Evidence for SARS-CoV-2 Delta and Omicron Coinfections and Recombination

Abstract

Between 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.

Funding Information: NIH RADx initiative funded a portion of this work. This work has been supported by the Centers for Disease Control and funded in part by CDC Contract 75D30121C12730 (Helix).

Conflict of Interests: A.B., T.B., S.W., A.D.R., D.W., E.K., H.D., T.C., K.T., J.N., J.R., S.C., E.T.C., K.S.B., N.L.W., S.J., E.S., D.B., J.T.L., M.I., W.L., and S.L. are all employees of Helix. K.H. is an employee of Thermo Fisher Scientific.

Ethical Approval: The Helix data analyzed and presented here were obtained through IRB protocol WIRB#20203438, which grants a waiver of consent for a limited dataset for the purposes of public health under section 164.512(b) of the Privacy Rule (45 CFR § 164.512(b)). All samples were de-identified before receipt by the study investigators.

Keywords: SARS-CoV-2, Delta, Omicron, co-infection, recombination, breakpoint, virus