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The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.25.006213 doi: bioRxiv preprint viruses. Lastly, we believe as more data accumulate for COVID-19 the evolutionary pattern 381 will become much clear. 382 The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.25.006213 doi: bioRxiv preprint coloured circle represents the country of origin of each isolate. The two isolates from Wuhan 589 are marked separately on the outside of the ring. B) SNP based phylogeny of SARS-CoV-2 590 isolates. Highly similar genomes of coronaviruses were taken as input by Parsnp. Whole-591 genome alignments were made using libMUSCLE aligner using the annotated genome of 592 MT121215 strain as reference. Parsnp identifies the maximal unique matches (MUMs) among 593 the query genomes provided in a single directory. As only genomes within a specified MUMI 594 distance threshold are recruited, option -c to force include all the strains was used. The output 595 phylogeny based on Single nucleotide polymorphisms was obtained following variant calling 596 on core-genome alignment. C) The minimum spanning tree generated using Maximum 597