Comprehensive comparative genomic and microsatellite analysis of SARS, MERS, BAT‐SARS, and COVID‐19 coronaviruses

Rehman, Hafiz Abdul; Ramzan, Farheen; Basharat, Zarrin; Shakeel, Muhammad; Khan, Muhammad Usman Ghani; Khan, Ishtiaq Ahmad

The coronavirus disease 2019 (COVID‐19) pandemic has spread around the globe very rapidly. Previously, the evolution pattern and similarity among the COVID‐19 causative organism severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) and causative organisms of other similar infections have been determined using a single type of genetic marker in different studies. Herein, the SARS‐CoV‐2 and related β coronaviruses Middle East respiratory syndrome coronavirus (MERS‐CoV), SARS‐CoV, bat coronavirus (BAT‐CoV) were comprehensively analyzed using a custom‐built pipeline that employed phylogenetic approaches based on multiple types of genetic markers including the whole genome sequences, mutations in nucleotide sequences, mutations in protein sequences, and microsatellites. The whole‐genome sequence‐based phylogeny revealed that the strains of SARS‐CoV‐2 are more similar to the BAT‐CoV strains. The mutational analysis showed that on average MERS‐CoV and BAT‐CoV genomes differed at 134.21 and 136.72 sites, respectively, whereas the SARS‐CoV genome differed at 26.64 sites from the reference genome of SARS‐CoV‐2. Furthermore, the microsatellite analysis highlighted a relatively higher number of average microsatellites for MERS‐CoV and SARS‐CoV‐2 (106.8 and 107, respectively), and a lower number for SARS‐CoV and BAT‐CoV (95.8 and 98.5, respectively). Collectively, the analysis of multiple genetic markers of selected β viral genomes revealed that the newly born SARS‐COV‐2 is closely related to BAT‐CoV, whereas, MERS‐CoV is more distinct from the SARS‐CoV‐2 than BAT‐CoV and SARS‐CoV.