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

Highlights

• Whole-genome sequencing of SARS-CoV-2 when Delta and Omicron variants co-circulated

• 18 samples (<0.1%) were confirmed to be Delta-Omicron co-infections

• Recombination of Delta and Omicron detected in one of the co-infection samples

• Infections by clonal Delta-Omicron recombinants was rare, only 2 samples

Summary

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 and the 3′ end from Omicron, including the majority of the spike protein gene, though the breakpoints were different.

Conclusions

Delta-Omicron recombinant viruses were rare, and there is currently no evidence that Delta-Omicron recombinant viruses are more transmissible between hosts compared with the circulating Omicron lineages.

Funding

This research was supported by the NIH RADx initiative and by the Centers for Disease Control Contract 75D30121C12730 (Helix).