Authors

1 Department of Microbiology, Golestan University of Medical Sciences. Gorgan, Iran.

2 Department of Microbiology, Golestan University of Medical Sciences, Gorgan, Iran

3 Senior Scientist, Enterprise-TTM, University of Pittsburgh Medical Center, Pittsburgh, PA

4 Dept. Microbiology. Faculty of Medicine, Golestan University of Medical Sciences

Abstract

Background: Molecular analysis of SARS-CoV-2 genome is important to predict viral pathogenicity. In addition to transmission, replication is a key factor in pathogenicity of the virus. Notably, mutations in non-structural proteins (NSP3 and NSP12) can affect host immune response and viral replication. Therefore, this study was conducted to investigate different mutations of SARS-CoV-2 NSP3, and NSP12 during different waves of COVID-19 infection.
Methods: We recruited 57 NGS sequences including 8 NGS sequences from Golestan SARS-CoV-2 RNA samples, obtained as part of clinical testing in different referral centers of Iran. After obtaining sequences from the global initiative on sharing all influenza data (GISAID), and evaluating and processing data, all sequences were aligned to the Wuhan variant genome (NC_045512.2) using MEGA6. The HDOCK server was used for molecular docking.
Results: In NSP3, mutations in positions (nts 315, 545, 2666, 3264) were more frequent and among them mutation in positions including nt 545 (aa182) and nt 2666 (aa889) were associated with an increase in codon usage. In the term of NSP12, mutations in positions such as nts 406 (aa137), 965 (aa323), 1233, 1653, 1836, 2733 were more frequent. The molecular docking results showed more affinity in some variants of NSP3 and NSP12 as well.
Conclusion: This study has assessed mutation in SARS-CoV-2 Nsp3, and NSP12 which are viral protease, and viral polymerase (RdRp). The mutations reported in this study may help this virus to replicate faster and evade the pharmaceutical agents which target viral polymerase activity and be very effective in viral pathogenesis. In addition, this study highlights the importance of ongoing genomic variation studies to be performed on SARS-CoV-2 variants.

Keywords

  1. Behboudi E, Shamsi A, Hamidi-Sofiani V, Oladnabi M. The effects of fasting in Ramadan on the risk factors of COVID-19 in adolescents: a brief review. International Journal of Pediatrics. 2021; 9(1):12835-42.
  2. Behboudi E, Hamidi V, Gholizadeh F, Grala EM, Ghelmani Y, Nakhaie M, Charostad J, Astani A. Association between ABO blood groups and rhesus antigen and susceptibility to COVID-19 in the Yazd hospital. New Microbes and New Infections. 2021; 44:100934.
  3. Behboudi E, Hamidi-Sofiani V. New mutations causing the 2019 novel Coronavirus (2019-nCoV) epidemic. Tehran University Medical Journal. 2020; 78(3):188.
  4. Behboudi E, Hamidi-Sofiani V, Zeynali P. Review of Therapeutic Candidates for the New CoronaVirus (COVID-19). Razi Journal of Medical Sciences. 2020; 27(8):65-77.
  5. Ruan Z, Liu C, Guo Y, He Z, Huang X, Jia X, Yang T. SARS‐CoV‐2 and SARS‐CoV: Virtual screening of potential inhibitors targeting RNA‐dependent RNA polymerase activity (NSP12). Journal of medical virology. 2021; 93(1):389-400.
  6. Shannon A, Le NT-T, Selisko B, Eydoux C, Alvarez K, Guillemot J-C, Decroly E, Peersen O, Ferron F, Canard B. Remdesivir and SARS-CoV-2: Structural requirements at both nsp12 RdRp and nsp14 Exonuclease active-sites. Antiviral research. 2020; 178:104793.
  7. Khailany RA, Safdar M, Ozaslan M. Genomic characterization of a novel SARS-CoV-2. Gene reports. 2020; 19:100682.
  8. Esmail S, Danter WR. Lung organoid simulations for modeling and predicting the effect of mutations on SARS-CoV-2 infectivity. Computational and Structural Biotechnology Journal. 2021; 19:1701-12.
  9. Lundstrom K, Seyran M, Pizzol D, Adadi P, Mohamed Abd El-Aziz T, Hassan S, Soares A, Kandimalla R, Tambuwala MM, Aljabali AA, Azad GK, Choudhury PP, Uversky VN, Sherchan SP, Uhal BD, Rezaei N, Brufsky AM. The importance of research on the origin of SARS-CoV-2. Multidisciplinary Digital Publishing Institute; 2020. p. 1203.
  10. Ayatollahi AA, Aghcheli B, Amini A, Nikbakht H, Ghassemzadehpirsala P, Behboudi E, Rajabi A, Tahamtan A. Association between blood groups and COVID-19 outcome in Iranian patients. Future Virology. 2021; 16(10):657-65.
  11. Erol A. Are the emerging SARS-COV-2 mutations friend or foe? Immunology Letters. 2021; 230:63.
  12. Zandi M, Behboudi E, Soltani S. Role of glycoprotein hemagglutinin-esterase in COVID-19 pathophysiology? Stem cell reviews and reports. 2021; 17(6):2359-60.
  13. Yadav R, Chaudhary JK, Jain N, Chaudhary PK, Khanra S, Dhamija P, Sharma A, Kumar A, Handu S. Role of structural and non-structural proteins and therapeutic targets of SARS-CoV-2 for COVID-19. Cells. 2021; 10(4):821.
  14. Raj R. Analysis of non-structural proteins, NSPs of SARS-CoV-2 as targets for computational drug designing. Biochemistry and biophysics reports. 2021; 25:100847.
  15. Behboudi E, Hamidi-Sofiani V. CD147: A missing key in the corona virus disease-2019 (COVID-19). Payesh (Health Monitor). 2020; 19(4):467-8.
  16. Mirza MU, Froeyen M. Structural elucidation of SARS-CoV-2 vital proteins: Computational methods reveal potential drug candidates against main protease, Nsp12 polymerase and Nsp13 helicase. Journal of pharmaceutical analysis. 2020; 10(4):320-8.
  17. McCallum M, Walls AC, Sprouse KR, Bowen JE, Rosen LE, Dang HV, Marco AD, Franko N, Tilles SW, Logue J, Miranda MC, Ahlrichs M, Carter L, Snell G, Pizzuto MS, Chu HY, Voorhis WCV, Corti D, Veesler D. Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants. Science. 2021; 374(6575):1621-6.
  18. Huang J, Song W, Huang H, Sun Q. Pharmacological therapeutics targeting RNA-dependent RNA polymerase, proteinase and spike protein: from mechanistic studies to clinical trials for COVID-19. Journal of clinical medicine. 2020; 9(4):1131.
  19. Zeng L, Li D, Tong W, Shi T, Ning B. Biochemical features and mutations of key proteins in SARS-CoV-2 and their impacts on RNA therapeutics. Biochemical Pharmacology. 2021; 189:114424.
  20. Wu R, Wang L, Kuo H-CD, Shannar A, Peter R, Chou PJ, Li S, Hudlikar R, Liu X, Liu Z, Poiani GJ, Amorosa L, Brunetti L, Kong AN. An update on current therapeutic drugs treating COVID-19. Current pharmacology reports. 2020; 6(3):56-70.
  21. Mohammadi E, Shafiee F, Shahzamani K, Ranjbar MM, Alibakhshi A, Ahangarzadeh S, Beikmohammadi L, Shariati L, Hooshmandi S, Ataei B, Javanmardj SH. Novel and emerging mutations of SARS-CoV-2: Biomedical implications. Biomedicine & Pharmacotherapy. 2021; 139:111599.
  22. Mutlu O, Ugurel OM, Sariyer E, Ata O, Inci TG, Ugurel E, Kocer S, Turgut-Balik D. Targeting SARS-CoV-2 Nsp12/Nsp8 interaction interface with approved and investigational drugs: an in silico structure-based approach. Journal of Biomolecular Structure and Dynamics. 2022; 40(2):918-30.
  23. Alam ARU, Islam OK, Hasan MS, Islam MR, Mahmud S, Al‐Emran HM, Jahid IK, Crandall KA, Hossain MA. Dominant clade‐featured SARS‐CoV‐2 co‐occurring mutations reveal plausible epistasis: An in silico based hypothetical model. Journal of medical virology. 2022; 94(3):1035-49.
  24. Zeng H-L, Dichio V, Horta ER, Thorell K, Aurell E. Global analysis of more than 50,000 SARS-CoV-2 genomes reveals epistasis between eight viral genes. Proceedings of the National Academy of Sciences. 2020; 117(49):31519-26.
  25. Angeletti S, Benvenuto D, Bianchi M, Giovanetti M, Pascarella S, Ciccozzi M. COVID‐2019: the role of the nsp2 and nsp3 in its pathogenesis. Journal of medical virology. 2020; 92(6):584-8.
  26. Claverie J-M. A putative role of de-mono-ADP-ribosylation of STAT1 by the SARS-CoV-2 Nsp3 protein in the cytokine storm syndrome of COVID-19. Viruses. 2020; 12(6):646.
  27. Tomaszewski T, DeVries RS, Dong M, Bhatia G, Norsworthy MD, Zheng X, Caetano-Anolles G. New pathways of mutational change in SARS-CoV-2 proteomes involve regions of intrinsic disorder important for virus replication and release. Evolutionary Bioinformatics. 2020; 16:1176934320965149.