Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America.
SARS-CoV-2
molecular epidemiology
phylogenetics
recombination
Journal
Cell host & microbe
ISSN: 1934-6069
Titre abrégé: Cell Host Microbe
Pays: United States
ID NLM: 101302316
Informations de publication
Date de publication:
10 08 2022
10 08 2022
Historique:
received:
14
12
2021
revised:
18
03
2022
accepted:
16
06
2022
pubmed:
20
7
2022
medline:
16
8
2022
entrez:
19
7
2022
Statut:
ppublish
Résumé
Although recombination is a feature of coronavirus evolution, previously detected recombinant lineages of SARS-CoV-2 have shown limited circulation thus far. Here, we present a detailed phylogenetic analysis of four SARS-CoV-2 lineages to investigate the possibility of virus recombination among them. Our analyses reveal well-supported phylogenetic differences between the Orf1ab region encoding viral non-structural proteins and the rest of the genome, including Spike (S) protein and remaining reading frames. By accounting for several deletions in NSP6, Orf3a, and S, we conclude that the B.1.628 major cluster, now designated as lineage XB, originated from a recombination event between viruses of B.1.631 and B.1.634 lineages. This scenario is supported by the spatiotemporal distribution of these lineages across the USA and Mexico during 2021, suggesting that the recombination event originated in this geographical region. This event raises important questions regarding the role and potential effects of recombination on SARS-CoV-2 evolution.
Identifiants
pubmed: 35853454
pii: S1931-3128(22)00315-8
doi: 10.1016/j.chom.2022.06.010
pmc: PMC9212848
pii:
doi:
Substances chimiques
Spike Glycoprotein, Coronavirus
0
spike protein, SARS-CoV-2
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1112-1123.e3Subventions
Organisme : Bill & Melinda Gates Foundation
ID : INV-034540
Pays : United States
Organisme : Medical Research Council
ID : MR/R015600/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/S019510/1
Pays : United Kingdom
Informations de copyright
Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of interests The authors declare no competing interests.
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