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

Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1002, Tunisia

Reasearch Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health”, LR20IPT02, Pasteur Institute, Tunis 1002, Tunisia

Centre de Recherche Médicale et Sanitaire (CERMES), BP: 10887—634 Bd de la Nation, Niamey YN034, Niger

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Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Institut Pasteur de Tunis (IPT), 13, Place Pasteur BP 74, University of Tunis-El Manar, Tunis 1002, Tunisia

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Institut Pasteur Dakar, 36 Avenue Pasteur, Dakar BP 220, Senegal

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Centre Pasteur of Cameroon, Centre Pasteur of Cameroon, 451 rue 2005, Yaoundé, Cameroon

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Institut Pasteur d’Algérie, 01 Rue du Petite Staouéli, Dély-Brahim, Algiers 16047, Algeria

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Institut Pasteur, Direction Internationale, Pôle Coopération Scientifique, 25 Rue du Dr Roux, 75015 Paris, France

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Pasteur Network Association, Institut Pasteur 25 Rue du Dr Roux, 75015 Paris, France

Author to whom correspondence should be addressed.

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These authors contributed equally to this work.

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Repair consortium: Alain, M., Beloufa, M.A., Dellagi, K., Dia, N., Dussart, P., Fares, W., Faye, M., Faye, O., Fy, S., Gdoura, M., Grayot, S., Haddad-Boubaker, S., Heraud, J.M., Kadjo, H., Jambou, R.,Kammoun Rebai, W., Loucoubar, C., Makiala, C., Nourlil, J., Razanajatovo, N., Rabenandrasana, N., Ranaivoson, C., Sall, A., Simon-Lorière, E., Tordo, N., Troupin, C., Vernet, G., Vernet, M.

Academic Editors: Judd F. Hultquist, Ramón Lorenzo-Redondo and Egon Anderson Ozer

Viruses 2022, 14(5), 1007; https://doi.org/10.3390/v14051007

Received: 6 April 2022 / Revised: 5 May 2022 / Accepted: 5 May 2022 / Published: 9 May 2022

(This article belongs to the Special Issue SARS-CoV-2 Genomics)

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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. View Full-Text

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

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MDPI and ACS Style

Chouikha, A.; Lagare, A.; Ghedira, K.; Diallo, A.; Njouom, R.; Sankhe, S.; Derrar, F.; Victoir, K.; Dellagi, K.; Triki, H.; Diagne, M.M., for the REPAIR Consortium. SARS-CoV-2 Lineage A.27: New Data from African Countries and Dynamics in the Context of the COVID-19 Pandemic. Viruses 2022, 14, 1007. https://doi.org/10.3390/v14051007

AMA Style

Chouikha A, Lagare A, Ghedira K, Diallo A, Njouom R, Sankhe S, Derrar F, Victoir K, Dellagi K, Triki H, Diagne MM for the REPAIR Consortium. SARS-CoV-2 Lineage A.27: New Data from African Countries and Dynamics in the Context of the COVID-19 Pandemic. Viruses. 2022; 14(5):1007. https://doi.org/10.3390/v14051007

Chicago/Turabian Style

Chouikha, Anissa, Adamou Lagare, Kais Ghedira, Amadou Diallo, Richard Njouom, Safietou Sankhe, Fawzi Derrar, Kathleen Victoir, Koussay Dellagi, Henda Triki, and Moussa M. Diagne for the REPAIR Consortium. 2022. "SARS-CoV-2 Lineage A.27: New Data from African Countries and Dynamics in the Context of the COVID-19 Pandemic" Viruses 14, no. 5: 1007. https://doi.org/10.3390/v14051007

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

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