Abstract
Objectives: To 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.
Methods: Since 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.
Results: Between 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.
Conclusions: This 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.
Keywords: Delta and Omicron VOC; Recombination; SARS-CoV-2 co-infection; Single nucleotide polymorphism screening; Whole genome sequencing.
【저자키워드】 Recombination, whole genome sequencing., Single nucleotide polymorphism screening, SARS-CoV-2 co-infection, Delta and Omicron VOC, 【초록키워드】 COVID-19, SARS-CoV-2, Mutation, VoC, Sequencing, Genetic, SNPs, variant, SARS-CoV-2 variant, Infection, polymorphism, Delta, omicron, virus, Epidemic, Whole genome sequencing, Health, Surveillance, Single nucleotide polymorphism, L452R, K417N, SARS-CoV-2 genome, Co-infection, Pandemics, France, SNP, circulation, WGS, single nucleotide, Respiratory samples, patients, chimeric, profile, sequence, PCR assay, primer sets, pathogenic, whole genome, recombination event, nasopharyngeal sample, collected, Sample, generate, was performed, screened, analysis, submitted, epidemiologically, S-gene mutation, 【제목키워드】 Sequencing, SARS-CoV-2 variant, Delta, omicron, Co-infection, evidence of,