Genomic and epidemiological analysis of SARS-CoV-2 variants isolated in Guinea: A routine sequencing implementation.

Abstract Background Several variants of SARS-CoV-2 have a demonstrated impact on public health, including high and increased transmissibility, severity of infection and immune escape. Therefore, this study aimed to describe the genetic modifications and distribution of SARS-CoV-2 lineages and better characterize the dynamics of the pandemic during the different waves that occurred in Guinea. Methods Nasopharyngeal samples of 24638 and socio Demographic data were collected from consent patients in consultation at the health centers of Gbessia, Kenien and Matam, in the Republic of Guinea. Virus quantification of nasopharyngeal samples was performed by quantitative PCR. 363 samples with Ct values under 30 were sequenced on Illumina iSeq 100 platform. The sequences were then analyzed using GeVarli pipeline to generate consensus sequences, variant s calling, and lineage classifications (using Nextclade and Pangolin) . The phylogenetic tree was constructed using Nextstain tools. Statistical analysis was done using R programming. Results The circulation of SARS-CoV-2 in Guinea can be distributed in three periods independent to waves. The first lasting from May to June 2020 was characterized by one lineage B1 (n=6). The second period from January 2021 to July 2021 was characterized by the lineages B.1.1.7 (Alpha, n=25), AY.122 (Delta; n=2), B.1.1.318 (n=8), R1 (n=7), B.1.525 (n=9) and B.1.629 (n=13). The third period, between December 2021 and March 2023, was characterized by the Omicron variant, with nine sub-variants in the majority. In addition, detection of variants in the period out of there circulation were documented. Conclusion In summary, SARS-CoV-2 genomic surveillance projects like AFROSCREEN help African scientists to contribute to describe the natural history of the COVID epidemic and to implement a routine sequencing capacity using next generation sequencing platforms. This successful implementation system for SARS-CoV-2 must be adapted for other diseases. However, the organization of sample collection and conservation is a big challenge in Africa.