Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America

Bernardo Gutierrez; Hugo G Castelán Sánchez; 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

doi:10.1016/j.chom.2022.06.010

Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America

Cell Host Microbe. 2022 Aug 10;30(8):1112-1123.e3. doi: 10.1016/j.chom.2022.06.010. Epub 2022 Jun 20.

Authors

Affiliations

¹ Department of Zoology, University of Oxford, Oxford, UK; Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex), México; Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador. Electronic address: [email protected].
² Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex), México; Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México.
³ Department of Zoology, University of Oxford, Oxford, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
⁴ Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
⁵ Hertzl 52, Jerusalem, Israel.
⁶ 10 rue de Dunkerque, 75010, Paris, France.
⁷ Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK; Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
⁸ Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex), México; Departamento de Ingeniería Genética, Unidad Irapuato, CINVESTAV, Irapuato, Mexico.
⁹ Department of Zoology, University of Oxford, Oxford, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK; The Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London, UK.
¹⁰ Department of Zoology, University of Oxford, Oxford, UK; Department of Pathobiology, Royal Veterinary College, London, UK. Electronic address: [email protected].
¹¹ Department of Zoology, University of Oxford, Oxford, UK; Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex), México. Electronic address: [email protected].

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.

Keywords: SARS-CoV-2; molecular epidemiology; phylogenetics; recombination.

MeSH terms

COVID-19* / epidemiology
Genome, Viral
Humans
Phylogeny
SARS-CoV-2* / genetics
Spike Glycoprotein, Coronavirus / chemistry
Spike Glycoprotein, Coronavirus / genetics

Substances

Spike Glycoprotein, Coronavirus
spike protein, SARS-CoV-2

Abstract

MeSH terms

Substances

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