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Dynamics of SARS-CoV-2 variants characterized during different COVID-19 waves in Mali

2022; Elsevier BV; Volume: 6; Linguagem: Inglês

10.1016/j.ijregi.2022.11.009

2772-7076

A. Koné, Dramane Diallo, Fousseyni Kané, Bassirou Diarra, Tenin Aminatou Coulibaly, Stephen Sameroff, Hawa Diarra, Mahamane Talphi Diakite, Fatoumata Camara, Oumou Ousmane Maiga, Daouda Keita, Oumar Dolo, Anou M. Somboro, Y. Coulibaly, Sidy Bane, Antieme Combo Georges Togo, Anou M. Somboro, Josué Togo, Mariam Coulibaly, Gagni Coulibaly, Mahamadou Koné, Boureima Degoga, Hawa Baye Dramé, Fah Gaoussou Traoré, Fatimata Diallo, Fanta Sanogo, Kadidia Kone, Ibrahima B. Diallo, M. Sanogo, Mahamadou Diakité, Nischay Mishra, Aaron Neal, Katy Saliba-Shaw, Ydrissa Sow, Lisa E. Hensley, H. Clifford Lane, Thomas Briese, W. Ian Lipkin, Seydou Doumbia,

Viral Infections and Outbreaks Research

The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants may have contributed to prolonging the pandemic, and increasing morbidity and mortality related to coronavirus disease 2019 (COVID-19). This article describes the dynamics of circulating SARS-CoV-2 variants identified during the different COVID-19 waves in Mali between April and October 2021.The respiratory SARS-CoV-2 complete spike (S) gene from positive samples was sequenced. Generated sequences were aligned by Variant Reporter v3.0 using the Wuhan-1 strain as the reference. Mutations were noted using the GISAID and Nextclade platforms.Of 16,797 nasopharyngeal swab samples tested, 6.0% (1008/16,797) tested positive for SARS-CoV-2 on quantitative reverse transcription polymerase chain reaction. Of these, 16.07% (162/1008) had a cycle threshold value ≤28 and were amplified and sequenced. The complete S gene sequence was recovered from 80 of 162 (49.8%) samples. Seven distinct variants were identified: Delta (62.5%), Alpha (1.2%), Beta (1.2%), Eta (30.0%), 20B (2.5%), 19B (1.2%) and 20A (1.2%).Several SARS-CoV-2 variants were present during the COVID-19 waves in Mali between April and October 2021. The continued emergence of new variants highlights the need to strengthen local real-time sequencing capacity and genomic surveillance for better and coordinated national responses to SARS-CoV-2.