Phylogenetic Analysis of the Novel Coronavirus Reveals Important Variants in Indian Strains

Aditi Joshi; Sushmita Paul

There has been a report on SNP mutations in SARS-CoV2 genome which majorly 63 demonstrated mutations frequent in European strains [20] . These mutations were 64 analysed in 28 submitted sequences from India. A previous report from India observed 65 unique mutation in spike protein (A930V (24351C>T)), this mutation was identified in 66 one (Sample 2) of the early infected patients' viral sequence [16] . The most common 67 SNP's that were observed in this analysis includes the previously reported mutation in 68 leader sequence (241C>T), Coronaviruses includes subgenomic identical 5 Leader 69 sequence which plays role in viral replication process. This mutation was seen to replicase-transcriptase complex at a very early stage of infection [8] . Spike protein has 89 been a hotspot in CoV2 genome since the beginning due to the presence of 90 receptor-binding domain. Contact point to the host includes the domains from S1 91 subunit of this S-protein [19] . The mutation observed 23403A>G (D614G) lies in tail 92 region of this S1 subunit and before the cleavage site of another subunit called S2 of 93 S-protein. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.14.041301 doi: bioRxiv preprint Talking in terms of RNA replication of SARS-CoV ORF1a and ORF1b 95 (replicase/transcriptase) which includes NSP8 and NSP4 genes have been highlighted. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.14.041301 doi: bioRxiv preprint SARS-CoV2 has been reported to have second highest identity (82.30%) with 146 SARS-COV. To identify the possible role and relevance of the region observing the 147 mutation, sequence alignment of NSP3 protein from SARS-CoV and SARS-CoV2 was 148 performed. NSP3 gene along with NSP4 are the key players for membrane 149 rearrangement in form of Double Membrane Vesicles (DMV) upon infection [2] . Report 150 on role of mutations in important glycosylation sites in NSP4 gene in SARS-Cov have 151 been observed and were indicative of localisation problems with other NSP protein like 152 NSP3 [5] . As per this there will be a requirement to observe the site of novel change for 153 its impact on NSP3 gene interactions, which may even serve as a potential candidate for 154 therapeutics, depending upon the mutational effect shown in NSP4 [5] . The other 155 predictive outcome can come as benefit to virus in terms of interaction. recognize purine bases more strongly than pyrimidine bases [9] . Though the very crucial 162 role of SUD-C has not been recognised in SARS-CoV but in few reports SUD-C has 163 been shown to have RNA-binding ability, and concerted actions by the subdomains of 164 SUD have been proposed to ensure specific RNA binding [9] .The complete deletion of 165 the SUD-C domain within the context of a SARS-CoV was found to have large 166 reduction of RNA synthesis, but some basal RTC activity remains [12] . PDB blast 167 confirmed the presence of mutation in SUD domain of SARS-CoV with 74% identity to 168 2KAF (PDB-ID). Using Swiss model this particular domain was modelled for Reference 169 Wuhan sequence (NC 045521)and the change was observed by insilco protein stability 170 tool DynaMut [15] . The change was predicted to be stabilising by DynaMut and The novel Coronavirus, being identified as a global threat have been the prime focus of 178 research and investigation around the globe. Since its outbreak in Wu