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

© 2022 The Author(s)..

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.

Media Type:

Electronic Article

Year of Publication:

2023

Publication:

2023

Contained In:

To Main Record - volume:6

Contained In:

IJID regions - 6(2023) vom: 07. März, Seite 24-28

Language:

English

Contributors:

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

Links:

Volltext

Keywords:

COVID-19
Journal Article
Mali
SARS-CoV-2
Sequencing
Variant

Notes:

Date Revised 02.11.2023

published: Print-Electronic

Citation Status PubMed-not-MEDLINE

doi:

10.1016/j.ijregi.2022.11.009

funding:

Supporting institution / Project title:

PPN (Catalogue-ID):

NLM349608318