Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in southern Africa has been characterised by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, whilst the second and third waves were driven by the Beta and Delta variants, respectively1-3. In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng Province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, predicted to influence antibody neutralization and spike function4. Here, we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.

The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Management Practices, Farmers’ Knowledge of Diseased Fish, and Their Occurrence in Fish Farms in Nyeri County, Kenya

In this study, fish farmers’ management practices, occurrence, and knowledge of fish diseases in Nyeri County, Kenya, were evaluated. Fish farming management practices for small-scale farmers in Kenya have numerous challenges which have led to disease occurrence and reduced production. Moreover, the impact and association of these challenges to farmers’ knowledge of fish diseases and their burden has not been fully studied. A semistructured questionnaire was used to capture farmers’ biodata, fish species farmed, and farmers’ management practices such as handling of nets, pond fertilization, and disposal of fish waste. Farmers’ knowledge of fish diseases was based on their ability to identify independent and dependent variable indicators. Independent variables included clinical signs, decreased feeding, bulging eyes, floating on water, abdominal swelling, bulging eyes, abnormal skin color, reduced growth, and abnormal swimming with fish death as were the dependent variable. A total of 208 farmers were interviewed and included those of tilapia (134), mixed tilapia and catfish (40), catfish (22), rainbow trout, and five dams under cooperative management. Tilapia was the most kept fish species (66.8%) followed by polyculture of tilapia and catfish (20%) and rainbow trout (2%). Most respondents were male (78.5%) over 51 years of age (50%). Fifty percent of the respondents had secondary school education. There was a significant association between deaths and sharing of nets in Kieni East subcounty (p=0.0049, chi-square), while on-farm fish waste disposing appeared to cause higher deaths compared to burning of the waste although not statistically significant (p=0.13). Few respondents observed decreased feed uptake (<20%) and poor growth. Fifty-seven percent of farmers reported mortalities. Fish poor growth, floating in water, and management practices in subcounties had significant effect on fish deaths. The farmers had knowledge of signs of diseased fish, but there was paucity of knowing the specific causes of disease. Farmers need to be empowered on best aquaculture husbandry to avoid disease transmission and specific fish disease signs to enhance proper reporting of disease for subsequent mitigation measures

Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa

DATA AVAILABILITY : All of the SARS-CoV-2 genomes generated and presented in this article are publicly accessible through the GISAID platform (https://www.gisaid.org/). The GISAID accession identifiers of the sequences analyzed in this study are provided as part of Supplementary Table 1. Other raw data for this study are provided as a supplementary dataset at https://github.com/krisp-kwazulu-natal/SARSCoV2_South_Africa_Omicron_BA4_BA5. The reference SARS-CoV-2 genome (MN908947.3) was downloaded from the National Center for Biotechnology Information database (https://www.ncbi.nlm.nih.gov/).CODE AVAILABILITY : All custom scripts to reproduce the analyses and figures presented in this article are available at https://github.com/krisp-kwazulu-natal/ SARSCoV2_South_Africa_Omicron_BA4_BA5.Three lineages (BA.1, BA.2 and BA.3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern predominantly drove South Africa’s fourth Coronavirus Disease 2019 (COVID-19) wave. We have now identified two new lineages, BA.4 and BA.5, responsible for a fifth wave of infections. The spike proteins of BA.4 and BA.5 are identical, and similar to BA.2 except for the addition of 69–70 deletion (present in the Alpha variant and the BA.1 lineage), L452R (present in the Delta variant), F486V and the wild-type amino acid at Q493. The two lineages differ only outside of the spike region. The 69–70 deletion in spike allows these lineages to be identified by the proxy marker of S-gene target failure, on the background of variants not possessing this feature. BA.4 and BA.5 have rapidly replaced BA.2, reaching more than 50% of sequenced cases in South Africa by the first week of April 2022. Using a multinomial logistic regression model, we estimated growth advantages for BA.4 and BA.5 of 0.08 (95% confidence interval (CI): 0.08–0.09) and 0.10 (95% CI: 0.09–0.11) per day, respectively, over BA.2 in South Africa. The continued discovery of genetically diverse Omicron lineages points to the hypothesis that a discrete reservoir, such as human chronic infections and/or animal hosts, is potentially contributing to further evolution and dispersal of the virus.The South African Medical Research Council (SAMRC) with funds received from the National Department of Health. Sequencing activities for the National Institute for Communicable Diseases (NICD) are supported by a conditional grant from the South African National Department of Health as part of the emergency COVID-19 response; a cooperative agreement between the NICD of the NHLS and the US Centers for Disease Control and Prevention (CDC) (U01IP001048 and 1 NU51IP000930); the African Society of Laboratory Medicine (ASLM) and Africa Centers for Disease Control and Prevention through a sub-award from the Bill and Melinda Gates Foundation (grant number INV-018978); the UK Foreign, Commonwealth and Development Office and Wellcome (221003/Z/20/Z); and the UK Department of Health and Social Care, managed by the Fleming Fund and performed under the auspices of the SEQAFRICA project. This research was also supported by the Coronavirus Aid, Relief, and Economic Security Act (CARES ACT) through the CDC and COVID International Task Force (ITF) funds through the CDC under the terms of a subcontract with the African Field Epidemiology Network (AFENET) (AF-NICD-001/2021). Sequencing activities at KRISP and the Centre for Epidemic Response and Innovation are supported, in part, by grants from the World Health Organization, the Rockefeller Foundation (HTH 017), the Abbott Pandemic Defense Coalition (APDC), the US National Institutes of Health (U01 AI151698) for the United World Antivirus Research Network (UWARN) and the INFORM Africa project through IHVN (U54 TW012041) and the South African Department of Science and Innovation (SA DSI) and the SAMRC under the BRICS JAF (2020/049). Sequencing at the Botswana Harvard AIDS Institute Partnership was supported by funding from the Bill and Melinda Gates Foundation, the Foundation for Innovation in Diagnostics, the National Institutes of Health Fogarty International Centre (3D43TW009610-09S1) and the HHS/NIH/ National Institute of Allergy and Infectious Diseases (NIAID) (5K24AI131928-04 and 5K24AI131924-04).http://www.nature.com/naturemedicineam2023Medical VirologySDG-03:Good heatlh and well-bein