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

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

Effect of breed types and castration on carcass characteristics of Boer and large frame indigenous Veld goats of Southern Africa

CITATION: Van Wyk, G. L., et al . 2020. Effect of breed types and castration on carcass characteristics of Boer and large frame indigenous veld goats of Southern Africa. Animals, 10(10):1884, doi:10.3390/ani10101884.The original publication is available at http://www.mdpi.comPublication of this article was funded by the Stellenbosch University Open Access FundWeaner male Boer Goats (BG; n = 36; 21 bucks and 15 wethers) and large frame Indigenous Veld Goats (IVG; n = 41; 21 bucks and 20 wethers) were raised on hay and natural grass ad libitum and the recommended amount of commercial pelleted diet to a live weight between 30 and 35 kg. Carcass quality characteristics (live weight, carcass weights, dressing %, chilling loss and eye muscle area) were measured. The right sides of the carcasses were divided into wholesale cuts and dissected into subcutaneous fat, meat and bone. Large frame Indigenous Veld Goat (IVG) wethers were slightly lighter than the IVG bucks with no significant difference observed between BG. Wethers compared to bucks had higher dressing %, subcutaneous fat % in all primal cuts, intramuscular fat %, kidney fat % and, overall, slightly less bone %. Some breed–wether interactions were noticed: IVG wethers were slightly lighter than the IVG bucks, but the IVG bucks tended to produce higher % meat compared to other test groups. Judged on the intramuscular fat % characteristics, it seems as if wethers should produce juicier and more flavorsome meat compared to bucks.https://www.mdpi.com/2076-2615/10/10/1884Publisher's versio

Street Pork Vendors’ Hygiene and Safety Practices and Their Determinants in the Cape Metropole District, South Africa

South Africa’s rapid urbanization and high unemployment rates pushed people into street food vending as an alternative source of livelihood. Hygiene and food safety have become a concern under these circumstances owing to foodborne illnesses and associated deaths. A survey tool with 38 structured questions was administered to 172 to assess pork vendors’ hygiene and safety practices and identify their determinants in five low-income high-density suburbs of the Cape Metropole District, South Africa. Overall, vendors washed their hands before and after handling meat (66% of respondents) and cleaned the working area daily (51%), pork storage area daily (60%), and utensils and equipment before and after use (36%) with most of them using detergents as the main cleaning agent (70%). A quarter of the interviewed vendors experienced meat spoilage during storage, and 80% had no training in hygiene and safe food handling. The marginal effects of logistic regression findings showed that vending income increased the vendor’s probability to wash hands, and clean vending stalls, storage areas, utensils, and equipment. The likelihood of vendors cleaning pork storage areas, utensils, and equipment increased with the increase in female participants. The likelihood of hand washing and vending stall cleaning increased by 1% for each extra year of schooling. Strategies aimed at improving meat hygiene and safety practices of vendors in the surveyed areas should target vulnerable groups, especially less educated females depending solely on vending income

Sustained Effects of Muscle Calpain System Genotypes on Tenderness Phenotypes of South African Beef Bulls during Ageing up to 20 Days

The most important factor that determines beef tenderness is its proteolytic activity, and the balance between calpain-1 protease activity and calpastatin inhibition is especially important, while contributions can also arise from calpain-2 and, possibly, calpain-3. The meat ageing process itself affects these processes. To determine whether genotypes in the calpain–calpastatin system can enhance tenderness through a 20-day ageing period, South African purebred beef bulls (n = 166) were genotyped using the Illumina BovineHD SNP BeadChip through a gene-based association analysis targeting the cast, capn3, capn2 and capn1 genes. The Warner–Bratzler shear force (WBSF) and myofibril fragment length (MFL) of Longissimus thoracis et lumborum (LTL) steaks were evaluated between d 3 and d 20 of ageing, with protease enzyme activity in the first 20 h post-mortem. Although several of the 134 SNPs are associated with tenderness, only seven SNP in the cast, capn2 and capn1 genes sustained genetic associations, additive to the ageing-associated increases in tenderness for at least three of the four ageing periods. While most genomic associations were relatively stable over time, some genotypes within the SNP responded differently to ageing, resulting in altered genomic effects over time. The level of ageing at which genomic associations are performed is an important factor that determines whether SNPs affect tenderness phenotypes