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

Effects of storage period on nutritive value of broilers feeds and their remedy through some dietary treatments

There is scarce information on the effects of feed storage period on poultry performance, which has not been investigated thus far. The aim of this study was to evaluate the effect of feeding broilers on feeds stored for different periods, with or without supplemental amino acids and vitamins. This study followed a factorial design (3 x 3), i.e. three dietary treatments and three feed storage periods. The three dietary treatments consisted of 1) a basal diet, 2) a basal diet including additional 5g methionine and 13 g lysine/kg, and 3) a basal diet including 3 g vitamin premix/kg. The 3 dietary treatments were tested with feeds stored for three different periods (Fresh, 4-months, and 6-months). A total of 450 one-day old broiler chicks were randomly assigned to the 9 treatments, each treatment contained 5 replicates of 10 chicks each (n = 50/group). The experiment lasted for 42 days. The results indicated that the final BWs of the birds received 4- or 6-months stored feed were greater than that of those fed fresh diets. The best total BWG was seen in the 4-month-stored feed group. There was no significant effect of storage period on total FC and FCR during period from 0 to 6 weeks of age, but the FCR tended to be better with the feed stored for 4 months. Haemoglobin was significantly higher in the birds fed fresh or 4-month stored feed. The percent of liver and spleen of the birds received 6-month-stored feed were the highest (P ˂ 0.01). Plasma content of albumin was higher in the birds received 4-or 6-month stored feed than the fresh diet. The use of additional amino acids increased the final BW and total BWG than those of the control and vitamin-supplemented treatments. The main effect of dietary treatments on percentages of immune organ weight was insignificant. The control (basal diet) recorded higher lymphocytes percentage, while T2 (BD + double level of amino acids) recorded higher eosinophil, heterophil and H/L ratio, whereas T3 (BD + double level of vitamins) recorded higher levels of haemoglobin, eosinophil, and monocytes. The main effect of dietary treatments on blood plasma proteins was insignificant. The tested treatments did not show a significant effect on broilers mortality. The detected values of AF1, AF2, AG1, and AG2 were very low in all 9 diets. In conclusion, enrichment of broiler feeds with higher levels of lysine and methionine (double level of NRC, 1994) together with antioxidants supplement could prolong their shelf-life to 6 months without any deleterious impact on productive performance of broiler chickens

SARS-CoV-2 vaccination modelling for safe surgery to save lives: data from an international prospective cohort study

Background: Preoperative SARS-CoV-2 vaccination could support safer elective surgery. Vaccine numbers are limited so this study aimed to inform their prioritization by modelling. Methods: The primary outcome was the number needed to vaccinate (NNV) to prevent one COVID-19-related death in 1 year. NNVs were based on postoperative SARS-CoV-2 rates and mortality in an international cohort study (surgical patients), and community SARS-CoV-2 incidence and case fatality data (general population). NNV estimates were stratified by age (18-49, 50-69, 70 or more years) and type of surgery. Best- and worst-case scenarios were used to describe uncertainty. Results: NNVs were more favourable in surgical patients than the general population. The most favourable NNVs were in patients aged 70 years or more needing cancer surgery (351; best case 196, worst case 816) or non-cancer surgery (733; best case 407, worst case 1664). Both exceeded the NNV in the general population (1840; best case 1196, worst case 3066). NNVs for surgical patients remained favourable at a range of SARS-CoV-2 incidence rates in sensitivity analysis modelling. Globally, prioritizing preoperative vaccination of patients needing elective surgery ahead of the general population could prevent an additional 58 687 (best case 115 007, worst case 20 177) COVID-19-related deaths in 1 year. Conclusion: As global roll out of SARS-CoV-2 vaccination proceeds, patients needing elective surgery should be prioritized ahead of the general population