In silico analysis of the substitution mutations and evolutionary trends of the SARS-CoV-2 structural proteins in Asia

Document Type : Original Article

Authors

1 Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran

2 Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran

3 Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran

4 Non communicable Diseases Research Center, Bam University of Medical sciences, Bam, Iran

5 Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran

6 Department of Biochemistry, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands

7 Department of Bioinformatics, Kish International Campus University of Tehran, Kish, Iran

Abstract

Objective(s): To address a highly mutable pathogen, mutations must be evaluated. SARS-CoV-2 involves changing infectivity, mortality, and treatment and vaccination susceptibility resulting from mutations.
Materials and Methods: We investigated the Asian and worldwide samples of amino-acid sequences (AASs) for envelope (E), membrane (M), nucleocapsid (N), and spike (S) proteins from the announcement of the new coronavirus 2019 (COVID-19) up to January 2022. Sequence alignment to the Wuhan-2019 virus permits tracking mutations in Asian and global samples. Furthermore, we explored the evolutionary tendencies of structural protein mutations and compared the results between Asia and the globe.
Results: The mutation analyses indicated that 5.81%, 70.63%, 26.59%, and 3.36% of Asian S, E, M, and N samples did not display any mutation. Additionally, the most relative mutations among the S, E, M, and N AASs occurred in the regions of 508 to 635 AA, 7 to 14 AA, 66 to 88 AA, and 164 to 205 AA in both Asian and total samples. D614G, T9I, I82T, and R203M were inferred as the most frequent mutations in S, E, M, and N AASs. Timeline research showed that substitution mutation in the location of 614 among Asian and total S AASs was detected from January 2020.
Conclusion: N protein was the most non-conserved protein, and the most prevalent mutations in S, E, M, and N AASs were D614G, T9I, I82T, and R203M. Screening structural protein mutations is a robust approach for developing drugs, vaccines, and more specific diagnostic tools.

Keywords

References

1. Grigoriadis A, Raisanen IT, Parnanen P, Tervahartiala T, Sorsa T, Sakellari D. Is There a Link between COVID-19 and Periodontal Disease? A Narrative Review. Eur J Dent 2022; 16: 514-520.
2. To KK, Tsang OT, Leung WS, Tam AR, Wu TC, Lung DC, et al. Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study. Lancet Infect Dis 2020; 20: 565-574.
3. Pachetti M, Marini B, Benedetti F, Giudici F, Mauro E, Storici P, et al. Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant. J Transl Med 2020; 18: 179-187.
4. Mercatelli D, Giorgi FM. Geographic and Genomic Distribution of SARS-CoV-2 Mutations. Front Microbiol 2020; 11: 1800.
5. Chan JF, Kok KH, Zhu Z, Chu H, To KK, Yuan S, et al. Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerg Microbes Infect 2020; 9: 221-236.
6. Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, et al. A new coronavirus associated with human respiratory disease in China. Nature 2020; 579: 265-269.
7. Yan R, Zhang Y, Li Y, Xia L, Guo Y, Zhou Q. Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science 2020; 367: 1444-1448.
8. Andersen KG, Rambaut A, Lipkin WI, Holmes EC, Garry RF. The proximal origin of SARS-CoV-2. Nat Med 2020; 26: 450-452.
9. Rahbar Z, Nazarian S, Dorostkar R, Sotoodehnejadnematalahi F, Amani J. Recombinant expression of SARS-CoV-2 Receptor Binding Domain (RBD) in Escherichia coli and its immunogenicity in mice. Iran J Basic Med Sci 2022; 25: 1110-1116.
10. Mandala VS, McKay MJ, Shcherbakov AA, Dregni AJ, Kolocouris A, Hong M. Structure and drug binding of the SARS-CoV-2 envelope protein transmembrane domain in lipid bilayers. Nat Struct Mol Biol 2020; 27: 1202-1208.
11. Peng Y, Du N, Lei Y, Dorje S, Qi J, Luo T, et al. Structures of the SARS-CoV-2 nucleocapsid and their perspectives for drug design. EMBO J 2020; 39: e105938.
12. Zheng Y, Zhuang M-W, Han L, Zhang J, Nan M-L, Zhan P, et al. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) membrane (M) protein inhibits type I and III interferon production by targeting RIG-I/MDA-5 signaling. Signal transduction and targeted therapy 2020; 5: 1-13.
13. Moya A, Elena SF, Bracho A, Miralles R, Barrio E. The evolution of RNA viruses: A population genetics view. Proc Natl Acad Sci U S A 2000; 97: 6967-6973.
14. Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, et al. Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell 2020; 182: 812-827.e819.
15. Kumar A, Dowling WE, Román RG, Chaudhari A, Gurry C, Le TT, et al. Status report on COVID-19 vaccines development. Curr Infect Dis Rep 2021; 23: 1-12.
16. Khare S, Gurry C, Freitas L, Schultz MB, Bach G, Diallo A, et al. GISAID’s Role in Pandemic Response. China CDC Wkly 2021; 3: 1049-1051.
17. Elbe S, Buckland‐Merrett G. Data, disease and diplomacy: GISAID’s innovative contribution to global health. Glob Chall 2017; 1: 33-46.
18. Shu Y, McCauley J. GISAID: Global initiative on sharing all influenza data–from vision to reality. Euro Surveill 2017; 22: 30494.
19. Majumdar P, Niyogi S. SARS-CoV-2 mutations: the biological trackway towards viral fitness. Epidemiol Infect 2021; 149: e110.
20. Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. The lancet 2020; 395: 565-574.
21. Abavisani M, Rahimian K, Khayami R, Mollapour Sisakht M, Mahmanzar M, Meshkat Z. Mutational insights among the structural proteins of SARS-CoV-2: frequencies and evolutionary trends in American countries. BioRxiv 2022; 1-16.
22. Wang R, Chen J, Hozumi Y, Yin C, Wei G-W. Decoding asymptomatic COVID-19 infection and transmission. J Phys Chem Lett 2020; 11: 10007-10015.
23. Pulakuntla S, Lokhande KB, Padmavathi P, Pal M, Swamy KV, Sadasivam J, et al. Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. VirusDisease 2021; 32: 690-702.
24. Wang Z, Schmidt F, Weisblum Y, Muecksch F, Barnes CO, Finkin S, et al. mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants. Nature 2021; 592: 616-622.
25. Chen RE, Zhang X, Case JB, Winkler ES, Liu Y, VanBlargan LA, et al. Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Nat Med 2021; 27: 717-726.
26. Weissman D, Alameh MG, de Silva T, Collini P, Hornsby H, Brown R, et al. D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. Cell Host Microbe 2021; 29: 23-31.
27. Ilmjärv S, Abdul F, Acosta-Gutiérrez S, Estarellas C, Galdadas I, Casimir M, et al. Epidemiologically most successful SARS-CoV-2 variant: concurrent mutations in RNA-dependent RNA polymerase and spike protein. MedRxiv 2020; 1-22.
28. Zhang L, Jackson CB, Mou H, Ojha A, Peng H, Quinlan BD, et al. SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. Nat Commun 2020; 11:6013.
29. Abavisani M, Rahimian K, khayami R, Kodori M, Sisakht MM, Mahmanzar M, et al. Investigating the mutations in the SARS-CoV-2 proteins among European countries. BioRxiv 2022; 1-19.
30. Li Q, Wu J, Nie J, Zhang L, Hao H, Liu S, et al. The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Cell 2020; 182: 1284-1294.
31. Cortey M, Li Y, Díaz I, Clilverd H, Darwich L, Mateu E. SARS-CoV-2 amino acid substitutions widely spread in the human population are mainly located in highly conserved segments of the structural proteins. BioRxiv 2020; 1-25.
32. Davies NG, Abbott S, Barnard RC, Jarvis CI, Kucharski AJ, Munday JD, et al. Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England.  2020.
33. Andreano E, Rappuoli R. SARS-CoV-2 escaped natural immunity, raising questions about vaccines and therapies. Nat Med 2021; 27: 759-761.
34. Focosi D, Maggi F. Neutralising antibody escape of SARS‐CoV‐2 spike protein: risk assessment for antibody‐based Covid‐19 therapeutics and vaccines. Rev Med Virol 2021; 31: e2231.
35.Planas D, Veyer D, Baidaliuk A, Staropoli I, Guivel-Benhassine F, Rajah MM, et al. Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization. Nature 2021; 596: 276-280.
36.Rahman MS, Hoque MN, Islam MR, Islam I, Mishu ID, Rahaman MM, et al. Mutational insights into the envelope protein of SARS-CoV-2. Gene Rep 2021; 22: 100997.
37.Timmers L, Peixoto JV, Ducati RG, Bachega JFR, de Mattos Pereira L, Caceres RA, et al. SARS-CoV-2 mutations in Brazil: from genomics to putative clinical conditions. Sci Rep 2021; 11: 11998.
38.Kerachian MA, Amel JamehDar S, Azghandi M, Keyvanlou N, Mazafffari Jovin S, Javadmanesh A, et al. Developing novel liquid biopsy by selective capture of viral RNA on magnetic beads to detect COVID-19. Iran J Basic Med Sci 2022; 25: 762-766.
39. Schoeman D, Fielding BC. Coronavirus envelope protein: current knowledge. Virol J 2019; 16: 1-22.
40. Hassan SS, Choudhury PP, Roy B. SARS-CoV2 envelope protein: Non-synonymous mutations and its consequences. Genomics 2020; 112: 3890-3892.
41. Keller MD, Harris KM, Jensen-Wachspress MA, Kankate VV, Lang H, Lazarski CA, et al. SARS-CoV-2–specific T cells are rapidly expanded for therapeutic use and target conserved regions of the membrane protein. Blood 2020; 136: 2905-2917.
42. Hebbani AV, Pulakuntla S, Pannuru P, Aramgam S, Badri KR, Reddy VD. COVID-19: comprehensive review on mutations and current vaccines. Arch Microbiol 2022; 204: 1-17.
43. Shen L, Bard JD, Triche TJ, Judkins AR, Biegel JA, Gai X. Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. Emerg Microbes Infect 2021; 10:885-893.
44. Shen L, Bard JD, Triche TJ, Judkins AR, Biegel JA, Gai X. Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. Emerg Microbes Infect 2021; 10: 1293-1299.
Iranian Journal of Basic Medical Sciences
Volume 25, Issue 11
November 2022
Pages 1299-1307

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