Preprint / Version 1

Mutations in structural proteins of SARS-CoV-2 and potential implications for the ongoing outbreak of infection in India




SARS-CoV-2 has spread in India very quickly from its first reported case on 30 January 2020 in Thrissur, Kerala. With the drastic increasing number of positive cases around the world WHO raised the importance in the assessment of the risk of spread and understanding genetic modifications that could have occurred in the SARS-CoV-2. Using available genome sequence in NCBI repository from the samples of different locations in India, we identified the regions (hotspots) of the viral genome with high rates of mutation. We analysed four regions of the genome encoding structural proteins Spike (S), Nucleocapsid (N), envelop (E) and Membrane (M) proteins. Through computational biology approach, we identified multiple substitution mutations in S and N proteins whereas there is only one substitution in E protein and none in M protein.  We showed most of these amino acid residues are evolutionary conserved. The changes in the conserved residues may have significant implication on the stability of the proteins and subsequent interaction with other elements, which are essential for virus propagation. This provides a basis for a better understanding of the genetic variation in SARS-CoV-2 circulating in the India, which might provide important clues for identifying potential therapeutic targets, development of efficient vaccines, antiviral drugs and diagnostic assays for controlling COVID-19.


COVID-19, SARS-CoV2, sequence alignment, Mutation


Download data is not yet available.


Becerra-Flores M, Cardozo T. SARS-CoV-2 viral spike G614 mutation exhibits higher case fatality rate. Int J Clin Pract. 00: e13525, 2020.

Domenico Benvenuto, Ayse Banu Demir, Marta Giovanetti, Martina Bianchi, Silvia Angeletti, Stefano Pascarella, Roberto Cauda, Massimo Ciccozzi, Antonio Cassone. Evolutionary analysis of SARS-CoV-2: how mutation of Non-Structural Protein 6 (NSP6) could affect viral autophagy, Journal of Infection 81, e24–e27, 2020

Chang C-k, Hou M-H, Chang C-F, Hsiao C-D and HuangT-HThe SARS coronavirus nucleocapsid protein – Forms and functions. Antivir. Res. 103, pp. 39–50, 2014

Dewald Schoeman and Burtram C. Fielding. Coronavirus envelope protein: current knowledge. Virology Journal 16,69, 2019

Sayantan Laha, Joyeeta Chakraborty, Shantanab Das, Soumen Kanti Manna, Sampa Biswas, Raghunath Chatterjee. Characterizations of SARS-CoV-2 mutational profile, spike protein stability and viral transmission. Infection, Genetics and Evolution 85, 104445, 2020.

Liu Z, Xiao X, Wei X, et al. Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS?CoV?2. J Med Virol. 92, pp.595–601, 2020.

Manish Tiwari, Divya Mishra. Investigating the genomic landscape of novel coronavirus (2019-nCoV) to identify non-synonymous mutations for use in diagnosis and drug design. Journal of Clinical Virology, 128, 104441, 2020

Surjit M, Kumar R, Mishra RN, Reddy MK, Chow VTK. The severe acute respiratory syndrome coronavirus nucleocapsid protein is phosphorylated localizes in the cytoplasm by 14-3-3-mediated translocation. J. Virol. 79, pp. 11476–11486, 2005

Tortorici, M.A., and Veesler, D. Structural insights into coronavirus entry. Adv. Virus Res. 105, pp. 93–116. 2019.

Alexandra C. Walls, Young-Jun Park, M. Alejandra Tortorici, Abigail Wall, Andrew T. McGuire, David Veesler. Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein; Cell 180, pp. 281–292, 2020.

Weihong Zeng, Guangfeng Liu, Huan Ma, Dan Zhao, Yunru Yang, Muziying Liu, Ahmed Mohammed, Changcheng Zhao, Yun Yang, Jiajia Xie, Chengchao Ding, Xiaoling Ma, Jianping Weng, Yong Gao, Hongliang He, Tengchuan Jin, Biochemical characterization of SARS-CoV-2 nucleocapsid protein. Biochemical and Biophysical Research Communications ,527, pp. 618-623, 2020