ArticleNature communications2022
Detection and prevalence of SARS-CoV-2 co-infections during the Omicron variant circulation in France.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers, 2 of them syntheses that pooled it.
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Who cites it
39 citing papers in PubMed, 2 syntheses or guidelines pooled it, 56 citations in OpenAlex.
- The relative prevalence of the Omicron variant within SARS-CoV-2 infected cohorts in different countries: A systematic review.Human vaccines & immunotherapeutics · 2023Pooled it
- Severity and outcomes of Omicron variant of SARS-CoV-2 compared to Delta variant and severity of Omicron sublineages: a systematic review and metanalysis.BMJ global health · 2023Pooled it
- Longitudinal characterization of mixed-genotype SARS-CoV-2 infections in a military cohort reveals compartmentalized viral populations.Microbiology spectrum · 2026Article
- Risk factors for acquisition of SARS-CoV-2 Omicron variant among a prospective cohort of French Healthcare Workers: impact of hybrid immunity.Scientific reports · 2026Article
- Integration of bioinformatic tools for the detection of SARS-CoV-2 co-infection cases.Microbial genomics · 2026Article
- Clinical characteristics of acute lower respiratory tract infection caused by Omicron, respiratory syncytial virus, and influenza virus a in children in Chengdu: a retrospective study.Italian journal of pediatrics · 2025Article
- Case-based evidence links increased SARS-CoV-2 diversity to impaired IFN-I response in severe COVID-19.Journal of human immunity · 2025Article
- Performance of Long-Read Single-Molecule Real-Time Sequencing for SARS-CoV-2 Genotyping in Clinical Samples.Journal of medical virology · 2025Article
- Genomics-based approach for detection and characterization of SARS-CoV-2 co-infections and diverse viral populations.Microbiology spectrum · 2025Article
- Article
- Identification of Various Recombinants in a Patient Coinfected With the Different SARS-CoV-2 Variants.Influenza and other respiratory viruses · 2024Article
- Update on Omicron variant and its threat to vulnerable populations.Public health in practice (Oxford, England) · 2024Review
- Review
- OASIS: An interpretable, finite-sample valid alternative to Pearson'sProceedings of the National Academy of Sciences of the United States of America · 2024Article
- COVID-19: On the threshold of the fifth year. The situation in Spain.Revista espanola de quimioterapia : publicacion oficial de la Sociedad Espanola de Quimioterapia · 2024Review
- Systematic detection of co-infection and intra-host recombination in more than 2 million global SARS-CoV-2 samples.Nature communications · 2024Article
- Mining genomic repositories to further our knowledge of the extent of SARS-CoV-2 co-infections.Microbial genomics · 2024Article
- Article
- Generation of quality-controlled SARS-CoV-2 variant stocks.Nature protocols · 2023Review
- OASIS: An interpretable, finite-sample valid alternative to Pearson'sbioRxiv : the preprint server for biology · 2023Article
Corrections and comments
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Authors and funding
13 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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