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

Burden and impacts of chronic hepatitis B infection in rural Senegal : study protocol of a cross-sectional survey in the area of Niakhar (AmBASS ANRS 12356)

Introduction Though Senegal has one of the highest estimated prevalence rates of chronic hepatitis B virus (HBV) infection worldwide, epidemiological data in the general population are lacking and consequences of the infection remain undocumented. The ANRS-12356 AmBASS study aims at evaluating the health and socioeconomic burden of chronic HBV infection at the individual, household and population level. Its specific objectives are (1) to document the epidemiology of chronic HBV infection, including prevalence and risk factors; (2) to assess the acceptability of home-based testing and first clinic visit; (3) to investigate the repercussions of chronic HBV infection on living conditions; and (4) to estimate the public health impact of chronic HBV infection at the population level and the feasibility of a decentralised model of HBV test and treat. Methods and analysis This multidisciplinary cross-sectional survey includes a twofold data collection: (1) home-based screening using dried blood spot (DBS) sampling and collection of sociodemographic, economic and behavioural data, and (2) additional clinical and biological data collection in chronic HBV carriers at the first clinic visit. The prevalence of chronic HBV infection will be estimated in the general population and in key subgroups. Risk factors for HBV acquisition in children will be explored using case-control analysis. HBV burden will be assessed through comparisons of health and economic outcomes between households affected by the disease versus non-affected households. Last, an economic evaluation will assess costs and health benefits of scaling-up HBV care. Ethics and dissemination This study was approved by the Senegalese National Ethical Committee for Research in Health, and received authorisation from the Senegalese Ministry of Health and the French Commission on Information Technology and Liberties (Senegalese Protocol Number: SEN17/15). The study results will be presented in peer-review journals, international conferences and at a workshop with national stakeholders in order to contribute to the design of programmes to address the HBV pandemic

Autoantibodies against type I IFNs in humans with alternative NF-κB pathway deficiency

: Patients with autoimmune polyendocrinopathy syndrome type 1 (APS-1) caused by autosomal recessive AIRE deficiency produce autoantibodies that neutralize type I interferons (IFNs)1,2, conferring a predisposition to life-threatening COVID-19 pneumonia3. Here we report that patients with autosomal recessive NIK or RELB deficiency, or a specific type of autosomal-dominant NF-κB2 deficiency, also have neutralizing autoantibodies against type I IFNs and are at higher risk of getting life-threatening COVID-19 pneumonia. In patients with autosomal-dominant NF-κB2 deficiency, these autoantibodies are found only in individuals who are heterozygous for variants associated with both transcription (p52 activity) loss of function (LOF) due to impaired p100 processing to generate p52, and regulatory (IκBδ activity) gain of function (GOF) due to the accumulation of unprocessed p100, therefore increasing the inhibitory activity of IκBδ (hereafter, p52LOF/IκBδGOF). By contrast, neutralizing autoantibodies against type I IFNs are not found in individuals who are heterozygous for NFKB2 variants causing haploinsufficiency of p100 and p52 (hereafter, p52LOF/IκBδLOF) or gain-of-function of p52 (hereafter, p52GOF/IκBδLOF). In contrast to patients with APS-1, patients with disorders of NIK, RELB or NF-κB2 have very few tissue-specific autoantibodies. However, their thymuses have an abnormal structure, with few AIRE-expressing medullary thymic epithelial cells. Human inborn errors of the alternative NF-κB pathway impair the development of AIRE-expressing medullary thymic epithelial cells, thereby underlying the production of autoantibodies against type I IFNs and predisposition to viral diseases