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