Emerging novel coronavirus (2019-nCoV)—current scenario, evolutionary perspective based on genome analysis and recent developments

Malik, Yashpal Singh; Sircar, Shubhankar; Bhat, Sudipta; Sharun, Khan; Dhama, Kuldeep; Dadar, Maryam; Tiwari, Ruchi; Chaicumpa, Wanpen

In this study, we also attempted to reveal the evolutionary perspective of the recently emerging 2019-nCoV based on the complete genome analysis. Phylogenetic analysis was done using the MEGA 7.0 version applying the Maximum likelihood method (ML) based General Time Reversible substitution model with the available whole genome sequences of 2019-nCoV available in the NCBI GenBank database till January 28 th , 2020. Pairwise identity of the current 2019-nCoV outbreak sequences was calculated using the MegAlign software of DNASTAR. In the whole genome phylogenetic analysis, the 2019-nCoV strains from China and the USA clustered in a monophyletic clade (Figure 3 ). The nearest neighbors of the 2019-nCoV isolates from China and USA were two Bat_SARS-like coronaviruses (Bat-SL-CoVZC45, Accession no. MG772933 and Bat-SL-CoVZXC21, Accession no. MG772934). These two Bat_SARS-like CoVs shared a 100% bootstrap support with 2019-nCoV strains of the current outbreak. Using the MegAlign and MEGA 7.0 software based Clustal W alignments, the nucleotide sequence identity of 2019-nCoV strains revealed the highest similarity of greater than 88.2% with two Bat_SARS_like CoVs. These findings were in accordance with report of Zhu and colleagues where a nearby sequence identity of 86.9% with previously published Bat_SARS-like CoV was reported . Contrarily, the genome of 2019-nCoV has also been reported to be 96% identical to the bat coronavirus based on Simplot analysis where it has been found closer to bat CoV isolate RaTG13 previously detected in Rhinolophus affinis (intermediate horseshoe bat) from Yunnan Province, indicating its origin from the bats (Zhou et al. 2020) . Based on the available information it is rather early to predict the origin of this novel coronavirus without a comprehensive analysis of emerging nCoV strains from different parts of the world. To note, the sequence identity based on the complete genome sequences between current outbreaks 2019-nCoV isolates from China and the USA ranges 99.8 to 100% on the nucleotide level indicating their common origin of evolution.