Identification of a Novel SARS-CoV-2 Delta-Omicron Recombinant Virus in the United States

Lacek, Kristine; Rambo-Martin, Benjamin L.; Batra, Dhwani; Zheng, Xiao-yu; Keller, Matthew W.; Wilson, Malania M.; Sheth, Mili; Davis, Morgan L; Burroughs, Mark; Gerhart, Jonathan; Hassell, Norman; Lee, Justin; Shepard, Samuel S.; Cook, Peter W.; Wentworth, David E; Barnes, John; Kondor, Rebecca; Paden, Clinton R.; Peacock, Thomas P.; Sakaguchi, Hitoshi

doi:10.1101/2022.03.19.484981

Cited by 27 publications

(35 citation statements)

References 11 publications

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“…Overall, infections from a recombinant Delta-Omicron virus remain rare: 2 out of 10,742 sequences between January 10 and February 13, 2022. Eight other sequences similar to RECOMB1 have been reported by the CDC from samples collected in the US from December 31, 2021 to February 12, 2022 (Lacek et al, 2022). We did not identify any recombinant with Omicron on the 5’-end and Delta on the 3’-end or any recombinant with two breakpoints in our dataset.…”

Section: Resultsmentioning

confidence: 74%

“…The sequences of the two recombinant viruses differ slightly. (Lacek et al, 2022). We did not identify any recombinant with Omicron on the 5'-end and Delta on the 3'-end or any recombinant with two breakpoints in our dataset.…”

Section: Infection With Clonal Delta-omicron Recombinantsmentioning

confidence: 65%

“…Our analysis is also limited by the fact that we do not have information whether the exposure and seed infection by the two distinct variants happened at the same time, or if they followed each other. *Recombination in this sample was also confirmed by an orthogonal genotyping array, and by long-read sequencing by an independent lab at the CDC (Lacek et al, 2022) .…”

Section: Co-infection With Delta and Omicron Variantsmentioning

confidence: 65%

“…These confirm that the 5’-end of the genome was from Delta and the 3’-end from Omicron. Lastly, RECOMB1 sample was also sent to the US Centers for Disease Control and Prevention (CDC) laboratory and results were confirmed via another sequencing technology (Lacek et al, 2022). Together, these experiments provide evidence that the two independent infections were caused by viruses resulting from the recombination of Delta and Omicron.…”

Section: Resultsmentioning

confidence: 99%

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

Bolze

White

Basler

et al. 2022

Preprint

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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.

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Section: Resultsmentioning

confidence: 74%

Section: Infection With Clonal Delta-omicron Recombinantsmentioning

confidence: 65%

Section: Co-infection With Delta and Omicron Variantsmentioning

confidence: 65%

Section: Resultsmentioning

confidence: 99%

See 2 more Smart Citations

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

Bolze

White

Basler

et al. 2022

Preprint

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“…Such genetic recombinations are extremely frequent for viruses of family Coronaviridae , and they have already been identified for endemic human coronaviruses (Lai, 1996; Zhang et al, 2015; So et al, 2019; Gribble et al, 2020). Regarding SARS-CoV-2, the occurrence of recombinations has been reported or suspected (Yi, 2019; Yeh and Contreras, 2020; Haddad et al, 2021; Ignatieva et al, 2021; Jackson et al, 2021; Taghizadeh et al, 2021; Varabyou et al, 2021; Kreier, 2022; Wertheim et al, 2022; He et al, 2022; Sekizuka et al, 2022; Colson et al, 2022b; Lacek et al, 2022; Lohrasbi-Nejad, 2022; Bolze et al, 2022; Ou et al, 2022; Belen Pisano et al, 2022; Burel et al, 2022). Very recently, we described the identification and culture of two SARS-CoV-2 recombinants, one between the B.1.160 and Alpha/20I variants in a patient chronically-infected with SARS-CoV-2 (Burel et al, 2022), and another between the Delta/21J AY.4 and Omicron 21K/BA.1 variants in patients infected approximately 10 weeks after the start of the period of co-detection of these two variants in our geographical area (Colson et al, 2022b).…”

Section: Introductionmentioning

confidence: 99%

A 21L/BA.2-21K/BA.1 “MixOmicron” SARS-CoV-2 hybrid undetected by qPCR that screen for variant in routine diagnosis

Colson

Delerce

Marion-Paris

et al. 2022

Preprint

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Among the multiple SARS-CoV-2 variants identified since summer 2020, several have co-circulated, creating opportunities for coinfections and potentially genetic recombinations that are common in coronaviruses. Viral recombinants are indeed beginning to be reported more frequently. Here, we describe a new SARS-CoV-2 recombinant genome that is mostly that of a Omicron 21L/BA.2 variant but with a 3-prime tip originating from a Omicron 21K/BA.1 variant. Two such genomes were obtained in our institute from adults sampled in February 2022 in university hospitals of Marseille, southern France, by next-generation sequencing carried out with the Illumina or Nanopore technologies. The recombination site was located between nucleotides 26,858-27,382. In the two genomic assemblies, mean sequencing depth at mutation-harboring positions was 271 and 1,362 reads and mean prevalence of the majoritary nucleotide was 99.3+/-2.2% and 98.8+/-1.6%, respectively. Phylogeny generated trees with slightly different topologies according to whether genomes were depleted or not of the 3-prime tip. This 3-prime terminal end brought in the Omicron 21L/BA.2 genome a short transposable element of 41 nucleotides named S2m that is present in most SARS-CoV-2 except a few variants among which the Omicron 21L/BA.2 variant and may be involved in virulence. Importantly, this recombinant is not detected by currently used qPCR that screen for variants in routine diagnosis. The present observation emphasizes the need to survey closely the genetic pathways of SARS-CoV-2 variability by whole genome sequencing, and it could contribute to gain a better understanding of factors that lead to observed differences between epidemic potentials of the different variants.

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Potential intervariant and intravariant recombination of Delta and Omicron variants

Wang

Zhou

Cheng

et al. 2022

Journal of Medical Virology

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Among numerous severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) variants of concerns, Omicron is more infectious and immune‐escaping, while Delta is more pathogenic. Here, we provide evidence for both intervariant and intravariant recombination of the rapidly evolving new SARS‐CoV‐2 genomes, including XD/XE/XF and BA.3, raising concerns of potential more infectious, immune‐escaping, and disease‐causing Omicron and Delta–Omicron variants.

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Identification of a Novel SARS-CoV-2 Delta-Omicron Recombinant Virus in the United States

Cited by 27 publications

References 11 publications

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

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

A 21L/BA.2-21K/BA.1 “MixOmicron” SARS-CoV-2 hybrid undetected by qPCR that screen for variant in routine diagnosis

Potential intervariant and intravariant recombination of Delta and Omicron variants

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