Search

The SARS-CoV-2 virus is responsible for the COVID-19 global public health emergency, and the disease it causes is highly variable in its clinical presentation. Clinical phenotypes are heterogeneous both in terms of presentation of symptoms in the host and response to therapy. Several studies and initiatives have been established to analyse and review host genetic epidemiology associated with COVID-19. Our research group curated these articles into a web-based database using the python application-server framework Django. The database provides a searchable research tool describing current literature surrounding COVID-19 host genetic factors associated with disease outcome. This paper describes the COHG-SA database and provides an overview of the analyses that can be derived from these data., (© 2022. The Author(s).)

This paper deals with the ways in which the intellectual and political history of AIDS can assist in the chronological conceptualization of a pandemic such as COVID-19 as it is unfolding. It problematizes the idea of pandemic "beginnings" and "ends" to show that such definitions are shaped by the disciplinary location and thematic foci of relevant scholars. Central to this analysis is the notion that ethical and political contexts affect research on a pandemic in different ways at national and global levels at various points in its trajectory. The article develops this argument in relation to two main themes: firstly, with reference to the history of AIDS research in South Africa; secondly, with the philosophical concept of bioagency to understand the ways in which viruses and humans co-shape the course of epidemics over time. I first make the case for the development of historically informed, long-term ethnographic studies of COVID-19. Using bioagency as a point of departure to consider viruses as social actors, the essay then critiques the notion of bioinformationalism as catalyzing the widening accessibility of biomedical research. Instead, I discuss the biotechnology and pharmaceutical industries as protagonists in the operation of biocapital. I argue that the history of AIDS in South Africa can provide methodological and theoretical insights into how to interpret an unfolding epidemic, outlining an ambitious transdisciplinary research agenda for thinking about the temporality of a pandemic spanning the different, interconnected, scales of life., (© The Author(s) 2024. Published by Oxford University Press.)

Respiratory syncytial virus (RSV) is the most predominant viral pathogen worldwide in children with lower respiratory tract infections. The Coronavirus disease 2019 (COVID-19) pandemic and resulting nonpharmaceutical interventions perturbed the transmission pattern of respiratory pathogens in South Africa. A seasonality shift and RSV resurgence was observed in 2020 and 2021, with several infected children observed. Conventional RSV-positive nasopharyngeal swabs were collected from various hospitals in the Free State province, Bloemfontein, South Africa, from children suffering from respiratory distress and severe acute respiratory infection between 2020 to 2021. Overlapping genome fragments were amplified and complete genomes were sequenced using the Illumina MiSeq platform. Maximum likelihood phylogenetic and evolutionary analysis were performed on both RSV-A/-B G-genes with published reference sequences from GISAID and GenBank. Our study strains belonged to the RSV-A GA2.3.2 and RSV-B GB5.0.5a clades. The upsurge of RSV was due to pre-existing strains that predominated in South Africa and circulating globally also driving these off-season RSV outbreaks during the COVID-19 pandemic. The variants responsible for the resurgence were phylogenetically related to pre-pandemic strains and could have contributed to the immune debt resulting from pandemic imposed restrictions. The deviation of the RSV season from the usual pattern affected by the COVID-19 pandemic highlights the need for ongoing genomic surveillance and the identification of genetic variants to prevent unforeseen outbreaks in the future., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)

Purpose: We sought to understand the impact of the initial COVID-19 mitigation strategies in 2020 on drug-resistant (DR) TB diagnoses in KwaZulu-Natal province (KZN), South Africa., Methods: We compared the number, spatial distribution, and characteristics of DR TB diagnoses before and after the initial COVID-19 lockdown on March 26th, 2020. Information on DR TB diagnoses was collected from the CONTEXT prospective cohort study and municipality characteristics were collected from Statistics South Africa. We used Bayesian conditional autoregressive models and relative-risk surface maps to examine spatial correlates and patterns of DR TB notifications., Results: Between October 2018 and February 2022, there were 693 individuals diagnosed with DR TB in KZN, South Africa. The rate of diagnoses per year was 274 and 155 prior and after to the initial lockdowns, respectively, corresponding to a 43 % decrease in the notification rate of cases. Compared to cases diagnosed before the lockdown, cases diagnosed after were less likely to have a fuel source for heating, piped water, a flush toilet, or own a phone (p-values≤0.02). Changes in notifications were not homogenously distributed, with predominantly rural northeastern and southwestern municipalities having significantly greater relative-risks after the lockdown., Conclusions: We found a reduction in the rate of DR TB diagnoses after the COVID-19 pandemic lockdowns and observed that individuals diagnosed after the lockdowns had worse living conditions, fewer household resources, and more adults living in their household compared to before the pandemic., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Since late 2019, COVID-19 has significantly impacted the world. Understanding the evolution of SARS-CoV-2 is crucial for protecting against future infectious pathogens. In this study, we conducted a comprehensive chronological analysis of SARS-CoV-2 evolution by examining mutation prevalence from the source countries of VOCs: United Kingdom, India, Brazil, South Africa, plus two countries: United States, Russia, utilizing genomic sequences from GISAID. Our methodological approach involved large-scale genomic sequence alignment using MAFFT, Python-based data processing on a high-performance computing platform, and advanced statistical methods the Maximal Information Coefficient (MIC), and also Long Short-Term Memory (LSTM) models for correlation analysis. Our findings elucidate the dynamics of SARS-CoV-2 evolution, highlighting the virus's changing behaviour over various pandemic stages. Key results include the discovery of three temporal mutation patterns-lineage distinct, long-span, and competitive mutations-with varying levels of impact on the virus. Notably, we observed a convergence of advantageous mutations in the spike protein, especially in the later stages of the pandemic, indicating a substantial evolutionary pressure on the virus. One of the most significant revelations is the predominant role of natural immunity over vaccination-induced immunity in driving these evolutionary changes. This emphasizes the critical need for regular vaccine updates to maintain efficacy against evolving strains. In conclusion, our study not only sheds light on the evolutionary trajectory of SARS-CoV-2 but also underscores the urgency for robust, continuous global data collection and sharing. It highlights the necessity for rapid adaptations in medical countermeasures, including vaccine development, to stay ahead of pathogen evolution. This research provides valuable insights for future pandemic preparedness and response strategies., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Many low- and middle-income countries (LMICs) grapple with shortages of health workers, a crucial component of robust health systems. The COVID-19 pandemic underscored the imperative for appropriate staffing of health systems and the occupational health (OH) threats to health workers. Issues related to accessibility, coverage, and utilization of OH services in public sector health facilities within LMICs were particularly accentuated during the pandemic. This paper draws on the observations and experiences of researchers engaged in an international collaboration to consider how the South African concept of Ubuntu provides a promising way to understand and address the challenges encountered in establishing and sustaining OH services in public sector health facilities. Throughout the COVID-19 pandemic, the collaborators actively participated in implementing and studying OH and infection prevention and control measures for health workers in South Africa and internationally as part of the World Health Organizations' Collaborating Centres for Occupational Health. The study identified obstacles in establishing, providing, maintaining and sustaining such measures during the pandemic. These challenges were attributed to lack of leadership/stewardship, inadequate use of intelligence systems for decision-making, ineffective health and safety committees, inactive trade unions, and the strain on occupational health professionals who were incapacitated and overworked. These shortcomings are, in part, linked to the absence of the Ubuntu philosophy in implementation and sustenance of OH services in LMICs., Competing Interests: The authors have no competing interests to declare., (Copyright: © 2024 The Author(s).)

The current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic capacity is limited in defined communities, posing a challenge in tracking and tracing new infections. Monitoring student residences, which are considered infection hotspots, with targeted wastewater surveillance is crucial. This study evaluated the efficacy of SARS-CoV-2 targeted wastewater surveillance for outbreak mitigation at Stellenbosch University's student residences in South Africa. Using torpedo-style passive sampling devices, wastewater samples were collected biweekly from manholes at twelve Stellenbosch University Tygerberg (SUT) campus and Stellenbosch University-Main (SUM) campus student residences. The surveillance led to an early warning detection of SARS-CoV-2 presence on campus, followed by an informed management strategy leading to restriction of student activities on campus and a delay in the onset of the third wave that was experienced throughout the country. Moreover, the study highlighted the extent of possible infections at defined locations even when a low number of confirmed coronavirus disease 2019 (COVID-19) cases were reported. The study also tracked the surge of the Delta and Omicron variants in the student residences using the Thermo Fisher TaqMan® RT-qPCR genotyping assay., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)

On the 26th of November 2021, the World Health Organization (WHO) designated the newly detected B.1.1.529 lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) the Omicron Variant of Concern (VOC). The genome of the Omicron VOC contains more than 50 mutations, many of which have been associated with increased transmissibility, differing disease severity, and potential to evade immune responses developed for previous VOCs such as Alpha and Delta. In the days since the designation of B.1.1.529 as a VOC, infections with the lineage have been reported in countries around the globe and many countries have implemented travel restrictions and increased border controls in response. We putatively detected the Omicron variant in an aircraft wastewater sample from a flight arriving to Darwin, Australia from Johannesburg, South Africa on the 25th of November 2021 via positive results on the CDC N1, CDC N2, and del(69-70) RT-qPCR assays per guidance from the WHO. The Australian Northern Territory Health Department detected one passenger onboard the flight who was infected with SARS-CoV-2, which was determined to be the Omicron VOC by sequencing of a nasopharyngeal swab sample. Subsequent sequencing of the aircraft wastewater sample using the ARTIC V3 protocol with Nanopore and ATOPlex confirmed the presence of the Omicron variant with a consensus genome that clustered with the B.1.1.529 BA.1 sub-lineage. Our detection and confirmation of a single onboard Omicron infection via aircraft wastewater further bolsters the important role that aircraft wastewater can play as an independent and unintrusive surveillance point for infectious diseases, particularly coronavirus disease 2019., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)

Currently, the global report of COVID-19 cases is around 110 million, and more than 2.43 million related death cases as of February 18, 2021. Viruses continuously change through mutation; hence, different virus of SARS-CoV-2 has been reported globally. The United Kingdom (UK), South Africa, Brazil, and Nigeria are the countries from which these emerged variants have been notified and now spreading globally. Therefore, these countries have been selected as a research sample for the present study. The datasets analyzed in this study spanned from March 1, 2020, to January 31, 2021, and were obtained from the World Health Organization website. The study used the Autoregressive Integrated Moving Average (ARIMA) model to forecast coronavirus incidence in the UK, South Africa, Brazil, and Nigeria. ARIMA models with minimum Akaike Information Criterion Correction (AICc) and statistically significant parameters were chosen as the best models in this research. Accordingly, for the new confirmed cases, ARIMA (3,1,14), ARIMA (0,1,11), ARIMA (1,0,10), and ARIMA (1,1,14) models were chosen for the UK, South Africa, Brazil, and Nigeria, respectively. Also, the model specification for the confirmed death cases was ARIMA (3,0,4), ARIMA (0,1,4), ARIMA (1,0,7), and ARIMA (Brown); models were selected for the UK, South Africa, Brazil, and Nigeria, respectively. The results of the ARIMA model forecasting showed that if the required measures are not taken by the respective governments and health practitioners in the days to come, the magnitude of the coronavirus pandemic is expected to increase in the study's selected countries., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Cai Li et al.)

The global circulation of newly emerging variants of SARS-CoV-2 is a new threat to public health due to their increased transmissibility and immune evasion. Moreover, currently available vaccines and therapeutic antibodies were shown to be less effective against new variants, in particular, the South African (SA) variant, termed 501Y.V2 or B.1.351. To assess the efficacy of the CT-P59 monoclonal antibody against the SA variant, we sought to perform as in vitro binding and neutralization assays, and in vivo animal studies. CT-P59 neutralized B.1.1.7 variant to a similar extent as to wild type virus. CT-P59 showed reduced binding affinity against a RBD (receptor binding domain) triple mutant containing mutations defining B.1.351 (K417N/E484K/N501Y) also showed reduced potency against the SA variant in live virus and pseudovirus neutralization assay systems. However, in vivo ferret challenge studies demonstrated that a therapeutic dosage of CT-P59 was able to decrease B.1.351 viral load in the upper and lower respiratory tracts, comparable to that observed for the wild type virus. Overall, although CT-P59 showed reduced in vitro neutralizing activity against the SA variant, sufficient antiviral effect in B.1.351-infected animals was confirmed with a clinical dosage of CT-P59, suggesting that CT-P59 has therapeutic potential for COVID-19 patients infected with SA variant., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier Inc. All rights reserved.)

New SARS-CoV-2 mutations are constantly emerging, raising concerns of increased transmissibility, virulence or escape from host immune response. We describe a nested RT-PCR assay (~1500 bps) to detect multiple nucleotide changes resulting in key spike protein mutations distinctive of the major known circulating SARS-CoV-2 variants, including the three Variants of Concern (VOCs) 20I/501Y.V1 (United Kingdom), 20H/501Y.V2 (South Africa), and 20 J/501Y.V3 (Brazil), as well as the 20E.EU1 variant (Spain), the CAL.20C recently identified in California, and the mink-associated variant (GR, lineage B.1.1.298). Prior to application to field samples, the discriminatory potential of this PCR assay was explored using GISAID and Nextclade. To extend variant detection to challenging matrices such as sewage, where the amplification of long fragments is problematic, two short nested RT-PCR assays (~300 bps) were also designed, targeting portions of the region spanned by the long nested assay. The three newly-designed assays were then tested on field samples, including 31 clinical samples (7 fully-sequenced swab samples, and 24 uncharacterized ones) and 34 urban wastewater samples, some of which collected in areas where circulation of VOCs had been reported. The long assay successfully amplified 29 of the 31 swabs (93%), allowing the correct identification of variants 20I/501Y.V1 and 20E.EU1 present in the panel of previously characterized samples. The Spanish variant was detected in 14/24 of the uncharacterized samples as well. The sequences obtained using the short assays were consistent with those obtained with the long assay. Mutations characteristic of VOCs (UK and Brazilian variant) and of other variant (Spanish) were detected in sewage samples. To our knowledge, this is the first evidence of the presence of sequences harboring key mutations of 20I/501Y.V1 and 20 J/501Y.V3 in urban wastewaters, highlighting the potential contribution of wastewater surveillance to explore SARS-CoV-2 diversity. The developed nested RT-PCR assays can be used as an initial rapid screening test to select clinical samples containing mutations of interest. This can speed up diagnosis and optimize resources since it allows full genome sequencing to be done only on clinically relevant specimens. The assays can be also employed for a rapid and cost-effective detection of VOCs or other variants in sewage for the purposes of wastewater-based epidemiology. The approach proposed here can be used to better understand SARS-CoV-2 variant diversity, geographic distribution and impact worldwide., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Objectives: The Network for Genomic Surveillance in South Africa (NGS-SA) was formed to investigate the introduction and understand the early transmission dynamics of the SARS-CoV-2 epidemic in South-Africa., Design: This paper presents the first results from this group, which is a molecular epidemiological study of the first 21 SARS-CoV-2 whole genomes sampled in the first port of entry - KwaZulu-Natal (KZN) - during the first month of the epidemic. By combining this with calculations of the effective reproduction number (R), it aimed to shed light on the patterns of infections in South Africa., Results: Two of the largest provinces - Gauteng and KZN - had a slow growth rate for the number of detected cases, while the epidemic spread faster in the Western Cape and Eastern Cape. The estimates of transmission potential suggested a decrease towards R = 1 since the first cases and deaths, but a subsequent estimated R average of 1.39 between 6-18 May 2020. It was also demonstrated that early transmission in KZN was associated with multiple international introductions and dominated by lineages B1 and B. Evidence for locally acquired infections in a hospital in Durban within the first month of the epidemic was also provided., Conclusion: The COVID-19 pandemic in South Africa was very heterogeneous in its spatial dimension, with many distinct introductions of SARS-CoV2 in KZN and evidence of nosocomial transmission, which inflated early mortality in KZN. The epidemic at the local level was still developing and NGS-SA aimed to clarify the dynamics in South Africa and devise the most effective measures as the outbreak evolved., (Copyright © 2020. Published by Elsevier Ltd.)

Background: The rising burden of the ongoing COVID-19 epidemic in South Africa has motivated the application of modeling strategies to predict the COVID-19 cases and deaths. Reliable and accurate short and long-term forecasts of COVID-19 cases and deaths, both at the national and provincial level, are a key aspect of the strategy to handle the COVID-19 epidemic in the country., Methods: In this paper we apply the previously validated approach of phenomenological models, fitting several non-linear growth curves (Richards, 3 and 4 parameter logistic, Weibull and Gompertz), to produce short term forecasts of COVID-19 cases and deaths at the national level as well as the provincial level. Using publicly available daily reported cumulative case and death data up until 22 June 2020, we report 5, 10, 15, 20, 25 and 30-day ahead forecasts of cumulative cases and deaths. All predictions are compared to the actual observed values in the forecasting period., Results: We observed that all models for cases provided accurate and similar short-term forecasts for a period of 5 days ahead at the national level, and that the three and four parameter logistic growth models provided more accurate forecasts than that obtained from the Richards model 10 days ahead. However, beyond 10 days all models underestimated the cumulative cases. Our forecasts across the models predict an additional 23,551-26,702 cases in 5 days and an additional 47,449-57,358 cases in 10 days. While the three parameter logistic growth model provided the most accurate forecasts of cumulative deaths within the 10 day period, the Gompertz model was able to better capture the changes in cumulative deaths beyond this period. Our forecasts across the models predict an additional 145-437 COVID-19 deaths in 5 days and an additional 243-947 deaths in 10 days., Conclusions: By comparing both the predictions of deaths and cases to the observed data in the forecasting period, we found that this modeling approach provides reliable and accurate forecasts for a maximum period of 10 days ahead.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a new strain of virus in the Coronavirus family that has not been previously identified. Since SARS-CoV-2 is a new virus, everyone is at risk of catching the Coronavirus disease 2019 (Covid-19). No one has immunity to the virus. Despite this, misconceptions about specific groups of people who are immune to Covid-19 emerged with the onset of the pandemic. This paper explores South African communities' misconceptions about who is most vulnerable to Covid-19. A rapid qualitative assessment was conducted remotely in Gauteng, KwaZulu-Natal and the Western Cape provinces of South Africa. Recruitment of study participants took place through established relationships with civil society organizations and contacts made by researchers. In total, 60 key informant interviews and one focus group discussion was conducted. Atlas.ti.8 Windows was used to facilitate qualitative data analysis. The qualitative data was coded, and thematic analysis used to identify themes. The results show a high level of awareness and knowledge of the transmission and prevention of SARS-CoV-2. Qualitative data revealed that there is awareness of elderly people and those with immunocompromised conditions being more vulnerable to catching Covid-19. However, misconceptions of being protected against the virus or having low or no risk were also evident in the data. We found that false information circulated on social media not only instigated confusion, fear and panic, but also contributed to the construction of misconceptions, othering and stigmatizing responses to Covid-19. The study findings bring attention to the importance of developing communication materials adapted to specific communities to help reduce misconceptions, othering and stigmatization around Covid-19., Competing Interests: The authors have declared that no competing interests exist.

South Africa's declaration of a state of pandemic on 27 March 2020 to combat the spread of the novel coronavirus disease (COVID-19) has elicited debates on the impact of government's policy responses, such as national lockdowns, on the economy of the country. Some pundits support lockdown measures by arguing that they save many lives. Others acknowledge the efficacy of lockdowns in combating the spread of COVID-19 but argue that they have a devastating impact on the economy and livelihoods. However, both pro- and anti-lockdown commentators neglect African indigenous approaches in combatting the spread of infectious diseases such as COVID-19. The current paper offers a consolidated approach on how African indigenous approaches might be practically and pragmatically integrated with South Africa's COVID-19 policy responses. Drawing on Afrocentric theory, this paper argues that a combination of Western and African indigenous approaches can be more successful in combating the spread of COVID-19 if they are incorporated into a synthesis that adopts useful elements of each. This paper argues that by insisting on national lockdowns, social distancing, self-isolation, and the use of facemasks and vaccines as the only means of combating COVID-19, the South African government is discrediting the use of indigenous African knowledge. [ABSTRACT FROM AUTHOR]

It is no doubt that the outbreak of the novel coronavirus caught the world including South Africa, off-guard. This statement refers in particular, to the fact that the outbreak of the pandemic firstly exposed the level of unpreparedness of government and its different departments, including the private sector to deal with unforeseen outbreaks like the coronavirus which leads to COVID-19. This is a typical example of systemic problems within the government and the private sector. Secondly and most importantly, this outbreak exposed the level of inequality between schools in rural areas and those in townships and affluent parts of the country which are mostly habited by black middle class and white people. The purpose of this paper is to investigate the systemic challenges and the emotional impact of this virus on the learners and their parents; the learners and their teachers, and to venture into the policymaking and implementation terrain of the Department of Basic education with a specific focus on how the DBE responded to the outbreak. Furthermore, this paper makes a case out of the emerging case by case approach of the government and the DBE in dealing with the threats which are posed by this pandemic to communities and schools. The researchers hold the view that this paper will expose the levels of inequality between schools in different parts of the country and advocate for a culture of foresight in the education management system; a culture that acknowledges that schools, like communities and business entities, are vulnerable and susceptible to external forces that may have long-lasting effects on their functionality. [ABSTRACT FROM AUTHOR]

In this paper, we explored how vulnerable, immunocompromised groups and caregivers of the elderly experienced and perceived the onset of the Covid-19 pandemic in South Africa. Semi-structured interviews were conducted remotely between the 5th andthe 18th of April 2020 in the three South African provinces hardest hit by Covid-19, namely Gauteng, KwaZulu-Natal and the Western Cape. In total, 60 qualitative key informant interviews and one focus group discussion were conducted. Study participants expressed concerns for elderly people and people with underlying health conditions because of their increased vulnerability to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). People living with HIV expressed an increased fear of infection following the advent of the Covid-19 pandemic in South Africa. The sidelining of healthcare services and stock-outs of medication proved to be an added concern in particular for vulnerable and immunocompromised groups. Overall, the data suggest that the fear of infection is ubiquitous for people who live in unstable environments such as overcrowded townships and informal settlements. Given the increased fears of infection brought on by the Covid-19 pandemic, the mental health of vulnerable communities and those caring for them becomes an added burden for people living in unstable environments. [ABSTRACT FROM AUTHOR]

COVID-19 arguably had far-reaching implications for Christianity and the church as an institution. Issues around social distancing and lockdown directly impacted articulation and religious expression, while understanding of the pandemic and the virus were mediated through constructions of religio-spiritual beliefs. Given this, the study sought to explore some neo-Pentecostal church leaders' messages in South Africa regarding the novel coronavirus or COVID-19, what this meant to their followers and the associated implications for the spread and effects of COVID-19. Methodologically, the researcher viewed and listened to uploaded YouTube video clips of news related to the church and COVID-19, uploaded by media outlets and the neo-Pentecostal church leaders themselves as well as online newspaper reports from the period 2 March to 19 June 2020. The findings of the study reveal that neo-Pentecostal church leaders attributed the origins of SARS-COV-2 to "evil" spirits. Neo-Pentecostal church leaders had mixed messages on the possible cure for COVID-19, with some emphasising miracles as the panacea for COVID-19, and a minority believing that God exhibits his power through epidemiologists. Prayer was also viewed as a tool for Christians to protect themselves from contracting COVID-19 through the invocation of divine powers. The paper concludes that the pervasive influence of church leaders and their emphasis on spiritual remedies such as prayer and miracles may have given Pentecostal followers a false sense of security, which might have affected their awareness of COVID-19. [ABSTRACT FROM AUTHOR]

On March 11, 2020, the outbreak of Novel Coronavirus (SARS‐CoV‐2) Disease, or COVID‐19, was officially declared a pandemic by the World Health Organization (WHO). As its effects roll through societies and economies across the globe, women are expected to bear the heaviest impact. Unfortunately, despite gender‐focused reporting on the consequences of the COVID‐19 crisis, few government policies and public health efforts have explicitly addressed the gendered impacts of the pandemic. This academic review paper presents literature, from both academic and media sources, on the early effects of the COVID‐19 crisis on women, specifically within the South African context. Preliminary research and reporting of the effects of COVID‐19 on the South African population indicate that inequitable gendered practices negatively impact women in the general economy, the workplace, and the home. These settings are discussed in this article, along with recommendations to ameliorate the lived experiences of South African women. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic has resulted in over 340 million infection cases (as of 21 January 2022) and more than 5.57 million deaths globally. In reaction, science, technology and innovation communities across the globe have organised themselves to contribute to national responses to COVID-19 disease. A significant contribution has been from the establishment of wastewater-based epidemiological (WBE) surveillance interventions and programmes for monitoring the spread of COVID-19 in at least 55 countries. Here, we examine and share experiences and lessons learnt in establishing such surveillance programmes. We use case studies to highlight testing methods and logistics considerations associated in scaling the implementing of such programmes in South Africa, the Netherlands, Turkey and England. The four countries were selected to represent different regions of the world and the perspective based on the considerable progress made in establishing and implementing their national WBE programmes. The selected countries also represent different climatic zones, economies, and development stages, which influence the implementation of national programmes of this nature and magnitude. In addition, the four countries’ programmes offer good experiences and lessons learnt since they are systematic, and cover extensive areas, disseminate knowledge locally and internationally and partnered with authorities (government). The programmes also strengthened working relations and partnerships between and among local and global organisations. This paper shares these experiences and lessons to encourage others in the water and public health sectors on the benefits and value of WBE in tackling SARS-CoV-2 and related future circumstances. [ABSTRACT FROM AUTHOR]

Understanding the factors that influence COVID-19 transmission is essential in assessing and mitigating the spread of the pandemic. This study focuses on modeling the impact of air pollution and meteorological parameters on the risk of COVID-19 transmission in Western Cape Province, South Africa. The data used in this study consist of air pollution parameters, meteorological variables, and COVID-19 incidence observed for 262 days from April 26, 2020, to January 12, 2021. Lagged data were prepared for modeling based on a 6-day incubation period for COVID-19 disease. Based on the overdispersion property of the incidence, negative binomial (NB) and generalised Poisson (GP) regression models were fitted. Stepwise regression was used to select the significant predictors in both models based on the Akaike information criterion (AIC). The residuals of both NB and GB regression models were autocorrelated. An autoregressive integrated moving average (ARIMA) model was fitted to the residuals of both models. ARIMA (7, 1, 5) was fitted to the residuals of the NB model while ARIMA (1, 1, 6) was fitted for the residuals of the GP model. NB + ARIMA (7, 1, 5) and GP + ARIMA (1, 1, 6) models were tested for performance using root mean square error (RSME). GP + ARIMA (1, 1, 6) was selected as the optimal model. The results from the optimal model suggest that minimum temperature, ambient relative humidity, ambient wind speed, PM 2.5 , and NO 2 at various lags are positively associated with COVID-19 incidence while maximum relative humidity, minimum relative humidity, solar radiation, maximum temperature, NO, PM load, PM 10 , SO 2 , and NO X at various lags have a negative association with COVID-19 incidence. Ambient wind direction and temperature showed a nonsignificant association with COVID-19 at all lags. This study suggests that meteorological and pollution parameters play a vital independent role in the transmission of the SARS-CoV-2 virus. [ABSTRACT FROM AUTHOR]

COVID-19, which originated in Wuhan, China, 2 years ago, became a pandemic, that continues to this day. The Journal of Disaster Research (JDR) edited a special issue, "Special Issue on COVID-19 and Historical Pandemics" at the end of 2020 and an electronic version of the issue was published in January 2021 (JDR Vol.16, No.1, pp. 1-117). Even though one year has passed, life has not yet returned to normal due to the continued spread of COVID-19. Although the percentage of the general public that has been vaccinated continues to increase and various drugs and treatments have been developed, the number of COVID-19 cases also continues to increase. A huge number of COVID-19 cases have been reported, especially in Europe and the Americas. Accordingly, we planned to publish Special Issue Part 2 and called for papers. This Special Issue Part 2 includes 18 manuscripts, which deal with general epidemiology, effects on socioeconomic or educational areas, and clinical medicine, including vaccines and medical treatments. The virus spike protein plays an important role in its intrusion into human cells and the onset of COVID-19 infection. Although SARS-CoV-2 (the pathogenic virus of COVID-19) originated in Wuhan, China, various variant strains with mutation in gene coding in the spike protein have appeared in multiple countries. The WHO classifies these variants into the categories of VOC (variant of concern), VOI (variant of interest), or VUM (variant under monitoring). The definitions of VOC and VOI are as follows. VOC: "A SARS-CoV-2 variant that meets the definition of a VOI and, through a comparative assessment, has been demonstrated to be associated with one or more changes in the degree of global public health significance." VOI: "Increase in transmissibility or detrimental change in COVID-19 epidemiology, increase in virulence or change in clinical disease presentation, or decrease in effectiveness of public health and social measures or available diagnostics, vaccines and therapeutics." The WHO uses Greek letters designating the variants. Accordingly as they have appeared, variants have been designated as alpha (α: the UK variant), beta (β: the South Africa variant), and delta (δ: the Indian variant). After the deadline for the manuscript of this special issue, a new variant, omicron (o) originated in South Africa and Botswana, and it immediately began spreading worldwide. Unfortunately, it was impossible to include the manuscript on the omicron variant in this Special Issue Part 2, as the deadline had already passed. As COVID-19 continues to spread, the JDR will plan to edit Part 3 of this COVID-19 special issue. [ABSTRACT FROM AUTHOR]

The novel coronavirus (COVID-19) pandemic continues to be a global health problem whose impact has been significantly felt in South Africa. With the global spread increasing and infecting millions, containment efforts by countries have largely focused on lockdowns and social distancing to minimise contact between persons. Social distancing has been touted as the best form of response in managing a rapid increase in the number of infected cases. In this paper, we present a deterministic model to describe the impact of social distancing on the transmission dynamics of COVID-19 in South Africa. The model is fitted to data from March 5 to April 13, 2020, on the cumulative number of infected cases, and a scenario analysis on different levels of social distancing is presented. The model shows that with the levels of social distancing under the initial lockdown level between March 26 and April 13, 2020, there would be a projected continued rise in the number of infected cases. The model also looks at the impact of relaxing the social distancing measures after the initial announcement of the lockdown. It is shown that relaxation of social distancing by 2% can result in a 23% rise in the number of cumulative cases whilst an increase in the level of social distancing by 2% would reduce the number of cumulative cases by about 18%. The model results accurately predicted the number of cases after the initial lockdown level was relaxed towards the end of April 2020. These results have implications on the management and policy direction in the early phase of the epidemic. [ABSTRACT FROM AUTHOR]

Purpose: This research examines the impact of lockdown stringency measures and COVID-19 cases on food and healthcare prices in six Brazil, Russia, India, China, South Africa and Turkey (BRICST) countries. This research is conducted in these countries since previous studies failed to examine the effect of COVID-19 reported cases on food and healthcare prices. Design/methodology/approach: To achieve the objectives of this study, food and healthcare services were regressed against CVC and lockdown stringency measures using the dynamic autoregressive distributed lag (DARDL) model. For this purpose, we used daily data for BRICST countries such as Brazil, Russia, India, China, South Africa and Turkey. Findings: The empirical evidence indicates that, in the long run, COVID-19 cases significantly and positively affect both food and healthcare prices in India, South Africa and China. In contrast, in the short run, COVID-19 positively affects food and healthcare prices in all countries except Russia and Turkey. Similarly, in the long run, the government stringency index (GSI) and Containment and Health Index (CHI) significantly affect health prices in India and South Africa. In contrast, GSI and CHI significantly affect healthcare prices in South Africa only in the short run. Finally, GSI and CHI significantly affect the food prices in the long run in India, South Africa and China and in the short run in South Africa only. Originality/value: The widespread impact of the new Coronavirus (COVID-19) has made the world panic. COVID-19 affected all spheres of life, including food supplies and healthcare services. However, most of the empirical research failed to examine the impact of COVID-19 cases on food and healthcare prices which is the main focus of this study. Moreover, in the given context, the authors use a recently developed model that the previous studies failed to use. [ABSTRACT FROM AUTHOR]

This study assesses the durability of severe acute respiratory coronavirus-2 (SARS-CoV-2) anti-nucleocapsid (anti-N) immunoglobulin G (IgG) after infection and examines its association with established risk factors among South African healthcare workers (HCWs). Blood samples were obtained from 390 HCWs with diagnosis of coronavirus disease 2019 (COVID-19) for assay of the SARS-CoV-2 anti-N IgG at two time points (Phase 1 and 2) between November 2020 and February 2021. Out of 390 HCWs with a COVID-19 diagnosis, 267 (68.5%) had detectable SARS-CoV-2 anti-N IgG antibodies at the end of Phase I. These antibodies persisted for 4–5 and 6–7 months in 76.4% and 16.1%, respectively. In the multivariate logistic regression model analysis, Black participants were more likely to sustain SARS-CoV-2 anti-N IgG for 4–5 months. However, participants who were HIV positive were less likely to sustain SARS-CoV-2 anti-N IgG antibodies for 4–5 months. In addition, individuals who were <45 years of age were more likely to sustain SARS-CoV-2 anti-N IgG for 6–7 months. Of the 202 HCWs selected for Phase 2, 116 participants (57.4%) had persistent SARS-CoV-2 anti-N IgG for an extended mean period of 223 days (7.5 months). Findings support the longevity of vaccine responses against SARS-CoV-2 in Black Africans. [ABSTRACT FROM AUTHOR]

Health care workers (HCWs) experienced greater risk of SARS-CoV-2 infection during the COVID-19 pandemic. This study applies a cost-of-illness (COI) approach to model the economic burden associated with SARS-CoV-2 infections among HCWs in five low- and middle-income sites (Kenya, Eswatini, Colombia, KwaZulu-Natal province, and Western Cape province of South Africa) during the first year of the pandemic. We find that not only did HCWs have a higher incidence of COVID-19 than the general population, but in all sites except Colombia, viral transmission from infected HCWs to close contacts resulted in substantial secondary SARS-CoV-2 infection and death. Disruption in health services as a result of HCW illness affected maternal and child deaths dramatically. Total economic losses attributable to SARS-CoV-2 infection among HCWs as a share of total health expenditure ranged from 1.51% in Colombia to 8.38% in Western Cape province, South Africa. This economic burden to society highlights the importance of adequate infection prevention and control measures to minimize the risk of SARS-CoV-2 infection in HCWs. Health care workers were at high risk of SARS-CoV-2 infection in the early stage of the pandemic, and this had knock-on effects including secondary infections and disruptions in health service delivery. Here, the authors estimate the economic impacts of SARS-CoV-2 infections in health care workers at the society level in five low- and middle-income country settings. [ABSTRACT FROM AUTHOR]

Background: Remdesivir is being studied and used to treat coronavirus disease 2019 (COVID-19). This study aimed to systematically identify, critically evaluate, and summarize the findings of the studies on the cost-effectiveness of remdesivir in the treatment of hospitalized patients with COVID-19. Methods: In this systematic review, PubMed, EMBASE, Web of Science, SCOPUS, and the Cochrane Library were searched for studies published between 2019 and 2022. We included all full economic evaluations of remdesivir for the treatment of hospitalized patients with COVID-19. Data were summarized in a structured and narrative manner. Results: Out of 616 articles obtained in this literature search, 12 studies were included in the final analysis. The mean score of the Quality of Health Economic Studies (QHES) for the studies was 87.66 (high quality). All studies were conducted in high-income countries (eight studies in the USA and one study in England), except for three studies from middle-to-high-income countries (China, South Africa, and Turkey). Six studies conducted their economic analysis in terms of a health system perspective; five studies conducted their economic analysis from a payer perspective; three studies from the perspective of a health care provider. The results of five studies showed that remdesivir was cost-effective compared to standard treatment. Furthermore, the therapeutic strategy of combining remdesivir with baricitinib was cost-effective compared to remdesivir alone. Conclusions: Based on the results of the present study, remdesivir appears to be cost-effective in comparison with the standard of care in China, Turkey, and South Africa. Studies conducted in the United States show conflicting results, and combining remdesivir with baricitinib is cost-effective compared with remdesivir alone. However, the cost-effectiveness of remdesivir in low-income countries remains unknown. Thus, more studies in different countries are required to determine the cost-effectiveness of this drug. [ABSTRACT FROM AUTHOR]

While vaccines are a well-established method of controlling the spread of infectious diseases, vaccine hesitancy jeopardizes curbing the spread of COVID-19. Through the Vaccine Information Network (VIN), this study explored barriers and motivators to COVID-19 vaccine uptake. We conducted 18 focus group discussions with male and female community members, stratified by country, age group, and—for Zimbabwe only—by HIV status. Participants' median age across both countries was 40 years (interquartile range of 22–40), and most (65.9%) were female. We conceptualized the key themes within the World Health Organization's Strategic Advisory Group of Experts on Immunization (SAGE) 3C (convenience, confidence, complacency) vaccine hesitancy model. Barriers to vaccine uptake—lack of convenience, low confidence, and high complacency—included inaccessibility of vaccines and vaccination sites, vaccine safety and development concerns, and disbelief in COVID-19's existence. Motivators to vaccine uptake—convenience, confidence, and low complacency—included accessibility of vaccination sites, user-friendly registration processes, trust in governments and vaccines, fear of dying from COVID-19, and knowing someone who had died from or become infected with COVID-19. Overall, vaccine hesitancy in South Africa and Zimbabwe was influenced by inconvenience, a lack of confidence, and high complacency around COVID-19 vaccines. [ABSTRACT FROM AUTHOR]

Background Reports on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread across Africa have varied, including among healthcare workers (HCWs). This study assessed the comparative SARS-CoV-2 burden and associated risk factors among HCWs in three African countries. Methods A multicentre study was conducted at regional healthcare facilities in Côte d'Ivoire (CIV), Burkina Faso (BF) and South Africa (SA) from February to May 2021. HCWs provided blood samples for SARS-CoV-2 serology and nasopharyngeal/oropharyngeal swabs for testing of acute infection by polymerase chain reaction and completed a questionnaire. Factors associated with seropositivity were assessed with logistic regression. Results Among 719 HCWs, SARS-CoV-2 seroprevalence was 34.6% (95% confidence interval 31.2 to 38.2), ranging from 19.2% in CIV to 45.7% in BF. A total of 20 of 523 (3.8%) were positive for acute SARS-CoV-2 infection. Female HCWs had higher odds of SARS-CoV-2 seropositivity compared with males, and nursing staff, allied health professionals, non-caregiver personnel and administration had higher odds compared with physicians. HCWs also reported infection prevention and control (IPC) gaps, including 38.7% and 29% having access to respirators and IPC training, respectively, in the last year. Conclusions This study was a unique comparative HCW SARS-CoV-2 investigation in Africa. Seroprevalence estimates varied, highlighting distinctive population/facility-level factors affecting COVID-19 burden and the importance of established IPC programmes to protect HCWs and patients. [ABSTRACT FROM AUTHOR]

Patients with cancer are presumed to be vulnerable to an increased risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and severe clinical outcomes due to the immunocompromised state mediated by their underlying malignancies and therapy. The aim of this study was to estimate the SARS-CoV-2 seroprevalence, following second to fourth waves in solid tumour patients attending the Steve Biko Academic Hospital (SBAH) for diagnosis and treatment of cancer. We used the single-prick COVID-19 IgG/IgM Rapid Test Cassettes to detect SARS-CoV-2 IgG/IgM antibodies in 760 patients with solid tumours who were asymptomatic and who had never tested positive for coronavirus disease 2019 (COVID-19). Out of the 760 patients, 277 were male (36.4%), 483 were female (63.6%), and the mean age was 55 years (range 18–92). The estimated total seroprevalence was 33.2%. The seroprevalence status of the COVID-19 IgG/IgM antibodies rose significantly from the second wave (11.3%) to the third (67.38%) and then the fourth (69.81%) waves with roughly similar counts. A significant number of the seropositive patients were asymptomatic to COVID-19 (96%). There was a higher rate of seropositivity in cancer patients with hypertension (p < 0.05). Patients with breast, gynaecologic, and prostate cancers exhibited increased SARS-CoV-2 seropositivity. Although oncology patients may be susceptible to SARS-CoV-2 infection, our data indicate that these patients remained asymptomatic throughout various waves with an overall COVID-19 IgG/IgM antibody seropositivity of 33.16%, suggesting no risk of severe or fatal cases of COVID-19. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic caused by SARS-CoV-2 has placed severe constraints on healthcare systems around the globe. The SARS-CoV-2 virus has caused upheaval in the healthcare and economic sectors worldwide. On the 20th of May 2020, the World Health Organisation declared COVID-19 a global pandemic due to the unprecedented number of cases reported around the globe. As of the 4th of November 2022, there were 637,117,429 coronavirus cases reported globally by Worldometer stats, with 6,602,572 related deaths. In South Africa, there were approximately 4,029,496 coronavirus cases and 102,311 associated deaths. As such, there is a need for efficacious therapeutic regimes. There has been a paucity of knowledge encompassing the use of effective and specific antiviral drug therapies for treating COVID-19 since the outbreak. In this review, we provide valuable insights into the repurposing of current drugs for COVID-19. Drug repurposing provides a suitable option for the discovery of efficacious drugs for COVID-19, thereby decreasing the costs and turnaround times of drug development strategies. This review provides an overview of ten drugs, including antimalarial, antiparasitic, anti-inflammatory, nucleoside analogue, monoclonal-antibody drugs, that were repurposed for the potential treatment of COVID-19. [ABSTRACT FROM AUTHOR]

Background: SARS-CoV-2 (Covid-19 virus) infection exposed the unpreparedness of African countries to health-related issues, South Africa included. Africa recorded more than 211 853 deaths as a consequence of Covid-19. When rare and deadly diseases require urgent hospitalisation strikes, governments and healthcare providers are usually caught unprepared, resulting in huge loss of lives. Usually, at the beginning of such pandemics, there is no rich data for health practitioners and academics to be able to forecast the number of patients or deaths related to the pandemic. This study aims to predict the number of deaths associated with Covid-19 infection. With the availability of the number of deaths on a daily basis, the results stemming from this study are important to inform and plan health policy.Methods: This study uses the daily number of deaths due to Covid-19 infection. Exploratory data analysis reveals that the data exhibits non-normality, three structural breaks and volatility clustering characteristics. The Markov switching (MS)-generalized autoregressive conditional heteroscedasticity (GARCH)-type model combined with heavy-tailed distributions is fitted to the returns of the data. Using available daily reported Covid-19-related deaths up until 26 August 2021, we report 10-day ahead forecasts of deaths. All forecasts are compared to the actual observed values in the forecasting period.Results: The Anderson-Darling Goodness of fit test confirms that the fitted models are adequate for the data. The Kupiec likelihood ratio test and the root mean square error (RMSE) were used to select the robust model at different risk levels. At 95% the MS(3)-GARCH(1,1) combined with Pearson's type IV distribution (PIVD) is the best model. This indicates that the proposed best-fitting model is reasonable and can be used for predicting the daily number of deaths due to Covid-19.Conclusion: The MS(3)-GARCH(1,1)-PIVD model provides a reliable and accurate method for predicting the minimum number of death due to Covid-19. The accuracy of the proposed model will assist policymakers, academics and health practitioners in forecasting the volatility of future health-related deaths in which the predictability of volatility plays an integral role in health risk management. [ABSTRACT FROM AUTHOR]

The onset of the COVID-19 pandemic created various challenges for individuals and families across the globe. Many countries went into a state of disaster and applied strict lockdown regulations to limit the spread of the novel coronavirus. Although the sudden changes in livelihoods impacted families globally, this research is limited to understanding how families connected and resolved conflict during the pandemic. The current study therefore aimed at exploring how family dynamics and resilience in South African families were affected by the COVID-19 pandemic. This study was conducted qualitatively in the Western Cape, South Africa, with 31 participants. The results indicated that families in the Western Cape had trouble adjusting to the imposed restrictions; however, some of these families used the time they had together to adapt and find new ways of building their relationships and strengthening their bonds. The main themes indicated that the most difficult challenges were the children's schooling, financial impact from job losses, and separation from extended family members due to restrictions on movement. Furthermore, familial support and connecting as a family through open and honest communication helped the families remain resilient and fostered positive relationships. [ABSTRACT FROM AUTHOR]

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. SARS-CoV-2 in South Africa: Emerging SARS-CoV-2 variants bring questions as to their potential spread in populations. To analyze the spread of SARS-CoV-2 in South Africa, Sun et al. made use of detailed data from two household cohorts, one rural and one urban, who had longitudinal SARS-CoV-2 infection tests and serology assessments from July 2020 to August 2021. Their epidemiological analysis provides insights into the transmission dynamics of pre-Omicron SARS-CoV-2 variants and the population immunity landscape, and an additional modeling study evaluated the fitness advantage–fueled spread of Omicron and hypothetical future variants in this population. [ABSTRACT FROM AUTHOR]

This article is devoted to applying bioinformatics and immunoinformatics approaches for the development of a multi-epitope mRNA vaccine against the spike glycoproteins of circulating SARS-CoV-2 variants in selected African countries. The study's relevance is dictated by the fact that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began its global threat at the end of 2019 and since then has had a devastating impact on the whole world. Measures to reduce threats from the pandemic include social restrictions, restrictions on international travel, and vaccine development. In most cases, vaccine development depends on the spike glycoprotein, which serves as a medium for its entry into host cells. Although several variants of SARS-CoV-2 have emerged from mutations crossing continental boundaries, about 6000 delta variants have been reported along the coast of more than 20 countries in Africa, with South Africa accounting for the highest percentage. This also applies to the omicron variant of the SARS-CoV-2 virus in South Africa. The authors suggest that bioinformatics and immunoinformatics approaches be used to develop a multi-epitope mRNA vaccine against the spike glycoproteins of circulating SARS-CoV-2 variants in selected African countries. Various immunoinformatics tools have been used to predict T- and B-lymphocyte epitopes. The epitopes were further subjected to multiple evaluations to select epitopes that could elicit a sustained immunological response. The candidate vaccine consisted of seven epitopes, a highly immunogenic adjuvant, an MHC I-targeting domain (MITD), a signal peptide, and linkers. The molecular weight (MW) was predicted to be 223.1 kDa, well above the acceptable threshold of 110 kDa on an excellent vaccine candidate. In addition, the results showed that the candidate vaccine was antigenic, non-allergenic, non-toxic, thermostable, and hydrophilic. The vaccine candidate has good population coverage, with the highest range in East Africa (80.44%) followed by South Africa (77.23%). West Africa and North Africa have 76.65% and 76.13%, respectively, while Central Africa (75.64%) has minimal coverage. Among seven epitopes, no mutations were observed in 100 randomly selected SARS-CoV-2 spike glycoproteins in the study area. Evaluation of the secondary structure of the vaccine constructs revealed a stabilized structure showing 36.44% alpha-helices, 20.45% drawn filaments, and 33.38% random helices. Molecular docking of the TLR4 vaccine showed that the simulated vaccine has a high binding affinity for TLR-4, reflecting its ability to stimulate the innate and adaptive immune response. [ABSTRACT FROM AUTHOR]

The increasing informal urbanism in Africa exposes its residents to multiple shocks, including urban public health pandemics. South Africa is not an exception due to the squalid living conditions, lack of essential services and amenities, and overcrowding characterizing informal settlements. We argue that such conditions compromise the liveability of the informal settlements and the wellbeing of the communities. The urban health inequality concept is used to analyse the risks and vulnerability of informal settlements to public health problems. This study uses the impact of the novel coronavirus (COVID-19) to investigate the exposure of the urban poor in South Africa's informal settlements to public health crises. This study is ethnographic and uses the case of Dinaweng informal settlement, Bloemfontein. Data was collected from secondary data sources triangulated with 60 in-depth interviews with household heads to enhance the validity of the findings. The study found that the poor in Dinaweng are disproportionately affected by disease pandemics that are exacerbated by the challenges in their daily lives characterized by their informal livelihoods. We conclude that informal settlements are complex spaces that require carefully considered strategies and responses for addressing pandemics such as COVID-19; otherwise, the residents in these settlements remain marginalized. [ABSTRACT FROM AUTHOR]

Since the outbreak of Novel coronavirus pneumonia(COVID-19), Novel coronavirus has undergone evolution and variation in the process of transmission, and has formed many variant strains. There are five variants of concern, Alpha, Beta, Gamma, Delta and Omicron. In November 9, 2021, South Africa firstly detected a variant strain (B.1.1.529) from a sample of cases. In November 26, the World Health Organization named it "Omicron variant strain", Currently, the Omicron variant strain has become the main epidemic variant strain in the world. Omicron variant strain consists of several subtypes, including BA.1, BA.2 and BA.3. The subtypes of Omicron variant strain have different mutation and infectivity. This article reviews the characteristics and immune escape mechanisms of each Omicron variant strain subtype. [ABSTRACT FROM AUTHOR]

Background People living with HIV (PLWH) have been reported to have a higher risk of more severe COVID-19 disease and death. We assessed the ability of the Ad26.CoV2.S vaccine to elicit neutralizing activity against the Delta variant in PLWH relative to HIV-negative individuals. We also examined effects of HIV status and suppression on Delta neutralization response in SARS-CoV-2—infected unvaccinated participants. Methods We enrolled participants who were vaccinated through the SISONKE South African clinical trial of the Ad26.CoV2.S vaccine in healthcare workers (HCWs). PLWH in this group had well-controlled HIV infection. We also enrolled unvaccinated participants previously infected with SARS-CoV-2. Neutralization capacity was assessed by a live virus neutralization assay of the Delta variant. Results Most Ad26.CoV2.S vaccinated HCWs were previously infected with SARS-CoV-2. In this group, Delta variant neutralization was 9-fold higher compared with the infected-only group and 26-fold higher relative to the vaccinated-only group. No decrease in Delta variant neutralization was observed in PLWH relative to HIV-negative participants. In contrast, SARS-CoV-2—infected, unvaccinated PLWH showed 7-fold lower neutralization and a higher frequency of nonresponders, with the highest frequency of nonresponders in people with HIV viremia. Vaccinated-only participants showed low neutralization capacity. Conclusions The neutralization response of the Delta variant following Ad26.CoV2.S vaccination in PLWH with well-controlled HIV was not inferior to HIV-negative participants, irrespective of past SARS-CoV-2 infection. In SARS-CoV-2—infected and nonvaccinated participants, HIV infection reduced the neutralization response to SARS-CoV-2, with the strongest reduction in HIV viremic individuals. [ABSTRACT FROM AUTHOR]

The continuing crisis caused by the novel coronavirus (COVID-19) outbreak has raised significant challenges for the higher education community globally. In South Africa, the government-forced lockdown measures and social distancing containment policy changed working arrangements across sectors and organisations. As a result, academics were forced to work from home (WFH), a task for which they were hardly prepared. Several researchers have engaged the WFH situation of academics to understand the relationship between WFH and productivity. As far as we know, very few studies have tried to describe academics' WFH experiences in relation to the challenges, including determining possible ways of improving their satisfaction with working from home. We examine in this article the experiences of academics working from home across selected universities in South Africa. Using a qualitative approach and applying Atlas.ti for data analysis, our findings show that working from home in academia is a daunting task requiring extensive organisational, personal, and social adjustments. The population comprised all academics irrespective of any demographic or personality characteristic within the management faculty of the participating universities to secure the anonymity of the respondents. Five themes—inability to adapt, lack of a home office, loneliness and isolation, inability to balance family and work, and improving satisfaction with work from home—were identified as significant variables from the participants' responses. Our analysis suggests that organisations need to customise approaches to engage with the experiences of academics who work from home during COVID-19 and to develop fit-for-purpose support for these academics. The study contributes to the growing research exploring the relationship between COVID-19 lockdown and work in higher education. [ABSTRACT FROM AUTHOR]

Several variants of SARS-CoV-2 have been identified in different parts of the world, including Gamma, detected in Brazil, Delta, detected in India, and the recent Omicron variant, detected in South Africa. The emergence of a new variant is a cause of great concern. This work considers an extended version of an SIRD model capable of incorporating the effects of vaccination, time-dependent transmissibility rates, mortality, and even potential reinfections during the pandemic. We use this model to characterise the Omicron wave in Brazil, South Africa, and Germany. During Omicron, the transmissibility increased by five for Brazil and Germany and eight for South Africa, whereas the estimated mortality was reduced by three-fold. We estimated that the reported cases accounted for less than 25 % of the actual cases during Omicron. The mortality among the nonvaccinated population in these countries is, on average, three to four times higher than the mortality among the fully vaccinated. Finally, we could only reproduce the observed dynamics after introducing a new parameter that accounts for the percentage of the population that can be reinfected. Reinfection was as high as 40 % in South Africa, which has only 29 % of its population fully vaccinated and as low as 13 % in Brazil, which has over 70 % and 80 % of its population fully vaccinated and with at least one dose, respectively. The calibrated models were able to estimate essential features of the complex virus and vaccination dynamics and stand as valuable tools for quantifying the impact of protocols and decisions in different populations. [ABSTRACT FROM AUTHOR]

Early detection of SARS-CoV-2 variants enables timely tracking of clinically important strains in order to inform the public health response. Current subtype-based variant surveillance depending on prior subtype assignment according to lag features and their continuous risk assessment may delay this process. We proposed a weighted network framework to model the frequency trajectories of mutations (FTMs) for SARS-CoV-2 variant tracing, without requiring prior subtype assignment. This framework modularizes the FTMs and conglomerates synchronous FTMs together to represent the variants. It also generates module clusters to unveil the epidemic stages and their contemporaneous variants. Eventually, the module-based variants are assessed by phylogenetic tree through sub-sampling to facilitate communication and control of the epidemic. This process was benchmarked using worldwide GISAID data, which not only demonstrated all the methodology features but also showed the module-based variant identification had highly specific and sensitive mapping with the global phylogenetic tree. When applying this process to regional data like India and South Africa for SARS-CoV-2 variant surveillance, the approach clearly elucidated the national dispersal history of the viral variants and their co-circulation pattern, and provided much earlier warning of Beta (B.1.351), Delta (B.1.617.2), and Omicron (B.1.1.529). In summary, our work showed that the weighted network modeling of FTMs enables us to rapidly and easily track down SARS-CoV-2 variants overcoming prior viral subtyping with lag features, accelerating the understanding and surveillance of COVID-19. [ABSTRACT FROM AUTHOR]

During the COVID‐19 pandemic, genetic variants of SARS‐CoV‐2 have been emerging and spreading around the world. Several SARS‐CoV‐2 endemic variants were found in United Kingdom, South Africa, Japan, and India between 2020 and April 2021. Studies have shown that many SARS‐CoV‐2 variants are more infectious than early wild strain and produce immune escape. These SARS‐CoV‐2 variants have brought new challenges to the prevention and control of COVID‐19. This review summarizes and analyzes the biological characteristics of different amino acid mutations and the epidemic characteristics and immune escape of different SARS‐CoV‐2 variants. We hope to provide scientific reference for the monitoring, prevention, and control measures of new SARS‐CoV‐2 variants and the development strategy of the second‐generation vaccine. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic has had a considerable impact on global health and economics. The impact in African countries has not been investigated thoroughly via fitting epidemic models to the reported COVID-19 deaths. We downloaded the data for the 12 most-affected countries with the highest cumulative COVID-19 deaths to estimate the time-varying basic reproductive number ( R 0 (t) ) and infection attack rate. We develop a simple epidemic model and fitted it to reported COVID-19 deaths in 12 African countries using iterated filtering and allowing a flexible transmission rate. We observe high heterogeneity in the case-fatality rate across the countries, which may be due to different reporting or testing efforts. South Africa, Tunisia, and Libya were most affected, exhibiting a relatively higher R 0 (t) and infection attack rate. Thus, to effectively control the spread of COVID-19 epidemics in Africa, there is a need to consider other mitigation strategies (such as improvements in socioeconomic well-being, healthcare systems, the water supply, and awareness campaigns). [ABSTRACT FROM AUTHOR]

Since 2020, the COVID-19 pandemic has spread worldwide, causing health, economic, and social distress. Containment strategies rely on rapid and consistent methodology for molecular detection and characterization. Emerging variants of concern (VOCs) are currently associated with increased infectivity and immune escape (natural defence mechanisms and vaccine). Several VOCs have been detected, including Alpha variant (B.1.1.7), Beta variant (B.1.351), Gamma variant (P.1/B.1.1.28.1) and Delta variant (B.1.617.2), first identified in the UK, South Africa, Brazil and India, respectively. Here, a rapid and low-cost technique was validated to distinguish the Alpha, Beta, Gamma, and Delta SARS-CoV-2 variants by detecting spike gene mutations using a real-time reverse transcription polymerase chain reaction methodology (RT-PCR). A total of 132 positive patients affected by coronavirus disease-19 (COVID-19) were analysed by employing RT-PCR to target single-nucleotide polymorphisms (SNPs) to screen spike protein mutations. All data were validated by the next-generation sequencing (NGS) methodology and using sequences from a public database. Among 132 COVID-19-positive samples, we were able to discriminate all of the investigated SARS-CoV-2 variants with 100% concordance when compared with the NGS method. RT-PCR -based assays for identifying circulating VOCs of SARS-CoV-2 resulted in a rapid method used to identify specific SARS-CoV-2 variants, allowing for a better survey of the spread of the virus and its transmissibility in the pandemic phase. [ABSTRACT FROM AUTHOR]

In late December 2019, pneumonia cases of unknown origin were reported in Wuhan, China. This virus was named SARS-CoV2 and the clinical syndrome was named coronavirus disease 19 (COVID-19). South Africa, despite strict and early lockdown has the highest infection rate in Africa. A key component of South Africa's response to SARSCoV2 was the rapid scale-up of diagnostic testing. The Abbott SARS-CoV2 assay detects IgG antibodies against the Nucleocapsid (N) protein of the SARS-CoV2 virus. This study undertook to validate and evaluate performance criteria of the Abbott assay and to establish whether this assay would show clinical utility in our population. Positive patients (n = 391) and negative controls (n = 139) were included. The Architect-i and Alinity-i systems were analyzers that were used to perform the SARS-CoV-2 IgG assay. In-house ELISA was incorporated into the study as a confirmatory serology test. A total of number of 530 participants was tested, 87% were symptomatic with infection and 13% were asymptomatic. When compared to RT-qPCR, the sensitivity of Architect and Alinity SARS-CoV2 assays was 69.5% and 64.8%, respectively. Specificity for Architect and Alinity assays was 95% and 90.3%, respectively. The Abbott assay was also compared to in house ELISA assay, with sensitivity for the Architect and Alinity assays of 94.7% and 92.5%, respectively. Specificity for Abbott Alinity assays was 91.7% higher than Abbott Architect 88.1%. Based on the current findings testing of IgG after 14 days is recommended in South Africa and supports other studies performed around the world. [ABSTRACT FROM AUTHOR]

Overview: Covid cases surge, worsening Q1 slowdown ▀ Although some of the initial worst fears about Omicron have proved unfounded, the unexpectedly large surge in global Covid‐19 cases is causing more cautious behaviour by individuals and greater disruption to businesses than envisaged. We have cut our Q1 GDP forecast again and now expect world GDP growth of 4.2% in 2022, down from 4.3% a month ago and the 5.8% estimated for 2021.▀ There remain plenty of unknowns regarding the Omicron variant and its health impact. But the evidence from economies such as South Africa, the UK and Denmark suggests that the Omicron wave is likely to be associated with much smaller rises in hospitalisations than earlier Covid waves. And for now, our initial assessment that there would only be a modest reimposition of mobility restrictions is correct.▀ Nonetheless, the rise in global Covid cases to more than double the previous peak has exceeded expectations of a month ago by a large margin and points to greater economic damage via increased voluntary social distancing and disruption to businesses from staff having to self‐isolate. In response, we have lowered global GDP growth further in Q1.▀ As with previous Covid waves, we expect activity to rebound quickly when cases start to fall back, so the downward revision to the outlook in Q1 will be largely offset by a bigger bounce in Q2. Nonetheless, the weak start to the year will dampen overall 2022 growth slightly.▀ Meanwhile, greater disruption in the near term — especially in China where a zerotolerance approach to Covid continues to be pursued— points to slower normalisation of supply‐chain pressures and potentially a slower transition of consumer spending from goods back to services. Partly due to this, we have lifted our 2022 global CPI inflation forecast by 0.3pp to 4.5%. But inflation is still expected to fall sharply over the course of year, limiting the need for aggressive monetary policy tightening. [ABSTRACT FROM AUTHOR]

The emergence of the global COVID-19 pandemic has continued to cause havoc and untold suffering worldwide. The pandemic's pattern of spreading has varied between continents and indeed within countries. Studies looking at the factors affecting the dynamics of COVID-19 in African countries are limited. In this study we attempt to assess and understand the differential spread of COVID-19 in Africa by looking at South Africa (Southern Africa), Senegal (West Africa), Egypt and Morocco (North Africa), Rwanda (Central Africa) and Kenya (East Africa). We observed a high prevalence of COVID-19 in South Africa, Morocco and Egypt. Furthermore, South Africa ranks first in the number of reported confirmed COVID-19 cases and related hospitalisations and deaths in Africa. Senegal (Western Africa) shows lower confirmed cases and death rates. Based on the findings, it is crucial for these countries' governments and health authorities to be vigilant in mobilising effective medical resources and to continue educating their citizens in order to curb the spread of the coronavirus. [ABSTRACT FROM AUTHOR]