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

• DOI: 10.1038/s41467-022-33910-9
• Publication Date: 2022-10-23T08:02:48Z
• Authors: Antonin Bal; Bruno Simon; Gregory Destras; Richard Chalvignac; Quentin Semanas; Antoine Oblette; Grégory Quéromès; Remi Fanget; Hadrien Regue; Florence Morfin; Martine Valette; Bruno Lina; Laurence Josset
• Keywords: 0301 basic medicine; 570; SARS-CoV-2; Coinfection; Science; Q; COVID-19; Article; 3. Good health; 03 medical and health sciences; NGS; [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology; Prevalence; Humans

AbstractFrom 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.