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

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 bioinformatic approach for the detection of co-infections. Implementing a specific SARS-CoV-2 lexicon in 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 (B.1.1.529) co-infections and Omicron lineages B.A.1 and B.A.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 B.A1/B.A2 co-infections were reported among ICU admitted 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.

Antonin Bal, Bruno Simon, Gregory Destras, Richard Chalviragñac, Quentin Semanas, Antoine Obtelet, Grégory Quéromès, Remi Fanget, Hadrien Regue, Florence Morfin, Martine Valette, Bruno Lina, Laurence Josset