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1. Characteristics of infections with ancestral, Beta and Delta variants of SARS-CoV-2 in the PHIRST-C community cohort study, South Africa, 2020-2021

Author: Cheryl Cohen, Jackie Kleynhans, Anne von Gottberg, Meredith L. McMorrow, Nicole Wolter, Jinal N. Bhiman, Jocelyn Moyes, Mignon du Plessis, Maimuna Carrim, Amelia Buys, Neil A. Martinson, Kathleen Kahn, Stephen Tollman, Limakatso Lebina, Floidy Wafawanaka, Jacques du Toit, Francesc Xavier Gómez-Olivé, Fatimah S. Dawood, Thulisa Mkhencele, for the PHIRST group, and Stefano Tempia
Subjects: SARS-CoV-2, South Africa, Epidemiology, Cohort study, Infectious and parasitic diseases, RC109-216
Abstract: Abstract Background Data on the characteristics of individuals with mild and asymptomatic infections with different SARS-CoV-2 variants are limited. We therefore compared the characteristics of individuals infected with ancestral, Beta and Delta SARS-CoV-2 variants in South Africa. Methods We conducted a prospective cohort study in a rural and an urban site during July 2020-August 2021. Mid-turbinate nasal swabs were collected twice-weekly from household members irrespective of symptoms and tested for SARS-CoV-2 using real-time reverse transcription polymerase chain reaction (rRT-PCR). Differences in demographic and clinical characteristics, shedding and cycle threshold (Ct) value of infection episodes by variant were evaluated using multinomial regression. Overall and age-specific incidence rates of infection were compared by variant. Results We included 1200 individuals from 222 households and 648 rRT-PCR-confirmed infection episodes (66, 10% ancestral, 260, 40% Beta, 322, 50% Delta). Symptomatic proportion was similar for ancestral (7, 11%), Beta (44, 17%), and Delta (46, 14%) infections (p=0.4). After accounting for previous infection, peak incidence shifted to younger age groups in successive waves (40-59 years ancestral, 19-39 years Beta, 13-18 years Delta). On multivariable analysis, compared to ancestral, Beta infection was more common in individuals aged 5-12 years (vs 19-39)(adjusted odds ratio (aOR) 2.6, 95% confidence interval (CI)1.1-6.6) and PCR cycle threshold (Ct) value 35)(aOR 3.2, 95%CI 1.3-7.9), while Delta was more common in individuals aged 35). Conclusions Consecutive SARS-CoV-2 waves with Beta and Delta variants were associated with a shift to younger individuals. Beta and Delta infections were associated with higher peak viral loads, potentially increasing infectiousness.
Published: 2024
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2. Transient increased risk of influenza infection following RSV infection in South Africa: findings from the PHIRST study, South Africa, 2016–2018

Author: Naomi R. Waterlow, Jackie Kleynhans, Nicole Wolter, Stefano Tempia, Rosalind M. Eggo, Orienka Hellferscee, Limakatso Lebina, Neil Martinson, Ryan G. Wagner, Jocelyn Moyes, Anne von Gottberg, Cheryl Cohen, and Stefan Flasche
Subjects: Influenza, RSV, Interaction, Competition, South Africa, Markov model, Medicine
Abstract: Abstract Background Large-scale prevention of respiratory syncytial virus (RSV) infection may have ecological consequences for co-circulating pathogens, including influenza. We assessed if and for how long RSV infection alters the risk for subsequent influenza infection. Methods We analysed a prospective longitudinal cohort study conducted in South Africa between 2016 and 2018. For participating households, nasopharyngeal samples were taken twice weekly, irrespective of symptoms, across three respiratory virus seasons, and real-time polymerase chain reaction (PCR) was used to identify infection with RSV and/or influenza. We fitted an individual-level hidden Markov transmission model in order to estimate RSV and influenza infection rates and their interdependence. Results Of a total of 122,113 samples collected, 1265 (1.0%) were positive for influenza and 1002 (0.8%) positive for RSV, with 15 (0.01%) samples from 12 individuals positive for both influenza and RSV. We observed a 2.25-fold higher incidence of co-infection than expected if assuming infections were unrelated. We estimated that infection with influenza is 2.13 (95% CI 0.97–4.69) times more likely when already infected with, and for a week following, RSV infection, adjusted for age. This equates to 1.4% of influenza infections that may be attributable to RSV in this population. Due to the local seasonality (RSV season precedes the influenza season), we were unable to estimate changes in RSV infection risk following influenza infection. Conclusions We find no evidence to suggest that RSV was associated with a subsequent reduced risk of influenza infection. Instead, we observed an increased risk for influenza infection for a short period after infection. However, the impact on population-level transmission dynamics of this individual-level synergistic effect was not measurable in this setting.
Published: 2023
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3. COVID-19 Vaccine Uptake and Effectiveness by Time since Vaccination in the Western Cape Province, South Africa: An Observational Cohort Study during 2020–2022

Author: Reshma Kassanjee, Mary-Ann Davies, Alexa Heekes, Hassan Mahomed, Anthony J. Hawkridge, Erna Morden, Theuns Jacobs, Cheryl Cohen, Harry Moultrie, Richard J. Lessells, Nicolette Van Der Walt, Juanita O. Arendse, Nicole Wolter, Sibongile Walaza, Waasila Jassat, Anne von Gottberg, Patrick L. Hannan, Daniel R. Feikin, Keith Cloete, and Andrew Boulle
Subjects: COVID-19, SARS-CoV-2, vaccine effectiveness, South Africa, cohort, observational, Medicine
Abstract: There are few data on the real-world effectiveness of COVID-19 vaccines and boosting in Africa, which experienced widespread SARS-CoV-2 infection before vaccine availability. We assessed the association between vaccination and severe COVID-19 in the Western Cape, South Africa, in an observational cohort study of >2 million adults during 2020–2022. We described SARS-CoV-2 testing, COVID-19 outcomes, and vaccine uptake over time. We used multivariable cox models to estimate the association of BNT162b2 and Ad26.COV2.S vaccination with COVID-19-related hospitalization and death, adjusting for demographic characteristics, underlying health conditions, socioeconomic status proxies, and healthcare utilization. We found that by the end of 2022, 41% of surviving adults had completed vaccination and 8% had received a booster dose. Recent vaccination was associated with notable reductions in severe COVID-19 during periods dominated by Delta, and Omicron BA.1/2 and BA.4/5 (sub)lineages. During the latest Omicron BA.4/5 wave, within 3 months of vaccination or boosting, BNT162b2 and Ad26.COV2.S were each 84% effective against death (95% CIs: 57–94 and 49–95, respectively). However, distinct reductions of effectiveness occurred at longer times post completing or boosting vaccination. Results highlight the importance of continued emphasis on COVID-19 vaccination and boosting for those at high risk of severe COVID-19, even in settings with widespread infection-induced immunity.
Published: 2024
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4. High prevalence of SARS-CoV-2 antibodies in pregnant women after the second wave of infections in the inner-city of Johannesburg, Gauteng Province, South Africa

Author: Shobna Sawry, Jean Le Roux, Nicole Wolter, Philile Mbatha, Jinal Bhiman, Jennifer Balkus, Anne von Gottberg, Cheryl Cohen, Matthew Chersich, Malolo Kekana, Thatcher Ndlovu, Angela Shipalana, Wendy Mthimunye, Faeezah Patel, Hermien Gous, Sibongile Walaza, Stefano Tempia, Helen Rees, and Lee Fairlie
Subjects: SARS-CoV-2 seroprevalence, Serosurveys, HIV, South Africa, COVID-19, Pregnant women, Infectious and parasitic diseases, RC109-216
Abstract: Objectives: After South Africa's second wave of COVID-19, this study estimated the SARS-CoV-2 seroprevalence among pregnant women in inner-city Johannesburg, South Africa. Methods: In this cross-sectional survey, 500 pregnant women who were non-COVID-19-vaccinated (aged ≥12 years) were enrolled, and demographic and clinical data were collected. Serum samples were tested using the Wantai SARS-CoV-2 spike antibody enzyme-linked immunosorbent assay and Roche Elecsys® anti-SARS-CoV-2 nucleocapsid antibody assays. Seropositivity was defined as SARS-CoV-2 antibodies on either (primary) or both (secondary) assays. Univariate Poisson regression assessed risk factors associated with seropositivity. Results: The median age was 27.4 years, and HIV prevalence was 26.7%. SARS-CoV-2 seroprevalence was 64.0% (95% confidence interval [CI]: 59.6-68.2%) on the primary and 54% (95% CI: 49.5-58.4%) on the secondary measure. Most (96.6%) women who were SARS-CoV-2-seropositive reported no symptoms. On the Roche assay, we detected lower seroprevalence among women living with HIV than women without HIV (48.9% vs 61.7%, P-value = 0.018), and especially low levels among women living with HIV with a clusters of differentiation 4
Published: 2022
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5. Assessing the clinical severity of the Omicron variant in the Western Cape Province, South Africa, using the diagnostic PCR proxy marker of RdRp target delay to distinguish between Omicron and Delta infections – a survival analysis

Author: Hannah Hussey, Mary-Ann Davies, Alexa Heekes, Carolyn Williamson, Ziyaad Valley-Omar, Diana Hardie, Stephen Korsman, Deelan Doolabh, Wolfgang Preiser, Tongai Maponga, Arash Iranzadeh, Sean Wasserman, Linda Boloko, Greg Symons, Peter Raubenheimer, Arifa Parker, Neshaad Schrueder, Wesley Solomon, Petro Rousseau, Nicole Wolter, Waasila Jassat, Cheryl Cohen, Richard Lessells, Robert J Wilkinson, Andrew Boulle, and Nei-yuan Hsiao
Subjects: SARS-CoV-2, Omicron variant, clinical severity, South Africa, RdRp target delay, Infectious and parasitic diseases, RC109-216
Abstract: Background: At present, it is unclear whether the extent of reduced risk of severe disease seen with SARS-Cov-2 Omicron variant infection is caused by a decrease in variant virulence or by higher levels of population immunity. Methods: RdRp target delay (RTD) in the Seegene AllplexTM 2019-nCoV PCR assay is a proxy marker for the Delta variant. The absence of this proxy marker in the transition period was used to identify suspected Omicron infections.Cox regression was performed for the outcome of hospital admission in those who tested positive for SARS-CoV-2 on the Seegene AllplexTM assay from November 1 to December 14, 2021 in the Western Cape Province, South Africa, in the public sector. Adjustments were made for vaccination status and prior diagnosis of infection. Results: A total of 150 cases with RTD and 1486 cases without RTD were included. Cases without RTD had a lower hazard of admission (adjusted hazard ratio [aHR], 0.56; 95% confidence interval [CI], 0.34-0.91). Complete vaccination was protective against admission, with an aHR of 0.45 (95% CI, 0.26-0.77). Conclusion: Omicron has resulted in a lower risk of hospital admission compared with contemporaneous Delta infection, when using the proxy marker of RTD. Under-ascertainment of reinfections with an immune escape variant remains a challenge to accurately assessing variant virulence.
Published: 2022
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6. Higher mortality associated with the SARS-CoV-2 Delta variant in the Western Cape, South Africa, using RdRp target delay as a proxy: a cross-sectional study. [version 1; peer review: 2 approved]

Author: Hannah Hussey, Mary-Ann Davies, Carolyn Williamson, Alexa Heekes, Diana Hardie, Ziyaad Valley-Omar, Deelan Doolabh, Stephen Korsman, Tongai Maponga, Wofgang Preiser, Susan Engelbrecht, Arash Iranzadeh, Neshaad Schrueder, Sean Wasserman, Greg Symons, Linda Boloko, Abraham Viljoen, Peter Raubenheimer, Cheryl Cohen, Arifa Parker, Richard Lessells, Waasila Jasat, Andrew Boulle, Robert J Wilkinson, and Marvin Hsiao
Subjects: SARS-CoV-2, Delta, B.1.617.2, clinical severity, RdRp target delay, South Africa, eng, Medicine
Abstract: Background: The SARS-CoV-2 Delta variant (B.1.617.2) has been associated with more severe disease, particularly when compared to the Alpha variant. Most of this data, however, is from high income countries and less is understood about the variant’s disease severity in other settings, particularly in an African context, and when compared to the Beta variant. Methods: A novel proxy marker, RNA-dependent RNA polymerase (RdRp) target delay in the Seegene AllplexTM 2019-nCoV (polymerase chain reaction) PCR assay, was used to identify suspected Delta variant infection in routine laboratory data. All cases diagnosed on this assay in the public sector in the Western Cape, South Africa, from 1 April to 31 July 2021, were included in the dataset provided by the Western Cape Provincial Health Data Centre (PHDC). The PHDC collates information on all COVID-19 related laboratory tests, hospital admissions and deaths for the province. Odds ratios for the association between the proxy marker and death were calculated, adjusted for prior diagnosed infection and vaccination status. Results: A total of 11,355 cases with 700 deaths were included in this study. RdRp target delay (suspected Delta variant) was associated with higher mortality (adjusted odds ratio [aOR] 1.45; 95% confidence interval [CI]: 1.13-1.86), compared to presumptive Beta infection. Prior diagnosed infection during the previous COVID-19 wave, which was driven by the Beta variant, was protective (aOR 0.32; 95%CI: 0.11-0.92) as was vaccination (aOR [95%CI] 0.15 [0.03-0.62] for complete vaccination [≥28 days post a single dose of Ad26.COV2.S or ≥14 days post second BNT162b2 dose]). Conclusion: RdRp target delay, a proxy for infection with the Delta variant, is associated with an increased risk of mortality amongst those who were tested for COVID-19 in our setting.
Published: 2022
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7. The importation and establishment of community transmission of SARS-CoV-2 during the first eight weeks of the South African COVID-19 epidemic

Author: Kerrigan M. McCarthy, Stefano Tempia, Tendesayi Kufa, Jackie Kleynhans, Nicole Wolter, Waasila Jassat, Joy Ebonwu, Anne von Gottberg, Linda Erasmus, Mazvita Muchengeti, Sibongile Walaza, Genevie Ntshoe, Andronica M. Shonhiwa, Pinky N. Manana, Yogan Pillay, Devanand Moonasar, Tshilidzi Muthivhi, Shadrack Mngemane, Koleka Mlisana, Kamy Chetty, Lucille H. Blumberg, Cheryl Cohen, and Nelesh P. Govender
Subjects: COVID-19, SARS-CoV-2, South Africa, Public Health, Lockdown, Epidemiology, Medicine (General), R5-920
Abstract: Background: We describe the epidemiology of COVID-19 in South Africa following importation and during implementation of stringent lockdown measures. Methods: Using national surveillance data including demographics, laboratory test data, clinical presentation, risk exposures (travel history, contacts and occupation) and outcomes of persons undergoing COVID-19 testing or hospitalised with COVID-19 at sentinel surveillance sites, we generated and interpreted descriptive statistics, epidemic curves, and initial reproductive numbers (Rt). Findings: From 4 March to 30 April 2020, 271,670 SARS-CoV-2 PCR tests were performed (462 tests/100,000 persons). Of these, 7,892 (2.9%) persons tested positive (median age 37 years (interquartile range 28–49 years), 4,568 (58%) male, cumulative incidence of 13.4 cases/100,000 persons). Hospitalization records were found for 1,271 patients (692 females (54%)) of whom 186 (14.6%) died. Amongst 2,819 cases with data, 489/2819 (17.3%) travelled internationally within 14 days prior to diagnosis, mostly during March 2020 (466 (95%)). Cases diagnosed in April compared with March were younger (median age, 37 vs. 40 years), less likely female (38% vs. 53%) and resident in a more populous province (98% vs. 91%). The national initial Rt was 2.08 (95% confidence interval (CI): 1.71–2.51). Interpretation: The first eight weeks following COVID-19 importation were characterised by early predominance of imported cases and relatively low mortality and transmission rates. Despite stringent lockdown measures, the second month following importation was characterised by community transmission and increasing disease burden in more populous provinces. Funding: Surveillance for SARS-CoV-2 is conducted by the National Institute for Communicable Diseases, and South African national and provincial health departments with funding, resources and material provided by the South African government and other sources as detailed in declaration of interest.
Published: 2021
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8. Detection of Victoria lineage influenza B viruses with K162 and N163 deletions in the hemagglutinin gene, South Africa, 2018

Author: Orienka Hellferscee, Florette Treurnicht, Lucinda Gaelejwe, Alexandra Moerdyk, Gary Reubenson, Meredith McMorrow, Stefano Tempia, Johanna McAnerney, Sibongile Walaza, Nicole Wolter, Anne vonGottberg, and Cheryl Cohen
Subjects: deletions, influenza B, South Africa, Victoria lineage, Medicine
Abstract: Abstract Background A group of Victoria lineage influenza B viruses with a two amino acid deletion in the hemagglutinin (HA) at residues K162 and N163, was detected during the 2016 to 2017 Northern Hemisphere influenza season and continues to spread geographically. We describe the first identification of viruses with these deletions from South Africa in 2018. Methods Nasopharyngeal samples were obtained from the syndromic surveillance programs. Real‐time reverse transcription‐polymerase chain reaction was used for virus detection and lineage determination. Influenza genetic characterization was done using next‐generation sequencing on the MiSeq platform. The duration of virus circulation was determined using thresholds calculated using the Moving Epidemic Method; duration was used as an indicator of disease transmissibility and impact. Results In 2018, 42% (426/1015) of influenza‐positive specimens were influenza B viruses. Of 426 influenza B‐positive samples, 376 (88%) had the lineage determined of which 75% (283/376) were Victoria lineage. The transmissibility of the 2018 South African influenza season was high for a few weeks, although the severity remained moderate through most of the season. The sequenced 2018 South African Victoria lineage influenza B viruses clustered in sub‐clade V1A.1 with the 162‐163 deletions. Conclusions We report the first detection of the 162‐163 deletion variant of influenza B/Victoria viruses from South Africa in 2018, and suggest that this deletion variant replaced the previous circulating influenza B/Victoria viruses. These deletions putatively affect the antigenic properties of the viruses because they border an immune‐dominant region at the tip of the HA. Therefore, close monitoring of these newly emerging viruses is essential.
Published: 2021
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9. Challenges and clinical relevance of molecular detection of Bordetella pertussis in South Africa

Author: Fahima Moosa, Mignon du Plessis, Nicole Wolter, Maimuna Carrim, Cheryl Cohen, Claire von Mollendorf, Sibongile Walaza, Stefano Tempia, Halima Dawood, Ebrahim Variava, and Anne von Gottberg
Subjects: Bordetella pertussis, South Africa, Severe respiratory illness, Influenza-like illness (ILI), Surveillance, Real-time PCR, Infectious and parasitic diseases, RC109-216
Abstract: Abstract Background We assessed the utility of a multi-target, real-time PCR assay for Bordetella pertussis detection and diagnosis in patients with severe respiratory illness (SRI), influenza-like illness (ILI), and asymptomatic controls. Methods Real-time PCR detection of IS481, pIS1001, hIS1001 and ptxS1 was performed on nasopharyngeal specimens (SRI, ILI and controls) and induced sputum (SRI) collected from June 2012 to May 2016 through respiratory illness surveillance. Using PCR cycle threshold (Ct) value cut-offs, IS481 positive cases were classified as confirmed (Ct
Published: 2019
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10. Responses to hypothetical health scenarios overestimate healthcare utilization for common infectious syndromes: a cross-sectional survey, South Africa, 2012

Author: Karen K. Wong, Adam L. Cohen, Neil A. Martinson, Shane A. Norris, Stefano Tempia, Claire von Mollendorf, Sibongile Walaza, Shabir A. Madhi, Meredith L. McMorrow, and Cheryl Cohen
Subjects: Pneumonia, Influenza, Diarrhea, Meningitis, South Africa, Healthcare utilization, Infectious and parasitic diseases, RC109-216
Abstract: Abstract Background Asking people how they would seek healthcare in a hypothetical situation can be an efficient way to estimate healthcare utilization, but it is unclear how intended healthcare use corresponds to actual healthcare use. Methods We performed a cross-sectional survey between August and September 2012 among households in Soweto and Klerksdorp, South Africa, to compare healthcare seeking behaviors intended for hypothetical common infectious syndromes (pneumonia, influenza-like illness [ILI], chronic respiratory illness, meningitis in persons of any age, and diarrhea in a child
Published: 2018
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11. Epidemiology and Molecular Identification and Characterization of Mycoplasma pneumoniae, South Africa, 2012–2015

Author: Maimuna Carrim, Nicole Wolter, Alvaro J. Benitez, Stefano Tempia, Mignon du Plessis, Sibongile Walaza, Fahima Moosa, Maureen H. Diaz, Bernard J. Wolff, Florette K. Treurnicht, Orienka Hellferscee, Halima Dawood, Ebrahim Variava, Cheryl Cohen, Jonas M. Winchell, and Anne von Gottberg
Subjects: Mycoplasma pneumoniae, community-acquired pneumonia, South Africa, severe respiratory illness, influenza-like illness, real-time PCR, Medicine, Infectious and parasitic diseases, RC109-216
Abstract: During 2012–2015, we tested respiratory specimens from patients with severe respiratory illness (SRI), patients with influenza-like illness (ILI), and controls in South Africa by real-time PCR for Mycoplasma pneumoniae, followed by culture and molecular characterization of positive samples. M. pneumoniae prevalence was 1.6% among SRI patients, 0.7% among ILI patients, and 0.2% among controls (p
Published: 2018
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12. Molecular Characterization of Corynebacterium diphtheriae Outbreak Isolates, South Africa, March–June 2015

Author: Mignon du Plessis, Nicole Wolter, Mushal Allam, Linda de Gouveia, Fahima Moosa, Genevie Ntshoe, Lucille Blumberg, Cheryl Cohen, Marshagne Smith, Portia Mutevedzi, Juno Thomas, Valentino Horne, Prashini Moodley, Moherndran Archary, Yesholata Mahabeer, Saajida Mahomed, Warren Kuhn, Koleka Mlisana, Kerrigan McCarthy, and Anne von Gottberg
Subjects: Corynebacterium diphtheriae, outbreak, South Africa, diphtheria, MLST, whole genome sequencing, Medicine, Infectious and parasitic diseases, RC109-216
Abstract: In 2015, a cluster of respiratory diphtheria cases was reported from KwaZulu-Natal Province in South Africa. By using whole-genome analysis, we characterized 21 Corynebacterium diphtheriae isolates collected from 20 patients and contacts during the outbreak (1 patient was infected with 2 variants of C. diphtheriae). In addition, we included 1 cutaneous isolate, 2 endocarditis isolates, and 2 archived clinical isolates (ca. 1980) for comparison. Two novel lineages were identified, namely, toxigenic sequence type (ST) ST-378 (n = 17) and nontoxigenic ST-395 (n = 3). One archived isolate and the cutaneous isolate were ST-395, suggesting ongoing circulation of this lineage for >30 years. The absence of preexisting molecular sequence data limits drawing conclusions pertaining to the origin of these strains; however, these findings provide baseline genotypic data for future cases and outbreaks. Neither ST has been reported in any other country; this ST appears to be endemic only in South Africa.
Published: 2017
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13. Healthcare seeking behaviour for common infectious syndromes among people in three administrative regions of Johannesburg, South Africa, 2015: a cross-sectional study

Author: Relebogile Mapuroma, Cheryl Cohen, Lazarus Kuonza, Alfred Musekiwa, Stefano Tempia, Akhona Tshangela, and Claire von Mollendorf
Subjects: disease surveillance, healthcare utilisation, respiratory illness, infectious diseases, household survey, south africa, Medicine
Abstract: INTRODUCTION: hospital-based surveillance programs only capture people presenting to facilities and may underestimate disease burden. We conducted a healthcare utilisation survey to characterise healthcare-seeking behaviour among people with common infectious syndromes in the catchment areas of two sentinel surveillance hospitals in Johannesburg, South Africa. METHODS: a cross-sectional survey was conducted within three regions of Johannesburg from August to November 2015. Premises were randomly selected from an enumerated list with data collected on household demographics and selected syndromes using a structured questionnaire. Fisher's exact or chi-square tests were used to determine association of characteristics among different regions. RESULTS: of 3650 selected coordinates, 3358 were eligible dwellings and 2930 (87%) households with 9850 individuals participated. Four percent of participants (431/9850) reported influenza-like illness (ILI) in the last 30 days; equal numbers of participants (0.2%, 20/9850) reported pneumonia or tuberculosis symptoms in the last year and 1% reported diarrhoea or meningitis symptoms. Sixty eight percent (295/431) of participants who reported ILI, 75% (6/8) of children with diarrhoea and all participants who reported pneumonia (20), tuberculosis (20) or meningitis (6) sought healthcare. For all syndrome most sought care at registered healthcare providers. Only 10% (24/237) attended sentinel hospitals, predominantly those that lived closer to the hospitals. In contrast, of patients with meningitis, 50% (3/6) sought care at sentinel hospitals. CONCLUSION: patterns of seeking healthcare differed by syndrome and distance from facilities. Surveillance programs are still relevant in collecting information on infectious syndromes and reflect a proportion of the hospital's catchment area.
Published: 2019
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14. Laboratory-based surveillance of Pneumocystis jirovecii pneumonia in South Africa, 2006–2010i

Author: Desiree du Plessis, Bhavani Poonsamy, Veerle Msimang, Leigh Davidsson, Cheryl Cohen, Nelesh Govender, Halima Dawood, Alan Karstaedt, and John Frean
Subjects: co-infection, developing countries, hiv infection, opportunistic infection, pjp, pneumocystis jirovecii, south africa, Infectious and parasitic diseases, RC109-216
Abstract: Background: We aimed to establish the characteristics of patients with confirmed Pneumocystis jirovecii pneumonia recruited by passive, sentinel laboratory-based surveillance. Method: The study design was prospective, observational, cross-sectional, laboratory-based sentinel surveillance. Laboratorybased surveillance of Pneumocystis jirovecii pneumonia (PJP), formerly known as Pneumocystis carinii pneumonia (PCP), was conducted in six South African provinces at 61 hospitals, of which 17 were sentinel sites, where surveillance officers collected clinical and demographic data from cases. A case was defined as a patient with a respiratory tract specimen that was confirmed positive for P. jirovecii by immunofluorescent microscopy or PCR test, either as a first diagnosis or ≥ 30 days after the last confirmed laboratory diagnosis of PJP. The chi-square test or Fisher’s exact test were used to compare the categorical variables. Results: From 2006–2010, 1 537 cases of PJP were recorded. Eighty-nine per cent (460/518) were found to be human immunodeficiency virus (HIV)-infected. This was a first diagnosis of HIV infection in 57% of the cases. The case fatality ratio was 34% (177/525). Recurrent infection was significantly more common in the 26- to 45-year age group, compared to children aged ≤ 5 years (odds ratio 1.7, 95% confidence interval: 1.1–2.8) (p 0.040). Treatment for tuberculosis was common in cases aged ≥ 5 years (37%, 85/229). Conclusion: PJP was the acquired immune deficiency syndrome-defining illness in more than half of the patients detected through laboratory-based surveillance. The high mortality rate and number of recurrent cases is noteworthy. This study may not have reflected the full spectrum of clinical presentation of the disease as case report forms were only completed for hospitalised patients at sentinel surveillance sites.
Published: 2016
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15. Epidemiology of Serotype 1 Invasive Pneumococcal Disease, South Africa, 2003–2013

Author: Claire von Mollendorf, Stefano Tempia, Cheryl Cohen, Susan Meiring, Linda de Gouveia, Vanessa Quan, Sarona Lengana, Alan Karstaedt, Halima Dawood, Sharona Seetharam, Ruth Lekalakala, Shabir A. Madhi, Keith P. Klugman, and Anne von Gottberg
Subjects: Streptococcus pneumoniae, serotype 1, South Africa, pneumococcal conjugate vaccine, PCV13, epidemiology, Medicine, Infectious and parasitic diseases, RC109-216
Abstract: In South Africa, 7-valent pneumococcal conjugate vaccine (PCV) was introduced in April 2009 and replaced with 13-valent PCV in April 2011. We describe the epidemiology of serotype 1 Streptococcus pneumoniae disease during the pre- and post-PCV eras (2003–2013). Using laboratory-based invasive pneumococcal disease (IPD) surveillance, we calculated annual incidences, identified IPD clusters, and determined serotype 1–associated factors. Of 46,483 IPD cases, 4,544 (10%) were caused by serotype 1. Two clusters of serotype 1 infection were detected during 2003–2004 and 2008–2012, but incidence decreased after 2011. Among children
Published: 2016
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16. Healthcare utilization for common infectious disease syndromes in Soweto and Klerksdorp, South Africa

Author: Karen Kai-Lun Wong, Claire von Mollendorf, Neil Martinson, Shane Norris, Stefano Tempia, Sibongile Walaza, Ebrahim Variava, Meredith Lynn McMorrow, Shabir Madhi, Cheryl Cohen, and Adam Lauren Cohen
Subjects: diarrhea, health services, meningitis, respiratory tract infections, south africa, Medicine
Abstract: INTRODUCTION: Understanding healthcare utilization helps characterize access to healthcare, identify barriers and improve surveillance data interpretation. We describe healthcare-seeking behaviors for common infectious syndromes and identify reasons for seeking care. METHODS: we conducted a cross-sectional survey among residents in Soweto and Klerksdorp, South Africa. Households were interviewed about demographic characteristics; recent self-reported episodes of pneumonia, influenza-like illness (ILI), chronic febrile respiratory illness and meningitis in individuals of all ages; recent diarrhea in children aged 5 years; and consultation with healthcare facilities and providers. RESULTS: from July-October 2012, we interviewed 1,442 households in Klerksdorp and 973 households in Soweto. Public clinics were consulted most frequently for pneumonia, ILI and diarrhea in a child 5 years old at both sites; public hospitals were most frequently consulted for chronic respiratory and meningitis syndromes. Of all illness episodes reported, there were 110 (35%) in Klerksdorp and 127 (32%) in Soweto for which the person did not seek care with a licensed medical provider. Pharmacies were often consulted by individuals with pneumonia (Klerksdorp: 17, 16%; Soweto: 38, 22%) or ILI (Klerksdorp: 35, 24%; 44, 28%). Patients who did not seek care with a licensed provider reported insufficient time (Klerksdorp: 7%; Soweto, 20%) and lack of medications at the facility (Klerksdorp: 4%; Soweto: 8%) as barriers. CONCLUSION: public government healthcare facilities are commonly consulted for infectious syndromes and pharmacies are frequently consulted particularly for respiratory diseases. Improving medication availability at healthcare facilities and streamlining healthcare delivery may improve access of licensed providers for serious illnesses.
Published: 2018
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17. Legionnaires’ Disease in South Africa, 2012–2014

Author: Nicole Wolter, Maimuna Carrim, Stefano Tempia, Cheryl Cohen, Sibongile Walaza, Philip Sahr, Linda de Gouveia, Florette K. Treurnicht, Orienka Hellferscee, Adam L. Cohen, Alvaro J. Benitez, Halima Dawood, Ebrahim Variava, Jonas M. Winchell, and Anne von Gottberg
Subjects: Legionella spp., Legionnaires’ disease, pneumonia, South Africa, Legionellosis, legionella, Medicine, Infectious and parasitic diseases, RC109-216
Abstract: During June 2012–September 2014, we tested patients with severe respiratory illness for Legionella spp. infection and conducted a retrospective epidemiologic investigation. Of 1,805 patients tested, Legionella was detected in samples of 21 (1.2%); most were adults who had HIV or tuberculosis infections and were inappropriately treated for Legionella.
Published: 2016
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18. Methods for early characterisation of the severity and dynamics of SARS-CoV-2 variants: a population-based time series analysis in South Africa

Author: Emily Reichert, Beau Schaeffer, Shae Gantt, Eva Rumpler, Nevashan Govender, Richard Welch, Andronica Moipone Shonhiwa, Chidozie Declan Iwu, Teresa Mashudu Lamola, Itumeleng Moema-Matiea, Darren Muganhiri, William Hanage, Mauricio Santillana, Waasila Jassat, Cheryl Cohen, and David Swerdlow
Subjects: Microbiology (medical), South Africa, Time Factors, Infectious Diseases, SARS-CoV-2, Virology, COVID-19, Humans, Middle Aged, Communicable Diseases, Microbiology
Abstract: Assessment of disease severity associated with a novel pathogen or variant provides crucial information needed by public health agencies and governments to develop appropriate responses. The SARS-CoV-2 omicron variant of concern (VOC) spread rapidly through populations worldwide before robust epidemiological and laboratory data were available to investigate its relative severity. Here we develop a set of methods that make use of non-linked, aggregate data to promptly estimate the severity of a novel variant, compare its characteristics with those of previous VOCs, and inform data-driven public health responses.Using daily population-level surveillance data from the National Institute for Communicable Diseases in South Africa (March 2, 2020, to Jan 28, 2022), we determined lag intervals most consistent with time from case ascertainment to hospital admission and within-hospital death through optimisation of the distance correlation coefficient in a time series analysis. We then used these intervals to estimate and compare age-stratified case-hospitalisation and case-fatality ratios across the four epidemic waves that South Africa has faced, each dominated by a different variant.A total of 3 569 621 cases, 494 186 hospitalisations, and 99 954 deaths attributable to COVID-19 were included in the analyses. We found that lag intervals and disease severity were dependent on age and variant. At an aggregate level, fluctuations in cases were generally followed by a similar trend in hospitalisations within 7 days and deaths within 15 days. We noted a marked reduction in disease severity throughout the omicron period relative to previous waves (age-standardised case-fatality ratios were consistently reduced by50%), most substantial for age strata with individuals 50 years or older.This population-level time series analysis method, which calculates an optimal lag interval that is then used to inform the numerator of severity metrics including the case-hospitalisation and case-fatality ratio, provides useful and timely estimates of the relative effects of novel SARS-CoV-2 VOCs, especially for application in settings where resources are limited.National Institute for Communicable Diseases of South Africa, South African National Government.
Published: 2022

19. Post-COVID-19 condition 3 months after hospitalisation with SARS-CoV-2 in South Africa: a prospective cohort study

Author: Murray Dryden, Caroline Mudara, Caroline Vika, Lucille Blumberg, Natalie Mayet, Cheryl Cohen, Stefano Tempia, Arifa Parker, Jeremy Nel, Rubeshan Perumal, Michelle J Groome, Francesca Conradie, Norbert Ndjeka, Louise Sigfrid, Laura Merson, and Waasila Jassat
Subjects: Adult, Cohort Studies, Hospitalization, Male, South Africa, SARS-CoV-2, Quality of Life, COVID-19, Humans, Female, Prospective Studies, General Medicine, Middle Aged
Abstract: Post COVID-19 condition (PCC), as defined by WHO, refers to a wide range of new, returning, or ongoing health problems in people who have had COVID-19, and it represents a rapidly emerging public health priority. We aimed to establish how this developing condition has affected patients in South Africa and which population groups are at risk.In this prospective cohort study, we used the DATCOV national hospital surveillance system to identify participants aged 18 years or older who had been hospitalised with laboratory-confirmed SARS-CoV-2 infection in South Africa. Participants underwent telephone follow-up assessment at 1 month and 3 months after hospital discharge. Participants were assessed using a standardised questionnaire for the evaluation of symptoms, functional status, health-related quality of life, and occupational status. We used negative binomial regression models to determine factors associated with PCC.Of 241 159 COVID-19 admissions reported to DATCOV between Dec 1, 2020, and Aug 23, 2021, 8309 were randomly selected for enrolment. Of the 3094 patients that we were able to contact, 2410 (77·9%) consented to participate in the study at 1 month after discharge. Of these, 1873 (77·7%) were followed up at 3 months after hospital discharge. Participants had a median age of 52 years (IQR 41-62) and 960 (51·3%) were women. At 3 months of follow-up, 1249 (66·7%) of 1873 participants reported new or persistent COVID-19-related symptoms, compared with 1978 (82·1%) of 2410 at 1 month after hospital discharge. The most common symptoms reported at 3 months were fatigue (50·3%), shortness of breath (23·4%), confusion or lack of concentration (17·5%), headaches (13·8%), and problems seeing or blurred vision (10·1%). On multivariable analysis, the factors associated with persistent symptoms after acute COVID-19 were being female (adjusted incident rate ratio 1·20, 95% CI 1·04-1·38) and admission to an intensive care unit (1·17, 1·01-1·37).Most participants in this cohort of individuals previously hospitalised with COVID-19 reported persistent symptoms 3 months after hospital discharge and a significant impact of PCC on their functional and occupational status. The large burden of PCC symptoms identified in this study emphasises the need for a national health strategy. This should include the development of clinical guidelines and training of health-care workers for identifying, assessing, and caring for patients affected by PCC; establishment of multidisciplinary health services; and provision of information and support to people who have PCC.BillMelinda Gates Foundation, UK Foreign, CommonwealthDevelopment Office, and Wellcome.
Published: 2022

20. Clinical severity of COVID-19 in patients admitted to hospital during the omicron wave in South Africa: a retrospective observational study

Author: Waasila Jassat, Salim S Abdool Karim, Caroline Mudara, Richard Welch, Lovelyn Ozougwu, Michelle J Groome, Nevashan Govender, Anne von Gottberg, Nicole Wolter, Milani Wolmarans, Petro Rousseau, Lucille Blumberg, and Cheryl Cohen
Subjects: South Africa, SARS-CoV-2, Influenza, Human, COVID-19, Humans, General Medicine, Pandemics, Hospitals
Abstract: Up to the end of January, 2022, South Africa has had four recognisable COVID-19 pandemic waves, each predominantly dominated by one variant of concern: the ancestral strain with an Asp614Gly mutation during the first wave, the beta variant (B.1.351) during the second wave, the delta variant (B.1.617.2) during the third wave, and lastly, the omicron variant (B.1.1.529) during the fourth wave. We aimed to assess the clinical disease severity of patients admitted to hospital with SARS-CoV-2 infection during the omicron wave and compare the findings with those of the preceding three pandemic waves in South Africa.We defined the start and end of each pandemic wave as the crossing of the threshold of weekly incidence of 30 laboratory-confirmed SARS-CoV-2 cases per 100 000 population. Hospital admission data were collected through an active national COVID-19-specific surveillance programme. We compared disease severity across waves by post-imputation random effect multivariable logistic regression models. Severe disease was defined as one or more of the following: acute respiratory distress, receipt of supplemental oxygen or mechanical ventilation, admission to intensive care, or death.We analysed 335 219 laboratory-confirmed SARS-CoV-2 hospital admissions with a known outcome, constituting 10·4% of 3 216 179 cases recorded during the four waves. During the omicron wave, 52 038 (8·3%) of 629 617 cases were admitted to hospital, compared with 71 411 (12·9%) of 553 530 in the Asp614Gly wave, 91 843 (12·6%) of 726 772 in the beta wave, and 131 083 (10·0%) of 1 306 260 in the delta wave (p0·0001). During the omicron wave, 15 421 (33·6%) of 45 927 patients admitted to hospital had severe disease, compared with 36 837 (52·3%) of 70 424 in the Asp614Gly wave, 57 247 (63·4%) of 90 310 in the beta wave, and 81 040 (63·0%) of 128 558 in the delta wave (p0·0001). The in-hospital case-fatality ratio during the omicron wave was 10·7%, compared with 21·5% during the Asp614Gly wave, 28·8% during the beta wave, and 26·4% during the delta wave (p0·0001). Compared with those admitted to hospital during the omicron wave, patients admitted during the other three waves had more severe clinical presentations (adjusted odds ratio 2·07 [95% CI 2·01-2·13] in the Asp614Gly wave, 3·59 [3·49-3·70] in the beta wave, and 3·47 [3·38-3·57] in the delta wave).The trend of increasing cases and admissions across South Africa's first three waves shifted in the omicron wave, with a higher and quicker peak but fewer patients admitted to hospital, less clinically severe illness, and a lower case-fatality ratio compared with the preceding three waves. Omicron marked a change in the SARS-CoV-2 epidemic curve, clinical profile, and deaths in South Africa. Extrapolations to other populations should factor in differing vaccination and previous infection levels.National Institute for Communicable Diseases.
Published: 2022

21. SARS-CoV-2 incidence, transmission, and reinfection in a rural and an urban setting: results of the PHIRST-C cohort study, South Africa, 2020–21

Author: Cheryl Cohen, Jackie Kleynhans, Anne von Gottberg, Meredith L McMorrow, Nicole Wolter, Jinal N Bhiman, Jocelyn Moyes, Mignon du Plessis, Maimuna Carrim, Amelia Buys, Neil A Martinson, Kathleen Kahn, Stephen Tollman, Limakatso Lebina, Floidy Wafawanaka, Jacques D du Toit, Francesc Xavier Gómez-Olivé, Fatimah S Dawood, Thulisa Mkhencele, Kaiyuan Sun, Cécile Viboud, Stefano Tempia, Linda de Gouveia, Jacques du Toit, Francesc X Gómez-Olivé, Kgaugelo P Kgasago, Retshidisitswe Kotane, Neil A. Martinson, and Tumelo Moloantoa
Subjects: Cohort Studies, South Africa, Infectious Diseases, SARS-CoV-2, Incidence, Reinfection, COVID-19, Humans, HIV Infections, Disease Susceptibility, Prospective Studies
Abstract: By August, 2021, South Africa had been affected by three waves of SARS-CoV-2; the second associated with the beta variant and the third with the delta variant. Data on SARS-CoV-2 burden, transmission, and asymptomatic infections from Africa are scarce. We aimed to evaluate SARS-CoV-2 burden and transmission in one rural and one urban community in South Africa.We conducted a prospective cohort study of households in Agincourt, Mpumalanga province (rural site) and Klerksdorp, North West province (urban site) from July, 2020 to August, 2021. We randomly selected households for the rural site from a health and sociodemographic surveillance system and for the urban site using GPS coordinates. Households with more than two members and where at least 75% of members consented to participate were eligible. Midturbinate nasal swabs were collected twice a week from household members irrespective of symptoms and tested for SARS-CoV-2 using real-time RT-PCR (RT-rtPCR). Serum was collected every 2 months and tested for anti-SARS-CoV-2 antibodies. Main outcomes were the cumulative incidence of SARS-CoV-2 infection, frequency of reinfection, symptomatic fraction (percent of infected individuals with ≥1 symptom), the duration of viral RNA shedding (number of days of SARS-CoV-2 RT-rtPCR positivity), and the household cumulative infection risk (HCIR; number of infected household contacts divided by the number of susceptible household members).222 households (114 at the rural site and 108 at the urban site), and 1200 household members (643 at the rural site and 557 at the urban site) were included in the analysis. For 115 759 nasal specimens from 1200 household members (follow-up 92·5%), 1976 (1·7%) were SARS-CoV-2-positive on RT-rtPCR. By RT-rtPCR and serology combined, 749 of 1200 individuals (62·4% [95% CI 58·1-66·4]) had at least one SARS-CoV-2 infection episode, and 87 of 749 (11·6% [9·4-14·2]) were reinfected. The mean infection episode duration was 11·6 days (SD 9·0; range 4-137). Of 662 RT-rtPCR-confirmed episodes (14 days after the start of follow-up) with available data, 97 (14·7% [11·9-17·9]) were symptomatic with at least one symptom (in individuals aged19 years, 28 [7·5%] of 373 episodes symptomatic; in individuals aged ≥19 years, 69 [23·9%] of 289 episodes symptomatic). Among 222 households, 200 (90·1% [85·3-93·7]) had at least one SARS-CoV-2-positive individual on RT-rtPCR or serology. HCIR overall was 23·9% (195 of 817 susceptible household members infected [95% CI 19·8-28·4]). HCIR was 23·3% (20 of 86) for symptomatic index cases and 23·9% (175 of 731) for asymptomatic index cases (univariate odds ratio [OR] 1·0 [95% CI 0·5-2·0]). On multivariable analysis, accounting for age and sex, low minimum cycle threshold value (≤30 vs30) of the index case (OR 5·3 [2·3-12·4]) and beta and delta variant infection (vs Wuhan-Hu-1, OR 3·3 [1·4-8·2] and 10·4 [4·1-26·7], respectively) were associated with increased HCIR. People living with HIV who were not virally supressed (≥400 viral load copies per mL) were more likely to develop symptomatic illness when infected with SAR-CoV-2 (OR 3·3 [1·3-8·4]), and shed SARS-CoV-2 for longer (hazard ratio 0·4 [95% CI 0·3-0·6]) compared with HIV-uninfected individuals.In this study, 565 (85·3%) SARS-CoV-2 infections were asymptomatic and index case symptom status did not affect HCIR, suggesting a limited role for control measures targeting symptomatic individuals. Increased household transmission of beta and delta variants was likely to have contributed to successive waves of SARS-CoV-2 infection, with more than 60% of individuals infected by the end of follow-up.US CDC, South Africa National Institute for Communicable Diseases, and Wellcome Trust.
Published: 2022

22. SARS-CoV-2 Seroprevalence after Third Wave of Infections, South Africa

Author: Jackie, Kleynhans, Stefano, Tempia, Nicole, Wolter, Anne, von Gottberg, Jinal N, Bhiman, Amelia, Buys, Jocelyn, Moyes, Meredith L, McMorrow, Kathleen, Kahn, F Xavier, Gómez-Olivé, Stephen, Tollman, Neil A, Martinson, Floidy, Wafawanaka, Limakatso, Lebina, Jacques D, du Toit, Waasila, Jassat, Mzimasi, Neti, Marieke, Brauer, Cheryl, Cohen, and Tumelo, Moloantoa
Subjects: Microbiology (medical), South Africa, Infectious Diseases, SARS-CoV-2, Seroepidemiologic Studies, Epidemiology, COVID-19, Humans
Abstract: By November 2021, after the third wave of severe acute respiratory syndrome coronavirus 2 infections in South Africa, seroprevalence was 60% in a rural community and 70% in an urban community. High seroprevalence before the Omicron variant emerged may have contributed to reduced illness severity observed in the fourth wave.
Published: 2022

23. Effectiveness of the Ad26.COV2.S vaccine in health-care workers in South Africa (the Sisonke study): results from a single-arm, open-label, phase 3B, implementation study

Author: Linda-Gail Bekker, Nigel Garrett, Ameena Goga, Lara Fairall, Tarylee Reddy, Nonhlanhla Yende-Zuma, Reshma Kassanjee, Shirley Collie, Ian Sanne, Andrew Boulle, Ishen Seocharan, Imke Engelbrecht, Mary-Ann Davies, Jared Champion, Tommy Chen, Sarah Bennett, Selaelo Mametja, Mabatlo Semenya, Harry Moultrie, Tulio de Oliveira, Richard John Lessells, Cheryl Cohen, Waasila Jassat, Michelle Groome, Anne Von Gottberg, Engelbert Le Roux, Kentse Khuto, Dan Barouch, Hassan Mahomed, Milani Wolmarans, Petro Rousseau, Debbie Bradshaw, Michelle Mulder, Jessica Opie, Vernon Louw, Barry Jacobson, Pradeep Rowji, Jonny G Peter, Azwi Takalani, Jackline Odhiambo, Fatima Mayat, Simbarashe Takuva, Lawrence Corey, Glenda E Gray, William Brumskine, Nivashnee Naicker, Disebo Makhaza, Vimla Naicker, Logashvari Naidoo, Elizabeth Spooner, Elane van Nieuwenhuizen, Kathryn Mngadi, Maphoshane Nchabeleng, James Craig Innes, Katherine Gill, Friedrich Georg Petrick, Shaun Barnabas, Sharlaa Badal-Faesen, Sheetal Kassim, Scott Hayden Mahoney, Erica Lazarus, Anusha Nana, Rebone Molobane Maboa, Philip Kotze, Johan Lombaard, Daniel Rudolf Malan, Sheena Kotze, Phuthi Mohlala, Amy Ward, Graeme Meintjes, Dorothea Urbach, Faeezah Patel, Andreas Diacon, Khatija Ahmed, Coert Grobbelaar, Pamela Mda, Thozama Dubula, Angelique Luabeya, Musawenkosi Bhekithemba Mamba, Lesley Burgess, and Rodney Dawson
Subjects: Adult, Male, South Africa, Vaccines, Ad26COVS1, Adolescent, SARS-CoV-2, COVID-19, Humans, Female, HIV Infections, General Medicine, Aged
Abstract: We aimed to assess the effectiveness of a single dose of the Ad26.COV2.S vaccine (JohnsonJohnson) in health-care workers in South Africa during two waves of the South African COVID-19 epidemic.In the single-arm, open-label, phase 3B implementation Sisonke study, health-care workers aged 18 years and older were invited for vaccination at one of 122 vaccination sites nationally. Participants received a single dose of 5 × 10Between Feb 17 and May 17, 2021, 477 102 health-care workers were enrolled and vaccinated, of whom 357 401 (74·9%) were female and 119 701 (25·1%) were male, with a median age of 42·0 years (33·0-51·0). 215 813 vaccinated individuals were matched with 215 813 unvaccinated individuals. As of data cutoff (July 17, 2021), vaccine effectiveness derived from the total matched cohort was 83% (95% CI 75-89) to prevent COVID-19-related deaths, 75% (69-82) to prevent COVID-19-related hospital admissions requiring critical or intensive care, and 67% (62-71) to prevent COVID-19-related hospitalisations. The vaccine effectiveness for all three outcomes were consistent across scheme A and scheme B. The vaccine effectiveness was maintained in older health-care workers and those with comorbidities including HIV infection. During the course of the study, the beta (B.1.351) and then the delta (B.1.617.2) SARS-CoV-2 variants of concerns were dominant, and vaccine effectiveness remained consistent (for scheme A plus B vaccine effectiveness against COVID-19-related hospital admission during beta wave was 62% [95% CI 42-76] and during delta wave was 67% [62-71], and vaccine effectiveness against COVID-19-related death during beta wave was 86% [57-100] and during delta wave was 82% [74-89]).The single-dose Ad26.COV2.S vaccine shows effectiveness against severe COVID-19 disease and COVID-19-related death after vaccination, and against both beta and delta variants, providing real-world evidence for its use globally.National Treasury of South Africa, the National Department of Health, Solidarity Response Fund NPC, The MichaelSusan Dell Foundation, The Elma Vaccines and Immunization Foundation, and the BillMelinda Gates Foundation.
Published: 2022

24. Direct and Indirect Effects of the Coronavirus Disease 2019 Pandemic on Private Healthcare Utilization in South Africa, March 2020–September 2021

Author: Amanda C Perofsky, Stefano Tempia, Jeremy Bingham, Caroline Maslo, Mande Toubkin, Anchen Laubscher, Sibongile Walaza, Juliet R C Pulliam, Cécile Viboud, and Cheryl Cohen
Subjects: sub-Saharan Africa, Microbiology (medical), SARS-CoV-2, social distancing, COVID-19, healthcare, Patient Acceptance of Health Care, lockdown, South Africa, AcademicSubjects/MED00290, Infectious Diseases, Communicable Disease Control, Major Article, Humans, Emergency Service, Hospital, Delivery of Health Care, Pandemics, Retrospective Studies
Abstract: Background The coronavirus disease 2019 (COVID-19) pandemic caused severe disruptions to healthcare in many areas of the world, but data remain scarce for sub-Saharan Africa. Methods We evaluated trends in hospital admissions and outpatient emergency department (ED) and general practitioner (GP) visits to South Africa’s largest private healthcare system during 2016–2021. We fit time series models to historical data and, for March 2020–September 2021, quantified changes in encounters relative to baseline. Results The nationwide lockdown on 27 March 2020 led to sharp reductions in care-seeking behavior that persisted for 18 months after initial declines. For example, total admissions dropped 59.6% (95% confidence interval [CI], 52.4–66.8) during home confinement and were 33.2% (95% CI, 29–37.4) below baseline in September 2021. We identified 3 waves of all-cause respiratory encounters consistent with COVID-19 activity. Intestinal infections and non–COVID-19 respiratory illnesses experienced the most pronounced declines, with some diagnoses reduced 80%, even as nonpharmaceutical interventions (NPIs) relaxed. Non-respiratory hospitalizations, including injuries and acute illnesses, were 20%–60% below baseline throughout the pandemic and exhibited strong temporal associations with NPIs and mobility. ED attendances exhibited trends similar to those for hospitalizations, while GP visits were less impacted and have returned to pre-pandemic levels. Conclusions We found substantially reduced use of health services during the pandemic for a range of conditions unrelated to COVID-19. Persistent declines in hospitalizations and ED visits indicate that high-risk patients are still delaying seeking care, which could lead to morbidity or mortality increases in the future.
Published: 2022

25. SARS-CoV-2 Seroprevalence in a Rural and Urban Household Cohort during First and Second Waves of Infections, South Africa, July 2020–March 2021

Author: Stephen Tollman, Limakatso Lebina, Cheryl Cohen, Anne von Gottberg, Mzimasi Neti, Amelia Buys, Kathleen Kahn, Neil A. Martinson, Jinal N. Bhiman, Jocelyn Moyes, Floidy Wafawanaka, Marieke Brauer, Meredith McMorrow, Waasila Jassat, Nicole Wolter, F. Xavier Gómez-Olivé, Jackie Kleynhans, Jacques du Toit, and Stefano Tempia
Subjects: Adult, Rural Population, Microbiology (medical), infection–fatality ratio, 2019-20 coronavirus outbreak, Epidemiology, coronaviruses, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Infectious and parasitic diseases, RC109-216, Limited access, respiratory infections, South Africa, Seroepidemiologic Studies, Humans, Medicine, Seroprevalence, viruses, SARS-CoV-2 Seroprevalence in a Rural and Urban Household Cohort during First and Second Waves of Infections, South Africa, July 2020–March 2021, Child, seroprevalence, Rural community, SARS-CoV-2, business.industry, Research, COVID-19, Middle Aged, Urban community, zoonoses, Infectious Diseases, coronavirus disease, Cohort, Age distribution, infection–hospitalization ratio, business, infection–case ratio, severe acute respiratory syndrome coronavirus 2, Demography
Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections may be underestimated because of limited access to testing. We measured SARS-CoV-2 seroprevalence in South Africa every 2 months during July 2020–March 2021 in randomly selected household cohorts in 2 communities. We compared seroprevalence to reported laboratory-confirmed infections, hospitalizations, and deaths to calculate infection–case, infection–hospitalization, and infection–fatality ratios in 2 waves of infection. Post–second wave seroprevalence ranged from 18% in the rural community children
Published: 2021

26. Clinical severity of SARS-CoV-2 Omicron BA.4 and BA.5 lineages compared to BA.1 and Delta in South Africa

Author: Nicole Wolter, Waasila Jassat, Sibongile Walaza, Richard Welch, Harry Moultrie, Michelle J. Groome, Daniel Gyamfi Amoako, Josie Everatt, Jinal N. Bhiman, Cathrine Scheepers, Naume Tebeila, Nicola Chiwandire, Mignon du Plessis, Nevashan Govender, Arshad Ismail, Allison Glass, Koleka Mlisana, Wendy Stevens, Florette K. Treurnicht, Kathleen Subramoney, Zinhle Makatini, Nei-yuan Hsiao, Raveen Parboosing, Jeannette Wadula, Hannah Hussey, Mary-Ann Davies, Andrew Boulle, Anne von Gottberg, and Cheryl Cohen
Subjects: South Africa, Multidisciplinary, SARS-CoV-2, COVID-19, Humans, General Physics and Astronomy, General Chemistry, General Biochemistry, Genetics and Molecular Biology
Abstract: Omicron lineages BA.4 and BA.5 drove a fifth wave of COVID-19 cases in South Africa. Here, we use the presence/absence of the S-gene target as a proxy for SARS-CoV-2 variant/lineage for infections diagnosed using the TaqPath PCR assay between 1 October 2021 and 26 April 2022. We link national COVID-19 individual-level data including case, laboratory test and hospitalisation data. We assess severity using multivariable logistic regression comparing the risk of hospitalisation and risk of severe disease, once hospitalised, for Delta, BA.1, BA.2 and BA.4/BA.5 infections. After controlling for factors associated with hospitalisation and severe outcome respectively, BA.4/BA.5-infected individuals had a similar odds of hospitalisation (aOR 1.24, 95% CI 0.98–1.55) and severe outcome (aOR 0.72, 95% CI 0.41–1.26) compared to BA.1-infected individuals. Newly emerged Omicron lineages BA.4/BA.5 showed similar severity to the BA.1 lineage and continued to show reduced clinical severity compared to the Delta variant.
Published: 2022

27. Human respiratory syncytial virus diversity and epidemiology among patients hospitalized with severe respiratory illness in South Africa, 2012–2015

Author: Florette K. Treurnicht, Cheryl Cohen, Senzo Mtshali, Ernest Mamorobela, Meredith McMorrow, Marthi Pretorius, Kathleen Kahn, Sibongile Walaza, Nicole Wolter, Ebrahim Variava, Orienka Hellferscee, Stefano Tempia, Anne von Gottberg, Halima Dawood, Ziyaad Valley-Omar, and Marietjie Venter
Subjects: Pulmonary and Respiratory Medicine, medicine.medical_specialty, Genotype, Epidemiology, Respiratory Syncytial Virus Infections, Logistic regression, medicine.disease_cause, Virus, South Africa, Internal medicine, Streptococcus pneumoniae, medicine, Humans, Prospective Studies, Respiratory system, Child, Phylogeny, Dominance (genetics), business.industry, Public Health, Environmental and Occupational Health, Infant, Odds ratio, Infectious Diseases, Respiratory Syncytial Virus, Human, business
Abstract: BACKGROUND We aimed to describe the prevalence of human respiratory syncytial virus (HRSV) and evaluate associations between HRSV subgroups and/or genotypes and epidemiologic characteristics and clinical outcomes in patients hospitalized with severe respiratory illness (SRI). METHODS Between January 2012 and December 2015, we enrolled patients of all ages admitted to two South African hospitals with SRI in prospective hospital-based syndromic surveillance. We collected respiratory specimens and clinical and epidemiological data. Unconditional random effect multivariable logistic regression was used to assess factors associated with HRSV infection. RESULTS HRSV was detected in 11.2% (772/6908) of enrolled patients of which 47.0% (363/772) were under the age of 6 months. There were no differences in clinical outcomes of HRSV subgroup A-infected patients compared with HRSV subgroup B-infected patients but among patients aged
Published: 2021

28. Risk factors for COVID-19-related in-hospital mortality in a high HIV and tuberculosis prevalence setting in South Africa: a cohort study

Author: Waasila Jassat, Cheryl Cohen, Stefano Tempia, Maureen Masha, Susan Goldstein, Tendesayi Kufa, Pelagia Murangandi, Dana Savulescu, Sibongile Walaza, Jamy-Lee Bam, Mary-Ann Davies, Hans W Prozesky, Jonathan Naude, Ayanda T Mnguni, Charlene A Lawrence, Hlengani T Mathema, Jarrod Zamparini, John Black, Ruchika Mehta, Arifa Parker, Perpetual Chikobvu, Halima Dawood, Ntshengedzeni Muvhango, Riaan Strydom, Tsholofelo Adelekan, Bhekizizwe Mdlovu, Nirvasha Moodley, Eunice L Namavhandu, Paul Rheeder, Jacqueline Venturas, Nombulelo Magula, Lucille Blumberg, Shaina Abdullah, Fiona Abrahams, Vincentius Adams, Fhima Adnane, Sonia Adoni, Dieketso Melitta Adoons, Veronique Africa, D Aguinaga, Susan Akach, Prisha Alakram Khelawon, George Aldrich, Olatunde Alesinloye, Mathale Biniki Aletta, Mametja Alice, Tebogo Aphane, Moherndran Archary, Felicity Arends, Shireen Arends, Munonde Aser, T Asmal, Mohammed Asvat, Theunis Avenant, Muvhali Avhazwivhoni, Magnolia Azuike, Johanna Baartman, Dlava Babalwa, Johan Badenhorst, Miranda Badenhorst, Bianca Badripersad, Lalihla Badul, M Bagananeng, Mncedisi Bahle, Liezl Balfour, T C Baloyi, S Baloyi, Tinyiko Baloyi, Tshepo Mpho Baloyi, Thokozani Banda, Shimon Barit, Nicole Bartsch, Junaid Bayat, Siyabulela Bazana, Marlene Beetge, Nosindiso Bekapezulu, Rammala Belebele, Phala Bella, Zanenkululeko Belot, Lindi Gladys Bembe, Sonja Bensch, Gishma Beukes, Karla Bezuidenhout, Themba Bhembe, N A Bikisha, Ben Bilenge, Leesa Bishop, Baphamandla Biyela, Cyntheola Blaauw, Mark Blaylock, Nicola Bodley, Power Bogale, Sibongile Bokolo, Stefan Bolon, Mary Booysen, Eldereze Booysen, Lia Boretti, Paula Borges, Millicent Boshoga, Natasha Bosman, Lucinda Bosvark, Nicky Botes, Adele Botha, Chantall Botha, Jana Botha, Chantall botha, Mandlakayise Irvin Botha, Alet Botha, Janet Bradbury, Zandisile Breakfast, Maria Breed, Molele Brenda, Moshito Brice, Jolene Britz, Amanda Brown, T Buchanan, Thozama Bucwa, Crystelle Burger, Ziyanda Busakwe, Nosiviwe Bushula, Zinhle Buthelezi, Dumsile Buthelezi, Thubelihle Buthelezi, Mpumelelo Basil Buthelezi, Fundiswa Lidwina Buthelezi, Nadia Bux, Christoff Buys, Anneline Buys, Ernestina Caka, Armando Sanchez Canal, Sithole Caroline, Monrick Casper, Shannon Cawood, Oratile Cebisa, Nothando Cele, Sboniso Cele, Sthembile Goodness Cele, Mkhacani Chauke, Pinkie Chauke, Nevil Chelin, Xiaohui Chen, Venmalla Chetty, Kerisse Chetty, Christinah Cheu, Vindana Chibabhai, Takudzwa Chirima, Mantwa ChisaleMabotja, Charity Chivenge, Ngoasheng Choene, Mbali Nosisa Choko, Martin Choshi, Sabbir Chowdhury, Anastacia Christoforou, S L S Chuene, T S Chueu, Dale Cilliers, Vanessa Cilliers, Marcel Claassen, Jeané Cloete, Chantelle Coelho, Carol Coetzee, Hans Jurgens Coetzee, Christine Coetzee, Marelize Coetzee, Dane Coetzer, Sizwe Coka, M Colane, Herkulaas Combrink, Songezo Conjwa, Colleen Contrad, Faith Cornelissen, Leezelle Cronje, Christine Crouse, Tshidi Dabi, Ziyanda Dandala, Ziyaad Dangor, Gildenhuys Daniel, Ngwana Daniel, Alfred Daumas, Madelein Dauth, Mongalo David, Wayne Davids, Nozuko Daweti, Wandisa Dayile, B De Bruin, Karin De Klerk, Tanya De la Rosa, Marice de Nysschen, Marie De vos, Darien De Wet, Mohith Debising, Darshan Deenadayalu, Babalwa Dekeda, Mofokeng Desiree, Annelise Deysel, Abram Dhlamini, Makgethwa Dhlala Diala, Mathapelo Diale, Bella Diketane, Nosisa Dingani, Siyabonga Diniso, Lesego Diphatse, Anele Diya, Zihloniphile Dladla, Nompumelelo Dladla, Mlungisi Dladla, Patience Dladla, Baphilie Dlamini, Nonhlanhla Dlamini, Linda Dlamini, Nonzwakazi Dlamini, Wendy Dlamini, Ncomeka Dlamini, Siyabonga Dlamini, Nicodemus Dlamini, Lebohang Dlamini, Motshedise Dlamini, Babalwa Christine Dlava, Phikiwe Dlova, Lindiwe Dlozi, Maenetja Doreen, Vumile Doyi, Athini Doyi, Belinda Du Plessis, Johanna Aletta du Plessis, Eddie du Plessis, Nicolette du Plessis, Karin du Plessis, Briette du Toit, Narissa du Toit, Jabulile Dube, Athayanda Dubula, Msomi Duduzile, Sechaba Duiker, Unati Bongile Duma, Kholiwe 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Gosa-Lufuta, Bernadett Gosnell, Sharleen Gouws, Christina Govender, Raksha Govender, Pearl Govender, Sally Govender, Roxanne Govender, K Govender, Savie Govender, Rashika Govinden, Luphumlo Gqabuza, Nomthandazo Gqaji, Maneo Gqetywa, Caroline Green, Nathan Green, Neera Green, Hendrik Grobler, Pamela Groenwald, Daniel Grootboom, Beatrice Gumede, Nomonde Gumede, Simphiwe Gumede, Slindile Gumede, Ntombikayise Gumede, Zenande Gumede, Thandiswa Gxotiwe, Makhubela H L, Nonhlanhla Hadebe, Skhumbuzo Hadebe, Christos Halkas, Ansie Hamer, Ebrahim Hamida, Juan Hammond, Sumayia Haniff, Annelise Hare, lorinda Hattingh, Thenjiwe Hendricks, Philip-George Henecke, Brends Henly-Smith, Glynis Herselman, Ansie Heymans, Chantel Heyns, Golekane Hlabahlaba, Lucky Hlabangwane, Simango Hlamarisa, Ntokozo Hlanzi, Hlengiwe Hlela, Katlego Hlokwe, Thembinkosi Hlongwa, Anele Hlongwana, Themba Hlubi, Tozama Hobo, Nare Nathaniel Hopane, Mariska House, Catharina Hudson, Marinda Huysamen, Jezreen Indheren, Samantha Ingle, Gavin Isaacs, T S Thekiso Isaacs, Maringa Itumeleng, Karien J van Rensburg, Saloshni Jackson, Neziswa Jacob, Burton Jacobs, Tshireletso Jacobs, Gugulethu Jacobs, Mesadi Jaftha, Zimkhitha Jaji, Sibusiso Jali, Gcobisa James, Gillian January, Andiswa Jeke, Laurent Jeremiah, L S Jeremiah, Mubeen Jhetam, Maureen John, Chuene John, Thandiwe Jola, Yolande Jonas, Anovick Jonas, Amilcar Juggernath, Eileen Kaba, Venetia Kabo, Disebo Kadi, Karabo Kaizer, Moshaya Peter Kambule, Lorraine Kapp, Tshepo Kau, Nchabeleng Keneth, O Kgabi, Tebogo Audrey Kgafela, Vincent Kgakgadi, Isabella Kgaswe, Tsholofelo Kgathlane, Vuyelwa Julia Kgetha, Mmaselloane Kgomojoo, B Kgoro, Christinah Kgosiemang, Gloria Kgosiencho, Stephen Khambula, Ariffa Khan, Refemetswe Khanare, Ncamsile Khanyase, Nokwethemba Khanyile, Fillip Kharatsi, Simangele Khawula, Themba Khohlakala, Letitia Khomo, Isabel Khoza, Sinethemba Khoza, Nombulelo Khukule, Busisiwe Khumalo, Tracy Khumalo, Zinhle khumalo, Vuyelwa Khumalo, Delisile 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Patrick Lekala, Motsitsi Lekhoaba, Tanki Shadrack Lekunutu, Galaletsang Lerefolo, N Letebele, Tsepo Patric Lethoba, Emission Letlalo, Ofentse Letlhage, D S V Letshufi, Dineo Fiona Letsoalo, Seleka Jones Letsoalo, Pennelope Letsoalo, Getrude Letwaba, Sobekwa Linda, Katleho Lipholo, Sabata Litabe, Harsha Lochan, Linda Lomax, Francina Lombaard, Elmarie Loots, Ariana Lourens, Celeste Louw, Rianna Louw, Zikhona Lubambo, Msebenzi Moises Lubambo, Gregory Ludada, Michael Lukas, Thembela Lungu, Nomvume Lupindo, Emmah Lusenga, Happiness Luthuli, Zoleka Sylvia Luvuno, Gwangwa M H, Mustafa Maarman, Buyisiwe Mabaso, Cynthia Mabaso, Morena Mabitle, Grace Mabogoane, Kgakgamatso Mabone, Rueben Mabuza, Velaphi Mabuza, Mogantla Madiseng, Thobile Madlala, Mashooase Madolo, Thabiso Madonsela, Lesetsa Madubanya, Amukelani Maepa, Namhla Mafumana, Caroline Mafumo, Pumeza Magadla, Viscah Magale, Nompumelelo Magaqa, Oberholzer Magda, Rakgoale Magdeline, Tswai Maggie, Bongeka Maginxa, Cathrine Maite Magoba, Caroline Magongwa, Agretia Magubane, Agretia Ntombizodwa Magubane, R Magwai, D I Mahabane, Padmini Mahabeer, Elsie Mahadulula, Lungiswa Mahanjana, Amy Maharaj, Qedusiza Mahlambi, Yvonne Mahlangu, Lerato Mahlangu, Ntombifikile Mahlangu, Makhosazana Mahlangu, Mahlatsi Mahlangu, Penelope Mahlasela, Thosago Mahlatse, Regina Mahlobo, Dikhing Mahole, Adam Mahomed, Mapeu Debora Mahubane, Peter Mahume, Lehlogonolo Maifo, Vincent Maimane, Petunia Maimele, Phakoe Maine, Patricia Senyanyathi Mainongwane, Nomalungisa Majamani, Amahle Majozini, Noluthando Makalima, Nomfundo Makam, Khanyisa Makamba, R Makan, Mashiane Makarapa, Malesela Makgahlela, Mogoiwa David Makgisa, Makgoba Makgomo, M A Makgopa, Mabone Makhalema, Lindokuhle Lizo Makhanya, Philile Valentia Makhanya, Tolerance Makharaedzha, Nathi Makhathini, Elizabeth Makhesi, Cinile Makhubela, Nkululeko Freedom Makhunga, Nomalinge Makhupula, R R Makhura, Rangwato Makola, Zingisa Makuba, Asanda Makubalo, Lonwabo Makumsha, George Makuya, Levy Mmachuene Malaka, Themba Malangeni, M L Malatji, Pelonomi Malebana-Metsing, Malek Malek, Luthando Malevu, Juanita Malgas, Dimakatso Malgas, Paul Makgasane Malope, Monyeki Malose, Katekani Maluleke, Kato Mambane, Nthabiseng Mamorobela, Kukami Manamela, Tshepo Manana, Sathiel Maneto, Aron Kabelo Manganye, Pheto Mangena, Anna Mangoale, Tinotenda Florence Mangozho, Pariva Manickchund, Zandisile Mankayi, Arthur Manning, Kelebogile Manyaapelo Manyaapelo, Tabea Manyane, Zoliswa Manzana, Milton Manzini, Busisiwe Mapasa-Dube, Siboniso Maphumulo, Ntombifuthi Maphumulo, Sindy Maponya, Khomotso Mumsy Maponya, Napjadi Maponya, Lami Maqubela, Lizeka Maqubela, Vuyo Maqungo, Marisa Marais, Chantal Marais, Nondumiso Maramba, Annelize Mare, Madumetsa Maredi, Afikile Martins, Johanna Marule, Refilwe Marumo, N N Masakona, Kedibone Vincentia Masehla, Eric Maseko, Tshilidzi Maselesele, Mojalefa Maselo, M Maseloa, M E Masemola, Thembi Masemola, Bella Mashaba, James Mashangwane, Mantebele Mashao, Shalom Mashego, Lerato Mashele, Ester Mashiane, Joyce Mashibini, J Mashilo, Tumi Mashiloane, Charity Mashishi, Ngazibini Mashiyi, Khomola Mashudu, Aluwani Masindi, Caroline Maslo, Nduduzo Masondo, Dumisile Masuku, Cry Matamela, Mirriam Matandela, Nontokozo Mathabela, T Mathabi, Keitumetse Mathe, Mathabo Mathebula, Catherine Mathebula, Mdungazi Andres Mathebula, Nqobizwe Mathenjwa, Jane Mathibe, Lebohang Mathibela, Makwela Mathilda, Khakhu Mathiva, Mokgadi Alinah Mathobela, Fikile Pearl Mathonsi, K P Mathonsi, Katlego Mathosa, Noluvo Matiwane, Emma Matjeke, Bella Matjiane, Thabang Matjila, Chidi Matlala, Petlo Matome, Nolusindiso Matoti, C Matseliso, Dineo Matsemela, Phumeza Matsha, Gaalebale Prudence Matshediso, Motsumi Matshediso, Esther Matshela, Bongeka Mavuma, Pearl Mavundla, Nomthandazo Mavuso, Lovender Mawasha, Rebecca Mawelela, Nelisiwe Mazibuko, Phumlani Mazibuko, Lindiwe Mazubane, Bavumile Mbanjwa, Ayanda Mbasa, Nosimilo Mbatha, Zanele Mbatha, Rudolph Zenzele Mbatha, Gift Mbedzi, Tatenda Trevor Mbizi, Khumbulani Mbonambi, Nondumiso Mboniswa, Nomfanelo Mbonisweni, Jody Mbuilu, Siyabonga Mbulawa, Zama Mbutho, Natasha Mbuzi, Nonkululeko Mchunu, Cyprian Mchunu, Nokuzola Mchunu, Masesi Thandeka Mchunu, Vuyokazi Mciteka, Solly Mdaka, Neho Mdakane, Siyabonga Mdediswa, Melusi Mdima, Nozipho Mdima Masondo, Siviwe Mdindana, Ntombizikhona Mdleleni, Sibusiso Mdletshe, Gcobisa Precious Mdoda, Ntombi Mdolo, Anele Mdontsane, Ruchikas Mehta, Philile Rittah Memela, Masande Methuse, Keatlaretse Metshile, Pheliswa Metuse, Anton Meyer, Gavin Meyer, Cameron Meyer, Sisonke Mfazwe, Andiswa Mfecane, Bongeka Mfecane, Nelisiwe Mfeka, Busisiwe Mgaga, Thandiwe Portia Mgauli, Thembekile Mgedezi, Vuyokazi Mgedezi, Kalipile Mgevane, Bongni Mgiba, Babalwa Mgoduka, Patrick Mhlaba, Zeldah Mhlaba, Ntombizodwa Mhlanga, Vangile Mhlinza, Nokuthula Mhlongo, sibongiseni Mhlongo, Unamandla Mhlotshana, Mabaso Mikateko, Helena Minnie, Karen Mintoor, Bongi Miyeni, Mabelane M J, Rosy Mjethu, Gloria Mkhize, Mvuselelo Mkhize, Ntokozo Siyabonga Mkhize, Victoria Mkhize, Nomkhosi Mkhize, Nokuthula Mkhize, Mathini Mkhwanazi, Nolwandle Mkile, Kholofelo Mkise, Nokwandiso Mkiya, Pearl Mkongi, Mnonopheli Mkungeka, Hlomile Mlahleki, Nolukholo Mlibali, Sakhumzi Mlungwana, Jonas Mmachele, Mashatole Mmateka, Molebatsi Mmokwa, Thembisa Mmutlane, Zanele Olive Mndebele, Nonhlanhla Mngomezulu, Noluthando Millicent Mnguni, Pumza Mngunyana, Nomxolisi Mngunyana, Ntombebongo Mngxekeza, Zenzele Mnisi, Hlengiwe Precious Mnqayi, Phumzile Mnqayi, Thabiso Mntungwa, Siya Mnyaka, Ntombikayise Mnyakeni, Vuyani Mnyamana, Nomzingisi Mnyipika, Koena Moabelo, Mmakgoshi Alseria Moatshe, Jennifer Mochaki-Senoge, Sharon Moche, Tebello Mocwagae, Koeikantse Modibane, Tebogo godfrey Modimoeng, Obakeng Modisa, Itumeleng Modisane, Olebogeng Modise, Makaepeaa Flovia Modjadji, Sharon Modupe, Maja Moeketsi, Ntswaki Moeketsi, Kereditse Kingsley Moeng, Naledi Nthabiseng Mofamere, Samuel Mofokeng, Thabo Mofokeng, Jonas 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Ntleki, Zanele Ntobela, Bandile Ntombela, Zamaswazi Ntombela, Khonelihle Zandile Ntombela, Praisegod Samkelo Thobani Ntombela, Lindiwe Ntonintshi, Dipuo Ntseane, Thobeka Ntseane, Xolelwa Ntsham, Mbalenhle Ntshele, Amanda Ntshewula, Zinzi Ntsoko, Athini Ntsoto, Nomsa Ntuli, Nokwazi Ntuli, Nomvula Ntuli, Andrew Diffar Ntuli, Faith Ntuli, Margrit Nurnberger, Ntsikelelo Nxala, Sithandiwe Nxasane, Thanda Nxumalo, Xolani Nyathi, Nontobeko Nyawula, Nhlakanipho Nzama, Maila Nkuneng Obed, Florence Ogwal, Maureen Olifant, B Oliphant, Monota Olive, Kagisho Olyn, Raymond Omoighe, Phumeza One, Ratombo Oscar, Nkuna Owen, Mailula P, Nalini Padayachee, Vasaily Padayachy, Ntombizakhe Pakade, Mosiuoa Palime, Jane Palisa, Lesenyeho Parkies, Andy Parrish, Nilesh Patel, Anastasia Pather, Mkhombo Tsakani Patience, Marisa Patzke, Akhumzi Pawuli, Ntandokazi Pelako, Phaswana Sibasa Penrose, Litha Peppeta, Santosh Pershad, Makheda Pertunia, Nkuna Pertunia, Dane Perumal, Mongameli Peter, Justin Peters, Vatiswa Petlane, Harideen Petrus, Kgomotso Phahladira, Matebesi John Phakisa, R Phale, Livhuwani Phathela, Sekate Daniel Phillip, Beverly Phiri, Mapule Precious Phiri, Thapelo Phokane, Frank Phokoane, Moele Pholosho, Sekoro Phooko, Sekodi Geoffrey Phooko, Maponya Phutiane, Faiza Pillay, Melanie Pillay, Sayuri Pillay, C R Pillay, Zikhona Plaatjie, James Pootona, Samantha Potgieter, Marius Potgieter, Mulaudzi Mulatedzi Precious, Paul Janus Pretorius, Hans Prozesky, Mokhethi Pule, Jayshina Punwasi, Dot Putzier, Lutho Qankqiso, Siphokazi Qebedu, Phozisa Qhola, Ntombesithathu Qotoyi, Sipho Victor Qotso, Zanele Qwabe, Helena Rabie, Phoebe Rabothata, Christina Rachoene, Mteteleli Radana, Maria Radebe, Dr. Valentino Radebe, Nonkululeko Radebe, Ella Radinne, Sherly Raduvha, Shamintha Raghunath, Claudine Rajagopaul, Mary Rakgwale, Malumbete Michael Ralethe, Kenneth Ralimo, Motlalepule Ramafoko, Maduvhahafani Ramagoma, Charlotte Raman, Dr Ramavhuya, Molly Rambally, Nivasha Ramdeen, Tanusha Ramdin, Sharita Rameshwarnath, Yeishna Ramkillawan, null Ramotlou, Faith Rampedi, Vijayluxmi Rampersad, Avhashoni Ramuima, Noluthando Ranone, Mabohlale Portia Rapasa, Mpharoane rapelang, Nika Raphaely, Lesiba Rashokeng, Caroline Rashopola, Tebogo Ratau, M Ratau, Mpfariseni David Ratshili, Elmari Rautenbach, Rofhiwa Ravele, Johannes Reachable, Peta Mmalahla Rebecca, Kessendri Reddy, Andrew Redfern, Robertha Reed, Mumsy Rees, Dr Reji, Gary Reubenson, Veena Rewthinarain, Nkonayani Rhulani, Mufamadi Richard, J S Rikhotso, Shatimone Beverley Rikhotso, Lavhelani Ndivhaleni Robert, Noncedo Roto, Gideon Ruder, Kapil Rugnath, Lizette Ruiters, Mina Ruiters, Sue Russell, Lynn Ruwiza, Molokoane R Y, Mandy Saaiman, Emmanuel Sabela, Lerato Sadiq, Litha Saki, Hyppolite Salambwa, Menitha Samjowan, Nazlee Samodien, Rakgolele Samuel, Fakudze Sandile, Cekuse Sanelisiwe, Mandlankosi Sani, Simangele Sawuka, Lelani Schoeman, Magriet Scholts, Ronel Schroder, Mamotetekoane Sebalabala, Selwalenkwe Collet Sebati, Jacoline Seboko, Wilheminah Sebuthoma, Annah Segami, Ruth Segokotlo, MR Sehloho, Khutjo Seisa, Antony Sekgobela, Monica Sekhosana, John Sekonyela, Mpho Sekoto, Naledi Sekulisa, Mokgadi Vanessa Sekwadi, Lebogo Selaelo, Johannes Selatlha, Kgomotso Selekolo, William Selfridge, Lucy Semenya, Ivy Sengakane, Masabata Sengata, Petronella Sentle, Malebo Seoketsa, Pratheesha Seonandan, Thomas Mambushi Serumula, Nkululeko Setheni, Refiloe Setlale, Tumediso Setlhodi, Barbara Setlhodi, Robert Setloghele, Aarthi Sewpersad, Ryan Sewpersadh, Phumlile Shabalala, Owen Shabangu, Kungesihe Shabangu, Harriet Sbonangaye Shabangu, Thokozani Shabangu, Clifford Shadi, Hasifa Shaik, Tseliso Shale, Qedani Shandu, Nomvelo Shandu, Ntswaki Marcia Shange, Abongile Shenxane, A Sherriff, Sebenzile Shezi, Thenjiwe Shezi, Scally Shihangule, Cheyeza Shikwambana, Lungisani Shoba, Kamogelo shokane, Nora Sibande, Lydia Sibeko, Xolani Sibeko, Zanele Sibiya, Mncedisi Sibiya, Sphamandla Sibuta, Thembakazi Sifumba, Sipho Sigcau, Lutho Sigila, Kayakazi Sihentshe, Bongani Sihlangu, Daisy Sikhakhane, Shaun Nhlanhla Sikhakhane, Mbali Siko, Sipho Sikonje, Khumbulekile Simanga, Nomsa Simango, Thulisile Simela, Ntombikayise Simelane, Sashah Singh, Marjorie Singh, Ragani Singh, Shash Singh, Anita Singh, Hitekani Sithole, Senzekile Sithole, Ntokozo Danielle Sithole, Koketso Maxwell Sithole, Jonnie Situma, Annie Sivraman, Katekani Siwela, Nonqubela Siyewuyewu, Maweya Sizeka, Nonceba Siziba, Andrew Skhosana, Khanyisile Skhosana, Rorisang Skhosana, Tandiwe Skoko, Sunet Slabbert, Ntombela Smangaliso, Christine Smedley, Lydia Smit, Natassia Smit, Lizelle Smit, Michelle Smit, Fasie Smith, Lizzie Smith, Sunell Smith, Cassius Smith, Stefan Smuts, Ayanda Sofe, Khobane Solomon, L J Solomon, chauke Sombani, Richard Songca, Anga Sontamo, Supriya Soorju, Zubenathi Sopazi, Brian Soqasha, Bongiwe Sosibo, Ntsika Sotsaka, Mandy Soula, Simon Spoor, Sarah Stacey, Asanda Stali, Mutele Mmboniseni Stephina, Myra Steup, Sinoxolo Steven, AW Stevens, Vincent Stevens, Dewald Steyn, Bianca Steyn, Pat Stocks, Henk Stolk, Alida Stoltz, Renate Strehlau, Anneke Stroebel, Loraine Strydom, Jean-Marie Strydom, Anton Strydom, Ursula Strydom, Midhu Sunnyraj, Nwabisa Swana, Winnie Swanepoel, Suzan Swanepoel, Elsie Swartbooi, Estley Swartz Swartz, Casandra Syce, Shihambi T E, Joyce Tabane, N E Tabane, Mrs Tawana, Ntene Tebello, Siphosetu Wiseman Tembe, Samantha Terblanche, Ntombifuthi Thabede, Nkhumeleni Thabelo, Sibusiso Thabethe, Lekhanya Thabo George, Keorapetse Thare, Makofane Thebogo, Lerato Thekiso, Lloyd Theko, Celimphilo Zandi Themba, Danie Theron, Henda Theron, Ilze Theron, Thandiwe Thingathinga, M M Thlabadira, Dikeledi Thoka, Zanele Thokwana, Gustav Thom, Mamphot Joel Thubakgale, Theodora Thwala, P Thys, Monethi Tieho, Matodzi Timothy, Ndlovu Tintswalo, Babalwa Tivana, Molefi Tladi, Bongiwe Tokota, Simthandile Toni, Ariel Torres, Mande Toubkin, Marinda Tsatsi, Khanyisile Tshabalala, Nozibele Tshamase, Gontse Tshefu, Makgoga Tshegofatjo, Given Tshikomba, Thapelo Tshilo, Lerato Tshira, S T Tshirado, Maipfi Tshisikule, G Tsoke, N TSOKE, Alatha Tsoko, Mosele Tsotetsi, Sandeva Tsubella, Noxolo Tuswa, Maipato Tutse, Nomayenzeke Tutu, Sphephelo Twala, Nhlanhla Twala, Simphiwe Twala, John Ubisi, Tefo Unathi, A Van Aswegen, Marietjie van der Merwe, Trudie van der Merwe, Patience van der Plank, Elmarie van der Spuy, Linda Van Der Westhuizen, Adele Van Der Westhuizen, Talana van der Westhuizen, Mene van der Westhuyzen, Thea Van Dyk, Ingrid van Heerden, Ryno van Jaarsveld, M Van Lill, Heidi van Niekerk, Ben van Niekerk, Amanda van Rensburg, Judy van Schallwyk, Zeitschke Yarnrich Van Sensie, Magda van Vuuren, Cloete van Vuuren, Olga Funiswa Vandu, Mandisa Vane, Lucia VanZyl, Ebrahim Variava, Mariam Veerus, Nokhwezi Velapi, Sebina Veleko, Z Velezantsi, Retha Venter, Corlia Vergottini, Inga Vermeulen, Liabara Lufuluvhi Vidah, Bongani Vilakazi, Treasure N Vilakazi, Mbalenhle Precious Vilakazi, Karen Viljoen, Werner Viljoen, Zuretha Volschenk, Angelo Vos, Matlala V V, Jacques Walters, Kate Webb, John Welsh, D Wessels, Judy Wheller, Fundile White, Priscilla White, Carmen Whyte, Ansie Willemse, Sape William, Daniel Williams, Kamielah Williams, Mercia Williams, Anne Williamson, Cherade Wilson, Boipelo Wolff, Michelle Wray, Ntombizonke B Xaba, Thabang Jabulani Xaba, Thanks Xiniwe, Mtshali Xoliswa, Funokwakhe Xulu, Gibson Xulu, Sandlakazi Yam, NM Zakhura, Mashela Zareloa, Sive Zinto, Dyibeni Zinziswa, Lulamile Ziselo, Zakhele Zitha, Emmanuel Zitha, Anele Zokufa, Innocent Zondi, Sikhumbuzo Bernard Zondi, Sbuyi Zondi, Thulani Zondi, Wandiswa Zongola, Liesl Zühlke, Zandile Zulu, Lungelo Zulu, Thandeka Zulu, Slindili Zulu, Nkosinathi Zulu, Angel Zuma, Precious Zungu, Pamela Zungu, Melusi Zungu, Priscilla Zungu, Bongo Lihle Zwakala, Antonia Zwane, Promise Zwane, Muziwendoda Zwane, Hlengiwe Priscila Zwane, and Nomgcobo Zwane
Subjects: Male, Pediatrics, medicine.medical_specialty, Tuberculosis, Epidemiology, Immunology, HIV Infections, Comorbidity, Disease, Cohort Studies, South Africa, Risk Factors, Virology, Diabetes mellitus, Prevalence, Humans, Medicine, Hospital Mortality, Asthma, SARS-CoV-2, business.industry, Public health, COVID-19, Articles, Odds ratio, medicine.disease, Infectious Diseases, Anti-Retroviral Agents, Female, business, Cohort study
Abstract: Summary Background The interaction between COVID-19, non-communicable diseases, and chronic infectious diseases such as HIV and tuberculosis is unclear, particularly in low-income and middle-income countries in Africa. South Africa has a national HIV prevalence of 19% among people aged 15–49 years and a tuberculosis prevalence of 0·7% in people of all ages. Using a nationally representative hospital surveillance system in South Africa, we aimed to investigate the factors associated with in-hospital mortality among patients with COVID-19. Methods In this cohort study, we used data submitted to DATCOV, a national active hospital surveillance system for COVID-19 hospital admissions, for patients admitted to hospital with laboratory-confirmed SARS-CoV-2 infection between March 5, 2020, and March 27, 2021. Age, sex, race or ethnicity, and comorbidities (hypertension, diabetes, chronic cardiac disease, chronic pulmonary disease and asthma, chronic renal disease, malignancy in the past 5 years, HIV, and past and current tuberculosis) were considered as risk factors for COVID-19-related in-hospital mortality. COVID-19 in-hospital mortality, the main outcome, was defined as a death related to COVID-19 that occurred during the hospital stay and excluded deaths that occurred because of other causes or after discharge from hospital; therefore, only patients with a known in-hospital outcome (died or discharged alive) were included. Chained equation multiple imputation was used to account for missing data and random-effects multivariable logistic regression models were used to assess the role of HIV status and underlying comorbidities on COVID-19 in-hospital mortality. Findings Among the 219 265 individuals admitted to hospital with laboratory-confirmed SARS-CoV-2 infection and known in-hospital outcome data, 51 037 (23·3%) died. Most commonly observed comorbidities among individuals with available data were hypertension in 61 098 (37·4%) of 163 350, diabetes in 43 885 (27·4%) of 159 932, and HIV in 13 793 (9·1%) of 151 779. Tuberculosis was reported in 5282 (3·6%) of 146 381 individuals. Increasing age was the strongest predictor of COVID-19 in-hospital mortality. Other factors associated were HIV infection (adjusted odds ratio 1·34, 95% CI 1·27–1·43), past tuberculosis (1·26, 1·15–1·38), current tuberculosis (1·42, 1·22–1·64), and both past and current tuberculosis (1·48, 1·32–1·67) compared with never tuberculosis, as well as other described risk factors for COVID-19, such as male sex; non-White race; underlying hypertension, diabetes, chronic cardiac disease, chronic renal disease, and malignancy in the past 5 years; and treatment in the public health sector. After adjusting for other factors, people with HIV not on antiretroviral therapy (ART; adjusted odds ratio 1·45, 95% CI 1·22–1·72) were more likely to die in hospital than were people with HIV on ART. Among people with HIV, the prevalence of other comorbidities was 29·2% compared with 30·8% among HIV-uninfected individuals. Increasing number of comorbidities was associated with increased COVID-19 in-hospital mortality risk in both people with HIV and HIV-uninfected individuals. Interpretation Individuals identified as being at high risk of COVID-19 in-hospital mortality (older individuals and those with chronic comorbidities and people with HIV, particularly those not on ART) would benefit from COVID-19 prevention programmes such as vaccine prioritisation as well as early referral and treatment. Funding South African National Government.
Published: 2021

29. An evaluation of an influenza vaccination campaign targeting pregnant women in 27 clinics in two provinces of South Africa, 2015 – 2018

Author: Stefano Tempia, Sarona Mhlanga, Susan Meiring, Azwifarwi Mathunjwa, Heather J. Zar, Sibongile Walaza, Johanna M. McAnerney, Katherine Bishop, Jackie Kleynhans, Meredith McMorrow, Liza Rossi, Cheryl Cohen, and Grace D. Appiah
Subjects: Prioritization, medicine.medical_specialty, Influenza vaccine, Logistic regression, Health administration, South Africa, Pregnancy, Environmental health, Influenza, Human, medicine, Humans, Pregnancy Complications, Infectious, Immunization Programs, business.industry, Research, Health Policy, Nursing research, Public health, Vaccination, Odds ratio, Pregnant women, South Africa, Influenza vaccines, Female, Pregnant Women, Public aspects of medicine, RA1-1270, business
Abstract: Introduction Despite prioritization, routine antenatal influenza vaccine coverage is Methods From 2015 through 2018, 40,230 additional doses of influenza vaccine were added to the available stock and administered as part of routine antenatal care. Educational talks were given daily and data were collected on women attending ANCs. We compared characteristics of vaccinated and unvaccinated women using multivariable logistic regression. Results We screened 62,979 pregnant women during the period when Southern Hemisphere influenza vaccines were available (27,068 in Gauteng and 35,911 in WC). Vaccine coverage at the targeted clinics was 78.7% (49,355/62682), although pregnant women in WC were more likely to be vaccinated compared to those in the Gauteng (Odds ratio (OR) =3.7 p 35 years were less likely to be vaccinated than women aged 18—24 years (OR = 0.9 p = 0.053; OR = 0.9 p < 0.001). HIV positive status was not associated with vaccination (OR = 1.0 p = 0.266). Reasons for not vaccinating included: vaccine stock-outs where ANCs depleted available stock of vaccines and/or were awaiting delivery of vaccines (54.6%, 6949/12723), refusal/indecision (25.8%, 3285), and current illness that contraindicated vaccination (19.6%, 2489). Conclusion Antenatal vaccination uptake was likely improved by the increased vaccine supply and vaccine education offered during our campaign.
Published: 2021

30. Difference in mortality among individuals admitted to hospital with COVID-19 during the first and second waves in South Africa: a cohort study

Author: Waasila Jassat, Caroline Mudara, Lovelyn Ozougwu, Stefano Tempia, Lucille Blumberg, Mary-Ann Davies, Yogan Pillay, Terence Carter, Ramphelane Morewane, Milani Wolmarans, Anne von Gottberg, Jinal N Bhiman, Sibongile Walaza, Cheryl Cohen, Shaina Abdullah, Fiona Abrahams, Vincentius Adams, FHIMA ADNANE, Sonia Adoni, Dieketso Melitta Adoons, Veronique Africa, Dr Aguinaga, Susan Akach, Prisha Alakram Khelawon, George Aldrich, Olatunde Alesinloye, Mathale Biniki Aletta, Mametja Alice, Tebogo Aphane, Moherndran Archary, Felicity Arends, Shireen Arends, Munonde Aser, T Asmal, Mohammed Asvat, Theunis Avenant, Muvhali Avhazwivhoni, Magnolia Azuike, Johanna Baartman, Dlava Babalwa, Johan Badenhorst, Miranda Badenhorst, Badenhorst, Bianca Badripersad (CEO), Lalihla Badul, M Bagananeng, Mncedisi Bahle, Liezl Balfour, TC Baloyi, S Baloyi, Tinyiko Baloyi, Tshepo Mpho Baloyi, Thokozani Banda, Shimon Barit, Nicole Bartsch, Junaid Bayat, Siyabulela Bazana, Marlene Beetge, Nosindiso Bekapezulu, Rammala Belebele, Phala Bella, Zanenkululeko Belot, Lindi Gladys Bembe, Sonja Bensch, Gishma Beukes, Karla Bezuidenhout, Themba Bhembe, N.A BIKISHA, Ben Bilenge, Leesa Bishop, Baphamandla Biyela, Cyntheola Blaauw, Mark Blaylock, Nicola Bodley, Power Bogale, Sibongile Bokolo, Stefan Bolon, Mary Booysen, Eldereze Booysen, Lia Boretti, Paula Borges, Millicent Boshoga, Natasha Bosman, Lucinda Bosvark, Nicky Botes, Adele Botha, CHANTALL BOTHA, Jana Botha, MANDLAKAYISE IRVIN BOTHA, Alet Botha, Janet Bradbury, Zandisile Breakfast, Maria Breed, Molele Brenda, Moshito Brice, Jolene Britz, Amanda brown, Ms T Buchanan, Thozama Bucwa, Crystelle Burger, Ziyanda Busakwe, Nosiviwe Bushula, Zinhle Buthelezi, Dumsile Buthelezi, Thubelihle Buthelezi, Mpumelelo Basil Buthelezi, Fundiswa Lidwina Buthelezi, Nadia Bux, Christoff Buys, Anneline Buys, Ernestina Caka, Armando Sanchez Canal, Sithole Caroline, Monrick Casper, Shannon Cawood, Oratile Cebisa, Nothando Cele, Sboniso Cele, Sthembile Goodness Cele, Mkhacani Chauke, Pinkie Chauke, Nevil Chelin, Xiaohui Chen, Venmalla Chetty, Kerisse Chetty, Christinah Cheu, Vindana Chibabhai, Takudzwa Chirima, Mantwa ChisaleMabotja, CHARITY CHIVENGE, Ngoasheng Choene, Mbali Nosisa Choko, Martin Choshi, Sabbir Chowdhury, Anastacia Christoforou, S.L.S Chuene, T.S Chueu, Dale Cilliers, Vanessa Cilliers, Marcel Claassen, Jeané Cloete, Chantelle Coelho, Carol Coetzee, Hans Jurgens Coetzee, Christine Coetzee, Marelize Coetzee, Dane Coetzer, Sizwe Coka, Mr M Colane, Herkulaas Combrink, Songezo Conjwa, Colleen Contrad, Faith Cornelissen, Leezelle Cronje, Christine Crouse, Moshai D.A, Ms Mahabane D.I, Tshidi Dabi, Ziyanda Dandala, Ziyaad Dangor, Gildenhuys Daniel, Ngwana Daniel, Alfred Daumas, Madelein Dauth, Mongalo David, Wayne Davids, Nozuko Daweti, Halima Dawood, Wandisa Dayile, B DE BRUIN, Karin De Klerk, Tanya De la Rosa, Marice de Nysschen, Marie De vos, Darien De Wet, Mohith Debising, Darshan Deenadayalu, Babalwa Dekeda, Mofokeng Desiree, Annelise Deysel, Abram Dhlamini, Makgethwa Dhlala Diala, Mathapelo Diale, Bella Diketane, Nosisa Dingani, Siyabonga Diniso, Lesego Diphatse, Anele Diya, Zihloniphile Dladla, Nompumelelo Dladla, Mlungisi Dladla, Patience Dladla, Baphilie Dlamini, NONHLANHLA DLAMINI, Linda Dlamini, Nonzwakazi Dlamini, Wendy Dlamini, Ncomeka Dlamini, Siyabonga Dlamini, Nicodemus Dlamini, Lebohang Dlamini, Motshedise Dlamini, Babalwa Christine Dlava, Phikiwe Dlova, Lindiwe Dlozi, Maenetja Doreen, Vumile Doyi, Athini Doyi, Belinda Du Plessis, Johanna Aletta du Plessis, Mr. Eddie du Plessis, Nicolette du Plessis, Karin du Plessis, Briette du Toit, Narissa du Toit, Jabulile Dube, Athayanda Dubula, Msomi Duduzile, Sechaba Duiker, Unati Bongile Duma, Kholiwe Duma, Kella Dunne, Kholeka Dyantyi, Avile Dyantyi, Simphiwe Dyasi, CHAUKE DYONDZO, Phelisa Dyubhele, B.J Dywili, Letitia Edwards Edwards, Madie Eksteen, Tersia Ellis, Tia Ellis, Glenda Emmerson, Theusia Enslin, ODIMULA EPULE, Lana Erasmus, Mathonsi Erick, Lerato Etsane, Shimange Eunice, Zanele Fani, Mariette Ferreira, K.L Finger-Motsepe, Fabion Floris, Tseko Fobo, Keresemetse Fokotsane, Duduzile Emmelda Fokwana, Genevieve Marion Fords, Juanita Fortein, Christine Fouche, Rulandi Fourie, Andrew Frean, Ludwig Fredericks, Wandile Funda, Kabelo Funjwa, Martha Futhane, Amanda Futuse, Dora Gabaediwe, Nonhlanhla Gabuza, Janycke Galant, Zanele Gama, Thobile Gano, Emma Cora Gardiner, Henri Gastrow, Kelly Gate, Ben Gaunt, Rikhotso Gavaza, Thapelo Gayi, Nkosinathi Gcakasi, Nomusa Gcobo, Leon Geffen, S Geldenhuys, Jenny George, Martha Gerber, Zolisa Getyengana, Nkululo Gigi, Radha Gihwala, Mitchell Gilliland, Zandile Gloria, Elitia Glover, Ellen Gokailemang, Suseth Goosen, Maria Gopane, Thandazile Gosa - Lufuta, Bernadett Gosnell, Sharleen Gouws, Christina Govender, Raksha Govender, Pearl Govender, Sally Govender, Roxanne Govender, K Govender, Mrs Savie Govender, Rashika Govinden, Luphumlo Gqabuza, Nomthandazo Gqaji, Maneo Gqetywa, Caroline Green, Nathan Green, Neera Green, Hendrik Grobler, Pamela Groenwald, Daniel Grootboom, Beatrice Gumede, Nomonde Gumede, Simphiwe Gumede, Slindile Gumede, Ntombikayise Gumede, Zenande Gumede, Thandiswa Gxotiwe, Makhubela H.L, Nonhlanhla Hadebe, Skhumbuzo Hadebe, Christos Halkas, Ansie Hamer, Ebrahim Hamida, Juan Hammond, Sumayia Haniff, Annelise Hare, lorinda Hattingh, Thenjiwe Hendricks, Philip-George Henecke, Brends Henly-Smith, Glynis Herselman, Ansie Heymans, Chantel Heyns, Golekane Hlabahlaba, Lucky Hlabangwane, Simango Hlamarisa, Ntokozo Hlanzi, Hlengiwe Hlela, Katlego Hlokwe, Thembinkosi hlongwa, Anele Hlongwana, Themba Hlubi, Tozama Hobo, Nare Nathaniel Hopane, Mariska House, Catharina Hudson, Marinda Huysamen, Jezreen Indheren, Samantha Ingle, Gavin Isaacs, TS Thekiso Isaacs, Maringa Itumeleng, Karien J van Rensburg, Saloshni Jackson, Neziswa Jacob, Burton Jacobs, Tshireletso Jacobs, Gugulethu Jacobs, Mesadi Jaftha, Zimkhitha Jaji, Sibusiso Jali, Gcobisa James, Gillian January, Andiswa Jeke, Laurent Jeremiah, LS Jeremiah, Mubeen Jhetam, Maureen John, Chuene John, Thandiwe Jola, Yolande Jonas, Anovick Jonas, Amilcar Juggernath, eileen kaba, Venetia Kabo, Disebo Kadi, Karabo Kaizer, Moshaya Peter Kambule, Lorraine Kapp, Tshepo Kau, Nchabeleng Keneth, O Kgabi, Tebogo Audrey Kgafela, Vincent Kgakgadi, Isabella Kgaswe, Tsholofelo Kgathlane, Vuyelwa Julia Kgetha, Mmaselloane Kgomojoo, MR B Kgoro, Christinah Kgosiemang, Gloria Kgosiencho, Stephen Khambula, Ariffa Khan, Refemetswe Khanare, Ncamsile Khanyase, Nokwethemba Khanyile(Data Capturer), Fillip Kharatsi, Simangele Khawula, Themba Khohlakala, Letitia Khomo, Isabel khoza, Sinethemba Khoza, Nombulelo Khukule, Busisiwe Khumalo, Tracy Khumalo, Zinhle khumalo, Vuyelwa Khumalo, Delisile Khumalo, Lebohang Khumalo, Boitumelo Khumalo, Thuli Khumalo, Gugu Khumalo, Bongiwe Khuzwayo, Thembhelihle Khuzwayo, Hennie Kidson, Jesne Kistan, Gugu Klaas, Marilyn Klassen, Josehine Koeberg, Marizel Koen, Simphiwe Koena, Ina Kok, Imraan Kola, Karabo Kolokoto, Ramachandra Konar, Dr Kotsedi, Jaline Kotze, MARTINS KOUPIS CDS, Sr Helen Kritzinger, Marlize Kruger, Henk Kruger, Tlangelani Kubayi, Thabisile Kubeka, Nonjabulo Kubheka, Melusi Kubheka, Sibusiso Clifford Kubheka, Erol Kubheka, Monica Kumalo, Thulani Kunene, Siphilile Candy Kunene, Yvette Kunneke, R.P KUPA, Rachel Kutama, Nompumelelo Kwakwazi, Lwanele Kweyama, Maureen Labuschagne, Marina Labuschagne, Prabha Lakshman, Lungelo Lamani, Thembela Lamani, Naomi Langa, Khangelani Langeni, Aphelele Langeni, Nwabisa Hazel Langeni, Gena Langeveldt, Anchen Laubscher, Laetitia Le Roux, Magagane Leah, Collen Lebea, Sello Lebea, Viyella Phumla Cynthia Lebenya, Lorraine lebogang, PK LEBOHO, Chantel Lee, Kelebogile Rejoice Lefakane, Zandile Legoabe, Patrick Lekala, Motsitsi Lekhoaba, Tanki Shadrack Lekunutu, Galaletsang Lerefolo, Mrs N Letebele, Tsepo Patric Lethoba, Emission Letlalo, Ofentse Letlhage, D.S.V Letshufi, Dineo Fiona Letsoalo, Seleka Jones Letsoalo, Pennelope Letsoalo, Getrude Letwaba, Sobekwa Linda, Katleho Lipholo, Sabata Litabe, Harsha Lochan, Linda Lomax, Francina Lombaard, Elmarie Loots, Ariana Lourens, Celeste Louw, Rianna Louw, Zikhona Lubambo, Msebenzi Moises Lubambo, Gregory Ludada, Michael Lukas, Thembela Lungu, Nomvume Lupindo, Emmah Lusenga, Happiness Luthuli, Zoleka Sylvia Luvuno, Sr Gwangwa M.H, Mustafa Maarman, Buyisiwe Mabaso, Cynthia Mabaso, Morena Mabitle, Grace Mabogoane, Kgakgamatso Mabone, Rueben Mabuza, Velaphi Mabuza, Mogantla Madiseng, Thobile Madlala, Mashooase Madolo, Thabiso Madonsela, Lesetsa Madubanya, Amukelani Maepa, Namhla Mafumana, Caroline Mafumo, Pumeza Magadla, Viscah Magale, Nompumelelo Magaqa, Oberholzer Magda, Rakgoale Magdeline, Tswai Maggie, Bongeka Maginxa, Cathrine Maite Magoba, Caroline Magongwa, AGRETIA MAGUBANE, Agretia Ntombizodwa Magubane, R Magwai, Padmini Mahabeer, Elsie Mahadulula, Lungiswa Mahanjana, Amy Maharaj, Qedusiza Mahlambi, Yvonne Mahlangu, Lerato Mahlangu, Ntombifikile Mahlangu, Makhosazana Mahlangu, Mahlatsi Mahlangu, Penelope Mahlasela, Thosago Mahlatse, Regina Mahlobo, Dikhing Mahole, Adam Mahomed, Mapeu Debora Mahubane, Peter Mahume, Lehlogonolo Maifo, Vincent Maimane, Petunia Maimele, Phakoe Maine, Patricia Senyanyathi Mainongwane, Nomalungisa Majamani, Amahle Majozini, Noluthando Makalima, Nomfundo Makam, Khanyisa Makamba, R Makan, Mashiane Makarapa, Malesela Makgahlela, Mogoiwa David Makgisa, Makgoba Makgomo, MA Makgopa, Mabone Makhalema, Lindokuhle Lizo Makhanya, Philile Valentia Makhanya, Tolerance Makharaedzha, Nathi Makhathini, Elizabeth Makhesi, Cinile Makhubela, Nkululeko Freedom Makhunga, Nomalinge Makhupula, RR Makhura, Rangwato Makola, Zingisa Makuba, Asanda Makubalo, Lonwabo Makumsha, George Makuya, Levy Mmachuene Malaka, Themba Malangeni, ML MALATJI, Pelonomi Malebana-Metsing, Malek Malek, Luthando Malevu, Juanita Malgas, Dimakatso Malgas, Paul Makgasane Malope, Monyeki Malose, Katekani Maluleke, Kato Mambane, Nthabiseng Mamorobela, Kukami Manamela, Tshepo Manana, Sathiel Maneto, Aron Kabelo Manganye, Pheto Mangena, Anna Mangoale, TINOTENDA FLORENCE MANGOZHO, Pariva Manickchund, Zandisile Mankayi, Arthur Manning, Kelebogile Manyaapelo Manyaapelo, Tabea Manyane, Zoliswa Manzana, Milton Manzini, Busisiwe Mapasa-Dube, Siboniso Maphumulo, Ntombifuthi Maphumulo, Sindy Maponya, Khomotso Mumsy Maponya, Napjadi Maponya, Lami Maqubela, Lizeka Maqubela, Vuyo Maqungo, Marisa Marais, Chantal Marais, Nondumiso Maramba, Annelize Mare, Madumetsa Maredi, Afikile Martins, Johanna Marule, Refilwe Marumo, NN Masakona, KEDIBONE VINCENTIA MASEHLA, Eric Maseko, Tshilidzi Maselesele, Mojalefa Maselo, M Maseloa, M.E Masemola, Thembi Masemola, Bella Mashaba, James Mashangwane, Mantebele Mashao, Shalom Mashego, Lerato Mashele, Ester Mashiane, Joyce Mashibini, J Mashilo, Tumi Mashiloane, Charity Mashishi, Ngazibini Mashiyi, Khomola Mashudu, aluwani masindi, Caroline Maslo, Nduduzo Masondo, Dumisile Masuku, Cry Matamela, Mirriam Matandela, Nontokozo Mathabela, T Mathabi, Keitumetse Mathe, Mathabo Mathebula, Catherine Mathebula, Mdungazi Andres Mathebula, Nqobizwe Mathenjwa, Jane Mathibe, Lebohang Mathibela, MAKWELA MATHILDA, Khakhu Mathiva, Mokgadi Alinah Mathobela, Fikile Pearl Mathonsi, KP Mathonsi, Katlego Mathosa, Noluvo Matiwane, Emma Matjeke, Bella Matjiane, Thabang Matjila, Sr Chidi Matlala, Petlo Matome, Nolusindiso Matoti, C. Matseliso, Dineo Matsemela, Phumeza Matsha, Gaalebale Prudence Matshediso, Motsumi Matshediso, Esther Matshela, Bongeka Mavuma, Pearl Mavundla, Nomthandazo Mavuso, Lovender Mawasha, Rebecca Mawelela, Nelisiwe Mazibuko, Phumlani Mazibuko, Lindiwe Mazubane, Bavumile Mbanjwa, Ayanda Mbasa, Nosimilo Mbatha, ZANELE MBATHA, Rudolph Zenzele Mbatha, Gift Mbedzi, Tatenda Trevor Mbizi, Khumbulani Mbonambi, Nondumiso Mboniswa, Nomfanelo Mbonisweni, Jody Mbuilu, Siyabonga Mbulawa, Zama Mbutho, Natasha Mbuzi, Nonkululeko Mchunu, Cyprian Mchunu, Nokuzola Mchunu, Masesi Thandeka Mchunu, Vuyokazi Mciteka, Solly Mdaka, Neho Mdakane, Siyabonga Mdediswa, Melusi Mdima, Nozipho Mdima Masondo, Siviwe Mdindana, Ntombizikhona Mdleleni, Sibusiso Mdletshe, Gcobisa Precious Mdoda, Ntombi Mdolo, Anele Mdontsane, Ruchikas Mehta, Philile Rittah Memela, Masande Methuse, Keatlaretse Metshile, Pheliswa Metuse, Anton Meyer, Gavin Meyer, Cameron Meyer, Sisonke Mfazwe, Andiswa Mfecane, Bongeka Mfecane, Nelisiwe Mfeka, Busisiwe Mgaga, Thandiwe Portia Mgauli, Thembekile Mgedezi, Vuyokazi Mgedezi, Kalipile Mgevane, Bongni Mgiba, Babalwa Mgoduka, PATRICK MHLABA, Zeldah Mhlaba, Ntombizodwa Mhlanga, Vangile Mhlinza, Nokuthula Mhlongo, sibongiseni Mhlongo, Unamandla Mhlotshana, Mabaso Mikateko, Helena Minnie, Karen Mintoor, Bongi Miyeni, Mabelane MJ, Rosy Mjethu, Gloria Mkhize, Mvuselelo Mkhize, Ntokozo Siyabonga Mkhize, Victoria Mkhize, Nomkhosi Mkhize, Nokuthula Mkhize, Mathini Mkhwanazi, Nolwandle Mkile, Kholofelo Mkise, Nokwandiso Mkiya, Pearl Mkongi, Mnonopheli Mkungeka, Hlomile Mlahleki, Nolukholo Mlibali, Sakhumzi mlungwana, Jonas Mmachele, Mashatole Mmateka, Molebatsi Mmokwa, Thembisa Mmutlane, Zanele Olive Mndebele, nonhlanhla mngomezulu, Noluthando Millicent Mnguni, Pumza Mngunyana, Nomxolisi Mngunyana, Ntombebongo Mngxekeza, ZENZELE MNISI, Hlengiwe Precious Mnqayi, PHUMZILE MNQAYI, Thabiso Mntungwa, Siya Mnyaka, Ntombikayise Mnyakeni, Vuyani Mnyamana, Nomzingisi Mnyipika, Koena Moabelo, Mmakgoshi Alseria Moatshe, Jennifer Mochaki-Senoge Mochaki-Senoge, Sharon Moche, Tebello Mocwagae, Koeikantse Modibane, Tebogo godfrey Modimoeng, Obakeng Modisa, Itumeleng Modisane, Olebogeng Modise, Makaepeaa Flovia Modjadji, Sharon Modupe, Maja Moeketsi, Ntswaki Moeketsi, Kereditse Kingsley Moeng, Naledi Nthabiseng Mofamere, Samuel Mofokeng, Thabo Mofokeng, Jonas Mofomme, VICKY MOGAKANE, Lehlohonolo Mogale, Audrey Mogapi, Thomas Mogashoa, Mphaka James Mogatla, Kgaladi Mogoale, Dikeledi Maggie Mohajane, Nkuba Mohapi, Mthoamihla Mohatsela, Irene Mohlala, Daphney Mohlala, Mpho Mohlamonyane, Bonolo Millord Mohutsiwa, Selemela Moipone, Tshepang Moisi, Nelly Mojalefa, Vuyo Moji, Buhle Mokangwana, Matloa Mokgabo, Manaka Mokgaetji, Jane Mokgaotsi, Neo Theodore Mokgoro, Thalitha Mokhatla, Lerato Lovedalia Mokhele, Sheila Mokhema, Mamoya Mokoena, Mojalefa Mokoena, Lleka Mokome, Cynthia Mokone, Ipeleng Mokono, Thabiso Mokonyama, Josiah Mokori, Dolores Mokuena, Danny Mokumo, Oddy Mokwena, Kgaogelo Mokwena, Kgantshi Sam Mokwena, Lebogang Mokwene, Thato Elliott Molate, Ditoche Molebalwa, Boingotlo Molefe, KGOPA STANLEY MOLEHE, Kgomotso Moleme, Sarah Moliane, FANYANA MOLOI, Retshepile Joseph Molorane, Glenda Tsholanang Molotsi, Lerato Molukanele, Joy Monareng, Thapelo Moncho, Modiadie Monica, Refilwe Monnane, Andile Monqo, Neo Montewa, Kgalalelo Montsioa, Reitumetse monyaki, Masekhobe Jeanett Monyane, Lipson Monyela, Yudeshan Moodley, Kriesen Moodley, Kaira Moodley, Boitumelo Donald Mooka, Prea Moonsamy, Simmi Moopanar, David Moore, Lineo Mophethe, Tshegohatso Moremedi, Kealeboga Moremong, nthangeni morgan, Egma Moripa, Lulamile Morris, Me. A.M. Mosala, Thabo Mosana, Alice Mosase, Yolanda Mose, Maponya Mosehlo, Mothusi Moseki, Mojalefa David Moshabe, Mbulelo Moshani, Pelisa Moshani, Ledwaba Mosima, Ezrom Mosima, M.P Mosoma, Lebohang Motaung, Mokete Motaung, Thozama Charmain Motaung Xhama, Purine Khethiwe Motha, Lerato Motimele, Boitumelo Motimeng, Shirley Motladiile, otsile Motlhabane, Joshua Motlhamme, Mandla Motloba, Kagiso Motse, Sophia Motshegoa, Edward Moutlana, Irma Mouton, Zanele Moya, Nomonde Moyake, Maja MP, Jenny Mpete, Luamba Meltha Mpfuni, Seputule Mphahlele Mphahlele, Mashadi Mphake, Ephraim Letlhogonolo Mphanya, Mashudu Mphaphuli, Tebogo Chwene Mphela, MS Mpontshane, Thabile Mqotyana, Babalwa Mqungquthu, Noluthando Busane Msane, Malusi Mseleku, Sibusiso Msibi, Mancele Msibi, Thulisile Msibi, Siyabonga Linda Msibi, Clement Nhlanhla Msiza, Lungelo Msomi, Mandlenkosi Mtatambi, Thembisa Mthathambi, December Mthembu, Nhlahla Mthembu, Fezile Mbali Mthembu, Lungiswa Mthembu, Nompumelelo Petunia Mthethwa, Khulekani Mthimkhulu, Lungani Percival Mthuli, Ashley Mthunzi, Xolani Sydney Mtolo, Nomonde Precious Mtolo, Linda Mtshali, Neliswa Mtwa, Fezeka Mtyobile, Kanyisa Mtyobile, Mpfariseni Mudau, Magwabeni Muemeleli, Isaac Mulaudzi, Rebecca Mulaudzi, Mhlelekedzeni Mulaudzi, Dakalo Rejoyce Muligwe, Blessing Muponda, Mmbangiseni Stella Mushadi, M Mushid, Konanani Muthaphuli, J Muthavhine, Mpho Muthika, Samkelisiwe Mvelase, Vusi Mvelase, LAURENT KAYUMBA MWEHU, Thabile Myaka, Magriet myburgh, Zimkhitha Mzamo, Fezeka Mzawuziwa, Mfundo Lunga Mzini, Oscar Mzizana, Ntokozo Mzobe, Thokozile Mzobe, Zamaswazi Mzobe, Mtimkulu Mzwandile, Fathima Naby, KESHNEE NAICKER, Pregashnie Naicker, Saroja Naicker, Pershen Naicker, Saiyen Virgil Naicker, RIA NAIDOO, Sam Naidoo, Mergan Naidoo, KAMALAMBAL NAIDOO, Aroomugam Naidoo, Sivuyile Naku, Firdose Nakwa, Masoga Nancy, Rita Nathan, Maritsa Naude, Gcobisa Ncaza, Aviwe Ncaza, Relebohile Ncha, Yanelisa Ncoyini, Snothile Ncube, Mrs Ndaba, VUSUMUZI NDABA, Mmapula Ndaba, Siziwe Ndawonde, Ziphozihle Ndevu, NONHLANHLA FAITH NDHLOVU, Simphiwe Ndima, Sindisiwe Ndlela, Thobsile P Ndlela, Nobuhle Ndlovu, Nwabisa Ndlovu, Virginia Dipuo Ndlovu, Sombekhaya Ndlumbini, Khululiwe Nduli, Priscilla Nontokozo Nduli, Michael Ndwambi, Jeremy Nel, Rina Nel, Lizelle Nel, Ntsundeni florah Nemanashi, Usinkhangwe Nyaphophi Nemudivhiso, Joyce Nemutavhanani Nemutavhanani, Jabu Nene, Xolani Nene, David Netshilonga, Rendani Netsianda, Charmaine Newton, Vuyo Leroy Ngalo, Ncumisa Ngani, Thabisa Monica Ngcakaza, Thamela Ngcobo, Trulove Nonhlanhla Ngcobo, Richards Ngcobo, Gcinile Ngcobo, Guguletu Ngcobo, Thozama Ngetu, Pinkie Ngewu, Tshepo Ngobeni, Providence Ngobeni, Khanyisile Ngobeni, Prudence Ngobeni, Thembisile Ngobese, Tracy Ngomane, Nolusindiso Ngondo, Nokukhanya Ngubane, Sithembiso Ngubane, Ntombizodwa Praxedise Nguse, Tholakele Ngwane, Elizabeth Ngwasheng, Siphamandla Ngwenya, Gugu Ngwenya, Nomthandazo Ngwenya, Themba Ngwenya, Eva Ngwenya, Zintlanu Ngxola, Tshegofatso Nhabe, Jabulile Nhlabathi, Ishmael Nhlangwana, Sithembile Nhlapo, Matlala nick, Vicky Niemand, Carina Nienaber, Louise Nix, Chumisa Njikelana, Masiza Njomi, Lucia Nkabinde, M NKABINDE, Boitumelo Nkabiti, Gugu Nkabule, Mankopodi Nkadimeng, Nonkanyiso Nkanjeni, Palesa Portia Nkatlo, Bongani Nkewana, Audrey Nkhwashu, Ngokoana Nkoana, Mmathapelo Nkoane, M Nkogatse, Fezile Nkomo, Ntando Nkomo, Nontobeko Nkonyane, Sydney Nkosi, Ntombikayise Nkosi, Phumzile Nkosi, Ntombifuthi Nkosi, TINTSWALO NKOSI, ML Nkosi, Godfrey Nkosi, Amukelani Nkosi, Fikile Vinoliah Nkosi, Mbali Nkosi, Nomcebo Lucia Nkosi, Siphokazi Nkosi, Amanda Nkuhlu, Phumzile Nkumane, Malebo Nkuna, Wendy Nkwakwha, Sesi Noge, Elizabeth Nolte, Peko Nomawabo, Malibongwe Nombita, Nandipha Nophale, Jeanetta Nothnagel, Bongiwe Novokoza, Zanele Nqaphi, Thobekile Nqondo, Siphokazi Nqwelo, Nkoana NS, Sindiswa Ntabeni, Mr Ntabeni, mawethu Ntampula, Mthutuzeli Ntebe, MOKWABO NTELA, Hezekiah Ntimbane, Xolisa Ntintsilana, Patrick Ntleki, Zanele Ntobela, Bandile Ntombela, Zamaswazi Ntombela, Khonelihle Zandile Ntombela, Praisegod Samkelo Thobani Ntombela, Lindiwe Ntonintshi, Dipuo Ntseane, Thobeka Ntseane, Xolelwa Ntsham, Mbalenhle Ntshele, Amanda Ntshewula, Zinzi Ntsoko, Athini Ntsoto, Nomsa Ntuli, Nokwazi Ntuli, Nomvula Ntuli, Andrew Diffar Ntuli, Faith Ntuli, Margrit Nurnberger, Ntsikelelo Nxala, Sithandiwe Nxasane, Mr Thanda Nxumalo, Xolani Nyathi, Nontobeko Nyawula, Nhlakanipho Nzama, Maila Nkuneng Obed, Florence Ogwal, Maureen Olifant, Mr B Oliphant, Monota Olive, Kagisho Olyn, Raymond Omoighe, Phumeza One, Ratombo Oscar, Nkuna Owen, Mailula P, Nalini Padayachee, Vasaily Padayachy, Ntombizakhe Pakade, Mosiuoa Palime, Jane Palisa, Arifa Parker, Lesenyeho Parkies, Andy Parrish, Nilesh Patel, Anastasia Pather, Mkhombo Tsakani Patience, Marisa Patzke, Akhumzi Pawuli, Ntandokazi Pelako, Phaswana Sibasa Penrose, Litha Peppeta, Santosh Pershad, Makheda Pertunia, Nkuna Pertunia, Dane Perumal, Mongameli Peter, Justin Peters, Vatiswa Petlane, Harideen Petrus, Kgomotso Phahladira, Matebesi John Phakisa, R Phale, Livhuwani Phathela, Sekate Daniel Phillip, Beverly Phiri, Mapule Precious Phiri, Thapelo Phokane, Frank Phokoane, Moele Pholosho, Sekoro Phooko, Sekodi Geoffrey Phooko, Maponya Phutiane, Faiza Pillay, Melanie Pillay, Sayuri Pillay, CR Pillay, Zikhona Plaatjie, James Pootona, Samantha Potgieter, Marius Potgieter, Mulaudzi Mulatedzi Precious, Paul Janus Pretorius, Hans Prozesky, Mokhethi Pule, Jayshina Punwasi, Dot Putzier, Lutho Qankqiso, Siphokazi Qebedu, Phozisa Qhola, Ntombesithathu Qotoyi, Sipho Victor Qotso, Zanele Qwabe, Helena Rabie, Phoebe Rabothata, Christina Rachoene, Mteteleli Radana, Maria Radebe, Dr. Valentino Radebe, Nonkululeko Radebe, Ella Radinne, Sherly Raduvha, Shamintha Raghunath, Claudine Rajagopaul, Mary Rakgwale, Malumbete Michael Ralethe, Kenneth ralimo, Motlalepule Ramafoko, Maduvhahafani Ramagoma, Charlotte Raman, Dr Ramavhuya, Molly Rambally, Nivasha Ramdeen, Tanusha Ramdin, Sharita Rameshwarnath, Yeishna Ramkillawan, null Ramotlou, Faith Rampedi, Vijayluxmi Rampersad, Avhashoni Ramuima, Noluthando Ranone, Mabohlale Portia Rapasa, Mpharoane rapelang, Nika Raphaely, Lesiba Rashokeng, Caroline Rashopola, Tebogo Ratau, M RATAU, Mpfariseni David Ratshili, Elmari Rautenbach, Rofhiwa Ravele, Johannes Reachable, Peta Mmalahla Rebecca, Kessendri Reddy, Andrew Redfern, Robertha Reed, Mumsy Rees, Dr Reji, Gary Reubenson, Veena Rewthinarain, Paul Rheeder, Nkonayani Rhulani, Mufamadi Richard, J.S Rikhotso, Shatimone Beverley Rikhotso, Lavhelani Ndivhaleni Robert, Noncedo Roto, Gideon Ruder, Kapil Rugnath, Lizette Ruiters, Mina Ruiters, Sue Russell, Lynn Ruwiza, Molokoane RY, Mandy Saaiman, Emmanuel Sabela, Lerato Sadiq, Litha Saki, HYPPOLITE SALAMBWA, Menitha Samjowan, Nazlee Samodien, Rakgolele Samuel, Fakudze Sandile, Cekuse Sanelisiwe, Mandlankosi Sani, Simangele Sawuka, Lelani Schoeman, Magriet Scholts, Ronel Schroder, Mamotetekoane Sebalabala, Selwalenkwe Collet Sebati, Jacoline Seboko, Wilheminah Sebuthoma, Annah Segami, Ruth Segokotlo, MR Sehloho, Khutjo Seisa, Antony Sekgobela, Monica Sekhosana, John Sekonyela, Mpho Sekoto, Naledi Sekulisa, Mokgadi Vanessa Sekwadi, Lebogo Selaelo, Johannes Selatlha, Kgomotso Selekolo, William Selfridge, Lucy Semenya, Ivy Sengakane, Masabata Sengata, Petronella Sentle, Malebo Seoketsa, Pratheesha Seonandan, Thomas Mambushi Serumula, Nkululeko Setheni, Refiloe Setlale, Tumediso Setlhodi, Barbara Setlhodi, Robert Setloghele, Aarthi Sewpersad, Ryan Sewpersadh, Phumlile Shabalala, Owen Shabangu, Kungesihe Shabangu, Harriet Sbonangaye Shabangu, Doctor Thokozani Shabangu, Clifford Shadi, Hasifa Shaik, Tseliso Shale, Qedani Shandu, Nomvelo Shandu, Ntswaki Marcia Shange, Abongile Shenxane, A Sherriff, Sebenzile Shezi, Thenjiwe Shezi, Scally Shihangule, Cheyeza Shikwambana, Lungisani Shoba, Kamogelo shokane, Nora Sibande, Lydia Sibeko, Xolani Sibeko, Zanele Sibiya, Mncedisi Sibiya, Sphamandla Sibuta, Thembakazi Sifumba, Sipho Sigcau, Lutho Sigila, Kayakazi Sihentshe, Bongani Sihlangu, Daisy Sikhakhane, Shaun Nhlanhla Sikhakhane, Mbali Siko, Sipho Sikonje, Khumbulekile Simanga, Nomsa Simango, Thulisile Simela, Ntombikayise Simelane, Sashah Singh, Marjorie Singh, Mrs Ragani Singh, Shash Singh, Anita Singh, Hitekani Sithole, Senzekile Sithole, Ntokozo Danielle Sithole, Koketso Maxwell Sithole, Jonnie Situma, Annie Sivraman, Katekani Siwela, Nonqubela Siyewuyewu, Maweya Sizeka, Nonceba Siziba, Andrew Skhosana, Khanyisile Skhosana, RORISANG SKHOSANA, Tandiwe Skoko, Sunet Slabbert, Ntombela Smangaliso, Christine Smedley, Lydia Smit, Natassia Smit, Lizelle Smit, Michelle Smit, Fasie Smith, Lizzie Smith, Sunell Smith, Cassius Smith, Stefan Smuts, Ayanda Sofe, Khobane Solomon, LJ Solomon, chauke Sombani, RICHARD SONGCA, Anga Sontamo, Supriya Soorju, Zubenathi Sopazi, Brian Soqasha, Bongiwe Sosibo, Ntsika Sotsaka, Mandy Soula, Simon Spoor, Sarah Stacey, Asanda Stali, Mutele Mmboniseni Stephina, Myra Steup, Sinoxolo Steven, AW Stevens, Vincent Stevens, Dewald Steyn, Bianca Steyn, Pat Stocks, Henk Stolk, Alida Stoltz, Renate Strehlau, Anneke Stroebel, Loraine Strydom, Jean-Marie Strydom, Anton Strydom, Ursula Strydom, Midhu Sunnyraj, Nwabisa Swana, Winnie Swanepoel, Suzan Swanepoel, Elsie Swartbooi, Estley Swartz Swartz, Casandra Syce, Shihambi T.E, Joyce Tabane, NE Tabane, Mrs Tawana, Ntene Tebello, Siphosetu Wiseman Tembe, Samantha Terblanche, Ntombifuthi Thabede, Nkhumeleni Thabelo, Sibusiso Thabethe, Lekhanya Thabo George, Keorapetse Thare, Makofane Thebogo, Lerato Thekiso, Lloyd Theko, Celimphilo Zandi Themba, Danie Theron, Henda Theron, Ilze Theron, Thandiwe Thingathinga, M.M THLABADIRA, Dikeledi Thoka, Zanele Thokwana, Gustav Thom, Mamphot Joel Thubakgale, Theodora Thwala, P Thys, Monethi Tieho, Matodzi Timothy, Ndlovu Tintswalo, Babalwa Tivana, Molefi Tladi, Bongiwe Tokota, Simthandile Toni, Ariel Torres, Mande Toubkin, Marinda Tsatsi, Khanyisile Tshabalala, Nozibele Tshamase, Gontse Tshefu, Makgoga Tshegofatjo, Given Tshikomba, Thapelo Tshilo, Lerato Tshira, S.T Tshirado, Maipfi Tshisikule, G Tsoke, N TSOKE, Alatha Tsoko, Mosele Tsotetsi, SANDEVA TSUBELLA, Noxolo Tuswa, Maipato Tutse, Nomayenzeke Tutu, Sphephelo Twala, Nhlanhla Twala, Simphiwe Twala, John Ubisi, Tefo Unathi, A Van Aswegen, Marietjie van der Merwe, Trudie van der Merwe, Patience van der Plank, Elmarie van der Spuy, Linda Van Der Westhuizen, Adele Van Der Westhuizen, Talana van der Westhuizen, Mene van der Westhuyzen, Thea Van Dyk, Ingrid van Heerden, Ryno van Jaarsveld, M Van Lill, Heidi van Niekerk, Ben van Niekerk, Amanda van Rensburg, Judy van Schallwyk, Zeitschke Yarnrich Van Sensie, Magda van Vuuren, Cloete van Vuuren, Olga Funiswa Vandu, Mandisa Vane, Lucia VanZyl, Ebrahim Variava, Mariam Veerus, Nokhwezi Velapi, Sebina Veleko, Z. Velezantsi, Retha Venter, Corlia Vergottini, Inga Vermeulen, Liabara Lufuluvhi Vidah, Bongani Vilakazi, Treasure N Vilakazi, Mbalenhle Precious Vilakazi, Karen Viljoen, Werner Viljoen, Zuretha Volschenk, Angelo Vos, Matlala VV, Jacques Walters, Kate Webb, John Welsh, D WESSELS, Judy Wheller, Fundile White, Priscilla White, Carmen Whyte, Ansie Willemse, Sape William, Daniel Williams, Kamielah Williams, Mercia Williams, Anne Williamson, Cherade Wilson, Boipelo Wolff, Michelle Wray, Ntombizonke B Xaba, Thabang Jabulani Xaba, Thanks Xiniwe, Mtshali Xoliswa, Funokwakhe Xulu, Gibson Xulu, Sandlakazi Yam, NM Zakhura, Mashela Zareloa, Sive Zinto, Dyibeni Zinziswa, Lulamile Ziselo, Zakhele Zitha, Emmanuel Zitha, Anele Zokufa, Innocent Zondi, Sikhumbuzo Bernard Zondi, Sbuyi Zondi, Thulani Zondi, Wandiswa Zongola, Liesl Zühlke, Zandile Zulu, LUNGELO ZULU, Thandeka Zulu, Slindili Zulu, Nkosinathi Zulu, Angel Zuma, precious Zungu, Pamela Zungu, Melusi Zungu, Priscilla Zungu, Bongo Lihle Zwakala, Antonia Zwane, Promise Zwane, Muziwendoda Zwane, Hlengiwe Priscila Zwane, and Nomgcobo Zwane
Subjects: Coronavirus disease 2019 (COVID-19), SARS-CoV-2, business.industry, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Incidence (epidemiology), COVID-19, Articles, General Medicine, Odds ratio, Logistic regression, Wave period, South Africa, Humans, Medicine, Prospective cohort study, business, Demography, Cohort study
Abstract: Background The first wave of COVID-19 in South Africa peaked in July, 2020, and a larger second wave peaked in January, 2021, in which the SARS-CoV-2 501Y.V2 (Beta) lineage predominated. We aimed to compare in-hospital mortality and other patient characteristics between the first and second waves. Methods In this prospective cohort study, we analysed data from the DATCOV national active surveillance system for COVID-19 admissions to hospital from March 5, 2020, to March 27, 2021. The system contained data from all hospitals in South Africa that have admitted a patient with COVID-19. We used incidence risk for admission to hospital and determined cutoff dates to define five wave periods: pre-wave 1, wave 1, post-wave 1, wave 2, and post-wave 2. We compared the characteristics of patients with COVID-19 who were admitted to hospital in wave 1 and wave 2, and risk factors for in-hospital mortality accounting for wave period using random-effect multivariable logistic regression. Findings Peak rates of COVID-19 cases, admissions, and in-hospital deaths in the second wave exceeded rates in the first wave: COVID-19 cases, 240·4 cases per 100 000 people vs 136·0 cases per 100 000 people; admissions, 27·9 admissions per 100 000 people vs 16·1 admissions per 100 000 people; deaths, 8·3 deaths per 100 000 people vs 3·6 deaths per 100 000 people. The weekly average growth rate in hospital admissions was 20% in wave 1 and 43% in wave 2 (ratio of growth rate in wave 2 compared with wave 1 was 1·19, 95% CI 1·18–1·20). Compared with the first wave, individuals admitted to hospital in the second wave were more likely to be age 40–64 years (adjusted odds ratio [aOR] 1·22, 95% CI 1·14–1·31), and older than 65 years (aOR 1·38, 1·25–1·52), compared with younger than 40 years; of Mixed race (aOR 1·21, 1·06–1·38) compared with White race; and admitted in the public sector (aOR 1·65, 1·41–1·92); and less likely to be Black (aOR 0·53, 0·47–0·60) and Indian (aOR 0·77, 0·66–0·91), compared with White; and have a comorbid condition (aOR 0·60, 0·55–0·67). For multivariable analysis, after adjusting for weekly COVID-19 hospital admissions, there was a 31% increased risk of in-hospital mortality in the second wave (aOR 1·31, 95% CI 1·28–1·35). In-hospital case-fatality risk increased from 17·7% in weeks of low admission (8000 admissions; aOR 1·24, 1·17–1·32). Interpretation In South Africa, the second wave was associated with higher incidence of COVID-19, more rapid increase in admissions to hospital, and increased in-hospital mortality. Although some of the increased mortality can be explained by admissions in the second wave being more likely in older individuals, in the public sector, and by the increased health system pressure, a residual increase in mortality of patients admitted to hospital could be related to the new Beta lineage. Funding DATCOV as a national surveillance system is funded by the National Institute for Communicable Diseases and the South African National Government.
Published: 2021

31. Excess Invasive Meningococcal Disease Associated With Seasonal Influenza, South Africa, 2003–2018

Author: Cheryl Cohen, Anne von Gottberg, Susan Meiring, Linda de Gouveia, Emanuel M. Dominic, Jo McAnerney, and Stefano Tempia
Subjects: Microbiology (medical), Veterinary medicine, Population, Meningococcal Vaccines, Neisseria meningitidis, medicine.disease_cause, Meningococcal disease, Virus, South Africa, Throat, Influenza, Human, medicine, Humans, education, education.field_of_study, business.industry, Ecological study, medicine.disease, Meningococcal Infections, Vaccination, Infectious Diseases, medicine.anatomical_structure, Attributable risk, Seasons, business
Abstract: Background Invasive meningococcal disease (IMD) is a devastating illness with high mortality rates. Like influenza, endemic IMD is seasonal, peaking in winter. Studies suggest that circulation of influenza virus may influence the timing and magnitude of IMD winter peaks. Methods This ecological study used weekly data from 2 nationwide surveillance programs: Viral Watch (proportion of outpatient influenza-positive cases from throat or nasal swab samples) and GERMS-SA (laboratory-confirmed cases of IMD), occurring across South Africa from 2003 through 2018 in all age bands. A bivariate time series analysis using wavelet transform was conducted to determine cocirculation of the diseases and the time lag between the peak seasons. We modeled excess meningococcal disease cases attributable to influenza cocirculation, using univariate regression spline models. Stata and R statistical software packages were used for the analysis. Results A total of 5256 laboratory-confirmed IMD cases were reported, with an average annual incidence of 0.23 episodes per 100 000 population and a mean seasonal peak during week 32 (±3 weeks). Forty-two percent of swab samples (10 421 of 24 741) were positive for influenza during the study period. The mean peak for all influenza occurred at week 26 (±4 weeks). There was an average lag time of 5 weeks between annual influenza and IMD seasons. Overall, 5% (1%–9%) of IMD cases can be attributable to influenza cocirculation, with, on average, 17 excess IMD cases per year attributable to influenza. Conclusions A quantifiable proportion of IMD in South Africa is associated with influenza cocirculation; therefore, seasonal influenza vaccination may have an effect on preventing a small portion of IMD in addition to preventing influenza.
Published: 2021

32. Cohort profile: A Prospective Household cohort study of Influenza, Respiratory syncytial virus and other respiratory pathogens community burden and Transmission dynamics in South Africa, 2016–2018

Author: Kathleen Kahn, Limakatso Lebina, Cheryl Cohen, Angela Mathee, Florette K. Treurnicht, Azwifari Mathunjwa, Floidy Wafawanaka, Anne von Gottberg, Katlego Motlhaoleng, Maimuna Carrim, Matebejane Moroe, Ryan G. Wagner, Stephen Tollman, Stefano Tempia, Brigitte Language, Jocelyn Moyes, Stuart Piketh, Nicole Wolter, Jackie Kleynhans, Lorens Maake, Sizzy Ngobeni, Meredith McMorrow, Thulisa Mkhencele, Orienka Hellferscee, Amelia Buys, Neil A. Martinson, and Francesc Xavier Gómez-Olivé
Subjects: Pulmonary and Respiratory Medicine, Epidemiology, respiratory syncytial virus, Respiratory Syncytial Virus Infections, Asymptomatic, Virus, burden, Serology, Cohort Studies, South Africa, Environmental health, Influenza, Human, Humans, Medicine, Prospective Studies, Index case, cohort profile, SARS-CoV-2, business.industry, Transmission (medicine), Incidence (epidemiology), transmission, Public Health, Environmental and Occupational Health, COVID-19, virus diseases, Original Articles, Infectious Diseases, Respiratory Syncytial Virus, Human, Cohort, Original Article, medicine.symptom, influenza, business, Cohort study
Abstract: Purpose The PHIRST study (Prospective Household cohort study of Influenza, Respiratory Syncytial virus, and other respiratory pathogens community burden and Transmission dynamics in South Africa) aimed to estimate the community burden of influenza and respiratory syncytial virus (RSV) including the incidence of infection, symptomatic fraction, and to assess household transmission. Participants We enrolled 1684 individuals in 327 randomly selected households in a rural and an urban site over three consecutive influenza and two RSV seasons. A new cohort of households was enrolled each year. Participants were sampled with nasopharyngeal swabs twice‐weekly during the RSV and influenza seasons of the year of enrolment. Serology samples were collected at enrolment and before and after the influenza season annually. Findings to Date There were 122 113 potential individual follow‐up visits over the 3 years, and participants were interviewed for 105 783 (87%) of these. Out of 105 683 nasopharyngeal swabs, 1258 (1%) and 1026 (1%) tested positive on polymerase chain reaction (PCR) for influenza viruses and RSV, respectively. Over one third of individuals had PCR‐confirmed influenza each year. Overall, there was influenza transmission to 10% of household contacts of an index case. Future Plans Future planned analyses include analysis of influenza serology results and RSV burden and transmission. Households enrolled in the PHIRST study during 2016–2018 were eligible for inclusion in a study of SARS‐CoV‐2 transmission initiated in July 2020. This study uses similar testing frequency to assess the community burden of SARS‐CoV‐2 infection and the role of asymptomatic infection in virus transmission.
Published: 2021

33. Costs of seasonal influenza vaccination in South Africa

Author: Heather Fraser, Winfrida Tombe‐Mdewa, Ciaran Kohli‐Lynch, Karen Hofman, Stefano Tempia, Meredith McMorrow, Philipp Lambach, Wayne Ramkrishna, Cheryl Cohen, Raymond Hutubessy, and Ijeoma Edoka
Subjects: Pulmonary and Respiratory Medicine, South Africa, Infectious Diseases, Influenza Vaccines, Epidemiology, Cost-Benefit Analysis, Influenza, Human, Vaccination, Public Health, Environmental and Occupational Health, Humans, Seasons
Abstract: Background:\ud Influenza accounts for a substantial number of deaths and hospitalisations annually in South Africa. To address this disease burden, the South African National Department of Health introduced a trivalent inactivated influenza vaccination programme in 2010.\ud \ud Methods:\ud We adapted and populated the WHO Seasonal Influenza Immunization Costing Tool (WHO SIICT) with country-specific data to estimate the cost of the influenza vaccination programme in South Africa. Data were obtained through key-informant interviews at different levels of the health system and through a review of existing secondary data sources. Costs were estimated from a public provider perspective and expressed in 2018 prices. We conducted scenario analyses to assess the impact of different levels of programme expansion and the use of quadrivalent vaccines on total programme costs.\ud \ud Results:\ud Total financial and economic costs were estimated at approximately USD 2.93 million and USD 7.91 million, respectively, while financial and economic cost per person immunised was estimated at USD 3.29 and USD 8.88, respectively. Expanding the programme by 5% and 10% increased economic cost per person immunised to USD 9.36 and USD 9.52 in the two scenarios, respectively. Finally, replacing trivalent inactivated influenza vaccine (TIV) with quadrivalent vaccine increased financial and economic costs to USD 4.89 and USD 10.48 per person immunised, respectively.\ud \ud Conclusion:\ud We adapted the WHO SIICT and provide estimates of the total costs of the seasonal influenza vaccination programme in South Africa. These estimates provide a basis for planning future programme expansion and may serve as inputs for cost-effectiveness analyses of seasonal influenza vaccination programmes.
Published: 2022

34. SARS-CoV-2 transmission, persistence of immunity, and estimates of Omicron’s impact in South African population cohorts

Author: Kaiyuan Sun, Stefano Tempia, Jackie Kleynhans, Anne von Gottberg, Meredith L. McMorrow, Nicole Wolter, Jinal N. Bhiman, Jocelyn Moyes, Mignon du Plessis, Maimuna Carrim, Amelia Buys, Neil A. Martinson, Kathleen Kahn, Stephen Tollman, Limakatso Lebina, Floidy Wafawanaka, Jacques D. du Toit, Francesc Xavier Gómez-Olivé, Thulisa Mkhencele, Cécile Viboud, and Cheryl Cohen
Subjects: South Africa, SARS-CoV-2, COVID-19, Humans, General Medicine, Pandemics
Abstract: Understanding the build-up of immunity with successive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and the epidemiological conditions that favor rapidly expanding epidemics will help facilitate future pandemic control. We analyzed high-resolution infection and serology data from two longitudinal household cohorts in South Africa to reveal high cumulative infection rates and durable cross-protective immunity conferred by prior infection in the pre-Omicron era. Building on the history of past exposures to different SARS-CoV-2 variants and vaccination in the cohort most representative of South Africa’s high urbanization rate, we used mathematical models to explore the fitness advantage of the Omicron variant and its epidemic trajectory. Modeling suggests that the Omicron wave likely infected a large fraction (44 to 81%) of the population, leaving a complex landscape of population immunity primed and boosted with antigenically distinct variants. We project that future SARS-CoV-2 resurgences are likely under a range of scenarios of viral characteristics, population contacts, and residual cross-protection.
Published: 2022

35. Temporal Variations in Respiratory Syncytial Virus Epidemics, by Virus Subtype, 4 Countries

Author: Ana Paula Rodrigues, Clarisse Demont, John Paget, Saverio Caini, Adam Meijer, Lisa Staadegaard, Cheryl Cohen, Sue Huang, and Jojanneke van Summeren
Subjects: Microbiology (medical), 2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), Epidemiology, respiratory syncytial virus, viruses, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 030231 tropical medicine, Respiratory Syncytial Virus Infections, Infectious and parasitic diseases, RC109-216, Biology, Temporal, epidemics, Virus, South Africa, 03 medical and health sciences, 0302 clinical medicine, Research Letter, Humans, 030212 general & internal medicine, Respiratory system, Portugal, the Netherlands, DNA Viruses, Infant, virus diseases, respiratory system, Virology, Temporal Variations in Respiratory Syncytial Virus Epidemics, by Virus Subtype, 4 Countries, Infectious Diseases, Respiratory Syncytial Virus, Human, surveillance, Medicine, New Zealand
Abstract: Temporal variation of respiratory syncytial virus (RSV) epidemics was recently reported to be determined by the dominant RSV subtype. However, when we repeated the analysis for 4 countries in the Northern and Southern Hemispheres, the dominant subtype did not seem to affect temporal variation of RSV epidemics.
Published: 2021

36. SARS-CoV-2 cases reported from long-term residential facilities (care homes) in South Africa: a retrospective cohort study

Author: Tracy Arendse, Beverley Cowper, Cheryl Cohen, Maureen Masha, Stefano Tempia, Civil Legodu, Sandhya Singh, Tebogo Ratau, Leon Geffen, Ansie Heymans, Dane Coetzer, Lucille Blumberg, Waasila Jassat, Department of Medicine, and Faculty of Health Sciences
Subjects: Adult, Staff, SARS-CoV-2, Residents, Public Health, Environmental and Occupational Health, COVID-19, Outbreak, Middle Aged, Long term care facilities, Long-Term Care, Residential Facilities, Disease Outbreaks, South Africa, Case fatality ratio, Humans, Pandemics, Retrospective Studies
Abstract: Background Globally, long-term care facilities (LTCFs) experienced a large burden of deaths during the COVID-19 pandemic. The study aimed to describe the temporal trends as well as the characteristics and risk factors for mortality among residents and staff who tested positive for SARS-CoV-2 in selected LTCFs across South Africa. Method We analysed data reported to the DATCOV sentinel surveillance system by 45 LTCFs. Outbreaks in LTCFs were defined as large if more than one-third of residents and staff had been infected or there were more than 20 epidemiologically linked cases. Multivariable logistic regression was used to assess risk factors for mortality amongst LTCF residents. Results A total of 2324 SARS-CoV-2 cases were reported from 5 March 2020 through 31 July 2021; 1504 (65%) were residents and 820 (35%) staff. Among LTCFs, 6 reported sporadic cases and 39 experienced outbreaks. Of those reporting outbreaks, 10 (26%) reported one and 29 (74%) reported more than one outbreak. There were 48 (66.7%) small outbreaks and 24 (33.3%) large outbreaks reported. There were 30 outbreaks reported in the first wave, 21 in the second wave and 15 in the third wave, with 6 outbreaks reporting between waves. There were 1259 cases during the first COVID-19 wave, 362 during the second wave, and 299 during the current third wave. The case fatality ratio was 9% (138/1504) among residents and 0.5% (4/820) among staff. On multivariable analysis, factors associated with SARS-CoV-2 mortality among LTCF residents were age 40–59 years, 60–79 years and ≥ 80 years compared to Conclusion The analysis of SARS-CoV-2 cases in sentinel LTCFs in South Africa points to an encouraging trend of decreasing numbers of outbreaks, cases and risk for mortality since the first wave. LTCFs are likely to have learnt from international experience and adopted national protocols, which include improved measures to limit transmission and administer early and appropriate clinical care.
Published: 2022

37. Case-fatality and sequelae following acute bacterial meningitis in South Africa, 2016 through 2020

Author: Susan Meiring, Cheryl Cohen, Linda de Gouveia, Mignon du Plessis, Vanessa Quan, Jackie Kleynhans, Colin Menezes, Gary Reubenson, Halima Dawood, Maphoshane Nchabeleng, Mohamed Said, Nomonde Mvelase, Prasha Mahabeer, Rispah Chomba, Ruth Lekalakala, Trusha Nana, Vindana Chibabhai, Marianne Black, and Anne von Gottberg
Subjects: Microbiology (medical), Male, Meningitis, Pneumococcal, Infant, HIV Infections, General Medicine, Meningitis, Meningococcal, Neisseria meningitidis, Haemophilus influenzae, Meningitis, Bacterial, South Africa, Infectious Diseases, Streptococcus pneumoniae, Disease Progression, Humans, Female, Hospital Mortality
Abstract: Providing country-specific estimates of case fatality and sequelae from bacterial meningitis (BM) is important to evaluate and monitor progress toward the World Health Organization's roadmap to "defeating meningitis by 2030".From 2016-2020, GERMS-SA conducted enhanced surveillance at 26 hospitals across South Africa. Episodes of laboratory-confirmed BM due to Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis were included. Risk factors for in-hospital death and sequelae at hospital discharge among survivors were analyzed.Of 12,717 invasive bacterial infections reported nationally, 39% (4980) were from enhanced surveillance sites, including 4159 pneumococcal, 640 H. influenzae, and 181 meningococcal infections. BM accounted for 32% (1319/4159) of pneumococcal, 21% (136/640) of H. influenzae, and 83% (151/181) of meningococcal invasive diseases. Clinical data were available for 91% (1455/1606) of BM: 26% (376/1455) were aged5 years, 50% (726/1455) were female, and 62% (723/1171) with known HIV results, were HIV-infected. In-hospital case fatality was 37% (534/1455), and 24% (222/921) of survivors had adverse sequelae. Risk factors for death included altered mental status, HIV infection, and comorbidities. Risk factors for adverse sequelae included altered mental status and antimicrobial nonsusceptibility.BM in South Africa has a high case fatality, and adverse sequelae frequently occur among survivors. Those with comorbidities (including HIV) are at the highest risk.
Published: 2022

38. COVID-19 vaccine hesitancy in rural South Africa: Deepening understanding to increase uptake and access

Author: Kathleen Kahn, Audrey Pettifor, Palesa Mataboge, Nicole K Kelly, Duduzile P Mashinini, Harish Nair, Harry Campbell, Cheryl Cohen, F Xavier Gómez-Olivé, and Stephen Tollman
Subjects: Adult, Male, History, Vaccines, COVID-19 Vaccines, Polymers and Plastics, SARS-CoV-2, Health Policy, Public Health, Environmental and Occupational Health, COVID-19, Industrial and Manufacturing Engineering, South Africa, Cross-Sectional Studies, Humans, Female, Business and International Management, Vaccination Hesitancy, Aged
Abstract: Background: To date, COVID-19 vaccine coverage in the African region falls far too short of global goals. Increasing vaccination rates requires understanding barriers to vaccination so that effective interventions that sensitively and effectively address barriers to vaccination can be implemented. Methods: To assess COVID-19 vaccination levels and identify major barriers to vaccine uptake we conducted a population-based, cross-sectional survey among 1662 adults 18 and older from August 25 to October 29 2021 in the Agincourt Health and Socio-Demographic Surveillance System (AHDSS) area, Mpumalanga, South Africa. Results: Half of participants reported receiving a COVID-19 vaccine (50.4%) with 41.1% being fully vaccinated and 9.3% being partially vaccinated; 49.6% were unvaccinated. More women than men were vaccinated (55.5% vs 42.8%, P
Published: 2022

39. Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa

Author: Cheryl Cohen, Harry Moultrie, Koleka Mlisana, Michelle J. Groome, Juliet R. C. Pulliam, N. Govender, Cari van Schalkwyk, Jonathan Dushoff, and Anne von Gottberg
Subjects: medicine.medical_specialty, Surveillance data, Multidisciplinary, SARS-CoV-2, business.industry, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Incidence (epidemiology), Public health, Hazard ratio, COVID-19, Context (language use), South Africa, Immunity, Reinfection, Epidemiology, medicine, Humans, business, Demography
Abstract: SummaryIntroductionGlobally, there have been more than 404 million cases of SARS-CoV-2, with 5.8 million confirmed deaths, as of February 2022. South Africa has experienced four waves of SARS-CoV-2 transmission, with the second, third, and fourth waves being driven by the Beta, Delta, and Omicron variants, respectively. A key question with the emergence of new variants is the extent to which they are able to reinfect those who have had a prior natural infection.RationaleWe developed two approaches to monitor routine epidemiological surveillance data to examine whether SARS-CoV-2 reinfection risk has changed through time in South Africa, in the context of the emergence of the Beta (B.1.351), Delta (B.1.617.2), and Omicron (B.1.1.529) variants. We analyze line list data on positive tests for SARS-CoV-2 with specimen receipt dates between 04 March 2020 and 31 January 2022, collected through South Africa’s National Notifiable Medical Conditions Surveillance System. Individuals having sequential positive tests at least 90 days apart were considered to have suspected reinfections. Our routine monitoring of reinfection risk included comparison of reinfection rates to the expectation under a null model (approach 1) and estimation of the time-varying hazards of infection and reinfection throughout the epidemic (approach 2) based on model-based reconstruction of the susceptible populations eligible for primary and second infections.Results105,323 suspected reinfections were identified among 2,942,248 individuals with laboratory-confirmed SARS-CoV-2 who had a positive test result at least 90 days prior to 31 January 2022. The number of reinfections observed through the end of the third wave in September 2021 was consistent with the null model of no change in reinfection risk (approach 1). Although increases in the hazard of primary infection were observed following the introduction of both the Beta and Delta variants, no corresponding increase was observed in the reinfection hazard (approach 2). Contrary to expectation, the estimated hazard ratio for reinfection versus primary infection was lower during waves driven by the Beta and Delta variants than for the first wave (relative hazard ratio for wave 2 versus wave 1: 0.71 (CI95: 0.60–0.85); for wave 3 versus wave 1: 0.54 (CI95: 0.45–0.64)). In contrast, the recent spread of the Omicron variant has been associated with an increase in reinfection hazard coefficient. The estimated hazard ratio for reinfection versus primary infection versus wave 1 was 1.75 (CI95: 1.48–2.10) for the period of Omicron emergence (01 November 2021 to 30 November 2021) and 1.70 (CI95: 1.44–2.04) for wave 4 versus wave 1. Individuals with identified reinfections since 01 November 2021 had experienced primary infections in all three prior waves, and an increase in third infections has been detected since mid-November 2021. Many individuals experiencing third infections had second infections during the third (Delta) wave that ended in September 2021, strongly suggesting that these infections resulted from immune evasion rather than waning immunity.ConclusionPopulation-level evidence suggests that the Omicron variant is associated with substantial ability to evade immunity from prior infection. In contrast, there is no population-wide epidemiological evidence of immune escape associated with the Beta or Delta variants. This finding has important implications for public health planning, particularly in countries like South Africa with high rates of immunity from prior infection. Further development of methods to track reinfection risk during pathogen emergence, including refinements to assess the impact of waning immunity, account for vaccine-derived protection, and monitor the risk of multiple reinfections will be an important tool for future pandemic preparedness.
Published: 2022

40. Epidemiology of Pertussis in Individuals of All Ages Hospitalized With Respiratory Illness in South Africa, January 2013—December 2018

Author: Florette K. Treurnicht, Ebrahim Variava, Anne von Gottberg, Orienka Hellferscee, Sibongile Walaza, Halima Dawood, Stefano Tempia, Meredith McMorrow, Mignon du Plessis, Nicole Wolter, Fahima Moosa, and Cheryl Cohen
Subjects: Adult, Microbiology (medical), Bordetella pertussis, medicine.medical_specialty, Pediatrics, Whooping Cough, Population, Logistic regression, South Africa, Epidemiology, medicine, Humans, Child, education, Pertussis Vaccine, education.field_of_study, biology, business.industry, Incidence, Incidence (epidemiology), Infant, medicine.disease, biology.organism_classification, Confidence interval, Pneumonia, Infectious Diseases, Relative risk, business
Abstract: Background Policy recommendations on pertussis vaccination need to be guided by data, which are limited from low- and middle-income countries. We aimed to describe the epidemiology of pertussis in South Africa, a country with high human immunodeficiency virus (HIV) prevalence and routine pertussis vaccination for 6 decades including the acellular vaccine since 2009. Methods Hospitalized patients of all ages were enrolled at 5 sentinel sites as part of a pneumonia surveillance program from January 2013 through December 2018. Nasopharyngeal specimens and induced sputum were tested by polymerase chain reaction (PCR) for Bordetella pertussis. In addition, demographic and clinical information were collected. Incidence rates were calculated for 2013–2016, and multivariable logistic regression performed to identify factors associated with pertussis. Results Over the 6-year period 19 429 individuals were enrolled, of which 239 (1.2%) tested positive for B. pertussis. Detection rate was highest in infants aged Conclusions Pertussis continues to be a significant cause of illness and hospitalization in South Africa, despite routine vaccination. The highest burden of disease and death occurred in infants; however, HIV-infected adults were also identified as an important group at risk of B. pertussis infection.
Published: 2021

41. A cost-effectiveness analysis of South Africa’s seasonal influenza vaccination programme

Author: Stefano Tempia, Heather Fraser, Ciaran Kohli-Lynch, Karen Hofman, Cheryl Cohen, Raymond Hutubessy, Ijeoma Edoka, Wayne Ramkrishna, Meredith McMorrow, and Philipp Lambach
Subjects: Adult, Adolescent, Influenza vaccine, Cost effectiveness, Cost-Benefit Analysis, 030231 tropical medicine, Article, Seasonal influenza, South Africa, Young Adult, 03 medical and health sciences, 0302 clinical medicine, Acquired immunodeficiency syndrome (AIDS), Pregnancy, Environmental health, Influenza, Human, medicine, Humans, 030212 general & internal medicine, Child, Aged, Cost–utility analysis, General Veterinary, General Immunology and Microbiology, Cost–benefit analysis, Immunization Programs, business.industry, Vaccination, Public Health, Environmental and Occupational Health, Cost-effectiveness analysis, Middle Aged, medicine.disease, Infectious Diseases, Influenza Vaccines, Molecular Medicine, Female, Quality-Adjusted Life Years, Seasons, business
Abstract: Background: \ud Seasonal influenza imposes a significant health and economic burden in South Africa, particularly in populations vulnerable to severe consequences of influenza. This study assesses the cost-effectiveness of South Africa’s seasonal influenza vaccination strategy, which involves vaccinating vulnerable populations with trivalent inactivated influenza vaccine (TIV) during routine facility visits. Vulnerable populations included in our analysis are persons aged ≥ 65 years; pregnant women; persons living with HIV/AIDS (PLWHA), persons of any age with underlying medical conditions (UMC) and children aged 6–59 months.\ud \ud Method: \ud We employed the World Health Organisation’s (WHO) Cost Effectiveness Tool for Seasonal Influenza Vaccination (CETSIV), a decision tree model, to evaluate the 2018 seasonal influenza vaccination campaign from a public healthcare provider and societal perspective. CETSIV was populated with existing country-specific demographic, epidemiologic and coverage data to estimate incremental cost-effectiveness ratios (ICERs) by comparing costs and benefits of the influenza vaccination programme to no vaccination.\ud \ud Results: \ud The highest number of clinical events (influenza cases, outpatient visits, hospitalisation and deaths) were averted in PLWHA and persons with other UMCs. Using a cost-effectiveness threshold of US$ 3 400 per quality-adjusted life year (QALY), our findings suggest that the vaccination programme is cost-effective for all vulnerable populations except for children aged 6–59 months. ICERs ranged from ~US$ 1 750 /QALY in PLWHA to ~US$ 7 500/QALY in children. In probabilistic sensitivity analyses, the vaccination programme was cost-effective in pregnant women, PLWHA, persons with UMCs and persons aged ≥65 years in >80% of simulations. These findings were robust to changes in many model inputs but were most sensitive to uncertainty in estimates of influenza-associated illness burden.\ud \ud Conclusion: \ud South Africa's seasonal influenza vaccination strategy of opportunistically targeting vulnerable populations during routine visits is cost-effective. A budget impact analysis will be useful for supporting future expansions of the programme.
Published: 2021

42. Decreased influenza activity during the COVID‐19 pandemic—United States, Australia, Chile, and South Africa, 2020

Author: Rodrigo Fasce Pineda, Sonja J Olsen, Alicia P Budd, Eduardo Azziz-Baumgartner, Sheena G. Sullivan, Cheryl Cohen, Lynnette Brammer, and Alicia M Fry
Subjects: 2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Physical Distancing, MEDLINE, Cdc Report, 030230 surgery, 03 medical and health sciences, South Africa, 0302 clinical medicine, Environmental health, Pandemic, Influenza, Human, Immunology and Allergy, Medicine, Humans, Pharmacology (medical), Chile, Pandemics, Health policy, Transplantation, business.industry, Health Policy, Australia, COVID-19, United States, Vaccination, Reports from the Cdc: MMWR, business
Abstract: Transplant recipients are among the groups for whom the updated recommendations for 2020–2021 influenza vaccination should generally be considered essential, notably in the face of the COVID‐19 pandemic.
Published: 2020

43. Study protocol for a population-based observational surveillance study of culture-confirmed neonatal bloodstream infections and meningitis in South Africa: Baby GERMS-SA

Author: Susan Meiring, Rudzani Mashau, Rindidzani Magobo, Olga Perovic, Vanessa Quan, Cheryl Cohen, Linda de Gouveia, Anne von Gottberg, Cheryl Mackay, Mphekwa Thomas Mailula, Rose Phayane, Angela Dramowski, and Nelesh P Govender
Subjects: South Africa, Perinatal Death, Sepsis, Infant, Newborn, Humans, Medicine, Meningitis, General Medicine, Communicable Diseases
Abstract: IntroductionWorldwide, neonatal mortality remains high accounting for 47% of childhood deaths in 2019 and including an estimated 500 000 deaths from neonatal infections. While 42% of global neonatal deaths occur in sub-Saharan Africa, there is limited understanding of population-level burden and aetiology of neonatal infections outside tertiary-level institutions.Methods and analysisWe aim to implement the first population-level surveillance for bloodstream infections and meningitis among neonates aged Ethics and disseminationEthics clearance was obtained from the Human Research Ethics Committee of the University of the Witwatersrand (M190320). Funding for the study was obtained through a grant from the Bill and Melinda Gates Foundation (OPP1208882). Baby GERMS-SA aims to impact on national policy, resource allocation and neonatal guidelines by describing the national burden of neonatal infections in South Africa. In addition, end-users in neonatal units will benefit from a facility-level dashboard displaying key indicators of the surveillance findings.
Published: 2022

44. Outcomes of flucytosine-containing combination treatment for cryptococcal meningitis in a South African national access programme: a cross-sectional observational study

Author: Rudzani C Mashau, Susan T Meiring, Vanessa C Quan, Jeremy Nel, Greg S Greene, Andrea Garcia, Colin Menezes, Denasha L Reddy, Michelle Venter, Sarah Stacey, Matamela Madua, Lia Boretti, Thomas S Harrison, Graeme Meintjes, Amir Shroufi, Laura Trivino-Duran, John Black, Nelesh P Govender, Shareef Abrahams, Vanessa Pearce, Masego Moncho, Jeanette Wadula, Motlatji Maloba, Anwar Hoosen, Charl Verwey, David Moore, Dina Pombo, Gary Reubenson, Grace Ntlemo, Lauren Richards, Maphoshane Nchabeleng, Merika Tsitsi, Moamokgethi Moshe, Mohammed Said, Molebogeng Kolojane, Lesego Mothibi, Nicolette Du Plessis, Rispah Chomba, Teena Thomas, Theunis Avenant, Trusha Nana, Vindana Chibabhai, Adhil Maharj, Douglas Wilson, Fathima Naby, Halima Dawood, Khine Swe Swe Han, Lisha Sookan, Nomonde Dlamini, Praksha Ramajathan, Prasha Mahabeer, Prathna Bhola, Romola Naidoo, Sumayya Haffejee, Surendra Sirkar, Yeishna Ramkillawan, Ken Hamese, Ngoaka Sibiya, Phetho Mangena, Ruth Lekalakala, Greta Hoyland, Sindi Ntuli, Ebrahim Variava, Ignatius Khantsi, Omphile Mekgoe, Adrian Brink, Elizabeth Prentice, Kessendri Reddy, Andrew Whitelaw, Ebrahim Hoosien, Inge Zietsman, Terry Marshall, Xoliswa Poswa, Chetna Govind, Juanita Smit, Keshree Pillay, Sharona Seetharam, Victoria Howell, Catherine Samuel, Marthinus Senekal, Colleen Bamford, Andries Dreyer, Louis Marcus, Warren Lowman, Anne von Gottberg, Anthony Smith, Azwifarwi Mathunjwa, Cecilia d'Abreu, Cecilia Miller, Cheryl Cohen, Farzana Ismail, Harry Moultrie, Husna Ismail, Jacqueline Weyer, Jackie Kleynhans, Jenny Rossouw, John Frean, Joy Ebonwu, Judith Mwansa-Kambafwile, Juno Thomas, Kate Bishop, Kerrigan McCarthy, Liliwe Shuping, Linda de Gouveia, Linda Erasmus, Adrian Puren, Lucille Blumberg, Marshagne Smith, Martha Makgoba, Michelle Groome, Mignon du Plessis, Mimmy Ngomane, Mokupi Manaka, Myra Moremi, Nazir Ismail, Neo Legare, Nicola Page, Nombulelo Hoho, Olga Perovic, Phuti Sekwadi, Rindidzani Magobo, Ruth Mpembe, Sibongile Walaza, Siyanda Dlamini, Sunnieboy Njikho, Tiisetso Lebaka, and Wendy Ngubane
Subjects: Adult, Male, South Africa, Infectious Diseases, Antifungal Agents, Cross-Sectional Studies, Flucytosine, Humans, Female, HIV Infections, Cryptococcosis, Meningitis, Cryptococcal, Fluconazole
Abstract: Although flucytosine is a key component of WHO-recommended induction treatment for HIV-associated cryptococcal meningitis, this antifungal agent is not widely available in low-income and middle-income countries due to limited production and cost. In 2018, a national flucytosine access programme was initiated in South Africa. We aimed to determine the effectiveness of flucytosine-containing induction regimens in routine care to motivate for the urgent registration of flucytosine and its inclusion in treatment guidelines.In this cross-sectional study, we compared outcomes of adults aged 18 years and older with incident laboratory-confirmed cryptococcal meningitis treated with or without flucytosine-containing regimens at 19 sentinel hospitals in South Africa. A case of cryptococcosis was defined as illness in an adult with: (1) positive cerebrospinal fluid (CSF) India ink microscopy; (2) a positive CSF cryptococcal antigen test; or (3) culture of Cryptococcus neoformans or Cryptococcus gattii from CSF or any other specimen. We excluded patients without a case report form, those with an unknown or negative HIV serology result, those with a recurrent episode, and those who did not receive antifungal treatment in hospital. We assessed cumulative in-hospital mortality at 14 days and 30 days and calculated the overall crude in-hospital case-fatality ratio. We used random-effects logistic regression to examine the association between treatment group and in-hospital mortality.From July 1, 2018, to March 31, 2020, 10 668 individuals were diagnosed with laboratory-confirmed cryptococcal meningitis, 7787 cases diagnosed at non-enhanced surveillance sites and 567 cases from eight enhanced surveillance sites with no access to flucytosine were excluded. Of 2314 adults with a first episode of cryptococcosis diagnosed at 19 facilities with access to flucytosine, 1996 had a case report form and of these, 1539 received induction antifungal treatment and were confirmed HIV-seropositive first-episode cases. Of 1539 patients who received antifungal therapy, 596 (38·7%) individuals received a flucytosine-containing regimen and 943 (61·3%) received another regimen. The median age was 36 years (IQR 32-43) and 906 (58·9%) participants were male and 633 (41·1%) were female. The crude in-hospital case-fatality ratio was 23·9% (95% CI 20·0-27·0; 143 of 596) in those treated with flucytosine-containing regimens and 37·2% (95% CI 34·0-40·0; 351 of 943) in those treated with other regimens. Patients admitted to non-academic hospitals (adjusted odds ratio [aOR] 1·95 [95% CI 1·53-2·48]; p0·0001) and those who were antiretroviral treatment-experienced (aOR 1·30 [1·02-1·67]; p=0·033) were more likely to receive flucytosine. After adjusting for relevant confounders, flucytosine treatment was associated with a 53% reduction in mortality (aOR 0·47 [95% CI 0·35-0·64]; p0·0001). Among survivors, the median length of hospital admission in the flucytosine group was 11 days (IQR 8-15) versus 17 days (13-21) in the comparison group (p=0·0010).In-hospital mortality among patients treated with a flucytosine-containing regimen was comparable to reduced mortality reported in patients receiving a flucytosine-containing regimen in a recent multicentre African clinical trial. Flucytosine-based treatment can be delivered in routine care in a middle-income country with a substantial survival benefit.National Institute for Communicable Diseases, a Division of the National Health Laboratory Service.For the Zulu translation of the abstract see Supplementary Materials section.
Published: 2022

45. Coronavirus Host Genomics Study: South Africa (COVIGen-SA)

Author: Andrew K. May, Heather Seymour, Harriet Etheredge, Heather Maher, Marta C. Nunes, Shabir A. Madhi, Simiso M. Sokhela, W. D. Francois Venter, Neil Martinson, Firdaus Nabeemeeah, Cheryl Cohen, Jocelyn Moyes, Sibongile Walaza, Stefano Tempia, Jackie Kleynhans, Anne von Gottberg, Jeremy Nel, Halima Dawood, Ebrahim Variava, Stephen Tollman, Kathleen Kahn, Kobus Herbst, Emily B. Wong, Caroline T. Tiemessen, Alex van Blydenstein, Lyle Murray, Michelle Venter, June Fabian, and Michéle Ramsay
Subjects: Male, South Africa, Article Subject, SARS-CoV-2, Epidemiology, Public Health, Environmental and Occupational Health, Humans, COVID-19, Female, Genomics, Genome-Wide Association Study
Abstract: Host genetic factors are known to modify the susceptibility, severity, and outcomes of COVID-19 and vary across populations. However, continental Africans are yet to be adequately represented in such studies despite the importance of genetic factors in understanding Africa’s response to the pandemic. We describe the development of a research resource for coronavirus host genomics studies in South Africa known as COVIGen-SA—a multicollaborator strategic partnership designed to provide harmonised demographic, clinical, and genetic information specific to Black South Africans with COVID-19. Over 2,000 participants have been recruited to date. Preliminary results on 1,354 SARS-CoV-2 positive participants from four participating studies showed that 64.7% were female, 333 had severe disease, and 329 were people living with HIV. Through this resource, we aim to provide insights into host genetic factors relevant to African-ancestry populations, using both genome-wide association testing and targeted sequencing of important genomic loci. This project will promote and enhance partnerships, build skills, and develop resources needed to address the COVID-19 burden and associated risk factors in South African communities.
Published: 2022
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46. Decreased Influenza Activity During the COVID-19 Pandemic — United States, Australia, Chile, and South Africa, 2020

Author: Sheena G. Sullivan, Cheryl Cohen, Rodrigo Fasce Pineda, Alicia P Budd, Lynnette Brammer, Sonja J Olsen, Eduardo Azziz-Baumgartner, and Alicia M Fry
Subjects: Health (social science), Epidemiology, Health, Toxicology and Mutagenesis, Pneumonia, Viral, 01 natural sciences, South Africa, 03 medical and health sciences, 0302 clinical medicine, Health Information Management, Influenza, Human, Pandemic, Influenza prevention, medicine, Humans, 030212 general & internal medicine, Full Report, Chile, 0101 mathematics, Pandemics, Southern Hemisphere, Health policy, Transmission (medicine), business.industry, Incidence (epidemiology), 010102 general mathematics, Australia, COVID-19, virus diseases, General Medicine, medicine.disease, United States, Vaccination, Pneumonia, Population Surveillance, Coronavirus Infections, business, Demography
Abstract: After recognition of widespread community transmission of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), by mid- to late February 2020, indicators of influenza activity began to decline in the Northern Hemisphere. These changes were attributed to both artifactual changes related to declines in routine health seeking for respiratory illness as well as real changes in influenza virus circulation because of widespread implementation of measures to mitigate transmission of SARS-CoV-2. Data from clinical laboratories in the United States indicated a 61% decrease in the number of specimens submitted (from a median of 49,696 per week during September 29, 2019-February 29, 2020, to 19,537 during March 1-May 16, 2020) and a 98% decrease in influenza activity as measured by percentage of submitted specimens testing positive (from a median of 19.34% to 0.33%). Interseasonal (i.e., summer) circulation of influenza in the United States (May 17-August 8, 2020) is currently at historical lows (median = 0.20% tests positive in 2020 versus 2.35% in 2019, 1.04% in 2018, and 2.36% in 2017). Influenza data reported to the World Health Organization's (WHO's) FluNet platform from three Southern Hemisphere countries that serve as robust sentinel sites for influenza from Oceania (Australia), South America (Chile), and Southern Africa (South Africa) showed very low influenza activity during June-August 2020, the months that constitute the typical Southern Hemisphere influenza season. In countries or jurisdictions where extensive community mitigation measures are maintained (e.g., face masks, social distancing, school closures, and teleworking), those locations might have little influenza circulation during the upcoming 2020-21 Northern Hemisphere influenza season. The use of community mitigation measures for the COVID-19 pandemic, plus influenza vaccination, are likely to be effective in reducing the incidence and impact of influenza, and some of these mitigation measures could have a role in preventing influenza in future seasons. However, given the novelty of the COVID-19 pandemic and the uncertainty of continued community mitigation measures, it is important to plan for seasonal influenza circulation in the United States this fall and winter. Influenza vaccination of all persons aged ≥6 months remains the best method for influenza prevention and is especially important this season when SARS-CoV-2 and influenza virus might cocirculate (1).
Published: 2020

47. Influenza disease burden among potential target risk groups for immunization in South Africa, 2013–2015

Author: Nicole Wolter, Jocelyn Moyes, Cheryl Cohen, Heather Fraser, Adam L. Cohen, Halima Dawood, Sibongile Walaza, Orienka Hellferscee, Meredith McMorrow, Johanna M. McAnerney, Ijeoma Edoka, Florette K. Treurnicht, Ebrahim Variava, Anne von Gottberg, and Stefano Tempia
Subjects: Adult, Adolescent, Cost-Benefit Analysis, 030231 tropical medicine, Population, Psychological intervention, Article, South Africa, Young Adult, 03 medical and health sciences, 0302 clinical medicine, Cost of Illness, Pregnancy, Influenza, Human, Humans, Medicine, 030212 general & internal medicine, Young adult, Child, education, Disease burden, Aged, education.field_of_study, General Veterinary, General Immunology and Microbiology, business.industry, Vaccination, Public Health, Environmental and Occupational Health, Infant, Middle Aged, medicine.disease, Infectious Diseases, Years of potential life lost, Immunization, Child, Preschool, Molecular Medicine, Female, business, Demography
Abstract: Background Data on influenza burden in risk groups for severe influenza are important to guide targeted influenza immunization, especially in resource limited settings. However, this information is limited overall and in particular in low- and middle-income countries. We sought to assess the mean annual national burden of medically and non-medically attended influenza-associated mild, severe-non-fatal and fatal illness among potential target groups for influenza immunization in South Africa during 2013–2015. Methods We used published mean national annual estimates of mild, severe-non-fatal, and fatal influenza-associated illness in South Africa during 2013–2015 and estimated the number of such illnesses occurring among the following risk groups: (i) children aged 6–59 months; (ii) individuals aged 5–64 years with HIV, and/or pulmonary tuberculosis (PTB), and/or selected underlying medical conditions (UMC); (iii) pregnant women; and (iv) individuals aged ≥65 years. We also estimated the number of individuals among the same risk groups in the population. Results During 2013–2015, individuals in the selected risk groups accounted for 45.3% (24,569,328/54,086,144) of the population and 43.5% (4,614,763/10,598,138), 86.8% (111,245/128,173) and 94.5% (10,903/11,536) of the mean annual estimated number of influenza-associated mild, severe-non-fatal and fatal illness episodes, respectively. The rates of influenza-associated illness were highest in children aged 6–59 months (23,983 per 100,000 population) for mild illness, in pregnant women (930 per 100,000 population) for severe-non-fatal illness and in individuals aged ≥65 years (138 per 100,000 population) for fatal illness. Conclusion Influenza immunization of the selected risk groups has the potential to prevent a substantial number of influenza-associated severe illness. Nonetheless, because of the high number of individuals at risk, South Africa, due to financial resources constrains, may need to further prioritize interventions among risk populations. Cost-burden and cost-effectiveness estimates may assist with further prioritization.
Published: 2020

48. Human Immunodeficiency Virus Infection Is Associated With Increased Meningococcal Carriage Acquisition Among First-year Students in 2 South African Universities

Author: Vanessa Quan, Cheryl Cohen, Anne von Gottberg, Susan Meiring, Jackie Kleynhans, Stefano Tempia, Linda de Gouveia, Mignon du Plessis, and Karistha Ganesh
Subjects: 0301 basic medicine, Microbiology (medical), Adolescent, Universities, 030106 microbiology, Population, Human immunodeficiency virus (HIV), HIV Infections, Neisseria meningitidis, medicine.disease_cause, 03 medical and health sciences, South Africa, 0302 clinical medicine, medicine, Prevalence, risk factors, Humans, 030212 general & internal medicine, education, Online Only Articles, Students, carriage, education.field_of_study, business.industry, Vaccination, Meningococcal Infections, Major Articles and Commentaries, Infectious Diseases, Carriage, AcademicSubjects/MED00290, Cross-Sectional Studies, Meningococcal carriage, Relative risk, meningococcus, Cohort, Carrier State, Female, business, Southern Africa, Demography
Abstract: Background Invasive meningococcal disease clusters occur among university students and may reflect higher carriage prevalence among this population. We aimed to measure meningococcal carriage prevalence, acquisition, and risk factors among first-year university students in South Africa. Methods In summer–autumn 2017, after consenting to participate, we collected oropharyngeal swabs and questionnaires on carriage risk factors and tested students for HIV at 2 universities, during registration week (survey 1) and 6–8 weeks later (survey 2). Meningococci were detected by culture and polymerase chain reaction. Results We enrolled 2120 students at registration. Mean age was 18.5 years, 59% (1252/2120) were female and 0.8% (16/1984) had HIV. Seventy-eight percent of students returned for survey 2 (1655/2120). Among the cohort, carriage prevalence was 4.7% (77/1655) at registration, increasing to 7.9% (130/1655) at survey 2: 5.0% (83) acquired new carriage, 2.8% (47) had persistent carriage, 1.8% (30) cleared the initial carriage, and 90.3% (1495) remained carriage free. At both surveys, nongenogroupable meningococci predominated, followed by genogroups Y, B, W, and C. On multinomial analysis, risk factors for carriage acquisition included attending nightclubs (adjusted relative risk ratio [aRRR], 2.1; 95% CI, 1.1–4.0), having intimate kissing partners (aRRR, 1.8; 95% CI, 1.1–2.9) and HIV (aRRR, 5.0; 95% CI, 1.1–24.4). Conclusions Meningococcal carriage among first-year university students increased after 2 months. Sociobehavioral risk factors were associated with increased carriage for all analyses. HIV was associated with carriage acquisition. Until vaccination programs become mandatory in South African universities, data suggest that students with HIV could benefit most from meningococcal vaccination., Meningococcal carriage prevalence among first-year South African university students increased over time, peaking at 8%. Human immunodeficiency virus infection was associated with carriage acquisition, while sociobehavioral risk factors were associated with carriage and acquisition. These data advocate for targeted meningococcal vaccination of students.
Published: 2020

49. Human surveillance and phylogeny of highly pathogenic avian influenza A(H5N8) during an outbreak in poultry in South Africa, 2017

Author: Reneé Pieterse, Mushal Allam, Mpho Seleka, Florette K. Treurnicht, Michelle Seutloali, Cheryl Cohen, Ziyaad Valley-Omar, Sibongile Walaza, Arshad Ismail, Yusrah Salie‐Bassier, N. Govender, Kerrigan McCarthy, Lesley S. van Helden, Tasneem Anthony, Orienka Hellferscee, Phillip Senzo Mtshali, Mikhail Smith, and Alicia Cloete
Subjects: Adult, Male, Pulmonary and Respiratory Medicine, Adolescent, Epidemiology, Animals, Wild, Human pathogen, 030312 virology, Biology, medicine.disease_cause, Disease Outbreaks, South Africa, Young Adult, 03 medical and health sciences, H5N8, Phylogenetics, Geese, Influenza, Human, medicine, Animals, Humans, Influenza A Virus, H5N8 Subtype, Clade, Pathogen, Phylogeny, Poultry Diseases, Struthioniformes, 0303 health sciences, Transmission (medicine), business.industry, Influenza A Virus, H3N2 Subtype, Public Health, Environmental and Occupational Health, Outbreak, Original Articles, Middle Aged, Poultry farming, Virology, Influenza A virus subtype H5N1, Ducks, Infectious Diseases, Influenza in Birds, Epidemiological Monitoring, Original Article, Female, avian influenza, business, Chickens
Abstract: Background In June 2017, an outbreak of the highly pathogenic avian influenza A(H5N8) was detected in commercial poultry farms in South Africa, which rapidly spread to all nine South African provinces. Objectives We conducted active surveillance for the transmission of influenza A(H5N8) to humans working with infected birds during the South African outbreak. Methods Influenza A(H5N8)‐positive veterinary specimens were used to evaluate the ability of real‐time PCR‐based assays to detect contemporary avian influenza A(H5N8) strains. Whole genome sequences were generated from these specimens by next‐generation sequencing for phylogenetic characterization and screening for mammalian‐adaptive mutations. Results Human respiratory samples from 74 individuals meeting our case definition, all tested negative for avian influenza A(H5) by real‐time PCR, but 2 (3%) were positive for human influenza A(H3N2). 54% (40/74) reported wearing personal protective equipment including overalls, boots, gloves, masks, and goggles. 94% (59/63) of veterinary specimens positive for H5N8 were detected on an influenza A(H5) assay for human diagnostics. A commercial H5N8 assay detected H5 in only 6% (3/48) and N8 in 92% (44/48). Thirteen (13/25; 52%) A(H5N8) genomes generated from veterinary specimens clustered in a single monophyletic clade. These sequences contained the NS (P42S) and PB2 (L89V) mutations noted as markers of mammalian adaptation. Conclusions Diagnostic assays were able to detect and characterize influenza A(H5N8) viruses, but poor performance is reported for a commercial assay. Absence of influenza A(H5N8) in humans with occupational exposure and no clear impression of molecular adaptation for mammalian infection suggest that this avian pathogen continues to be low‐risk human pathogen.
Published: 2020

50. A cost-effectiveness analysis of antenatal influenza vaccination among HIV-infected and HIV-uninfected pregnant women in South Africa

Author: Joni Steinberg, Jocelyn Moyes, Carrie Reed, Meredith McMorrow, Cheryl Cohen, Adam L. Cohen, Paul Hutchinson, Sibongile Walaza, Charles Stoecker, Stefano Tempia, Matthew Biggerstaff, and Florette K. Treurnicht
Subjects: Male, Pediatrics, medicine.medical_specialty, Cost effectiveness, Cost-Benefit Analysis, 030231 tropical medicine, Population, Human immunodeficiency virus (HIV), HIV Infections, medicine.disease_cause, Article, South Africa, 03 medical and health sciences, 0302 clinical medicine, Pregnancy, Hiv infected, Influenza, Human, medicine, Humans, 030212 general & internal medicine, education, education.field_of_study, General Veterinary, General Immunology and Microbiology, business.industry, Vaccination, Infant, Newborn, Public Health, Environmental and Occupational Health, Cost-effectiveness analysis, Quality-adjusted life year, Infectious Diseases, Cohort, Molecular Medicine, Female, business, Monte Carlo Method
Abstract: BACKGROUND: Pregnant women and infants are at increased risk of severe disease from influenza. Antenatal influenza vaccination is safe and can reduce the risk of illness for women and their infants. We evaluated for South Africa the health effects of antenatal influenza vaccination among pregnant women and their infants aged
Published: 2019

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