Molecular epidemiology of Omicron's CH.1.1 lineage: evidence of recombination event

Abstract

The genome of the Omicron (B.1.1.529) variant is highly modified and contagious because of natural selection, which has resulted in rapid genomic evolution and the emergence of several lineages. The spike (S) protein's high number of amino acid variations in the receptor binding domain (RBD) have increased its binding affinity to the host angiotensin-converting enzyme 2 (ACE2) receptor and thus the transmissibility. However, recombination is a critical event in the evolution of RNA viruses, especially the positive single-stranded RNA viruses such as the viruses of the Coronaviridae family. The recombination event is caused by co-infection, which occurs when the genomes of lineages combine within a host cell, giving rise to a lineage with new genomic characteristics. This molecular epidemiological study demonstrates that CH.1.1, a designated lineage primarily found in Europe, is a possible recombinant derived from the likely parental BM.4 and BA.2.75.2 Omicron lineages. Regarding the genomic analysis for the possible recombination, the genomes of Wuhan/WIV04, CH.1.1, BM.4, and BA.2.75.2 were uploaded as FASTA file from the GISAID platform and aligned by UGEN software. Dissimilarity percentages were counted based on the Distance Matrix Hamming dissimilarity count. Through the genomic analysis, we identified significant amino acid variations from the hypothetical parental lineages and CH.1.1. However, the hypothesis of the possibility that CH.1.1 arises from these parental lineages is supported by their circulation simultaneously in Austria in July 2022. The dissimilarity percentage between CH.1.1 and the parental lineages, in addition to the shared inherited amino acid variations in CH.1.1.