Structural, glycosylation and antigenic variation between 2019 novel coronavirus (2019-nCoV) and SARS coronavirus (SARS-CoV)

Abstract

The emergence of 2019 novel coronavirus (2019-nCoV) is of global concern and might have emerged from RNA recombination among existing coronaviruses. CoV spike (S) protein which is crucial for receptor binding, membrane fusion via conformational changes, internalization of the virus, host tissue tropism and comprises crucial targets for vaccine development, remain largely uncharacterized. Therefore, the present study has been planned to determine the sequence variation, structural and antigenic divergence of S glycoprotein which may be helpful for the management of 2019-nCoV infection. The sequences of spike glycoprotein of 2019-nCoV and SARS coronavirus (SARS-CoV) were used for the comparison. The sequence variations were determined using EMBOSS Needle pairwise sequence alignment tools. The variation in glycosylation sites was predicted by NetNGlyc 1.0 and validated by N-GlyDE server. Antigenicity was predicted by NetCTL 1.2 and validated by IEDB Analysis Resource server. The structural divergence was determined by using SuperPose Version 1.0 based on cryo-EM structure of the SARS coronavirus spike glycoprotein. Our data suggests that 2019-nCoV is newly spilled coronavirus into humans in China is closely related to SARS-CoV, which has only 12.8% of difference with SARS-CoV in S protein and has 83.9% similarity in minimal receptor-binding domain with SARS-CoV. Addition of a novel glycosylation sites were observed in 2019-nCoV. In addition, antigenic analysis proposes that great antigenic differences exist between both the viral strains, but some of the epitopes were found to be similar between both the S proteins. In spite of the variation in S protein amino acid composition, we found no significant difference in their structures. Collectively, for the first time our results exhibit the emergence of human 2019-nCoV is closely related to predecessor SARS-CoV and provide the evidence that 2019-nCoV uses various novel glycosylation sites as SARS-CoV and may have a potential to become pandemic owing its antigenic discrepancy. Further, demonstration of novel Cytotoxic T lymphocyte epitopes may impart opportunities for the development of peptide based vaccine for the prevention of 2019-nCoV.

Keywords: 2019-nCoV; Antigenicity; COVID-19; Coronavirus; Glycosylation; S glycoprotein; SARS-CoV; Structural divergence.

Fig. 1

Phylogeny of 2019-nCoV. The phylogenetic tree was constructed by molecular evolutionary genetic analysis (MEGA) software based on the spike gene sequences, showing the evolutionary relationship of 2019-nCoV with predecessors strains of SARS-coronaviruses. The phylogenetic analysis showing that 2019-nCoV is closely related with Bat SARS-like coronavirus. However, both 2019-nCoV and Bat SARS-like coronavirus emerged from the SARS coronavirus. The accession number of the sequences used for the phylogenetic analysis is represented at the tip of the branches, where Japanese encephalitis virus has been used as the outgroup

Fig. 2

Sequence variation of spike glycoprotein. a The complete amino acid sequences of spike glycoprotein of 2019-nCoV and SARS-CoV are shown as described earlier. Standard single-letter abbreviations for the amino acids were used. The collinear sequences were aligned by online use of Clustal Omega. Amino acid alignment exhibits non-conservative substitutions (“.”), conservative substitutions (“:”) and semi-conservative substitutions (“.”). Conserved regions are represented as (“”). There are 76.2% identity, 87.2% similarity and 2% Gaps in 1273 positions. b The tertiary structure of minimal RBD (residues 270–510)

Fig. 3

Structural divergence of spike glycoprotein. The PDB structures of spike glycoprotein of 2019-nCoV (PDBA) and SARS-CoV (PDBB) were based on cryo-EM structure of the SARS coronavirus spike glycoprotein (PDB ID 6ACC). Models were superimposed using SuperPose which was visualized by Chimera where green color showing the S glycoprotein of SARS coronavirus and cyan color represents the S glycoprotein of 2019-nCoV. The analysis suggests that both the structures exhibits insignificant divergence with 1.39 A° deviation