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

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IJID Reg


. 2022 Nov 25.
doi: 10.1016/j.ijregi.2022.11.009. Online ahead of print.
Dynamics of SARS-CoV-2 variants characterized during different COVID-19 waves in Mali


Amadou Koné ¹ , Dramane Diallo ¹ , Fousseyni Kané ¹ , Bassirou Diarra ¹ , Tenin Aminatou Coulibaly ¹ , Stephen C Sameroff ² , Hawa B Diarra ¹ , Mahamane T Diakité ¹ , Fatoumata Camara ¹ , Oumou Maiga ¹ , Daouda Keita ¹ , Oumar Dolo ¹ , Amadou Somboro ¹ , Youssouf Coulibaly ¹ , Sidy Bane ¹ , Antieme C G Togo ¹ , Anou M Somboro ¹ , Josué Togo ¹ , Mariam Coulibaly ¹ , Gagni Coulibaly ¹ , Mahamadou Kone ¹ , Boureima Degoga ¹ , Hawa Baye Dramé ¹ , Fah Gaoussou Traoré ¹ , Fatimata Diallo ¹ , Fanta Sanogo ¹ , Kadidia Kone ¹ , Ibrahima B Diallo ¹ , Moumine Sanogo ¹ , Mahamadou Diakité ¹ , Nischay Mishra ² , Aaron Neal ³ , Katy Saliba-Shaw ³ , Ydrissa Sow ³ , Lisa Hensley ⁴ , H Clifford Lane ³ , Thomas Briese ² , W Ian Lipkin ² , Seydou Doumbia ¹



Affiliations

• PMID: 36448028
• PMCID: PMC9691504
• DOI: 10.1016/j.ijregi.2022.11.009

Abstract

Background: Emergence of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants may contribute to prolonging the pandemic and increasing morbidity, and mortality related to coronavirus disease 2019 (COVID-19). We describe the dynamics of circulating SARS-CoV-2 variants identified during the different COVID-19 waves that occurred in Mali between April 2021 and October 2021.
Methods: We sequenced respiratory SARS-CoV-2 complete spike (S) gene from positive samples. Generated sequences were aligned by Variant Reporter v3.0 using Wuhan-1 strain as a reference. Mutations were noted using the GISAID and Nextclade platforms.
Results: Of 16,797 nasopharyngeal swab samples tested, 6.0 % (1008/16,797) were RT-qPCR positive for SARS-CoV-2. Of these, 16.07% (162/1008) had a Ct value ≤ 28 and were amplified and sequenced. We recovered complete S-gene sequence from 80 of 162 [49.8%] samples. We identified seven distinct variants including Delta [62.5%], Alpha [1.2%], Beta [1.2%], Eta [30.0%], 20B [2.5%], 19B and 20A [1.2% each].
Conclusion and perspectives: Our results show the presence of several SARS-CoV-2 variants during 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.