H3Africa PI: Seydou Doumbia
Institution: Faculté de médecine et d’Odontostomatologie, Université des Sciences des Techniques et des Tecnologie de Bamako
Project Affiliation: West African Center of Excellence for Global Health Bioinformatics Research Training
Background: The use of real-time genomic epidemiology has enabled the tracking of the global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), informing evidence-based public health decision making. Mali has experienced five waves of the Coronavirus Disease 2019 (COVID-19) between April 2020 and November 2022. However, the low capacity for local genetic sequencing limited SARS-CoV-2 genomic surveillance.
Objective: The objective of this work was to follow the dynamics of variants emergence by sequencing of SARS-CoV-2 genomes from samples using Oxford Nanopore Technology.
Methods: We performed a random sampling among samples collected between November 2021 and October 2022 stored at the UCRC. All pre-selected samples had a CT value lower than 30. The library preparation, ligation and barcoding were performed following the NEBNext® ARTIC SARS-CoV-2 Companion Kit workflow. The nf-core/viralrecon pipeline was used for the bioinformatics analysis (Sequencing QC, Aggregate pre-demultiplexed, alignment, Downstream variant analysis).
Results: A total of 37 genomes were sequenced with an estimated median genomic coverage of 90.7.48% IQ (85.1% – 96.1%). The average total number of reads was 61249 ± 25348 with 61249 ± 25348 reads mapped. The average number of SNPs was 35±11.09. The variants were dominated by delta n=32 (86.49%) composed by clades B.1.617.2; AY.133; AY.34.1; AY.34; AY.36 followed by Eta (clade= B.1.525) n=3 8.11% and Omicron (clade= BQ.1.10; BA.2) n=2 (5.41%).
Conclusion: Different SARS-CoV-2 variants are circulating in Mali. Genomic epidemiology integration within public health response allows tracking of variants and mutations that potentially affect disease outcome and vaccine efficacy.
Key words: NGS, Nanopore sequencing, Sars-Cov2, Mali