Genomic epidemiology of SARS-CoV-2 in Senegal in 2020-2021
DOI:
https://doi.org/10.3855/jidc.17796Keywords:
COVID-19, SARS-CoV-2, Senegal, genomic diversity, waveAbstract
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.
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Copyright (c) 2024 Adjiratou Aissatou BA, Romain Coppée, Assane DIENG, Jarra Manneh, Mengue FALL, Khadim GUEYE, Pauline Yacine SENE, Samba NDIOUR, Dianké SAMATE, Pascaline MANGA, Oumy DIOP, Abdoulaye CAMARA, Abdou PADANE, Sada DIALLO; Sokhna Bousso GUEYE; Makhtar CAMARA, Abdul Sesay, Coumba Toure Kane Toure Kane , Souleymane Mboup, Charlotte CHARPENTIER , Halimatou DIOP
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