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Mutations have driven the evolution and development of new variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with potential implications for increased transmissibility, disease severity and vaccine escape among others. Genome sequencing is a technique that allows scientists to read the genetic code of an organism and has become a powerful tool for studying emerging infectious diseases. Here, we conducted a cross-sectional study in selected districts of the Eastern Province of Zambia, from November 2021 to February 2022. We analyzed SARS-CoV-2 samples ( n = 76) using high-throughput sequencing. A total of 4097 mutations were identified in 69 SARS-CoV-2 genomes with 47% (1925/4097) of the mutations occurring in the spike protein. We identified 83 unique amino acid mutations in the spike protein of the seven Omicron sublineages (BA.1, BA.1.1, BA.1.14, BA.1.18, BA.1.21, BA.2, BA.2.23 and XT). Of these, 43.4% (36/83) were present in the receptor binding domain, while 14.5% (12/83) were in the receptor binding motif. While we identified a potential recombinant XT strain, the highly transmissible BA.2 sublineage was more predominant (40.8%). We observed the substitution of other variants with the Omicron strain in the Eastern Province. This work shows the importance of pandemic preparedness and the need to monitor disease in the general population.

Enteric infections due to viral pathogens are a major public health concern. Detecting the risk areas requires a strong surveillance system for pathogenic viruses in sources such as wastewater. Towards building an environmental surveillance system in Zambia, we aimed to identify group A rotavirus (RVA) and human adenovirus (HAdV) in wastewater. Convenient sampling was conducted at four study sites every Tuesday for five consecutive weeks. The research team focused on three different methods of viral concentration to determine the suitability in terms of cost and applicability for a regular surveillance system: the bag-mediated filtration system (BMFS), polyethylene glycol-based (PEG) precipitation, and skimmed milk (SM) flocculation. We screened 20 wastewater samples for HAdV and RVA using quantitative polymerase chain reaction (qPCR) and conventional polymerase chain reaction (cPCR). Of the 20 samples tested using qPCR, 18/20 (90%) tested positive for HAdV and 14/20 (70%) tested positive for RVA. For the genetic sequencing, qPCR positives were subjected to cPCR, of which 12 positives were successfully amplified. The human adenovirus was identified with a nucleotide identity range of 98.48% to 99.53% compared with the reference genome from GenBank. The BMFS and SM flocculation were the most consistent viral concentration methods for HAdV and RVA, respectively. A statistical analysis of the positives showed that viral positivity differed by site ( p < 0.001). SM and PEG may be the most appropriate options in resource-limited settings such as Zambia due to the lower costs associated with these concentration methods. The demonstration of HAdV and RVA detection in wastewater suggests the presence of the pathogens in the communities under study and the need to establish a routine wastewater surveillance system for the identification of pathogens.

Objectives: The study aim was to evaluate vaccine effectiveness (VE) of COVID-19 vaccines in preventing symptomatic COVID-19 among healthcare workers (HCWs) in Zambia. We sought to answer the question, 'What is the vaccine effectiveness of a complete schedule of the SARS-CoV-2 vaccine in preventing symptomatic COVID-19 among HCWs in Zambia?', Design/setting: We conducted a test-negative case-control study among HCWs across different levels of health facilities in Zambia offering point of care testing for COVID-19 from May 2021 to March 2022., Participants: 1767 participants entered the study and completed it. Cases were HCWs with laboratory-confirmed SARS-CoV-2 and controls were HCWs who tested SARS-CoV-2 negative. Consented HCWs with documented history of vaccination for COVID-19 (vaccinated HCWs only) were included in the study. HCWs with unknown test results and unknown vaccination status, were excluded., Primary and Secondary Outcome Measures: The primary outcome was VE among symptomatic HCWs. Secondary outcomes were VE by: SARS-CoV-2 variant strains based on the predominant variant circulating in Zambia (Delta during May 2021 to November 2021 and Omicron during December 2021 to March 2022), duration since vaccination and vaccine product., Results: We recruited 1145 symptomatic HCWs. The median age was 30 years (IQR: 26-38) and 789 (68.9%) were women. Two hundred and eighty-two (24.6%) were fully vaccinated. The median time to full vaccination was 102 days (IQR: 56-144). VE against symptomatic SARS-CoV-2 infection was 72.7% (95% CI: 61.9% to 80.7%) for fully vaccinated participants. VE was 79.4% (95% CI: 58.2% to 90.7%) during the Delta period and 37.5% (95% CI: -7.0% to 63.3%) during the Omicron period., Conclusions: COVID-19 vaccines were effective in reducing symptomatic SARS-CoV-2 among Zambian HCWs when the Delta variant was circulating but not when Omicron was circulating. This could be related to immune evasive characteristics and/or waning immunity. These findings support accelerating COVID-19 booster dosing with bivalent vaccines as part of the vaccination programme to reduce COVID-19 in Zambia., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2023. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Background: Rare cancers are difficult to study owing to their infrequent diagnosis. Using aggregate incidence data from population-based cancer registries in Europe, the Surveillance of Rare Cancers in Europe project compiled a list of clinically relevant, topography and morphology defined rare cancers operationally defined as having a crude annual incidence rate of <6 per 100,000 persons. In 2020, this list of rare cancers was updated. The objective of this study was to assess the utility of a rare cancer recode variable for use in the Cancer in North America (CiNA) dataset and to provide a first look at the burden of rare cancers in Canada and the United States., Methods: Data were obtained from 62 registries in Canada and the United States that met North American Association of Central Cancer Registries (NAACCR) high-quality data standards. The list of rare cancers was programmed as a Rare Cancer Classification variable within SEER*Stat. SEER*Stat was used to estimate case counts and crude and age-specific incidence rates per 100,000 for cancers diagnosed 2015-2019 by age at diagnosis, country, and country-specific geographic regions in Canada and the United States, and by race/ethnicity in the United States., Results: In Canada and the United States, 21% and 22% of all invasive cancers were classified as rare, respectively. The percentage of rare cancers ranged between 18% to 21% across geographic regions in Canada and the United States. Children (aged 0-14 years) had the highest percentage and lowest incidence rates of rare cancers. The percentage of rare cancers decreased, and incidence increased with increasing age. In the United States, Hispanics had the highest percentage (27%) and non-Hispanic Whites and non-Hispanic Blacks the lowest percentage (21%) of rare cancers., Conclusions: While individual rare cancers are infrequently diagnosed, in aggregate, they account for a substantial percentage of all cancers diagnosed in the population and pose a substantial public health burden. We report variations in percentage of rare cancers by age, and race/ethnicity (United States only). Such variations in the burden of these cancers may suggest possible areas for public health research., (© 2023 National Cancer Registrars Association.)

Introduction: since March 2020, Zambia has been experiencing a SARS-CoV-2 epidemic. Little data has been reported on cases and deaths arising from COVID-19 in Africa. We described the demographic characteristics of these cases and deaths in Zambia., Methods: we analyzed data on all persons testing positive for SARS-CoV-2 from 18 th March 2020 to 25 th April 2021 in Zambia. COVID-19 cases were identified through port-of-entry surveillance, contact-tracing, health-care-worker testing, health-facility-based and community-based screening and community-death screening. All diagnoses were confirmed using real-time-polymerase-chain-reaction and rapid-antigen-test-kits of nasopharyngeal specimens. We analyzed age, sex, and date-of-reporting according to whether the cases or deaths occurred during the first wave (1 st July to 15 th September 2020) or the second wave (15 th December 2020 to 10 th April 2021). We computed Mann-Whitney-U-test to compare medians of continuous variables and chi-square tests to compare differences between proportions using R., Results: a total 1,246 (1.36%) deaths were recorded among 91,378 confirmed cases during March 2020-April 2021 in Zambia. Persons who died were older than those who did not (median age 50 years versus 32.0 years, p< 0.001). Although only 4.7% of cases were among persons aged >60 years, most deaths (31.6%) occurred in this age group (p<0.001). More deaths (83.5%) occurred in the community than in health facilities (p<0.001)., Conclusion: during the SARS-CoV-2 epidemic in Zambia, most deaths occurred in the community, indicating potential gaps in public health messaging about COVID-19. Improving health-seeking behaviors for COVID-19 through public messaging campaigns and engaging key community stakeholders in Zambia might reduce avoidable mortality. As the group most impacted by COVID-19 mortality, older persons might need enhanced outreach and linkage to care., Competing Interests: The authors declare no competing interests., (Copyright: Stephen Longa Chanda et al.)

Introduction: Zambia experienced a major cholera outbreak in 2017-2018, with more than 5905 cases reported countrywide, predominantly from the peri-urban slums of Lusaka city. The WHO recommends the use of oral cholera vaccines (OCVs) together with traditional control measures, including health promotion, provision of safe water and improving sanitation, in cholera endemic areas and during cholera outbreaks. In response to this outbreak, the Zambian government implemented the OVC campaign and administered the Euvichol-plus vaccine in the high-risk subdistricts of Lusaka. Although OCVs have been shown to be effective in preventing cholera infection in cholera endemic and outbreak settings, the effectiveness of the Euvichol-plus vaccine has not yet been evaluated in Zambia. This study aimed to determine the effectiveness of two doses of OCV administered during the 2017/2018 vaccination campaign., Methods: We conducted a matched case-control study involving 79 cases and 316 controls following the mass vaccination campaign in the four subdistricts of Lusaka (Chawama, Chipata, Kanyama and Matero). Matching of controls was based on the place of residence, age and sex. Conditional logistic regression was used for analysis. Adjusted OR (AOR), 95% CI and vaccine effectiveness (1-AOR) for two doses of Euvichol-plus vaccine and any dose were estimated (p < 0.05)., Results: The AOR vaccine effectiveness for two doses of Euvichol-plus OCV was 81.0% (95% CI 66.0% to 78.0%; p<0.01). Secondary analysis showed that vaccine effectiveness for any dose was 74.0% (95% CI 50.0% to 86.0%; p<0.01)., Conclusion: These findings show that two doses of Euvichol-plus OCV are effective in a cholera outbreak setting in Lusaka, Zambia. The findings also indicate that two doses are more effective than a single dose and thus support the use of two doses of the vaccine as part of an integrated intervention to cholera control during outbreaks., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY. Published by BMJ.)

During a COVID-19 outbreak in a prison in Zambia from December 14 to 19, 2021, a case-control study was done to measure vaccine effectiveness (VE) against infection and symptomatic infection, when the Omicron variant was the dominant circulating variant. Among 382 participants, 74.1% were fully vaccinated, and the median time since full vaccination was 54 days. There were no hospitalizations or deaths. COVID-19 VE against any SARS-CoV-2 infection was 64.8%, and VE against symptomatic SARS-CoV-2 infection was 72.9%. COVID-19 vaccination helped protect incarcerated persons against SARS-CoV-2 infection during an outbreak while Omicron was the dominant variant in Zambia. These findings provide important local evidence that might be used to increase COVID-19 vaccination in Zambia and other countries in Africa.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) have significantly impacted the global epidemiology of the pandemic. From December 2020 to April 2022, we conducted genomic surveillance of SARS-CoV-2 in the Southern Province of Zambia, a region that shares international borders with Botswana, Namibia, and Zimbabwe and is a major tourist destination. Genetic analysis of 40 SARS-CoV-2 whole genomes revealed the circulation of Alpha (B.1.1.7), Beta (B.1.351), Delta (AY.116), and multiple Omicron subvariants with the BA.1 subvariant being predominant. Whereas Beta, Delta, and Omicron variants were associated with the second, third, and fourth pandemic waves, respectively, the Alpha variant was not associated with any wave in the country. Phylogenetic analysis showed evidence of local transmission and possible multiple introductions of SARS-CoV-2 VOCs in Zambia from different European and African countries. Across the 40 genomes analysed, a total of 292 mutations were observed, including 182 missense mutations, 66 synonymous mutations, 23 deletions, 9 insertions, 1 stop codon, and 11 mutations in the non-coding region. This study stresses the need for the continued monitoring of SARS-CoV-2 circulation in Zambia, particularly in strategically positioned regions such as the Southern Province which could be at increased risk of introduction of novel VOCs.

Since its first discovery in December 2019 in Wuhan, China, COVID-19, caused by the novel coronavirus SARS-CoV-2, has spread rapidly worldwide. While African countries were relatively spared initially, the initial low incidence of COVID-19 cases was not sustained for long due to continuing travel links between China, Europe and Africa. In preparation, Zambia had applied a multisectoral national epidemic disease surveillance and response system resulting in the identification of the first case within 48 h of the individual entering the country by air travel from a trip to France. Contact tracing showed that SARS-CoV-2 infection was contained within the patient's household, with no further spread to attending health care workers or community members. Phylogenomic analysis of the patient's SARS-CoV-2 strain showed that it belonged to lineage B.1.1., sharing the last common ancestor with SARS-CoV-2 strains recovered from South Africa. At the African continental level, our analysis showed that B.1 and B.1.1 lineages appear to be predominant in Africa. Whole genome sequence analysis should be part of all surveillance and case detection activities in order to monitor the origin and evolution of SARS-CoV-2 lineages across Africa., (Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Zambia is a landlocked, lower-middle income country in southern Africa, with a population of 17 million (1). The first known cases of coronavirus disease 2019 (COVID-19) in Zambia occurred in a married couple who had traveled to France and were subject to port-of-entry surveillance and subsequent remote monitoring of travelers with a history of international travel for 14 days after arrival. They were identified as having suspected cases on March 18, 2020, and tested for COVID-19 after developing respiratory symptoms during the 14-day monitoring period. In March 2020, the Zambia National Public Health Institute (ZNPHI) defined a suspected case of COVID-19 as 1) an acute respiratory illness in a person with a history of international travel during the 14 days preceding symptom onset; or 2) acute respiratory illness in a person with a history of contact with a person with laboratory-confirmed COVID-19 in the 14 days preceding symptom onset; or 3) severe acute respiratory illness requiring hospitalization; or 4) being a household or close contact of a patient with laboratory-confirmed COVID-19. This definition was adapted from World Health Organization (WHO) interim guidance issued March 20, 2020, on global surveillance for COVID-19 (2) to also include asymptomatic contacts of persons with confirmed COVID-19. Persons with suspected COVID-19 were identified through various mechanisms, including port-of-entry surveillance, contact tracing, health care worker (HCW) testing, facility-based inpatient screening, community-based screening, and calls from the public into a national hotline administered by the Disaster Management and Mitigation Unit and ZNPHI. Port-of-entry surveillance included an arrival screen consisting of a temperature scan, report of symptoms during the preceding 14 days, and collection of a history of travel and contact with persons with confirmed COVID-19 in the 14 days before arrival in Zambia, followed by daily remote telephone monitoring for 14 days. Travelers were tested for SARS-CoV-2, the virus that causes COVID-19, if they were symptomatic upon arrival or developed symptoms during the 14-day monitoring period. Persons with suspected COVID-19 were tested as soon as possible after evaluation for respiratory symptoms or within 7 days of last known exposure (i.e., travel or contact with a confirmed case). All COVID-19 diagnoses were confirmed using real-time reverse transcription-polymerase chain reaction (RT-PCR) testing (SARS-CoV-2 Nucleic Acid Detection Kit, Maccura) of nasopharyngeal specimens; all patients with confirmed COVID-19 were admitted into institutional isolation at the time of laboratory confirmation, which was generally within 36 hours. COVID-19 patients were deemed recovered and released from isolation after two consecutive PCR-negative test results ≥24 hours apart. A Ministry of Health memorandum was released on April 13, 2020, mandating testing in public facilities of 1) all persons admitted to medical and pediatric wards regardless of symptoms; 2) all patients being admitted to surgical and obstetric wards, regardless of symptoms; 3) any outpatient with fever, cough, or shortness of breath; and 4) any facility or community death in a person with respiratory symptoms, and 5) biweekly screening of all HCWs in isolation centers and health facilities where persons with COVID-19 had been evaluated. This report describes the first 100 COVID-19 cases reported in Zambia, during March 18-April 28, 2020., Competing Interests: All authors have completed and submitted the International Committee of Medical Journal Editors form for disclosure of potential conflicts of interest. No potential conflicts of interest were disclosed.

Background:  Congenital cytomegalovirus (CMV) infection is the major infectious cause of birth defects and hearing loss globally. There is a growing recognition of the potential clinical impact of congenital CMV infections in high-seroprevalence settings., Methods:  A cross-sectional study of neonatal admissions at a large referral center in sub-Saharan Africa to determine the prevalence of both symptomatic and asymptomatic congenital CMV infection was performed. Real-time polymerase chain reaction was used to screen DNA-extracted sera, urine, and saliva, and an enzyme-linked immunosorbent assay was used to screen serum samples for anti-CMV immunoglobulin M. Multivariate binary logistic regression was used to identify risk factors associated with increased odds of congenital CMV infection., Results:  Congenital CMV was detected in 3.8% (15/395) of neonates. Among these infants, 6 of 15 (40%) presented with jaundice, 1 of whom also had petechiae. Congenital CMV infection was detected in 9 of 79 (11.4%; 95% confidence interval [CI], 6.1%-20.3%) neonates born to human immunodeficiency virus (HIV)-infected mothers, and both maternal HIV (odds ratio [OR], 6.661 [95% CI, 2.126-20.876], P = .001) and jaundice (OR, 5.701 [95% CI, 1.776-18.306], P = .003) were independently linked with significantly increased odds of congenital CMV infection., Conclusions:  Congenital and early infant CMV infections may have important consequences for child health in sub-Saharan Africa and other high HIV and CMV seroprevalence populations globally.

Background: Human immunodeficiency virus (HIV) and human cytomegalovirus (HCMV) coinfections have been shown to increase infant morbidity, mortality, and AIDS progression. In HIV-endemic regions, maternal HIV-exposed but HIV-uninfected infants, which is the majority of children affected by HIV, also show poor growth and increased morbidity. Although nutrition has been examined, the effects of HCMV infection have not been evaluated. We studied the effects of HCMV infection on the growth, development, and health of maternally HIV-exposed and unexposed infants in Zambia., Methods: Infants were examined in a cohort recruited to a trial of micronutrient-fortified complementary foods. HIV-infected mothers and infants had received perinatal antiretroviral therapy to prevent mother-to-child HIV transmission. Growth, development, and morbidity were analyzed by linear regression analyses in relation to maternal HIV exposure and HCMV infection, as screened by sera DNA for viremia at 6 months of age and by antibody for infection at 18 months., Results: All HCMV-seropositive infants had decreased length-for-age by 18 months compared with seronegative infants (standard deviation [z]-score difference: -0.44 [95% confidence interval {CI}, -.72 to -.17]; P = .002). In HIV-exposed infants, those who were HCMV positive compared with those who were negative, also had reduced head size (mean z-score difference: -0.72 [95% CI, -1.23 to -.22]; P = .01) and lower psychomotor development (Bayley test score difference: -4.1 [95% CI, -7.8 to -.5]; P = .03). HIV-exposed, HCMV-viremic infants were more commonly referred for hospital treatment than HCMV-negative infants. The effects of HCMV were unaffected by micronutrient fortification., Conclusion: HCMV affects child growth, development, and morbidity of African infants, particularly in those maternally exposed to HIV. HCMV is therefore a risk factor for child health in this region.