A 21L/BA.2-21K/BA.1 "MixOmicron" SARS-CoV-2 hybrid undetected by qPCR that screen for variant in routine diagnosis.

ABSTRACT: Among the multiple SARS-CoV-2 variants identified since summer 2020, several have co-circulated, creating opportunities for coinfections and potentially genetic recombinations that are common in coronaviruses. Viral recombinants are indeed beginning to be reported more frequently. Here, we describe a new SARS-CoV-2 recombinant genome that is mostly that of a Omicron 21L/BA.2 variant but with a 3' tip originating from a Omicron 21K/BA.1 variant. Two such genomes were obtained in our institute from adults sampled in February 2022 in university hospitals of Marseille, southern France, by next-generation sequencing carried out with the Illumina or Nanopore technologies. The recombination site was located between nucleotides 26,858-27,382. In the two genomic assemblies, mean sequencing depth at

SUBMITTER: Colson P 

PROVIDER: S-EPMC9444252 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature