Have a personal or library account? Click to login
The Worldwide Search for the New Mutations in the RNA-Directed RNA Polymerase Domain of SARS-CoV-2 Cover

The Worldwide Search for the New Mutations in the RNA-Directed RNA Polymerase Domain of SARS-CoV-2

Open Access
|Mar 2021

References

  1. 1. Wu, Z., Yang, L., Ren, X., He, G., Zhang, J., Yang, J., Qian, Z., et al. (2016). Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases. ISME J. 10(3): 609-620. https://doi.org/10.1038/ismej.2015.138 PMid:26262818 PMCid:PMC481768610.1038/ismej.2015.138481768626262818
  2. 2. Huang, J., Song, W., Huang, H., Sun, Q. (2020). Pharmacological therapeutics targeting RNA-dependent RNA polymerase, proteinase and spike protein: from mechanistic studies to clinical trials for COVID-19. J Clin Med. 9(4): 1131. https://doi.org/10.3390/jcm9041131 PMid:32326602 PMCid:PMC723116610.3390/jcm9041131723116632326602
  3. 3. Ge, X.Y., Li, J.L., Yang, X.L., Chmura, A.A., Zhu, G., Epstein, J.H., Mazet, J.K., et al. (2013). Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature 503(7477): 535-538. https://doi.org/10.1038/nature12711 PMid:24172901 PMCid:PMC538986410.1038/nature12711538986424172901
  4. 4. Oreshkova, N., Molenaar, R.J., Vreman, S., Harders, F., Munnink, B.B.O., Hakze R., Gerhards, N., et al. (2020). SARS-CoV2 infection in farmed mink, Netherlands, April 2020 [Internet]. Microbiology; 2020 May [cited 2020 May 23]. Available from: http://biorxiv.org/lookup/doi/10.1101/2020.05.18.101493https://doi.org/10.1101/2020.05.18.101493
  5. 5. Gretebeck, L.M., Subbarao, K. (2015). Animal models for SARS and MERS coronaviruses. Curr Opin Virol. 13, 123-129. https://doi.org/10.1016/j.coviro.2015.06.009 PMid:26184451 PMCid:PMC455049810.1016/j.coviro.2015.06.009455049826184451
  6. 6. Dabravolski, S. (2020). The worldwide search for the new mutations in the RNA-directed RNA polymerase domain of SARS-CoV-2 [Supplementary data and figures]. Available at: https://osf.io/xtz6a/. https://doi.org/10.17605/OSF.IO/XTZ6A
  7. 7. Edgar, R.C. (2004). Muscle: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5, 113. https://doi.org/10.1186/1471-2105-5-113 PMid:15318951 PMCid:PMC51770610.1186/1471-2105-5-11351770615318951
  8. 8. Okonechnikov, K., Golosova, O., Fursov, M. (2012). Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 28(8): 1166-1167. https://doi.org/10.1093/bioinformatics/bts091 PMid:2236824810.1093/bioinformatics/bts09122368248
  9. 9. Buchan, D.W.A., Jones, D.T. (2019). The PSIPRED protein analysis workbench: 20 years on. Nucleic Acids Res. 47(W1): W402-W407. https://doi.org/10.1093/nar/gkz297 PMid:31251384 PMCid:PMC660244510.1093/nar/gkz297660244531251384
  10. 10. Laimer, J., Hiebl-Flach, J., Lengauer, D., Lackner, P. (2016). MAESTRO web: a web server for structure-based protein stability prediction. Bioinformatics 32(9): 1414-1416. https://doi.org/10.1093/bioinformatics/btv769 PMid:2674350810.1093/bioinformatics/btv76926743508
  11. 11. Rodrigues, C.H.M., Pires, D.E.V., Ascher, D.B. (2018). DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability. Nucleic Acids Res. 46(W1): W350-W355. https://doi.org/10.1093/nar/gky300 PMid:29718330 PMCid:PMC603106410.1093/nar/gky300603106429718330
  12. 12. Pires, D.E.V., Ascher, D.B., Blundell, T.L. (2014). DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach. Nucleic Acids Res. 42(W1):W314-W319. https://doi.org/10.1093/nar/gku411 PMid:24829462 PMCid:PMC408614310.1093/nar/gku411408614324829462
  13. 13. Duffy, S. (2018). Why are RNA virus mutation rates so damn high? PLOS Biol. 16(8): e3000003. https://doi.org/10.1371/journal.pbio.3000003 PMid:30102691 PMCid:PMC610725310.1371/journal.pbio.3000003610725330102691
  14. 14. Smith, E.C., Denison, M.R. (2013). Coronaviruses as DNA wannabes: a new model for the regulation of RNA virus replication fidelity. PLoS Pathog. 9(12): e1003760. https://doi.org/10.1371/journal.ppat.1003760 PMid:24348241 PMCid:PMC385779910.1371/journal.ppat.1003760385779924348241
  15. 15. Irwin, K.K., Renzette, N., Kowalik, T.F., Jensen, J.D. (2015). Antiviral drug resistance as an adaptive process. Virus Evol. 2(1): vew014. https://doi.org/10.1093/ve/vew014 PMid:28694997 PMCid:PMC549964210.1093/ve/vew014549964228694997
  16. 16. Frappier, V., Chartier, M., Najmanovich, R.J. (2015). ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability. Nucleic Acids Res. 43(W1): W395-400. https://doi.org/10.1093/nar/gkv343 PMid:25883149 PMCid:PMC448926410.1093/nar/gkv343448926425883149
  17. 17. Bao, L., Deng, W., Huang, B., Gao, H., Liu, J., Ren, L., Wei, Q., et al. (2020). The pathogenicity of SARS-CoV-2 in hACE2 transgenic mice. Nature 583(7818): 830-833. https://doi.org/10.1038/s41586-020-2312-y PMid:3238051110.1038/s41586-020-2312-y32380511
  18. 18. Zhou, P., Yang, X.L., Wang, X.G., Hu, B., Zhang, L., Zhang, W., Si, H.R., et al. (2020). A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579(7798): 270-273.
  19. 19. Sexton, N.R., Smith, E.C., Blanc, H., Vignuzzi, M., Peersen, O.B., Denison, M.R. (2016). Homology-based identification of a mutation in the coronavirus RNA-dependent RNA polymerase that confers resistance to multiple mutagens. J Virol. 90(16): 7415-7428. https://doi.org/10.1128/JVI.00080-16 PMid:27279608 PMCid:PMC498465510.1128/JVI.00080-16498465527279608
  20. 20. Ruan, Z., Liu, C., Guo, Y., He, Z., Huang, X., Jia, X. (2020). Potential inhibitors targeting RNA-dependent RNA polymerase activity (NSP12) of SARS-CoV-2 [Internet]. Preprints 2020030024 [cited 2020 May 23]. Available from: https://www.preprints.org/manuscript/202003.0024/v1https://doi.org/10.20944/preprints202003.0024.v110.20944/preprints202003.0024.v1
  21. 21. Pfeiffer, J.K., Kirkegaard, K. (2003). A single mutation in poliovirus RNA-dependent RNA polymerase confers resistance to mutagenic nucleotide analogs via increased fidelity. Proc Natl Acad Sci U S A. 100(12): 7289-7294. https://doi.org/10.1073/pnas.1232294100 PMid:12754380 PMCid:PMC16586810.1073/pnas.123229410016586812754380
  22. 22. Neogi, U., Hill, K.J., Ambikan, A.T., Heng, X., Quinn, T.P., Byrareddy, S.N., Sönnerborg, A., et al. (2020). Feasibility of known RNA polymerase inhibitors as Anti-SARS-CoV-2 drugs. Pathogens 9(5): 320. https://doi.org/10.3390/pathogens9050320 PMid:32357471 PMCid:PMC728137110.3390/pathogens9050320728137132357471
  23. 23. Shannon, A., Le, N.T.T., Selisko, B., Eydoux, C., Alvarez, K., Guillemot, J.C., Decroly, E., et al. (2020). Remdesivir and SARS-CoV-2: Structural requirements at both nsp12 RdRp and nsp14 Exonuclease active-sites. Antiviral Res. 178, 104793. https://doi.org/10.1016/j.antiviral.2020.104793 PMid:32283108 PMCid:PMC715149510.1016/j.antiviral.2020.104793715149532283108
  24. 24. Gao, Y., Yan, L., Huang, Y., Liu, F., Zhao, Y., Cao, L., Wang, T., et al. (2020). Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Science 368(6492): 779-782. https://doi.org/10.1126/science.abb7498 PMid:32277040 PMCid:PMC716439210.1126/science.abb7498716439232277040
  25. 25. Wang, M., Cao, R., Zhang, L., Yang, X., Liu, J., Xu, M., Shi, Z., et al. (2020). Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res. 30(3): 269-271. https://doi.org/10.1038/s41422-020-0282-0 PMid:32020029 PMCid:PMC705440810.1038/s41422-020-0282-0705440832020029
  26. 26. Pachetti, M., Marini, B., Benedetti, F., Giudici, F., Mauro, E., Storici, P., Masciovecchio, C., et al. (2020). Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant. J Transl Med. 18(1): 179. https://doi.org/10.1186/s12967-020-02344-6 PMid:32321524 PMCid:PMC717492210.1186/s12967-020-02344-6717492232321524
  27. 27. Coppée, F., Lechien, J.R., Declèves, A.E., Tafforeau, L., Saussez, S. (2020). Severe acute respiratory syndrome coronavirus 2: virus mutations in specific European populations. New Microbes New Infect. 36, 100696. https://doi.org/10.1016/j.nmni.2020.100696 PMid:32509310 PMCid:PMC723899710.1016/j.nmni.2020.100696723899732509310
  28. 28. Chand, G.B., Banerjee, A., Azad, G.K. (2020). Identification of novel mutations in RNA-dependent RNA polymerases of SARS-CoV-2 and their implications on its protein structure. PeerJ. 8, e9492. https://doi.org/10.7717/peerj.9492 PMid:32685291 PMCid:PMC733703210.7717/peerj.9492733703232685291
Language: English
Page range: 87 - 94
Submitted on: Jun 24, 2020
Accepted on: Nov 12, 2020
Published on: Mar 15, 2021
Published by: Ss. Cyril and Methodius University in Skopje
In partnership with: Paradigm Publishing Services
Publication frequency: 2 issues per year

© 2021 Siarhei A. Dabravolski, Yury K. Kavalionak, published by Ss. Cyril and Methodius University in Skopje
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.