[vc_row][vc_column][vc_single_image image=”13544″ img_size=”medium” alignment=”center” style=”vc_box_rounded” css=”.vc_custom_1673273304227{margin-top: 36px !important;}”][\/vc_column][\/vc_row][vc_row][vc_column][vc_column_text]<\/p>\n
Institution: Facult\u00e9 de m\u00e9decine et d’Odontostomatologie, Universit\u00e9 des Sciences des Techniques et des Tecnologie de Bamako<\/p>\n
Project Affiliation: West African Center of Excellence for Global Health Bioinformatics Research Training<\/p>\n
Background<\/strong>: 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.<\/p>\n Objective<\/strong>: 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.<\/p>\n Methods<\/strong>: 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\u00ae 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).<\/p>\n Results<\/strong>: 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 \u00b1 25348 with 61249 \u00b1 25348 reads mapped. The average number of SNPs was 35\u00b111.09. 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%).<\/p>\n Conclusion:<\/strong> 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.<\/p>\n \u00a0<\/strong>Key words: <\/strong>NGS, Nanopore sequencing, Sars-Cov2, Mali<\/p>\n [\/vc_column_text][vc_column_text]<\/p>\n [\/vc_column_text][vc_basic_grid post_type=”page” max_items=”-1″ element_width=”3″ item=”5653″ grid_id=”vc_gid:1673274102820-7d487c0f9074df94aa036e88b8137b5b-0″ taxonomies=”201″][\/vc_column][\/vc_row]<\/p>\n","protected":false},"excerpt":{"rendered":" [vc_row][vc_column][vc_single_image image=”13544″ img_size=”medium” alignment=”center” style=”vc_box_rounded” css=”.vc_custom_1673273304227{margin-top: 36px !important;}”][\/vc_column][\/vc_row][vc_row][vc_column][vc_column_text] Fousseyni Kan\u00e9 [\u2026]<\/span><\/p>\n","protected":false},"author":2,"featured_media":13544,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_coblocks_attr":"","_coblocks_dimensions":"","_coblocks_responsive_height":"","_coblocks_accordion_ie_support":"","footnotes":""},"categories":[],"tags":[201],"class_list":["post-13821","page","type-page","status-publish","has-post-thumbnail","hentry","tag-20th_fellows"],"_links":{"self":[{"href":"https:\/\/h3africa.org\/index.php\/wp-json\/wp\/v2\/pages\/13821","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/h3africa.org\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/h3africa.org\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/h3africa.org\/index.php\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/h3africa.org\/index.php\/wp-json\/wp\/v2\/comments?post=13821"}],"version-history":[{"count":5,"href":"https:\/\/h3africa.org\/index.php\/wp-json\/wp\/v2\/pages\/13821\/revisions"}],"predecessor-version":[{"id":13826,"href":"https:\/\/h3africa.org\/index.php\/wp-json\/wp\/v2\/pages\/13821\/revisions\/13826"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/h3africa.org\/index.php\/wp-json\/wp\/v2\/media\/13544"}],"wp:attachment":[{"href":"https:\/\/h3africa.org\/index.php\/wp-json\/wp\/v2\/media?parent=13821"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/h3africa.org\/index.php\/wp-json\/wp\/v2\/categories?post=13821"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/h3africa.org\/index.php\/wp-json\/wp\/v2\/tags?post=13821"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}Other Fellows<\/h3>\n