Genetic variation of SARS-CoV-2 circulating worldwide and its association for altering disease fatality
The emergence of SARS-CoV-2 has resulted in > 36,361,054 infections and > 1,056,186 deaths worldwide. Using publicly available genome sequences of patient samples from different geographical regions, a study has been conducted to co-relate mutational frequency with disease transmission and fatality rate. Seven hundred genome sequences were randomly chosen from different countries. The regions of the genome encoding structural proteins Spike (S), Nucleocapsid (N), envelop (E) and Membrane (M) proteins and ORF8 were studied here. Through Insilco approach, this study showed that several evolutionary conserved amino acid residues underwent mutations. Some of these mutations are common in multiple geographies. Quite a few region-specific mutations are also identified. This study highlights that mutational rate is proportional to disease transmission and inversely proportional to disease fatality. The changes in the conserved residues have significant implication on the stability of the proteins and subsequent interaction, which are essential for virus propagation. This provides a better understanding of the genetic variation in SARS-CoV-2 across the countries and its association with reducing disease fatality.
Keywords:SARS-CoV-2, Disease Fatality, Mutation
Farkas C, Fuentes-Villalobos F, Garrido JL, Haigh J, Barría MI. 2020. Insights on early mutational events in SARSCoV-2 virus reveal founder effects across geographical regions. PeerJ 8:e9255. https://doi.org/10.7717/peerj.9255
Lu R, Zhao X, Li J, Niu P, Yang B. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet 395, pp. 565–574, 2020
Zhu N, Zhang D, Wang W, Li X, Yang B et al. A Novel Coronavirus from Patients with Pneumonia in China, 2019. New Eng. J. Med. 382, pp. 727–733, 2020
Chinazzi M, Davis JT, Ajelli M, Gioannini C, Litvinova M. The effect of travel restrictions on the spread of the 2019 novel coronavirus (COVID-19) outbreak. Science 368, pp. 395–400, 2020
Zhang T, Wu Q and Zhang Z. Probable pangolin origin of SARS-CoV-2 associated with the COVID-19 outbreak. Curr. Biol. 30, pp. 1346–1351, 2020
Song, Z.; Xu, Y.; Bao, L.; Zhang, L.; Yu, P.; Qu, Y.; Zhu, H.; Zhao, W.; Han, Y.; Qin, C. From SARS to MERS, Thrusting Coronaviruses into the Spotlight. Viruses 2019, 11, 59
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. https://doi.org/10.1016/j.cell.2020.02.05827
Becerra-Flores M, Cardozo T. SARS-CoV-2 viral spike G614 mutation exhibits higher case fatality rate. Int J Clin Pract. 00: e13525, 2020. https://doi.org/10.1111/ijcp.13525
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. https://doi.org/10.1016/j.jinf.2020.03.058
Dasgupta, R. Comparative genomics of receptor binding domains of S protein and host receptor interaction in COVID-19 patient. International Journal of Creative Research Thoughts (IJCRT), Volume.8, Issue 8, pp.2571-2575, August 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
Dasgupta R. Mutational Analysis Of Structural Proteins In Sars-Cov-2 Viral RNA Of Covid-19 In India. Research Journal Of Life Sciences, Bioinformatics, Pharmaceutical and chemical Sciences. Vol 6, Issue 5, 2020. DOI: 10.26479/2020.0605.01
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
Li JY, Liao CH, Wang Q, Tan YJ, Luo R, Qiu Y, Ge XY. The ORF6, ORF8 and nucleocapsid proteins of SARS-CoV-2 inhibit type I interferon signaling pathway. Virus Res. 2020 Sep;286:198074. https://doi.org/10.1016/j.virusres.2020.198074
Dewald Schoeman and Burtram C. Fielding. Coronavirus envelope protein: current knowledge. Virology Journal 16,69, 2019. https://doi.org/10.1186/s12985-019-1182-0
Jalali S, Bhadra B, Dasgupta S. Significance of Mutation Rate of Structural and Non-Structural Proteins of SARS-Cov-2 Showed with Lower Death Rate of COVID-19. Sci J Biol. 2020;3(1): 017-022. https://dx.doi.org/10.37871/sjb.id18
Samir Kumar Patra. “Perspective on Accelerating the Mutation Rate of SARS-CoV-2 for a Better Way of COVID-19 Treatment; Enhanced Mutation Therapy of COVID-19”. AIJR Preprints, 62, version 1, 2020. https://preprints.aijr.org/index.php/ap/preprint/view/62
Copyright (c) 2020 Rimjhim Dasgupta
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
Any non-commercial use, distribution, adaptation, and reproduction in any medium is permitted as long as the original work is properly cited. However, caution and responsibility are required when reusing as the articles on the preprint server are not peer-reviewed. Readers are advised to check for the availability of any updated or peer-reviewed version.