Recombinant Variants of SARS-CoV-2 Identified in the South of Western Siberia During the COVID-19 Pandemic

Recombination is one of the mechanisms driving SARS-CoV-2 evolution and can generate genomes with novel combinations of characteristics inherited from parental lineages. We analyzed a total of 1963 genomes available SARS-CoV-2 genome sequences collected in the south of Western Siberia between March 2020 and 5 May 2023. Initial screening with Nextclade identified five potentially recombinant genomes. The consensus assemblies were re-examined by the originating laboratories and the absence of co-infection was confirmed. Recombinant origin was assessed with RecombinHunt and independently evaluated with 3SEQ and RDP5. EPI_ISL_11742584 was excluded because of numerous undetermined nucleotides. For EPI_ISL_15919275 the laboratory of origin did not confirm the reproducibility of the build. EPI_ISL_20438394 contained BA.2.35-like and XBB.3.1-like components but the signal did not survive correction for multiple comparisons. Recombination was confirmed for two sequences. EPI_ISL_17317906 presumably originated from CR.1-like and XBB.1.15-like lineages and was assigned to the recombinant lineage XBV. EPI_ISL_16287253 carried a BA.2-derived segment on a BA.1-derived background. These findings indicate that automated classification should be followed by statistical validation, verification of genome assembly quality and the confirmed absence of co-infection. Incomplete and uneven genomic surveillance may still limit reconstruction of the exact origins of rare recombinant variants.