Analysis of the genetic diversity of SARS-CoV-2 genomes carrying the Omicron B.1.1.529 mutation

Abstract

In this work, we evaluated the levels of genetic diversity in 95 genomes of the carriers of the Omicron B.1.1.529 mutation in SARS-CoV-2 from South Africa, Asia, Massachusetts-USA, Rhode Island-USA, United Kingdom and Germany. All with 29,996pb extension and recovered from GENBANK and publicly available at the National Center for Biotechnology and Information (NCBI). All gaps and conserved sites were extracted for the construction of a phylogenetic tree and for specific methodologies of estimates of paired FST, Molecular Variance (AMOVA), Genetic Distance, Incompatibility, demographic expansion analyses, molecular diversity and of evolutionary divergence time analyses, always with 20,000 random permutations. The results revealed the presence of only 75 parsimony-informative sites, sites among the 29,996bp analyzed. The analyses based on FST values, confirmed the absence of distinct genetic structuring with fixation index of 98% and with a greater component of population variation (6%) for a "p" 0.05. Tau variations (related to the ancestry of the groups), did not reveal significant moments of divergence, supported by the incompatible analysis of the observed distribution (τ = 0%). It is safe to say that the large number of existing polymorphisms reflects major changes in the protein products of viral populations in all countries and especially In South Africa. This consideration provides the safety that, because there are large differences between the haplotypes studied, these differences are minimal within the populations analyzed geographically and, therefore, it does not seem safe to extrapolate the results of polymorphism and molecular diversity levels found in the Variant Omicron B.1.529 of SARS-CoV-2 for wild genomes or other mutants. This warns us that, due to their higher transmission speed and infection, possible problems of molecular adjustments in vaccines already in use may be necessary in the near future.

Detection and Characterisation of SARS-CoV-2 in Eastern Province of Zambia: A Retrospective Genomic Surveillance Study

“…This present study found that there was high genetic diversity in the S gene. High genetic diversity in the S gene has also been reported in other studies [ 53 , 54 , 55 ]. The areas of high diversity indicate highly mutated genes.…”