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

We furthermore extended the analysis targeting the Spike (S) glycoprotein gene of the CoVs from human SARS, animal-origin CoVs including MERSV (camel), bovine coronavirus, canine coronavirus, bat_coronaviruses and the current outbreak nCoVs from different regions. The sequences of nCoV available in the NCBI GenBank database till January 28 th , 2020 were retrieved. Phylogenetic analysis was done using the MEGA 7.0 version applying the Maximum likelihood method (ML) based General Time Reversible substitution model with gamma distribution. Pairwise identity of the current 2019-nCoV outbreak sequences was calculated using the MegAlign software of DNASTAR. In the S-gene based phylogeny, 10 Chinese and 5 USA nCoV isolates (Figure 4) revealed that all the isolates are nearly identical across the Sgene based phylogeny constituting a monophyletic clade (Figure 4) . The two Bat_SARS-like CoVs (Bat-SL-CoVZC45, MG772933 and bat-SL-CoVZXC21, MG772934) shared 100% bootstrap support with 2019-nCoV isolates of the current outbreaks. Based on the MegAlign and MEGA 7.0 software based Clustal W alignments, the sequence identity of 2019-nCoV strains revealed Bat SARS-like CoVs (Bat-SL-CoVZC45, MG772933 and bat-SL-CoVZXC21, MG772934) as the nearest neighbors with 77.6 to 78.2% sequence identity on nucleotide basis. In the phylogenetic tree, the current outbreak nCoV isolates were fairly distinct than the previously reported SARS-CoV or BatSARS-CoV strains but were clustering inside a common major clade which includes strains from subgenus Sarbecovirus. The per cent identity with other SARS-CoV or BatSARS-CoV strains was 70.8 to 74.7% (Supplementary data 1) . The per cent similarity on nucleotide basis between nCoV isolates and canine respiratory coronaviruses (CRCoV) and bovine coronaviruses (BCoV) of subgenus Embecovirus ranged between 40.8 to 41.5%. Furthermore, the per cent identity of nCoV isolates was found lower (40.2%) with the mild respiratory human coronavirus isolate HCoV-OC43 of same subgenus Embecovirus containing animal-origin coronaviruses. Additionally, for S-gene, per cent similarity range pattern was evaluated in amino acid based index where 2019-nCoV isolates from China and USA were 100% identical. The range varied between 81.2 to 81.8% and 77.0 to 78.1% for 2019-nCoV isolates with Bat_SARS-like CoVs and other SARS like CoVs, respectively. The per cent identity with human coronavirus isolate HCoV-OC43 was also found lower (28.0%) (Supplementary data 2) .