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

Preferences for antiretroviral therapy services: Qualitative evidence from people living with HIV in Ghana

Antiretroviral therapy (ART) is one of the interventions meant to prolong the progression from HIV to AIDS for People Living with HIV (PLHIVs). Although ART was introduced in Ghana in 2003, there is little or no information about the preferences of those on ART services. The main objective of the study therefore was to examine the preferences of PLHIVs concerning ART services. The data were extracted from a nationwide qualitative study conducted by the Ghana AIDS Commission (GAC) which covered 12 cities/towns sampled from the three ecological zones of Ghana. Focus Group Discussions (FGD) and In-Depth Interviews (IDI) were the methods used in the data collection. A total of 145 FGDs and 171 IDIs were conducted in all the study sites among a wide range of target groups. The data were transcribed and analysed using NUD*IST (Non-numerical Data* Indexing Searching and Theorizing) version 6. The results showed that the hospital was the most preferred place for ART medications and most PLHIVs preferred to receive ART drugs from health personnel, trained PLHIVs or ‘foreigners’. PLHIVs preferred to access ART services free of charge and abhorred delays at ART centres. The preferences of PLHIVs regarding ART services must be considered in policies and programmes aimed at increasing enrolment, retention and coverage of ART in the country

Performance and Nutrient Utilization Responses in Broilers Fed Phytase Supplemented Mash or Pelleted Corn-Soybean Meal-Based Diets

Effect of phytase produced by thermo-protective coating technology (coated phytase) on performance and nutrient utilization of broiler chicks fed a corn-soybean meal-based pelleted diet was investigated. A total of 144-one-day-old male broiler (Ross) chicks were divided in 24 groups and fed 4 diets (6 groups per diet) for 21 days. The diets included a mash or pelleted basal diet without or with the coated phytase at 500FTU/kg in a 2×2 factorial arrangement. Calcium and non-phytate P values in the basal diet were 22 and 51% lower compared with NRC (1994) recommended values, respectively. All the diets contained titanium oxide as an indigestible marker. There was no interaction (P>0.05) between diet form and phytase on any of response criteria measured in this study except body weight gain and feed intake such that phytase supplementation improved (P<0.05) these 2 response criteria, but improvements were greater for pelleted diet than mash diet. Phytase supplementation increased (P<0.05) tibia ash and ileal P digestibility, by 10.5 and 38.1%, respectively. Phytase supplementation did not, however, affect (P>0.05) the ileal digestibilities of Ca, crude protein and amino acids. In conclusion, coated phytase supplementation to corn-soybean meal-based diet for broilers resulted in improved growth performance, bone mineralization and P digestibility regardless of diet type (mash versus pellet). These findings suggest that the efficacy of the coated phytase used in the current study was not influenced by the pelleting process