Frequent homologous recombination limited to the Omicron BA.1 lineage among SARS-CoV-2 variants
DOI:
https://doi.org/10.51094/jxiv.1021Keywords:
COVID-19, Omicron variant, reverse mutation, homologous recombination, sequence exchangeAbstract
Since the emergence of SARS-CoV-2, variants carrying new mutations have played significant roles in global transmission. Among them, the Omicron variant, which surfaced in November 2021, stands out due to its unprecedented number of mutations, particularly in the spike protein. This paper investigates the anomaly of the BA.1 lineage of the Omicron variant, focusing on the presence of reverse mutations and potential homologous recombination. Using sequence data from GenBank, the study analyzes the mutation patterns of various Omicron subvariants and compares them with each other and with other major variants such as Alpha and Delta. The results reveal a notable peak of triple reverse mutations and relatively high frequencies in the emergence of quadruple or more reverse mutations in BA.1 lineage as traces of homologous recombination. The study also addresses the possibility of contamination by Delta variant sequences, ruling out this explanation based on the accompanying mutations. Given the unique recombination patterns observed only in the BA.1 lineage and the absence of such events in other variants, the study raises concerns about the potential lab origin of the Omicron BA.1 lineage, underscoring the need for rigorous oversight in facilities handling SARS-CoV-2.
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Submitted: 2025-01-03 04:33:44 UTC
Published: 2025-01-09 01:04:45 UTC
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Hideki Kakeya
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