Detection and prevalence of SARS-CoV-2 co-infections during the Omicron variant circulation in France

Antonin Bal, Bruno Simon, Gregory Destras, Richard Chalvignac, Quentin Semanas, Antoine Oblette, Grégory Quéromès, Remi Fanget, Hadrien Regue, Florence Morfin, Martine Valette, Bruno Lina and Laurence Josset ()
Additional contact information
Antonin Bal: Hospices Civils de Lyon
Bruno Simon: Hospices Civils de Lyon
Gregory Destras: Hospices Civils de Lyon
Richard Chalvignac: Hospices Civils de Lyon
Quentin Semanas: Hospices Civils de Lyon
Antoine Oblette: Hospices Civils de Lyon
Grégory Quéromès: Hospices Civils de Lyon
Remi Fanget: Hospices Civils de Lyon
Hadrien Regue: Hospices Civils de Lyon
Florence Morfin: Hospices Civils de Lyon
Martine Valette: Hospices Civils de Lyon
Bruno Lina: Hospices Civils de Lyon
Laurence Josset: Hospices Civils de Lyon

Nature Communications, 2022, vol. 13, issue 1, 1-9

Abstract: Abstract From December 2021-February 2022, an intense and unprecedented co-circulation of SARS-CoV-2 variants with high genetic diversity raised the question of possible co-infections between variants and how to detect them. Using 11 mixes of Delta:Omicron isolates at different ratios, we evaluated the performance of 4 different sets of primers used for whole-genome sequencing and developed an unbiased bioinformatics method for the detection of co-infections involving genetically distinct SARS-CoV-2 lineages. Applied on 21,387 samples collected between December 6, 2021 to February 27, 2022 from random genomic surveillance in France, we detected 53 co-infections between different lineages. The prevalence of Delta and Omicron (BA.1) co-infections and Omicron lineages BA.1 and BA.2 co-infections were estimated at 0.18% and 0.26%, respectively. Among 6,242 hospitalized patients, the intensive care unit (ICU) admission rates were 1.64%, 4.81% and 15.38% in Omicron, Delta and Delta/Omicron patients, respectively. No BA.1/BA.2 co-infections were reported among ICU admitted patients. Among the 53 co-infected patients, a total of 21 patients (39.6%) were not vaccinated. Although SARS-CoV-2 co-infections were rare in this study, their proper detection is crucial to evaluate their clinical impact and the risk of the emergence of potential recombinants.

Date: 2022
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DOI: 10.1038/s41467-022-33910-9

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