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

Research output: Contribution to journalArticlepeer-review


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.
Original languageEnglish
Pages (from-to)1-12
Number of pages12
JournalCell Host & Microbe
Issue number8
Early online date19 Jun 2022
Publication statusPublished - 10 Aug 2022


  • SARS-CoV-2
  • recombination
  • phylogenetics
  • molecular epidemiology


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