Emergence and Widespread Circulation of a Recombinant SARS-CoV-2 Lineage in North America

Overview

Journal Cell Host Microbe

Publisher Cell Press

Specialties Infectious Diseases
Microbiology

Date 2022 Jul 19

PMID 35853454

Authors

Bernardo Gutierrez

Hugo G Castelan Sanchez

Darlan da Silva Candido

Ben Jackson

Shay Fleishon

Renaud Houzet

Christopher Ruis

Luis Delaye

Nuno R Faria

Andrew Rambaut

Oliver G Pybus

Marina Escalera-Zamudio

Affiliations

Soon will be listed here.

Abstract

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.

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