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

Evaluation of the analytical performance of six rapid diagnostic tests for the detection of viral hepatitis B and C in Lubumbashi, Democratic Republic of Congo.

Rapid diagnostic tests (RDTs) are widely used in Lubumbashi for the diagnosis of viral hepatitis B and C. To date, there are no works that have been carried out in Lubumbashi to independently assess the performance of such tests. This study aimed at assessing the effectiveness of RDTs for the detection of HBsAg and anti-HCV antibodies in order to identify infected blood donors in Lubumbashi. A total of 300 serum samples (100 HBsAg positive samples; 100 anti-HCV positive samples and 100 HBsAg and anti-HCV negative samples) were tested simultaneously using the 6 locally used RDTs and as gold standard the chemiluminescent assays for HBsAg and the RT-TMA for HCV.detection. The six evaluated RDTs demonstrated a sensitivity and a negative predictive value (NPV) of 100% whereas the specificity and positive predictive value (PPV) varied from 46% to 98.1%. SB BioLine HBsAg test performed best in this study with 100% of sensitivity, 97.1% of specificity,100% of NPV and 96.9% of PPV. Furthermore, sensitivity, specificity, NPV and PPV for SB BioLine HCV test were as follows: 100%, 98,1%, 100% and 93.9%. Therefore, SD BioLine tests (HBsAg, HCV) would be selected as the first line RDTs for the detection and the diagnostic of hepatitis B and C. They can prevent blood-borne transmission of HBV and HCV in areas with limited incomes as Lubumbashi

Epidemiological aspects and molecular characterization of the hepatitis B virus among blood donors in Lubumbashi, Democratic Republic of Congo.

OBJECTIVES : The strains of HBV circulating among blood donors in Lubumbashi, Democratic Republic of Congo (DRC), are not yet characterized. The purpose of this study was to determine seroprevalence, changes in biochemical parameters during HBV infection and molecular characterization of HBV in blood donors in Lubumbashi. METHODS : The detection of HBsAg was carried out by rapid diagnostic test then confirmed by the Liaison XL® Quant HBsAg technique. PCR targeting the P gene was carried out on LightCycler® 96 and genotyping by the sequencing technique on ABI 3500. RESULTS : The seroprevalence was 7.9%. The genotypes E (53.1%), A (41.8%), A3/E (3.8%), A1/E (1.3%) and some drug resistance mutations were identified. Disturbances of HDL-cholesterol, direct bilirubin, transaminases (ASAT and ALAT), PAL, GGT and albumin have been observed in HBsAg positive blood donors. CONCLUSION : The results of our study indicated that Lubumbashi is in a region with high endemicity for HBV and report for the first time HBV of genotypes A, E, A1/E and A3/E. They highlight the need to implement strategies to improve transfusion safety in blood transfusion centers and hospital blood banks in Lubumbashi in order to reduce HBV infection in recipients. They could also contribute to the implementation of treatment strategies and the development of mapping of circulating HBV genotypes in the DRC.[Aspects épidémiologiques et caractérisation moléculaire du virus de l’hépatite B chez les donneurs de sang à Lubumbashi, République démocratique du Congo] OBJECTIFS : Les souches du virus de l’hépatite B (VHB), circulant parmi les donneurs de sang à Lubumbashi, en République démocratique du Congo (RDC), ne sont pas encore caractérisées. Le but de cette étude était de déterminer la séroprévalence et les changements des paramètres biochimiques au cours de l’infection par le VHB et la caractérisation moléculaire du VHB chez les donneurs de sang à Lubumbashi. METHODES : La détection de l’AgHBs a été réalisée par le test de diagnostic rapide, puis confirmée par la technique Liaison XL® Quant HBsAg. La PCR ciblant le gène P a été réalisée sur LightCycler® 96 et le génotypage par la technique de séquençage sur ABI 3500. RESULTATS : La séroprévalence était de 7,9 %. Les génotypes E (53,1 %), A (41,8 %), A3/E (3,8 %), A1/E (1,3 %) et certaines mutations de résistance aux médicaments ont été identifiées. Des perturbations du cholestérol HDL, de la bilirubine directe, des transaminases (ASAT et ALAT), de la PAL, de la GGT et de l’albumine ont été observées chez des donneurs de sang AgHBs positif. CONCLUSION : Les résultats de notre étude avaient indiqué que Lubumbashi se trouve dans une région de forte endémicité pour le VHB et rapportent, pour la première fois, le VHB des génotypes A, E, A1/E et A3/E. Ils soulignent la nécessité de mettre en œuvre des stratégies pour améliorer la sécurité transfusionnelle dans les centres de transfusion sanguine et les banques de sang des hôpitaux de Lubumbashi, afin de réduire l’infection par le VHB chez les receveurs. Ils pourraient également contribuer à la mise en œuvre de stratégies de traitement au développement de la cartographie des génotypes circulants en RDC