126
Views
6
CrossRef citations to date
0
Altmetric
Review

Effect of Genomic and Amino Acid Sequence Mutation on Virulence and Therapeutic Target of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS COV-2)

, , ORCID Icon & ORCID Icon
Pages 2187-2192 | Published online: 14 Jun 2021

References

  • Ma X, Ph D, Wang D, et al. A novel coronavirus from patients with pneumonia in China, 2019. New Engl J Med Br. 2020;382(8):727–733. doi:10.1056/NEJMoa2001017
  • Ruan S. Likelihood of survival of coronavirus disease 2019 Scientific and ethical basis for social-distancing interventions against COVID-19. Lancet Infect Dis. 2020;20(6):630–631. doi:10.1016/S1473-3099(20)30257-7.32240633
  • Guan W, Liang W, Ou C, Du B. Clinical characteristics of coronavirus disease 2019 in China. New Engl J Med Orig. 2020;382(18):1–14.
  • Wang D, Bo H, Chang H, et al. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus–infected pneumonia in Wuhan, China. JAMA. 2020;323(11):1061–1069. doi:10.1001/jama.2020.158532031570
  • Wang C, Horby PW, Hayden FG, Gao GF. A novel coronavirus outbreak of global health concern. Lancet. 2020;395(10223):15–18. doi:10.1016/S0140-6736(20)30185-931908271
  • Koyama T, Platt D, Parida L. Variant analysis of SARS-CoV-2 genomes. Bull World Heal Organ. 2020;2(June):495–504. doi:10.2471/BLT.20.253591
  • World Health Organization. Infection prevention and control during health care when COVID-19 is suspected. Interim Guid. 2020;(March):1–5.
  • World Health Organization. COVID-19 weekly epidemiological update; 2020 (11).
  • Richardson S, Hirsch JS, Narasimhan M, Crawford JM, Mcginn T, Davidson KW. Presenting characteristics, comorbidities, and outcomes among 5700 patients hospitalized with COVID-19 in the New York City Area. JAMA. 2020;10022(20):2052–2059. doi:10.1001/jama.2020.6775
  • Chen N, Zhou M, Dong X, et al. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet. 2020;395(10223):507–513. doi:10.1016/S0140-6736(20)30211-732007143
  • Yang X, Yu Y, Xu J, et al. Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study. Lancet Respir. 2020;8(5):475–481. doi:10.1016/S2213-2600(20)30079-5
  • Toyoshima Y, Nemoto K, Matsumoto S, Nakamura Y, Kiyotani K. SARS-CoV-2 genomic variations associated with mortality rate of. J Hum Genet. 2020;65(7):1075–1082. doi:10.1038/s10038-020-0808-9.32699345
  • Pachetti M, Marini B, Benedetti F, et al. Emerging SARS ‑ CoV ‑ 2 mutation hot spots include a novel RNA ‑ dependent ‑ RNA polymerase variant. J Transl Med. 2020;18(1):1–9. doi:10.1186/s12967-020-02344-631900168
  • Mousavizadeh L, Ghasemi S. Genotype and phenotype of COVID-19: their roles in pathogenesis. J Microbiol Immunol Infect. 2020;54(2):4. doi:10.1016/j.jmii.2020.03.02232773286
  • Tao Z, Tian J, Pei Y, Yuan M, Zhang Y, Dai F. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579(March):265–269. doi:10.1038/s41586-020-2008-332015508
  • Zhou P, Yang X, Wang X, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020;579(March):270–273. doi:10.1038/s41586-020-2012-732015507
  • Kaushal N, Gupta Y, Goyal M, Khaiboullina SF. Mutational frequencies of SARS-CoV-2 genome during the beginning months of the outbreak in USA. Pathogens. 2020;565(9):1–16.
  • Huang Y, Yang C, Xu X, Xu W, Liu S. Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19. Acta Pharmacol Sin. 2020;41(July):1141–1149. doi:10.1038/s41401-020-0485-432747721
  • Subissi L, Posthuma CC, Collet A, Zevenhoven-dobbe JC, Gorbalenya AE. One severe acute respiratory syndrome coronavirus protein complex integrates processive RNA polymerase and exonuclease activities. Proc Natl Acad Sci USA. 2014;111(E):3900–3909. doi:10.1073/pnas.132370511124567381
  • Jia Y, Shen G, Zhang Y, et al. Analysis of the mutation dynamics of SARS-CoV-2 reveals the spread history and emergence of RBD mutant with lower ACE2 binding affinity. bioRxiv. 2020;1–17.
  • Laha S, Chakraborty J, Das S, Kanti S. Characterizations of SARS-CoV-2 mutational profile, spike protein stability and viral transmission. elsevier. 2020;85(104445):1–12.
  • Biswas SK, Mudi SR. RNA-dependent RNA polymerase and spike protein mutant variants of SARS-CoV-2 predominate in severely affected COVID-19 patients. 2020;(7):1–15.
  • Phan T. Infection, genetics and evolution genetic diversity and evolution of SARS-CoV-2. Infect Genet Evol. 2020;81(February):104260. doi:10.1016/j.meegid.2020.10426032092483
  • Yoshimoto FK. The proteins of severe acute respiratory syndrome coronavirus-2 (SARS CoV-2 or n-COV19), the cause of COVID‑19. Protein J. 2020;39(23):198–216. doi:10.1007/s10930-020-09901-432447571
  • Duffy S. Why are RNA virus mutation rates so damn high? PLOS Biol. 2018;16(8):1–6. doi:10.1371/journal.pbio.3000003
  • Lu R, Zhao X, Li J, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet. 2020;395(10224):565–574. doi:10.1016/S0140-6736(20)30251-832007145
  • Aftab SO, Ghouri MZ, Masood MU, et al. Analysis of SARS-CoV-2 RNA-dependent RNA polymerase as a potential therapeutic drug target using a computational approach. J Transl Med. 2020;18(275):1–15. doi:10.1186/s12967-020-02439-031900168
  • Maria A, Sébastien B, Paul G, et al. A recurrent mutation at position 26,340 of SARS-CoV-2 is associated with failure of the E-gene qRT-PCR utilized in a commercial dual-target diagnostic assay. J Clin Microbiol. 2020;2(July):1–18.
  • Tahamtan A, Ardebili A. Real-time RT-PCR in COVID-19 detection: issues affecting the results. Expert Rev Mol Diagn. 2020;00(0):1–2. doi:10.1080/14737159.2020.1757437
  • Rehman S, Mahmood T, Aziz E, Batool R. Identification of novel mutations in SARS-COV-2 isolates from Turkey. Res Sq. 2020;00:1–21.
  • Begum F, Mukherjee D, Das S, et al. Specific mutations in SARS-CoV2 RNA dependent RNA polymerase and helicase alter protein structure, dynamics and thus function: effect on viral RNA replication. bioRxiv. 2020.
  • Khan MI, Khan ZA, Baig MH, et al. Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: an in silico insight. PLoS One. 2020;3(september):1–18. doi:10.1371/journal.pone.0238344
  • Rahman MS, Islam MR, Alam AS, et al. Evolutionary dynamics of SARS-CoV-2 nucleocapsid protein (N protein) and its consequences. bioRxiv. 2020;1–39.
  • Benvenuto D, Angeletti S, Giovanetti M, et al. Evolutionary analysis of SARS-CoV-2: how mutation of Non-Structural Protein 6 (NSP6) could affect viral autophagy. J Infect. 2020;81(1):e24–7. doi:10.1016/j.jinf.2020.03.058
  • Isabel S, Miraglia LG, Gutierrez JM. Evolutionary and structural analyses of SARS - CoV - 2 D614G spike protein mutation now documented worldwide. Sci Rep. 2020;10(14031):1–9. doi:10.1038/s41598-020-70827-z31913322
  • Watanabe Y, Berndsen ZT, Raghwani J, et al. Vulnerabilities in coronavirus glycan shields despite extensive glycosylation. Nat Commun. 2020:1–10. doi:10.1038/s41467-020-16567-031911652
  • Saha P, Banerjee AK, Tripathi PP, Srivastava AK, Ray U. A virus that has gone viral: amino acid mutation in S protein of Indian isolate of Coronavirus COVID-19 might impact receptor binding, and thus, infectivity. Portl Press. 2020;19:1–8.
  • Li Q, Wu J, Nie J, et al. The impact of mutations in SARS-CoV-2 spike on viral infectivity and antigenicity llll article the impact of mutations in SARS-CoV-2 spike on viral infectivity and antigenicity. Cell Press. 2020;182(9):1284–1294.
  • Hu J, He C-L, Gao Q-Z, et al. D614G mutation of SARS-CoV-2 spike protein enhances viral infectivity. bioRxiv. 2020;1–37.
  • Ou J, Zhou Z, Dai R, et al. Emergence of RBD mutations in circulating SARS-CoV-2 strains enhancing the structural stability and human ACE2 receptor affinity of the spike protein JunxianOu. bioRxiv. 2020;1–30.
  • Volz E, Hill V, McCrone JT, et al. Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity. medRxiv. 2020;44:1–41.
  • Eaaswarkhanth M, Al MA, Al-mulla F. Could the D614G substitution in the SARS-CoV-2 spike (S) protein be associated with higher COVID-19 mortality? Int J Infect Dis. 2020;96:459–460. doi:10.1016/j.ijid.2020.05.07132464271
  • Korber B, Wm F, Gnanakaran S, et al. Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2 Introduction. bioRxiv. 2020;(April):1–33.
  • Zhang L, Jackson CB, Mou H, Ojha A, Rangarajan ES. The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity. bioRxiv. 2020.
  • Wang L, Wang L, Zhuang H. Pro fi ling and characterization of SARS-CoV-2 mutants ’ infectivity and antigenicity. Signal Transduct Target Ther. 2020;(August):1–2. doi:10.1038/s41392-020-00302-832296011
  • Xu W, Wang M, Yu D, Zhang X. Variations in SARS-CoV-2 spike protein cell epitopes and glycosylation profiles during global transmission course of COVID-19. Front Immunol. 2020;11(September):1–12. doi:10.3389/fimmu.2020.56527832038653
  • Chand GB, Banerjee A, Azad GK. Identi fi cation of novel mutations in RNA-dependent RNA polymerases of SARS-CoV-2 and their implications on its protein structure. PeerJ. 2020;8(9492):1–11. doi:10.7717/peerj.9492
  • Karakülah G, Suner A. RdRp mutations are associated with SARS-CoV-2 genome evolution. PeerJ. 2020;8(9587):1–14.
  • Wang Y, Anirudhan V, Du R, Cui Q, Rong L. RNA‐dependent RNA polymerase of SARS‐CoV‐2 as a therapeutic target. J Med Virol. 2020;(July):1–11.
  • Ruan Z, Liu C, Guo Y, He Z, Huang X, Jia X. Potential inhibitors targeting RNA-dependent RNA polymerase activity (NSP12) of SARS-CoV-2. NOT PEER-REVIEWED. 2020;(March):1–16.
  • Goldhill DH, Aartjan JW, Fletcher RA, Langat P, Zambon M, Lackenby A. The mechanism of resistance to favipiravir in influenza. Proc Natl Acad Sci U S A. 2018;115(45):11613–11618. doi:10.1073/pnas.181134511530352857
  • Delang L, Froeyen M, Herdewijn P, Neyts J. Identification of a novel resistance mutation for benzimidazole inhibitors of the HCV RNA-dependent RNA polymerase. Antiviral Res. 2012;93(1):30–38. doi:10.1016/j.antiviral.2011.10.01222033247
  • Badua CL. Genomic and proteomic mutation landscapes of SARS‐CoV‐2.pdf. Wiley. 2020;1(september):1–20.
  • Padhi AK, Shukla R, Tripathi T. Rational design of the remdesivir binding site in the RNA-dependent RNA polymerase of SARS-CoV-2: implications for potential resistance. bioRxiv. 2020;1–26.
  • Agostini ML, Andres EL, Sims AC, et al. Coronavirus susceptibility to the antiviral remdesivir(GS- 5734) is mediated by the viral polymerase and the. Am Soc Microbiol. 2018;9(2):1–15.
  • Holland LA, Kaelin EA, Maqsood R, et al. An 81-nucleotide deletion in SARS-CoV-2 ORF7a identified from sentinel surveillance in Arizona (January to March 2020). J Virol. 2020;94(14). doi:10.1128/JVI.00711-20.
  • Bal A, Destras G, Gaymard A, et al. Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino acid deletion in nsp2 (Asp268del). Clin Microbiol Infect. 2020;26(7):960–962. doi:10.1016/j.cmi.2020.03.02032234449
  • Benedetti F, Snyder GA, Giovanetti M, et al. Emerging of a SARS-CoV-2 viral strain with a deletion in nsp1. J Transl Med. 2020;18(1). doi:10.1186/s12967-020-02507-5.