SARS-CoV-2 Lineage A.27: New Data from African Countries and Dynamics in the Context of the COVID-19 Pandemic

SARS-CoV-2 is constantly evolving with lineages emerging and others eclipsing. Some lineages have an important epidemiological impact and are known as variants of interest (VOIs), variants under monitoring (VUMs) or variants of concern (VOCs). Lineage A.27 was first defined as a VUM since it holds m...

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Published in:Viruses 2022-05, Vol.14 (5), p.1007
Main Authors: Chouikha, Anissa, Lagare, Adamou, Ghedira, Kais, Diallo, Amadou, Njouom, Richard, Sankhe, Safietou, Derrar, Fawzi, Victoir, Kathleen, Dellagi, Koussay, Triki, Henda, Diagne, Moussa Moise
Format: Article
Language:English
Subjects:
Bioinformatics
clade 19B
Consortia
Coronavirus Nucleocapsid Proteins - genetics
Coronaviruses
COVID-19
COVID-19 - epidemiology
COVID-19 - virology
Disease transmission
Epidemiology
Genomes
Humans
lineage A.27
Mutation
Pandemics
Phosphoproteins - genetics
Phylogenetics
Phylogeny
phylogeography
SARS-CoV-2
SARS-CoV-2 - genetics
Severe acute respiratory syndrome coronavirus 2
Software
Spike Glycoprotein, Coronavirus - genetics
tMRCA
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Summary:SARS-CoV-2 is constantly evolving with lineages emerging and others eclipsing. Some lineages have an important epidemiological impact and are known as variants of interest (VOIs), variants under monitoring (VUMs) or variants of concern (VOCs). Lineage A.27 was first defined as a VUM since it holds mutations of concern. Here, we report additional lineage A.27 data and sequences from five African countries and describe the molecular characteristics, and the genetic history of this lineage worldwide. Based on the new sequences investigated, the most recent ancestor (tMRCA) of lineage A.27 was estimated to be from April 2020 from Niger. It then spread to Europe and other parts of the world with a peak observed between February and April 2021. The detection rate of A.27 then decreased with only a few cases reported during summer 2021. The phylogenetic analysis revealed many sub-lineages. Among them, one was defined by the substitution Q677H in the spike (S) gene, one was defined by the substitution D358N in the nucleoprotein (N) gene and one was defined by the substitution A2143V in the ORF1b gene. This work highlights the importance of molecular characterization and the timely submission of sequences to correctly describe the circulation of particular strains in order to be proactive in monitoring the pandemic.
ISSN:1999-4915
1999-4915
DOI:10.3390/v14051007