Background: After its initial detection in Wuhan, China, in December 2019, SARS-CoV-2 has spread rapidly, causing successive epidemic waves worldwide. This study aims to provide a genomic epidemiology of SARS-CoV-2 in Burkina Faso. Methods: Three hundred and seventy-seven SARS-CoV-2 genomes obtained from PCR-positive nasopharyngeal samples (PCR cycle threshold score < 35) collected between 5 May 2020, and 31 January 2022 were analyzed. Genomic sequences were assigned to phylogenetic clades using NextClade and to Pango lineages using pangolin. Phylogenetic and phylogeographic analyses were performed to determine the geographical sources and time of virus introduction in Burkina Faso. Results: The analyzed SARS-CoV-2 genomes can be assigned to 10 phylogenetic clades and 27 Pango lineages already described worldwide. Our analyses revealed the important role of cross-border human mobility in the successive SARS-CoV-2 introductions in Burkina Faso from neighboring countries. Conclusions: This study provides additional insights into the genomic epidemiology of SARS-CoV-2 in West Africa. It highlights the importance of land travel in the spread of the virus and the need to rapidly implement preventive policies. Regional cross-border collaborations and the adherence of the general population to government policies are key to prevent new epidemic waves.

Background: After its initial detection in Wuhan, China, in December 2019, SARS-CoV-2 has spread rapidly, causing successive epidemic waves worldwide. This study aims to provide a genomic epidemiology of SARS-CoV-2 in Burkina Faso. Methods: Three hundred and seventy-seven SARS-CoV-2 genomes obtained from PCR-positive nasopharyngeal samples (PCR cycle threshold score <35) collected between May 5, 2020, and January 31, 2022 were analysed. Genomic sequences were assigned to phylogenetic clades using NextClade and to Pango lineages using pangolin. Phylogenetic and phylogeographic analyses were performed to determine the geographical sources and time of virus introduction in Burkina Faso. Results: The analyzed SARS-CoV-2 genomes could be assigned to 10 phylogenetic clades and 27 Pango lineages already described worldwide. Our analyses revealed the important role of cross-border human mobility in the successive SARS-CoV-2 introductions in Burkina Faso from neighboring countries. Conclusion: This study provides additional insights into the genomic epidemiology of SARS-CoV-2 in West Africa. It highlights the importance of land travel in the spread of the virus and the need to rapidly implement preventive policies. Regional cross-border collaborations and the adherence of the general population to government policies are key to prevent new epidemic waves.

The human gut virome is a critical yet understudied component of the microbiome that shapes microbial community structure and host-microbe interactions. However, most existing human gut virome reference databases have been constructed predominantly from populations in high-income countries, resulting in the substantial underrepresentation of African populations. To help address this disparity, we developed the Kenyan Human Gut Virome Catalogue (KHGVC), the first comprehensive human gut virome resource for Kenya and the first country-specific human gut virome catalogue from Africa. Using a standardized viromics pipeline applied to 626 fecal metagenomes spanning infants and adults across three Kenyan counties, we reconstructed 116,968 viral operational taxonomic units (vOTUs). Cross-catalogue comparisons revealed extensive novelty where 65.6% of KHGVC's vOTUs larger than 10 kb lacked matches in five major human gut virome databases, and 95% remained unique relative to the Unified Human Gut Virome (UHGV). Temperate bacteriophages accounted for ~ 70% of vOTUs, supporting a major role for lysogeny in gut ecosystem stability. Functional annotation assigned putative roles to ~ 27% of predicted viral proteins, primarily structural and replication-associated functions. Application of KHGVC revealed pronounced age-dependent virome structuring in which infant viromes were less diverse and enriched in Bifidobacterium-infecting phages, including Bifidobacterium longum, whereas adult viromes exhibited greater diversity and expansion of Prevotella-associated phages. Together, the KHGVC substantially expands known human gut viral diversity and provides a foundational reference for Kenyan and African virome research. The KHGVC can be accessed freely through a publicly available interactive web interface (https://igmr.org/software/kenyavirocat).

Background: HIV infection is a major public health problem in sub-Saharan Africa, particularly in Burkina Faso. This study aimed to describe the socio-demographic characteristics of newly person living with HIV initiating antiretroviral treatment at the Adult Day Hospital of Bobo-Dioulasso over a five-year period. Materials and methods: A descriptive cross-sectional study was conducted from 1 January 2016 to 31 December 2020 at the Adult Day Hospital of Bobo-Dioulasso. People newly diagnosed with HIV after confirmatory testing and initiating antiretroviral therapy were included in this study. Results: Women represented 66.74% (586/878) of this study population (878), the average age of the study population was 41 ± 14.30 years-old and the age group of 35-52 years-old was the most represented at the initial visit. The majority of this study population were not schooled (48.86%) and housemaids accounted for 37.70%. The majority of the participants were infected with HIV-1 (84.51%). Conclusion: This study pointed out that HIV continues to infect the disadvantaged social and demographic groups. HIV awareness and screening campaigns are required to better control the infection in these groups.

Background: The use of alternative technique such as rapid antigen diagnostic tests (Ag‐RDTs) is needed in countries with limited resources for fast tracking of COVID‐19 cases. This study evaluated the performance of the STANDARD Q COVID‐19 antigen test compared with reverse transcriptase polymerase chain reaction (RT‐PCR) among suspected COVID‐19 cases using nasopharyngeal and/or oropharyngeal swabs in Bobo‐Dioulasso, Burkina Faso. Methods: A cross‐sectional study was conducted from April to September 2021. The respiratory secretions of suspected COVID‐19 cases were collected at the Virology Laboratory of Sourô Sanou University Hospital in Bobo‐Dioulasso. The respiratory secretions consisted of nasopharyngeal or combined nasopharyngeal/oropharyngeal swabs. Each sample was analyzed using the STANDARD Q COVID‐19 Ag test and RT‐PCR on the Abbott m2000 RealTime system. Results: A total of 152 respiratory specimens were collected from suspected COVID‐19 cases and processed in this study. The sensitivity and specificity of the Ag‐RDT were 26.32% (9.15–57.20) and 98.65% (92.7–99.9), respectively, in the suspected cases with nasopharyngeal swabs from suspected cases, while a sensitivity of 25.0% (3.2–65.1) and a specificity of 98.65% (92.7–99.9) were shown with combined nasopharyngeal/oropharyngeal swabs from suspected cases. The accuracy and Cohen′s kappa of the test were 83.87% and 0.36 in suspected cases with nasopharyngeal swabs from suspected cases, while they were 83.37% and 0.32 in oropharyngeal swabs. In our study, Ag‐RDT was not sensitive on the specimens of suspected COVID‐19 cases with Ct values ≥ 20, whereas its sensitivity increased to 41.18% (18.4–67.1) on specimens with Ct < 20. Conclusion: The study findings have shown that the Ag‐RDT is useful in suspected COVID‐19 cases. However, the sensitivity of the STANDARD Q COVID‐19 Ag test was low with minimal agreement in comparison to RT‐PCR on the Abbott m2000rt system.