Journal
CELL HOST & MICROBE
Volume 30, Issue 8, Pages 1112-+Publisher
CELL PRESS
DOI: 10.1016/j.chom.2022.06.010
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Funding
- National Council for Science and Technology - Mexico (CONACyT)
- Leverhulme Trust ECR Fellowship [ECF-2019542]
- Secretariat for Higher Education, Science, Technology, and Innovation of the Republic of Ecuador
- Sir Henry Dale Fellowship [204311/Z/16/Z]
- Medical Research Council-Sao Paulo Research Foundation (FAPESP) CADDE partnership award [MR/S0195/1, FAPESP 18/143890]
- Bill & Melinda Gates Foundation [INV-034540]
- Oxford Martin School
- Bill and Melinda Gates Foundation [INV-034540] Funding Source: Bill and Melinda Gates Foundation
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This study presents a phylogenetic analysis of SARS-CoV-2 lineages and identifies a recombination event between B.1.631 and B.1.634 lineages, resulting in the formation of the B.1.628 major cluster (lineage XB). The spatiotemporal distribution supports the conclusion that the recombination event originated in the USA and Mexico.
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 (5) 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.
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