ArticleClinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases2022
Evidence of co-infections during Delta and Omicron SARS-CoV-2 variants co-circulation through prospective screening and sequencing.
Article in Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 1 of them a synthesis that pooled it.
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Who cites it
32 citing papers in PubMed, 1 synthesis or guideline pooled it, 56 citations in OpenAlex.
- An updated meta-analysis of Chinese herbal medicine for the prevention of COVID-19 based on Western-Eastern medicine.Frontiers in pharmacology · 2023Pooled it
- Virus variant quantification with Orthanq.BMC bioinformatics · 2026Article
- Integration of bioinformatic tools for the detection of SARS-CoV-2 co-infection cases.Microbial genomics · 2026Article
- 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
- Molecular characterization, phylogenetic and variation analyses of SARS-CoV-2 strains in India.Virusdisease · 2024Article
- A program for real-time surveillance of SARS-CoV-2 genetics.Scientific reports · 2024Article
- The evaluation of risk factors for prolonged viral shedding during anti-SARS-CoV-2 monoclonal antibodies and long-term administration of antivirals in COVID-19 patients with B-cell lymphoma treated by anti-CD20 antibody.BMC infectious diseases · 2024Article
- Identification of Various Recombinants in a Patient Coinfected With the Different SARS-CoV-2 Variants.Influenza and other respiratory viruses · 2024Article
- Review
- Evaluation of the PrimeFlow RNA assay as a method of detection of SARS-CoV-2 single and dual Infections.Cytotechnology · 2024Article
- Exploration of low-frequency allelic variants of SARS-CoV-2 genomes reveals coinfections in Mexico occurred during periods of VOCs turnover.Microbial genomics · 2024Article
- Omicron and Delta variant prevalence detection and identification during the fourth COVID-19 wave in Mexico using wastewater-based epidemiology.IJID regions · 2024Article
- 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
- Mastering DNA chromatogram analysis in Sanger sequencing for reliable clinical analysis.Journal, genetic engineering & biotechnology · 2023Review
- Resurgence of SARS-CoV-2 Delta after Omicron variant superinfection in an immunocompromised pediatric patient.Virology journal · 2023Article
- "Nano COVID-19": Nanopore sequencing of spike gene to identify SARS-CoV-2 variants of concern.Experimental biology and medicine (Maywood, N.J.) · 2023Article
- SARS-CoV-2 Co-Infections and Recombinations Identified by Long-Read Single-Molecule Real-Time Sequencing.Microbiology spectrum · 2023Article
- Systematic genomic analysis of SARS-CoV-2 co-infections throughout the pandemic and segregation of the strains involved.Genome medicine · 2023Article
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Authors and funding
16 authors at 9 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
objectivesTo describe Delta/Omicron SARS-CoV-2 variants co-infection detection and confirmation during the fifth wave of COVID-19 pandemics in France in 7 immunocompetent and epidemiologically unrelated patients.
methodsSince December 2021, the surveillance of Delta/Omicron SARS-CoV-2 variants of concern (VOC) circulation was performed through prospective screening of positive-samples using single nucleotide polymorphism (SNP) PCR assays targeting SARS-CoV-2 S-gene mutations K417N (Omicron specific) and L452R (Delta specific). Samples showing unexpected mutational profiles were further submitted to whole genome sequencing (WGS) using three different primer sets.
resultsBetween weeks 49-2021 and 02-2022, SARS-CoV-2 genome was detected in 3831 respiratory samples, of which 3237 (84.5%) were screened for VOC specific SNPs. Unexpected mutation profiles suggesting a dual Delta/Omicron population were observed in 7 nasopharyngeal samples (0.2%). These co-infections were confirmed by WGS. For 2 patients, the sequence analyses of longitudinal samples collected 7 to 11 days apart showed that Delta or Omicron can outcompete the other variant during dual infection. Additionally, for one of these samples, a recombination event between Delta and Omicron was detected.
conclusionsThis work demonstrates that SARS-CoV-2 Delta/Omicron co-infections are not rare in high virus co-circulation periods. Moreover, co-infections can further lead to genetic recombination which may generate new chimeric variants with unpredictable epidemic or pathogenic properties that could represent a serious health threat.
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