Phylogenetic Analysis of Omicron Variants and their Evolutionary Relationship with SARS-CoV-2 Spike Glycoprotein

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is one of the most serious pandemics that has invaded the world in recent years. The virus responsible for this pandemic was isolated for the first time in China in 2019, and then it spread throughout the world, where it caused up today about over 7 million deaths and about 800 million confirmed cases. Therefore, several efforts have been made to study this virus. In about one year, has been sequenced the whole genome of SARS-CoV-2 and has been elucidated its mechanism of infection and duplication in host cells and its physiological effect on humans. Furthermore, the S spike glycoprotein has been identified as the main protein involved in the viral infection mechanism and it has been used as an antigen to develop several vaccines, including new generation mRNA-based ones. The data from World Health Organization (WHO) indicated that approximately 14 billion doses of vaccines have been dispensed far.

Since the beginning of the pandemic, SARS-CoV-2 has evolved by accumulating mutations in the genome, resulting in new virus versions showing different characteristics, and which have replaced the pre-existing variants. To date, hundreds of variants of the virus have been isolated. As a general trend, the SARS-CoV-2 variants identified so far have increased their spread and reduced their danger and mortality. More than 15 million viral sequences have been carried out to monitor the virus spreading and its variability.

Among all new variants, a new group of variants was isolated in early 2022.They were named omicron, and in a few months replaced all the variants present up to then, because they were characterized by high transmissibility. We study the omicron variants (BA.1, BA.2, BA.2.12.1, BA.4 and BA.5) and their derivative variants (BQ.1, BQ.1.18 (CH.1.1), XBF, XBB, XBB.1.5, XBB.1.9 and XBB.1.16), from a phylogenetic point of view. We generate a multiple alignment of the spike sequences and analyzed the mutations exhibited by these variants. Based on these results, we proposed a new phylogenetic tree of omicron variants, which includes several possible unidentified intermediate variants, proving insight into the origin of omicron variants.

SARS-CoV-2 has been characterized as a virus that has accumulated a high number of mutations in the genome that have drastically modified the infection mechanism by increasing the spread of the virus and reducing its mortality, transforming the pandemic form of SARS-CoV-2 into an endemic infection.