Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination.

ABSTRACT:

Background

Between November 2021 and February 2022, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta and Omicron variants co-circulated in the United States, allowing for co-infections and possible recombination events.

Methods

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.

Findings

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 a

SUBMITTER: Bolze A 

PROVIDER: S-EPMC9581791 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature