Phylogenetic Analysis of the Novel Coronavirus Reveals Important Variants in Indian Strains

Aditi Joshi; Sushmita Paul

14 Changchuan [20] presented a method for effectively genotyping SARS-CoV-2 viruses 15 using complete genomes. 16 In this report, an analysis of 468 novel and early virus genome is presented. The 440 17 sequences are from different parts of the world including countries from Europe, USA, 18 Middle East, Asia and 28 sequences submitted from India with 11 sequenced in Iran. 19 The data was downloaded from GenBank, GISAID, and SRA. Data was collected for 20 this study last as of 9th April 2020, with 440 genome sequence of the novel and early 21 strains from the world along with 28 sequences from India. The MEGAX tool [11] has 22 been used to perform the analysis. It is based on Tamura-Nei model and 23 Neighbour-Joining method along with 100 bootstrap. This study adds up a novel 24 non-synonymous mutation 4809C>T (S1515F) in NSP3 gene only observed in strains 25 obtained from India. Various studies revealed that the NSP3 gene harbours many 26 mutations as this gene has been reported with extensive positive selection towards 27 evolution in Betacoronaviruses [18] , [7] . Common mutations among different strains 28 were also identified and reported. The sequence containing the mutation was used to 29 build protein model using SWISS-Model. Followed by the usage of the DynaMut tool to 30 study effect of mutation on protein stability. The results indicate the clade of variations 31 in the Indian SARS-CoV2. Also, potential region of mutations in near future along with 32 the effect of non-synonymous mutation at the protein level. This paper represents the 33 initial observations on submitted 28 sequences of Indian viral strains.