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

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

doi:10.1016/j.ijregi.2022.11.009

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

IJID Reg. 2023 Mar:6:24-28. doi: 10.1016/j.ijregi.2022.11.009. Epub 2022 Nov 25.

Authors

Amadou Koné¹, Dramane Diallo¹, Fousseyni Kané¹, Bassirou Diarra¹, Tenin Aminatou Coulibaly¹, Stephen C Sameroff², Hawa B Diarra¹, Mahamane T Diakité¹, Fatoumata Camara¹, Oumou Maiga¹, Daouda Keita¹, Oumar Dolo¹, Amadou Somboro¹, Youssouf Coulibaly¹, Sidy Bane¹, Antieme C G Togo¹, Anou M Somboro¹, Josué Togo¹, Mariam Coulibaly¹, Gagni Coulibaly¹, Mahamadou Kone¹, Boureima Degoga¹, Hawa Baye Dramé¹, Fah Gaoussou Traoré¹, Fatimata Diallo¹, Fanta Sanogo¹, Kadidia Kone¹, Ibrahima B Diallo¹, Moumine Sanogo¹, Mahamadou Diakité¹, Nischay Mishra², Aaron Neal³, Katy Saliba-Shaw³, Ydrissa Sow³, Lisa Hensley⁴, H Clifford Lane³, Thomas Briese², W Ian Lipkin², Seydou Doumbia¹

Affiliations

¹ University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
² Center for Infection and Immunity, Columbia University, New York, NY, USA.
³ Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
⁴ Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA.

Abstract

Background: 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.

Methods: 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.

Results: 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%).

Conclusions and perspectives: 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.

Keywords: COVID-19; Mali; SARS-CoV-2; Sequencing; Variant.

Abstract

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