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Dynamics of SARS-CoV-2 variants characterized during different COVID-19 waves in Mali.
Koné, Amadou; Diallo, Dramane; Kané, Fousseyni; Diarra, Bassirou; Coulibaly, Tenin Aminatou; Sameroff, Stephen C; Diarra, Hawa B; Diakité, Mahamane T; Camara, Fatoumata; Maiga, Oumou; Keita, Daouda; Dolo, Oumar; Somboro, Amadou; Coulibaly, Youssouf; Bane, Sidy; Togo, Antieme C G; Somboro, Anou M; Togo, Josué; Coulibaly, Mariam; Coulibaly, Gagni; Kone, Mahamadou; Degoga, Boureima; Dramé, Hawa Baye; Traoré, Fah Gaoussou; Diallo, Fatimata; Sanogo, Fanta; Kone, Kadidia; Diallo, Ibrahima B; Sanogo, Moumine; Diakité, Mahamadou; Mishra, Nischay; Neal, Aaron; Saliba-Shaw, Katy; Sow, Ydrissa; Hensley, Lisa; Lane, H Clifford; Briese, Thomas; Lipkin, W Ian; Doumbia, Seydou.
  • Koné A; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Diallo D; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Kané F; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Diarra B; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Coulibaly TA; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Sameroff SC; Center for Infection and Immunity, Columbia University, New York, New York, United States of America.
  • Diarra HB; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Diakité MT; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Camara F; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Maiga O; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Keita D; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Dolo O; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Somboro A; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Coulibaly Y; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Bane S; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Togo ACG; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Somboro AM; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Togo J; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Coulibaly M; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Coulibaly G; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Kone M; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Degoga B; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Dramé HB; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Traoré FG; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Diallo F; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Sanogo F; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Kone K; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Diallo IB; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Sanogo M; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Diakité M; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
  • Mishra N; Center for Infection and Immunity, Columbia University, New York, New York, United States of America.
  • Neal A; Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America.
  • Saliba-Shaw K; Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America.
  • Sow Y; Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America.
  • Hensley L; Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, United States of America.
  • Lane HC; Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America.
  • Briese T; Center for Infection and Immunity, Columbia University, New York, New York, United States of America.
  • Lipkin WI; Center for Infection and Immunity, Columbia University, New York, New York, United States of America.
  • Doumbia S; University Clinical Research Center (UCRC), International Centers for Excellence in Research (ICER), University of Sciences, Techniques, and Technologies of Bamako (USTTB) Bamako, Mali.
IJID Reg ; 2022 Nov 25.
Article in English | MEDLINE | ID: covidwho-2242278
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

Full text: Available Collection: International databases Database: MEDLINE Topics: Variants Language: English Year: 2022 Document Type: Article Affiliation country: J.ijregi.2022.11.009

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Full text: Available Collection: International databases Database: MEDLINE Topics: Variants Language: English Year: 2022 Document Type: Article Affiliation country: J.ijregi.2022.11.009