In this study, we report the first case of intra-host SARS-CoV-2 recombination during a coinfection by the variants of concern (VOC) AY.33 (Delta) and P.1 (Gamma) supported by sequencing reads harboring a mosaic of lineage-defining mutations. By using next-generation sequencing reads intersecting regions that simultaneously overlap lineage-defining mutations from Gamma and Delta, we were able to identify a total of six recombinant regions across the SARS-CoV-2 genome within a sample. Four of them mapped in the spike gene and two in the nucleocapsid gene. We detected mosaic reads harboring a combination of lineage-defining mutations from each VOC. To our knowledge, this is the first report of intra-host RNA-RNA recombination between two lineages of SARS-CoV-2, which can represent a threat to public health management during the COVID-19 pandemic due to the possibility of the emergence of viruses with recombinant phenotypes.
【저자키워드】 COVID-19, SARS-CoV-2, Coinfection, Recombination, iSNVs, 【초록키워드】 viruses, public health, Mutation, VoC, knowledge, COVID-19 pandemic, Sequencing, mutations, variants of concern, Delta, variants, Coinfection, Region, spike gene, SARS-CoV-2 genome, P.1, management, Next-generation sequencing, Lineage, Gamma, Nucleocapsid gene, Combination, Phenotypes, overlap, mosaic, SARS-CoV-2 recombination, identify, supported, mapped, emergence of virus, sequencing read, the SARS-CoV-2 genome, 【제목키워드】 Delta, emergence, Gamma, recombinant, report,