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. 2022 May 9;14(5):1007.
doi: 10.3390/v14051007.

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

Anissa Chouikha  1   2 , Adamou Lagare  3 , Kais Ghedira  4 , Amadou Diallo  5 , Richard Njouom  6 , Safietou Sankhe  5 , Fawzi Derrar  7 , Kathleen Victoir  8 , Koussay Dellagi  9 , Henda Triki  1   2 , Moussa Moise Diagne  5 ; REPAIR Consortium
Affiliations

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

Anissa Chouikha et al. Viruses. .

Abstract

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.

Keywords: SARS-CoV-2; clade 19B; lineage A.27; phylogeny; phylogeography; tMRCA.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Geographic distribution of SARS-CoV-2 lineage A.27 from November 2020 to November 2021 based on 682 sequences from 38 different countries.
Figure 2
Figure 2
Timeline of SARS-CoV-2 lineage A.27 detection worldwide per epidemiological week based on 643 sequences as of 12 November 2021.
Figure 3
Figure 3
Phylogenetic tree of 280 whole genomes of SARS-CoV-2 lineage A.27. The tree was constructed using the maximum likelihood method using the IQ tree web server and visualized by FigTree. Topology was supported by 1000 bootstrap replicates.
Figure 4
Figure 4
Phylogeographic analysis of SARS-CoV-2 lineage A.27 based on 330 S genes from 27 countries.
See this image and copyright information in PMC

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