Comparative Genomic Analysis of Rapidly Evolving SARS CoV-2 Viruses Reveal Mosaic Pattern of Phylogeographical Distribution

Roshan Kumar; Helianthous Verma; Nirjara Singhvi; Utkarsh Sood; Vipin Gupta; Mona Singh; Rashmi Sharma; Princy Hira; Shekhar Nagar; Chandni Talwar; Namita Nayyar; Shailly Anand; Charu Dogra Rawat; Mansi Verma; Ram Kishan Negi; Yogendra Singh; Rup Lal

The strains formed a monophyletic clade, in which MT093571.1 (South Korea) and 210 MT039890.1 (Sweden) were most diverged. Focusing on the edge-connection between the 211 neighboring countries from where the transmission is more likely to occur, we noted a strain 212 from Taiwan (MT066176) closely clustered with another from China (MT121215.1). With the 213 exception of these two strains, we did not find any connection between strains of neighboring 214 countries. Thus, most strains belonging to the same country clustered distantly from each other 215 and showed relatedness with strains isolated from distant geographical locations ( Figure 1A & 216 B). For instance, a SARS-CoV-2 strain isolated from Nepal (MT072688) clustered with a strain 217 8 from USA (MT039888). Also, strains from Wuhan (LR757998 and LR757995), where the 218 virus was originated, showed highest identity with USA as well as China strains; strains from 219 India, MT012098 and MT050493 clustered closely with China and USA strains, respectively 220 ( Figure 1A & B) . Similarly, Australian strain (MT007544) showed close clustering with USA 221 strain ( Figure 1A & B) and one strain from Taiwan (MT066175) clustered nearly with Chinese 222 isolates ( Figure 1B ). Isolates from Italy (MT012098) and Brazil (MT126808) clustered with 223 different USA strains ( Figure 1A & B) . Notably, isolates from same country or geographical 224 location formed a mosaic pattern of phylogenetic placements of countries' isolates. For viral 225 transmission, contact between the individuals is also an important factor, supposedly due to 226 which the spread of identical strains across the border of neighboring countries is more likely. 227