Evidence for SARS-CoV-2 Delta and Omicron co-infections 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. Our sequencing protocol uses hybridization capture and is thus less subject to artifacts observed in amplicon-based approaches that may lead to spurious signals for recombinants. We identified 20 co-infections, one of which displayed evidence of a low 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 both cases, the 5'-end of the viral genome was from the Delta genome, and the 3'-end from Omicron, though the breakpoints were different. Delta-Omicron recombinant viruses were rare, and there is currently no evidence that the two Delta-Omicron recombinant viruses identified are more transmissible between hosts compared to the circulating Omicron lineages.

Detection and prevalence of SARS-CoV-2 co-infections during the Omicron variant circulation, France, December 2021 - February 2022

“…The evaluation of the primer sets was performed using a previously published method based on a curated list of mutations specific to Delta and to Omicron derived from co-variants [5][6][7] (Table S2 and Fig 1). More than 90% of the Delta-specific mutations were found in all mixes with the 4 primer sets.…”

“…The resulting prevalence of about 0.1% for Delta/Omicron is highly consistent with the prevalence found herein. However, no BA.1/BA.2 co-infection was reported by the authors as they specifically looked for Delta/Omicron co-infections using a curated list of mutations 7 . In contrast, the unbiased coinfection detection script presented herein and validated on mixed Delta:Omicron isolates was defined to detect likely co-infections whatever lineages are present in the sample and can be applied for all SARS-CoV-2 co-infections.…”

“…In addition, ICU admission and vaccination status information was lacking for some Flash cases, limiting the clinical characterization of co-infected patients. Finally, additional sequencing methods were not tested, such as metagenomics or hybrid capture which are less prone to amplification-bias toward specific lineages 7 . However, these techniques have lower sensitivity and lower throughput and were therefore not suitable as first-line sequencing methods in our laboratory 20 .…”

“…Thus, the unprecedented sustained co-circulation of genetically divergent lineages observed from November 2021 to February 2022 may have been suitable for co-infections with a risk of subsequent recombination events. Few cases of Delta and Omicron variant co-infections have been reported recently but a systematic assessment of the prevalence of SARS-CoV-2 co-infections, including BA.1/BA.2 co-infections, has not been explored on a large data set [5][6][7] . As Omicron and Delta have been associated with distinct COVID-19 severity, the clinical spectrum of these co-infections also needs to be determined 8,9 .…”

“…Detection of SARS-CoV-2 co-infection using whole-genome sequencing (WGS) is not trivial and can be hampered by several problems: i) uneven performances of primer sets used to amplify SARS-CoV-2 genome with possible amplification bias of some genomic regions of specific variants 10,11 ; ii) possible sample contamination during the sequencing process which requires independent validation on duplicate extracts 12,13 ; and iii) lack of unbiased and validated bioinformatics methods able to systematically detect co-infections. Previously published reports on SARS-CoV-2 Delta/Omicron co-infections were based on manually curated lists of divergent mutations and visual examination of their relative frequencies along the genome [5][6][7] . De-novo assembly methods have also been described to assemble different viral genomes present in one sample 14 but are computationally intensive.…”