Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination
Author:
Bolze AlexandreORCID, Basler Tracy, White Simon, Rossi Andrew Dei, Wyman DanaORCID, Roychoudhury PavitraORCID, Greninger Alexander L.ORCID, Hayashibara Kathleen, Beatty Mark, Shah Seema, Stous Sarah, Kil Eric, Dai Hang, Cassens Tyler, Tsan Kevin, Nguyen Jason, Ramirez Jimmy, Carter Scotty, Cirulli Elizabeth T.ORCID, Barrett Kelly SchiaborORCID, Washington Nicole L.ORCID, Belda-Ferre Pedro, Jacobs Sharoni, Sandoval Efren, Becker David, Lu James T.ORCID, Isaksson Magnus, Lee WilliamORCID, Luo ShishiORCID
Abstract
AbstractBetween November 2021 and February 2022, SARS-CoV-2 Delta and Omicron variants co-circulated in the United States, allowing for co-infections and possible recombination events. We sequenced 29,719 positive samples during this period and analyzed the presence and fraction of reads supporting mutations specific to either the Delta or Omicron variant. We identified 18 co-infections, one of which displayed evidence of a low Delta-Omicron recombinant viral population. We also identified two independent cases of infection by a Delta-Omicron recombinant virus, where 100% of the viral RNA came from one clonal recombinant. In the three cases, the 5’-end of the viral genome was from the Delta genome, and the 3’-end from Omicron including the majority of the spike protein gene, though the breakpoints were different. Delta-Omicron recombinant viruses were rare, and there is currently no evidence that Delta-Omicron recombinant viruses are more transmissible between hosts compared to the circulating Omicron lineages.
Publisher
Cold Spring Harbor Laboratory
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