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

Association of rs1319868, rs1567811 and rs8041224 of gene with infection among sickle cell anemia Tunisian patients

Background and aimSickle cell anemia (SCA) is characterized by variable patterns of clinical expression. Polymorphisms linked to different genes have been associated with specific complications of the disease. Herein, we focused on the study of the association of 4 polymorphisms of Insulin like Growth Factor 1 receptor (IGF1R) gene with infections, which are the major cause of death in SCA.Material and methodsThis study involved 116 sickle cell patients among whom 58 SS have the same confirmed infectious phenotype. Allele-Specific PCR was performed for the study of rs1319868, whereas the PCR/sequencing method was carried out for rs1567811, rs2872060 and rs8041224.ResultsThe results showed that rs1319868 and rs1567811 were associated with a decreased risk of infection among SS patients (p=0.038, RR=0.54; p=0.044, RR=0.56, respectively). Interestingly, the combination of different genotypes showed the association of the genotype GT of rs1319868 and the genotype CC of rs8041224 with further decreased infection risk in SCA (p=0.028, RR=0.04).ConclusionThese significant associations of IGF1R SNPs with infection suggest that this gene could play an important role in the immune function in SCA