ABSTRACT
INTRODUCTION: In Senegal, molecular diagnosis was widely used for the detection and management of COVID-19 patients. However, genomic surveillance was very limited in the public sector. This study aimed to share the experience of a Senegalese public sector laboratory in response to the COVID-19 pandemic, and to describe the distribution of variants circulating in 2020 and 2021. METHODOLOGY: From July 2020 to December 2021, SARS-CoV-2 qRT-PCR was performed on nasopharyngeal samples from travelers and symptomatic patients at the Bacteriology and Virology Laboratory (LBV) of the Aristide le Dantec University Teaching Hospital. Samples with a cycle threshold (Ct) ≤ 30 were selected for whole-genome sequencing (WGS) using the Nanopore technology. In-house scripts were developed to study the spatial and temporal distribution of SARS-CoV-2 variants in Senegal, using our sequences and those retrieved from the GISAID database. RESULTS: Of 8,207 patients or travelers screened for SARS-CoV-2, 970 (11.8%) were positive and 386 had a Ct ≤ 30. WGS was performed on 133 samples. Concomitantly with high-quality sequences deposited in the GISAID database covering nine cities in Senegal in 2020 and 2021 (n = 1,539), we observed a high circulation of the 20A (B.1, B.1.416 and B.1.620) and 20B (B.1.1.420) lineages in 2020, while most of the samples belonged to Delta variants (AY34 and AY.34.1, 22%) in 2021. CONCLUSIONS: Despite its late involvement, COVID-19 diagnosis was routinely performed in LBV, but genomic characterization remained challenging. The genomic diversity of SARS-CoV-2 strains in Senegal reflected that observed worldwide during the first waves of the pandemic.
Subject(s)
COVID-19 , Genome, Viral , SARS-CoV-2 , Humans , Senegal/epidemiology , COVID-19/epidemiology , COVID-19/virology , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Whole Genome Sequencing , Molecular Epidemiology , Nasopharynx/virology , Adult , Male , Female , Phylogeny , Middle AgedABSTRACT
â¢Omicron variant continues to progress in Senegal with the appearance of new contaminations.â¢IRESSEF detected the first positive case of the Omicron variant on Friday, December 3, 2021.â¢Since this date, the number of Omicron variant infections has increased over the weeks.â¢Molecular surveillance of the Omicron variant allowed us to identify a strong variation of this variant in our country.
