Detection and prevalence of SARS-CoV-2 co-infections during the Omicron variant circulation, France, December 2021 - February 2022

Abstract

In Dec 2021-Feb 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 we developed an unbiased bioinformatics method which can detect all co-infections irrespective of the SARS-CoV-2 lineages involved. Applied on 21,387 samples collected between weeks 49-2021 and 08-2022 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. 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.

Sotrovimab drives SARS-CoV-2 Omicron variant evolution in immunocompromised patients

“…As sotrovimab is one of the few monoclonal antibodies that retains efficacy against the widely circulating BA.1 sublineage (Omicron variant), monitoring the prevalence of these mutations is crucial 3 . As part of routine genomic surveillance at the National Reference Center from December 2021 to March 2022 4 , we detected S:340 and/or S:337 mutations in 24 out of 18,882 (0 •13%) and 1 out of 4,025 (0 •02%) Omicron BA.1 and BA.2 lineages, respectively. These 25 samples corresponded to 18 patients viruses carrying either S:P337 or S:E340 mutations (Table S1).…”

Sotrovimab drives SARS-CoV-2 omicron variant evolution in immunocompromised patients

“… 1 , 2 Given that sotrovimab is one of the few monoclonal antibodies that retains efficacy against the widely circulating omicron BA.1 sublineage, monitoring the prevalence of these mutations is crucial. 3 As part of routine genomic surveillance at the French National Reference Center for respiratory Viruses at the Hospices Civils de Lyon (Lyon, France) from December, 2021, to March, 2022, 4 we detected mutations in the spike protein at positions 340 and 337 in 24 (0·13%) of 18 882 omicron BA.1 lineages and in one (0·02%) of 4025 omicron BA.2 lineages. These 25 samples corresponded to 18 patients infected with SARS-CoV-2 variants carrying either P337 or E340 mutations (appendix p 5).…”

SPLASH: a statistical, reference-free genomic algorithm unifies biological discovery

“…Similarly, scripts to perform supplemental analysis can be found on the pipeline repository. (17). C. Protein profile analysis of NOMAD significant anchors from California data (SRR15881549), before viral strain divergence in the spike had been reported ( 22) serving as a negative control.…”

“…B. Protein profile analysis of NOMAD significant anchors from France data, Oropharyngeal swabs from patients with SARS-CoV-2 from 2021-12-6 to 2022-2-27 in France (SRP365166), a period of known Omicron-Delta coinfection ( 17 ).…”