Co-infection with SARS-COV-2 Omicron and Delta Variants Revealed by Genomic Surveillance

Rockett, Rebecca; Draper, Jenny; Gall, Mailie; E, Sim; Arnott, Alicia; Agius, Jessica E; Johnson-Mackinnon, Jessica; Martínez, Elena; Drew, Alexander P.; Lee, Clement; Ngo, Christine Ngoc; Ramsperger, Marc; Ginn, Andrew N.; Wang, Qinning; Fennell, Michael; Ko, Danny; Huston, Linda; Kairaitis, Lukas; Holmes, Edward C.; O’Sullivan, Matthew; Chen, Sharon C‐A; Kok, Jen; Dwyer, Dominic E.; Sintchenko, Vitali

doi:10.1101/2022.02.13.22270755

Cited by 18 publications

(20 citation statements)

References 12 publications

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“…Analysis of follow-up samples showed that Delta or Omicron can outcompete the other, as previously reported although in immunocompromised patients [8]. Complementary analyses, such as neutralizing antibody levels against the two variants, could help to better understand if the ability of variants to evade immunity after vaccination could explain why one variant outcompetes the other after co-infection.…”

Section: Discussionsupporting

confidence: 66%

“…This work shows that co-infection with two SARS-CoV-2 VOC can occur, particularly during a major epidemic wave marked by a co-circulation of two highly transmissible variants in the same region as occurred in December 2021 in France [6]. Few cases of SARS-CoV-2 coinfections have been reported [7][8][9]. The detection of co-infections could be underestimated by the differences in VOC screening strategies between laboratories and countries.…”

Section: Discussionmentioning

confidence: 99%

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Evidence of co-infection during Delta and Omicron variants of concern co-circulation, weeks 49-2021 to 02-2022, France

Combes

Bisseux

Bal

et al. 2022

Preprint

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We report evidence of Delta/Omicron SARS-CoV-2 co-infections during the fifth wave of COVID-19 pandemics in France for 7 immunocompetent and epidemiologically unrelated patients. These co-infections were detected by PCR assays targeting SARS-CoV-2 S-gene mutations K417N and L452R and confirmed by whole genome sequencing which allowed the proportion estimation of each subpopulation. For 2 patients, the analyses of longitudinal samples collected 7 to 11 days apart showed that Delta or Omicron can outcompete the other variant during dual infection.

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Section: Discussionsupporting

confidence: 66%

Section: Discussionmentioning

confidence: 99%

Evidence of co-infection during Delta and Omicron variants of concern co-circulation, weeks 49-2021 to 02-2022, France

Combes

Bisseux

Bal

et al. 2022

Preprint

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“…Co-infections with two variants were reported including recently with SARS-CoV-2 Delta and Omicron variants. [10][11][12][13] Furthermore, genetic recombinations were reported or suspected, based on the concurrent detection in consensus genomes of signature mutations of different mutants or variants. 10,12,[14][15][16][17][18][19][20][21][22][23][24] A study detected up to 1,175 (0.2%) putative recombinant genomes among 537,360 genomes and estimated that up to 5% SARS-CoV-2 having circulated in the USA and UK could be recombinants.…”

Section: Text Introductionmentioning

confidence: 99%

“…Therefore, the frequency of creation of recombinants between two variants depends on the duration of their co-circulation, on the time until viral clearance, and on the number of people exposed to both viruses. Co-infections with two variants were reported including recently with SARS-CoV-2 Delta and Omicron variants (Jackson et al, 2021; Francisco et al, 2021; Taghizadeh et al, 2021; Rockett et al, 2022). Furthermore, genetic recombinations were reported or suspected, based on the concurrent detection in consensus genomes of signature mutations of different mutants or variants (Yi, 2020; Yeh and Contreras, 2020; VanInsberghe et al, 2020; Gallaher, 2020; Jackson et al, 2021; Haddad et al, 2021; Makarenkov et al, 2021; Varabyou et al, 2021; Leary et al, 2021; Taghizadeh et al, 2021; Lohrasbi-Nejad, 2022; Kreier, 2022; Ignatieva et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Culture and identification of a “Deltamicron” SARS-CoV-2 in a three cases cluster in southern France

Colson

Fournier

Delerce

et al. 2022

Preprint

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Multiple SARS-CoV-2 variants have successively, or concommitantly spread worldwide since summer 2020. A few co-infections with different variants were reported and genetic recombinations, common among coronaviruses, were reported or suspected based on co-detection of signature mutations of different variants in a given genome. Here were report three infections in southern France with a Delta 21J/AY.4-Omicron 21K/BA.1 “Deltamicron” recombinant. The hybrid genome harbors signature mutations of the two lineages, supported by a mean sequencing depth of 1,163-1,421 reads and mean nucleotide diversity of 0.1-0.6%. It is composed of the near full-length spike gene (from codons 156-179) of an Omicron 21K/BA.1 variant in a Delta 21J/AY.4 lineage backbone. It is similar to those reported for 15 other patients sampled since January 2022 in Europe. Importantly, we cultured an isolate of this recombinant and sequenced its genome. It was observed by scanning electron microscopy. As it is misidentified with current variant screening qPCR, we designed and implemented for routine diagnosis a specific duplex qPCR. Finally, structural analysis of the recombinant spike suggested its hybrid content could optimize viral binding to the host cell membrane. These findings prompt further studies of the virological, epidemiological, and clinical features of this recombinant.

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“…Regarding SARS-CoV-2, coinfection in the same patient with distinct variants has been reported [8][9][10][11][12][13][14]. In addition, several studies have described or suspected genetic recombinations for this virus [10,[13][14][15][16][17][18][19][20][21][22][23][24][25].…”

Section: Introductionmentioning

confidence: 99%

Sequential appearance and isolation of a SARS-CoV-2 recombinant between two major SARS-CoV-2 variants in a chronically infected immunocompromised patient

Burel

Colson

Lagier

et al. 2022

Preprint

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Genetic recombination is a major evolutionary mechanism among RNA viruses, and it is common in coronaviruses, including those infecting humans. A few SARS-CoV-2 recombinants have been reported to date whose genome harbored combinations of mutations from different mutants or variants, but a single patient sample was analyzed, and the virus was not isolated. Here, we report the gradual creation of a hybrid genome of B.1.160 and Alpha variants in a lymphoma patient chronically infected for 14 months, and we isolated the recombinant virus. The hybrid genome was obtained by next-generation sequencing, and recombination sites were confirmed by PCR. This consisted of a parental B.1.160 backbone interspersed with two fragments, including the spike gene, from an Alpha variant. Analysis of seven sequential samples from the patient decoded the recombination steps, including the initial infection with a B.1.160 variant, then a concurrent infection with this variant and an Alpha variant, the generation of hybrid genomes, and eventually the emergence of a predominant recombinant virus isolated at the end of the patient follow-up. This case exemplifies the recombination process of SARS-CoV-2 in real life, and it calls for intensifying genomic surveillance in patients coinfected with different SARS-CoV-2 variants, and more generally with several RNA viruses, as this may lead to the creation of new viruses.

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Co-infection with SARS-COV-2 Omicron and Delta Variants Revealed by Genomic Surveillance

Cited by 18 publications

References 12 publications

Evidence of co-infection during Delta and Omicron variants of concern co-circulation, weeks 49-2021 to 02-2022, France

Evidence of co-infection during Delta and Omicron variants of concern co-circulation, weeks 49-2021 to 02-2022, France

Culture and identification of a “Deltamicron” SARS-CoV-2 in a three cases cluster in southern France

Sequential appearance and isolation of a SARS-CoV-2 recombinant between two major SARS-CoV-2 variants in a chronically infected immunocompromised patient

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