Phylogenetic Study of Surface Glycoprotein (S1 Spike Protein) Sequence of SARS-CoV-2 Virus

In the recent times, the resultant pandemic of severe acute respiratory syndrome caused due to the infection of coronavirus 2 (SARS-CoV-2) accounted for a major global health emergency termed as COVID-19 disease-WHO. Different countries globally witnessed the rapid spread of COVID-19 disease to date, primarily due to the continuous emergence of mutant variants of the SARS-CoV-2 virus. In order to control the COVID-19 disease, it is important to understand the origin and the rate of emergence of mutant variants. With this aim the present study intends to analyze the phylogeny of the SARS-CoV-2 virus, to determine its association with other viruses, and to aid in the search for potential treatment regimens against SARS-CoV-2 virus infection. Surface glycoprotein (S1) sequences of various strains of the SARS-CoV-2 virus from different regions of the globe have been considered for building the genetic tree. A character-based phylogenetic tree applying Jones-Taylor-Thornton (JTT) based Maximum Likelihood (ML) Method was developed to compare the standard SARS-CoV-2 strain (WEU54352) with other 99 selected variants of SARS-CoV-2 virus sequences representing the different countries of the globe. Phylogenetic results were validated by applying 500 bootstrapping. The study reported that the developed phylogenetic tree displayed two major clades with 58 and 42 identical mutant sequences respectively. Among the 99 sequences of S1 Spike Protein, 6 sequences displayed higher similarity with the standard sequence displaying minimum divergence. Among the 6 sequences, the sequence UZD77448 and UZD77771 obtained from USA (California) and USA(New Jersey) on 22/10/2022 respectively displayed the very closest similarity with that of the standard sequence with a bootstrap value of 53 and was present in the same major clade with the standard sequence. With the evidence, the study concludes that the inferences of the present study can help in understating the mutation rates of the virus and further aid in the process of control of SARS-CoV-2 virus infections by selecting a suitable treatment regimens.