An Insight Into SARS-CoV-2 Phylogenetics and Genomics for Sixty Isolates Occurring in India

Introduction: Analysis of genome sequences to search for encoded proteins and motifs is a most widely used technique for the prediction of new drug and vaccine targets. It can effectively leverage computational techniques to deliver effective and pragmatic advantages in the search of new drug and vaccines. Materials and Methods: The diversity and evolution of the SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) isolates have been examined from different geographical parts of India using phylogenetic tree analysis. A dataset of 172 Indian SARS-CoV-2 genome sequences were collected from a database and a phylogenetic tree was constructed. Results: From the phylogenetic analysis, six different clusters were identified and from each cluster 10 genome sequences were chosen to find open reading frames (ORFs) and common encoded proteins. Four encoded proteins that are common among the 60 genome sequences and correspond to ORF7a protein, Membrane glycoprotein, Surface glycoprotein and Nucleocapsid phosphoproteins were found. Our results highlight that there are six conserved motifs with high frequency of occurrence suggesting a potential of being useful in further studies. Conclusions: The encoded proteins and their detected sequential motifs might be useful for screening potential drugs and vaccine candidates of the SARS-CoV-2 Indian isolates in the current epidemic situation.