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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.
Affiliation
  • Koné A; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Diallo D; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Kané F; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Diarra B; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Coulibaly TA; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Sameroff SC; Center for Infection and Immunity, Columbia University, New York, NY, USA.
  • Diarra HB; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Diakité MT; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Camara F; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Maiga O; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Keita D; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Dolo O; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Somboro A; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Coulibaly Y; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Bane S; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Togo ACG; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Somboro AM; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Togo J; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Coulibaly M; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Coulibaly G; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Kone M; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Degoga B; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Dramé HB; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Traoré FG; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Diallo F; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Sanogo F; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Kone K; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Diallo IB; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Sanogo M; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Diakité M; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
  • Mishra N; Center for Infection and Immunity, Columbia University, New York, NY, USA.
  • Neal A; Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
  • Saliba-Shaw K; Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
  • Sow Y; Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
  • Hensley L; Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA.
  • Lane HC; Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
  • Briese T; Center for Infection and Immunity, Columbia University, New York, NY, USA.
  • Lipkin WI; Center for Infection and Immunity, Columbia University, New York, NY, USA.
  • Doumbia S; University Clinical Research Center, International Centers for Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
IJID Reg ; 6: 24-28, 2023 Mar.
Article in En | MEDLINE | ID: mdl-36448028
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.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Language: En Journal: IJID Reg Year: 2023 Type: Article Affiliation country: Mali
Fulltext
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XML
PubMed Links
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Full text: 1 Collection: 01-internacional Database: MEDLINE Language: En Journal: IJID Reg Year: 2023 Type: Article Affiliation country: Mali