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Thinking Outside the Triangle: Replication Fidelity of the Largest RNA Viruses
Abstract
When judged by ubiquity, adaptation, and emergence of new diseases, RNA viruses are arguably the most successful biological organisms. This success has been attributed to a defect of sorts: high mutation rates (low fidelity) resulting in mutant swarms that allow rapid selection for fitness in new environments. Studies of viruses with small RNA genomes have identified fidelity determinants in viral RNA-dependent RNA polymerases and have shown that RNA viruses likely replicate within a limited fidelity range to maintain fitness. In this review we compare the fidelity of small RNA viruses with that of the largest RNA viruses, the coronaviruses. Coronaviruses encode the first known viral RNA proofreading exoribonuclease, a function that likely allowed expansion of the coronavirus genome and that dramatically increases replication fidelity and the range of tolerated variation. We propose models for regulation of coronavirus fidelity and discuss the implications of altered fidelity for RNA virus replication, pathogenesis, and evolution.
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“This editing efficiency at a specific site is a few orders of magnitude higher compared with the estimated ~ 10–6–10–7 random incorporation error rate for Coronaviruses replication53.”
From The roles of APOBEC-mediated RNA editing in SARS-CoV-2 mutations, replication and fitness (2022) · cites this paper as [53]
Citations
Cites
Selforganization of matter and the evolution of biological macromolecules
Eigen, M. (1971) · Die Naturwissenschaften · doi:10.1007/bf00623322 · Cited by 3,788
Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor
Ge, X.-Y., Li, J.-L., Yang, X.-L., Chmura, A. A., Zhu, G., Epstein, J. H., Mazet, J. K., Hu, B., Zhang, W., Peng, C., et al. (2013) · Nature · doi:10.1038/nature12711 · Cited by 1,778
Mutation rates among RNA viruses
Drake, J. W., & Holland, J. J. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.24.13910 · Cited by 1,143
Vignuzzi, M., Stone, J. K., Arnold, J. J., Cameron, C. E., & Andino, R. (2006) · Nature · doi:10.1038/nature04388 · Cited by 1,116
Domingo, E., Sheldon, J., & Perales, C. (2012) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.05023-11 · Cited by 1,009
Kunkel, T. A., & Bebenek, K. (2000) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.69.1.497 · Cited by 1,003
Kunkel, T. A. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.r400006200 · Cited by 754
Lack of evidence for proofreading mechanisms associated with an RNA virus polymerase
Steinhauer, D. A., Domingo, E., & Holland, J. J. (1992) · Gene · doi:10.1016/0378-1119(92)90216-c · Cited by 415
Arnold, J. J., & Cameron, C. E. (2004) · Biochemistry · doi:10.1021/bi035212y · Cited by 178
Flagged first, then by citations
Research works printed but not linked: 113
- 10.1128/JVI.00694-10 · DOI
- 10.1534/genetics.113.154963 · DOI
- 10.1038/nrmicro3143 · DOI
- 10.1128/JVI.00906-12 · DOI
- 10.3201/eid1509.090224 · DOI
- 10.3390/v4123689 · DOI
- 10.1128/JVI.79.3.1595-1604.2005 · DOI
- 10.1007/s00705-005-0573-2 · DOI
- 10.1016/S0140-6736(03)13077-2 · DOI
- 10.1056/NEJMoa1211721 · DOI
- 10.3181/0903-MR-94 · DOI
- 10.1016/j.antiviral.2013.10.013 · DOI
- 10.1128/JVI.03273-12 · DOI
- 10.1128/CMR.00017-06 · DOI
- 10.1016/j.antiviral.2013.08.015 · DOI
- 10.1016/S1473-3099(13)70690-X · DOI
- 10.1128/mBio.01002-14 · DOI
- 10.1016/S1473-3099(13)70304-9 · DOI
- 10.1016/S0140-6736(13)61492-0 · DOI
- 10.1038/nrmicro2147 · DOI
- 10.1002/j.1460-2075.1987.tb02713.x · DOI
- 10.1371/journal.pbio.0030172 · DOI
- 10.1016/S0022-2836(03)00865-9 · DOI
- 10.1099/0022-1317-81-4-853 · DOI
- 10.1073/pnas.1000378107 · DOI
- 10.1038/sj.emboj.7601368 · DOI
- 10.1093/nar/gkr893 · DOI
- 10.1093/nar/gkp904 · DOI
- 10.1016/j.virol.2005.02.017 · DOI
- 10.1007/s00705-012-1404-x · DOI
- 10.1017/S1355838200000728 · DOI
- 10.1128/JVI.78.14.7833-7838.2004 · DOI
- 10.1073/pnas.0808790106 · DOI
- 10.1073/pnas.0508200103 · DOI
- 10.1073/pnas.0403127101 · DOI
- 10.1128/JVI.00407-08 · DOI
- 10.1038/nsmb999 · DOI
- 10.1128/JVI.02805-06 · DOI
- 10.1371/journal.ppat.1000863 · DOI
- 10.1073/pnas.1201130109 · DOI
- 10.1371/journal.ppat.1002059 · DOI
- 44. Chen Y, Su C, Ke M, Jin X, Xu L, et al. 2011. Biochemical and structural insights into the mechanisms of SARS coronavirus RNA ribose 2′-O-methylation by nsp16/nsp10 protein complex. PLoS Pathog. 7:e1002294 · DOI
- 10.1093/nar/gkg916 · DOI
- 10.1016/S0022-2836(02)01033-1 · DOI
- 10.1111/j.1574-6976.2012.00338.x · DOI
- 10.1073/pnas.88.16.7160 · DOI · Paper page
- 10.2174/1874404400903010009 · DOI
- 10.1016/S0092-8674(04)00252-1 · DOI
- 10.1002/anie.200504296 · DOI
- 10.1016/S0092-8674(01)00367-1 · DOI
- 10.1016/j.virusres.2004.11.004 · DOI
- 10.1016/j.sbi.2009.10.012 · DOI
- 10.1016/j.jmb.2011.04.078 · DOI
- 10.1016/j.str.2012.06.012 · DOI
- 10.1073/pnas.88.21.9473 · DOI
- 10.1002/j.1460-2075.1989.tb08516.x · DOI
- 10.1038/cr.2008.4 · DOI
- 10.1016/j.virusres.2006.01.017 · DOI
- 10.1371/journal.ppat.1003565 · DOI
- 10.1128/JVI.01296-07 · DOI
- 10.1371/journal.ppat.1000896 · DOI
- 10.1038/nm.2972 · DOI
- 10.1016/j.coviro.2011.12.004 · DOI
- 10.1371/journal.ppat.1001005 · DOI
- 10.1016/j.virusres.2011.09.018 · DOI
- 10.1038/nrmicro3003 · DOI
- 10.1073/pnas.1204022109 · DOI
- 10.1073/pnas.0501062102 · DOI
- 10.1128/JVI.79.18.11555-11558.2005 · DOI
- Lee CH, 1997, J. Virol., 71, 3636, 10.1128/jvi.71.5.3636-3640.1997 · DOI
- 10.1371/journal.ppat.0010011 · DOI
- 10.1038/nm1726 · DOI
- 10.1098/rspb.2012.2047 · DOI
- Schaaper RM, 1998, Genetics, 148, 1579, 10.1093/genetics/148.4.1579 · DOI
- Muzyczka N, 1972, J. Biol. Chem., 247, 7116, 10.1016/S0021-9258(19)44602-4 · DOI
- Gillin FD, 1976, J. Biol. Chem., 251, 5219, 10.1016/S0021-9258(17)33149-6 · DOI
- 10.1073/pnas.1232294100 · DOI
- 10.1073/pnas.1111650108 · DOI
- 10.1128/JVI.01374-07 · DOI
- 10.1074/jbc.M503444200 · DOI
- 10.1371/journal.ppat.1003877 · DOI
- 10.1016/j.antiviral.2013.07.008 · DOI
- 92. Zeng J, Wang H, Xie X, Li C, Zhou G, et al. 2014. Ribavirin-resistant variants of foot-and-mouth disease virus: the effect of restricted quasispecies diversity on viral virulence. J. Virol. 88:4008–20 · DOI
- 10.1074/jbc.M113.484428 · DOI
- 10.1016/j.virusres.2013.06.019 · DOI
- 10.1128/JVI.02139-12 · DOI
- 10.1074/jbc.C112.401471 · DOI
- 10.1128/JVI.01297-08 · DOI
- 10.1371/journal.ppat.1001163 · DOI
- 10.1128/JVI.01606-06 · DOI
- 10.1371/journal.ppat.1002215 · DOI
- 10.1128/mBio.00077-11 · DOI
- 10.1093/nar/29.5.1017 · DOI
- 10.1128/JVI.00061-13 · DOI
- 10.1371/journal.ppat.1003760 · DOI
- 10.1073/pnas.1016404108 · DOI
- 10.1371/journal.ppat.1002433 · DOI
- 10.1016/j.molimm.2011.03.004 · DOI
- 10.1128/JVI.02220-08 · DOI
- 10.1038/ng1621 · DOI · Paper page
- 10.1038/280445a0 · DOI · Paper page
- 10.1371/journal.ppat.1003500 · DOI
- 10.1371/journal.pone.0000459 · DOI
- 10.1371/journal.pone.0003299 · DOI
- 10.1016/j.virusres.2007.11.017 · DOI
- 10.1016/j.antiviral.2013.11.006 · DOI
- 10.1101/cshperspect.a012799 · DOI
- Studwell-Vaughan PS, 1993, J. Biol. Chem., 268, 11785, 10.1016/S0021-9258(19)50268-X · DOI
- 10.1128/JB.186.9.2774-2780.2004 · DOI
- 10.1099/0022-1317-82-2-385 · DOI
- 10.1016/j.bbapap.2009.06.018 · DOI
- 10.1038/ni.1979 · DOI · Paper page
- 10.1073/pnas.0307877101 · DOI
Cited by
Sorted by citations
Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody
Pinto, D., Park, Y.-J., Beltramello, M., Walls, A. C., Tortorici, M. A., Bianchi, S., Jaconi, S., Culap, K., Zatta, F., De Marco, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2349-y · Cited by 1,885
Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant
Yurkovetskiy, L., Wang, X., Pascal, K. E., Tomkins-Tinch, C., Nyalile, T. P., Wang, Y., Baum, A., Diehl, W. E., Dauphin, A., Carbone, C., et al. (2020) · Cell · doi:10.1016/j.cell.2020.09.032 · Cited by 1,025
Walls, A. C., Fiala, B., Schäfer, A., Wrenn, S., Pham, M. N., Murphy, M., Tse, L. V., Shehata, L., O’Connor, M. A., Chen, C., et al. (2020) · Cell · doi:10.1016/j.cell.2020.10.043 · Cited by 532
Lessons for COVID-19 immunity from other coronavirus infections
Sariol, A., & Perlman, S. (2020) · Immunity · doi:10.1016/j.immuni.2020.07.005 · Cited by 317
The roles of APOBEC-mediated RNA editing in SARS-CoV-2 mutations, replication and fitness
Kim, K., Calabrese, P., Wang, S., Qin, C., Rao, Y., Feng, P., & Chen, X. S. (2022) · Scientific Reports · doi:10.1038/s41598-022-19067-x · Cited by 115
Metadata
- Authors
- Smith, E. C., Sexton, N. R., & Denison, M. R.
- Affiliations
- Department of Pediatrics,
- Department of Pathology, Microbiology, and Immunology, and
- Venue
- Annual Review of Virology
- Publisher
- Annual Reviews
- Published
- 2014-11-03
- Volume
- 1
- Issue
- 1
- Pages
- 111-132
- ISSN
- 2327-056X
- 2327-0578
- Cited by
- 127
- References
- 9
- Language
- en
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