Genomic and epidemiological analysis of SARS-CoV-2 variants isolated in Guinea: a routine sequencing implementation DOI Creative Commons
Aminata Mbaye,

Haby Diallo,

Thibaut Armel Cherif Gnimadi

et al.

BMC Infectious Diseases, Journal Year: 2025, Volume and Issue: 25(1)

Published: Jan. 2, 2025

Abstract Background Several variants of SARS-CoV-2 have a demonstrated impact on public health, including high and increased transmissibility, severity infection, immune escape. Therefore, this study aimed to determine the lineages better characterize dynamics pandemic during different waves in Guinea. Methods Whole genome sequencing 363 samples with PCR cycle threshold (Ct) values under thirty was undertaken between May 2020 2023. The Illumina iSeq 100 technology used. sequences were then analyzed using GeVarli pipeline generate consensus variant calling. All isolated Guinea available GISAID included analysis for phylogenetic tree phylodynamic determination. Nextstain tools used these analyses. Statistical done GraphPad Prism version 10. Results circulation can be distributed three periods. first, lasting from June 2020, characterized by B1 B.1.1. second period, January 2021 July 2021, B.1.1.7 (Alpha), AY.122, B.1.1.318, R1, B.1.525 B.1.629. third December 2023, Omicron variant, nine subvariant majorities found. In addition, detecting period out their documented. importation exportation investigation showed strong movement viral association Senegal one hand Nigeria other. Conclusion summary, contributes understanding epidemic disease describing significant that circulated Guinee distribution population. It also shows virus pandemic. Sub-sampling degradation observed. Organization collaboration laboratories are needed good sample-collecting storage system future direction.

Language: Английский

Genomic and epidemiological analysis of SARS-CoV-2 variants isolated in Guinea: a routine sequencing implementation DOI Creative Commons
Aminata Mbaye,

Haby Diallo,

Thibaut Armel Cherif Gnimadi

et al.

BMC Infectious Diseases, Journal Year: 2025, Volume and Issue: 25(1)

Published: Jan. 2, 2025

Abstract Background Several variants of SARS-CoV-2 have a demonstrated impact on public health, including high and increased transmissibility, severity infection, immune escape. Therefore, this study aimed to determine the lineages better characterize dynamics pandemic during different waves in Guinea. Methods Whole genome sequencing 363 samples with PCR cycle threshold (Ct) values under thirty was undertaken between May 2020 2023. The Illumina iSeq 100 technology used. sequences were then analyzed using GeVarli pipeline generate consensus variant calling. All isolated Guinea available GISAID included analysis for phylogenetic tree phylodynamic determination. Nextstain tools used these analyses. Statistical done GraphPad Prism version 10. Results circulation can be distributed three periods. first, lasting from June 2020, characterized by B1 B.1.1. second period, January 2021 July 2021, B.1.1.7 (Alpha), AY.122, B.1.1.318, R1, B.1.525 B.1.629. third December 2023, Omicron variant, nine subvariant majorities found. In addition, detecting period out their documented. importation exportation investigation showed strong movement viral association Senegal one hand Nigeria other. Conclusion summary, contributes understanding epidemic disease describing significant that circulated Guinee distribution population. It also shows virus pandemic. Sub-sampling degradation observed. Organization collaboration laboratories are needed good sample-collecting storage system future direction.

Language: Английский

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