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

Infections par des virus transmissibles par le sang chez des hémophiles en Tunisie

International audienceIn this work, we proposed to evaluate prevalences of hepatitis B and C viruses and Parvovirus B19 among 70 Tunisian haemophiliacs treated with clotting factors imported from Europe and/or locally produced cryoprecipitate; among them 6 (8.6%) are known HIV positive patients. HBs antigen, anti-HBc antibodies and anti-Parvovirus B19 antibodies were detected in 7.1%, 52.9% and 91.8%, respectively. HCV prevalence, defined as positive ELISA with positive Immunoblot and/or PCR was 50.0%. Prevalences of these viral infections in haemophiliacs are higher than prevalences detected among general population and in the control group of the study. HCV infection is less frequent in haemophiliacs born after 1985, the year of introduction of the inactivation procedures in the production of coagulation factors concentrates; it decreases more considerably after 1994, date of introduction of systematic screening of HCV among blood donors. In contrast, despite the inactivation of the factors concentrates and the systematic screening of the blood donations against HBs antigen, since 1973, the risk of HBV infection contamination remains high in the Tunisian haemophiliacs. The introduction in 1995 of hepatitis B vaccination in the national schedule of new-born vaccination may resolve in the future the problem of HBV infection in haemophiliacs and in the other categories of the Tunisian population.Dans ce travail, nous nous sommes proposés d'évaluer les prévalences des infections par les virus des hépatites B et C et le parvovirus B19 chez 70 hémophiles tunisiens traités avec les facteurs de coagulation importés d'Europe et/ou le cryoprécipité fabriqué localement ; parmi eux six patients (8,6 %) sont connus VIH positifs. L'antigène HBs, les anticorps anti-HBc et les anticorps anti-Parvovirus B19 ont été retrouvés chez 7,1, 52,9 et 91,8 % des patients, respectivement. La prévalence de l'infection par le VHC, définie par un test Elisa positif avec Immunoblot et/ou PCR positifs, a été de 50,0 %. Les prévalences de ces infections virales sont plus élevées chez les hémophiles que dans la population générale et la population témoin admise dans ce travail. L'infection à VHC est plus faible chez les sujets hémophiles nés après 1985, date d'introduction des procédés d'inactivation virale dans la fabrication des concentrés de facteurs de coagulation. Elle est encore plus faible chez les patients nés après 1994, date d'introduction du dépistage systémique du VHC chez les donneurs de sang tunisiens. En revanche, malgré l'inactivation des concentrés de facteurs et le dépistage systématique des dons du sang vis-à-vis de l'AgHBs depuis 1973, un risque élevé de contamination par le VHB persiste chez les hémophiles tunisiens. L'introduction depuis 1995 de la vaccination anti-hépatite B dans le calendrier national de vaccination des nouveau-nés devrait prochainement résoudre le problème de l'infection à VHB aussi bien chez les hémophiles que chez d'autres catégories de la population tunisienne

Molecular characterization of erythrocyte glucose-6-phosphate dehydrogenase deficiency in Tunisia

International audienceScreening of G6PD deficiency was carried out on 79 unrelated subjects (32 females and 47 males), all coming from out consultation. DNA from deficient subject (11 females and 30 males) was analyzed for the presence of G6PD mutation. Known mutations were studied by the appropriate restriction enzyme digestion of fragment amplified by PCR. Where the mutation could not be identified in this way, the samples were subjected to SSCP analysis and abnormal fragments were sequenced. Through these methods, seven different mutations have been identified. Among deficient females, eight had the African variant A-(tow of them were homozygous) and three had the Mediterranean variant, one of them was homozygous and have had a haemolytic crisis after ingestion of fava beans showing at birth manifestation of neonatal jaundice. Among deficient males, four were hospitalized and transfused after a haemolytic crisis due to ingestion of fava beans. All of them have had manifestation of neonatal jaundice. Of them, one carried the Mediterranean variant and three others had the African variant A- Among the remaining deficient males, 15 had A-variant, two had the Aures mutation. SSCP analysis of nine mild deficient males, revealed the presence of the association of 1311 C (R) T/93 T (R) C in two subjects, a newly described silent mutation in the exon 12 associated with the polymorphism in the intron 1193 T (R) C in one subject and tow single intronic base deletion. The first is IVS V 17 (-C) found in two subjects and the second is IVS VIII 43 (-G) encountered in four subjects. (C) 2007 Elsevier Masson SAS. All fights reserved