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

IRON DEFICIENCY IN RURAL GHANAlAN CHILDREN

Objectives: To compare the prevalence d iron deficiency among Ghanaian cbidren indifferent residential settings and to see whether 200n1g ferrous fumerate B.P. could correctiron deficiency anaemia in observed cases of iron deficiency.Design: Prospcctivc case-tinding study using an Iron-deficiency society questionnaire,laboratory data add general practice records. Crude prevalence was calcl~lated using thehospital's mid-year estimates.Setting: Nkoranza in the Brong Ahafo Rcgionof Ghana, Komfo Anokye Teaching Hospital.Kumasi, GhanaSubject: Rural-dwelling children entering as ou t-patienh, urban-dwelling children enteringas controls and new-ly diagnosed iron-deficient children cntering as in-patients.hfuit~ outconic mearirres: Crudc prevalence rates (per quinquennia) for three grnups ofchildren. Correctud deficiencies espresscd as percentage aftcr management. Age,haernoglobin, iron status, residential status, svmptoms at entry and after therapy.Results: Following u 30-day adminbtration d ferrous furnarvte, the mcan serum iron for therural children increased significantly by 3.3 p o V l representing an improved iron status uf20.09 I P<O.U(101). Iron deficiency anacmia defined by serum Hh<lZ.Og/dl and Fed2.5mmoY 1 decreased by 10%: in the rural subjects. Comparatively. iron deficielicy among [henewly diagnosed anaemia group, fell by 17.6% whilst their ambulant urban counterpartsemployed as the control Croup had an iron deficiency anocmiu of O.D%.Conclusion: l'he study clearly indicates that the prevalence of iron deficiency anaemiaamong children in rural Ghana is about ten times that of the urban-dwelling children andthat iron-deficiency anaemia accounts for a greater percentage of all anaemic cases amongchildren in n ~ ~ r hrlspitals. It was alsushownthnt taking appropriate iran supplen~ents like 204mg of ferruw fumcrate for thirty days can subs tan ti all^ improve the iron status of irondeficientchildre

Physiological correlates of intellectual function in children with sickle cell disease: hypoxemia, hyperaemia and brain infarction

Lowered intelligence relative to controls is evident by mid-childhood in children with sickle cell disease. There is consensus that brain infarct contributes to this deficit, but the subtle lowering of IQ in children with normal MRI scans might be accounted for by chronic systemic complications leading to insufficient oxygen delivery to the brain. We investigated the relationship between daytime oxyhaemoglobin saturation (SpO2), cerebral blood flow velocity (CBFV) and intellectual function (IQ) using path-analysis in 30 adolescents with sickle cell disease (mean age 17.4 years, SD 4.2). Initial analyses revealed that the association between SpO2 and Full Scale IQ (FSIQ) was fully mediated by increased CBFV, whereby SpO2 was negatively correlated with CBFV and CBFV was negatively correlated with FSIQ, i.e. decreases in oxygen saturation are associated with increases in velocity, and increased velocity is associated with lowered IQ scores. The mediated relationship suggests that lowered IQ may be a function of abnormal oxygen delivery to the brain. Further analyses showed that the association between CBFV and IQ was significant for verbal but not for performance IQ. The pathophysiology characteristic of SCD can interfere with brain function and constrain intellectual development, even in the absence of an infarct. This supports the hypothesis that lowered intellectual function is partly explained by chronic hypoxia, and has wider implications for our understanding of SCD pathophysiology