The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Rampant C→U Hypermutation in the Genomes of SARS-CoV-2 and Other Coronaviruses: Causes and Consequences for Their Short- and Long-Term Evolutionary Trajectories
Published version of a preprint
Abstract
The wealth of accurately curated sequence data for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), its long genome, and its low substitution rate provides a relatively blank canvas with which to investigate effects of mutational and editing processes imposed by the host cell. The finding that a large proportion of sequence change in SARS-CoV-2 in the initial months of the pandemic comprised C→U mutations in a host APOBEC-like context provides evidence for a potent host-driven antiviral editing mechanism against coronaviruses more often associated with antiretroviral defense. In evolutionary terms, the contribution of biased, convergent, and context-dependent mutations to sequence change in SARS-CoV-2 is substantial, and these processes are not incorporated by standard models used in molecular epidemiology investigations.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Recent analysis of SARS-CoV-2 and rubella vaccine virus genome data derived from patients show predominant mutational patterns with specific signatures rather than random genetic variations, suggesting that the host-factor induced mutations play an important role in shaping the viral genomic RNA mutational outcome and evolution11–14.”
From The roles of APOBEC-mediated RNA editing in SARS-CoV-2 mutations, replication and fitness (2022) · cites this paper as [12]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Prior bioinformatic analysis of the SARS-CoV-2 sequences suggested that some of the C-to-U mutations may be caused by APOBEC proteins instead of the random mutations caused by viral RNA polymerase during replication or ROS11,12,14,27,51,52.”
From The roles of APOBEC-mediated RNA editing in SARS-CoV-2 mutations, replication and fitness (2022) · cites this paper as [12]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“Interestingly, the database analysis of SARS-CoV-2 genomic variations showed an overwhelmingly high C-to-U mutation rate, account for about 40% of all single nucleotide variations, which was interpreted as a result of RNA editing by host APOBECs rather than random mutations11,12,14,27.”
From The roles of APOBEC-mediated RNA editing in SARS-CoV-2 mutations, replication and fitness (2022) · cites this paper as [12]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
A novel coronavirus from patients with pneumonia in China, 2019
Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., Zhao, X., Huang, B., Shi, W., Lu, R., et al. (2020) · New England Journal of Medicine · doi:10.1056/nejmoa2001017 · Cited by 28,244
Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia
Li, Q., Guan, X., Wu, P., Wang, X., Zhou, L., Tong, Y., Ren, R., Leung, K. S. M., Lau, E. H. Y., Wong, J. Y., et al. (2020) · New England Journal of Medicine · doi:10.1056/nejmoa2001316 · Cited by 16,575
A new coronavirus associated with human respiratory disease in China
Wu, F., Zhao, S., Yu, B., Chen, Y.-M., Wang, W., Song, Z.-G., Hu, Y., Tao, Z.-W., Tian, J.-H., Pei, Y.-Y., et al. (2020) · Nature · doi:10.1038/s41586-020-2008-3 · Cited by 11,688
Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts
Mangeat, B., Turelli, P., Caron, G., Friedli, M., Perrin, L., & Trono, D. (2003) · Nature · doi:10.1038/nature01709 · Cited by 1,486
Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G
Sawyer, S. L., Emerman, M., & Malik, H. S. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020275 · Cited by 485
Flagged first, then by citations
Research works printed but not linked: 36
- 10.1038/s41586-020-2012-7 · DOI · Paper page
- Mavian C, Marini S, Manes C, Capua I, Prosperi M, Salemi M. 20 March 2020. Regaining perspective on SARS-CoV-2 molecular tracing and its implications. medRxiv https://www.medrxiv.org/content/10.1101/2020.03.16.20034470v1. · DOI
- 10.1371/journal.ppat.1003565 · DOI
- 10.1371/journal.ppat.1000896 · DOI
- 10.1128/JVI.01296-07 · DOI
- 10.1128/jvi.78.3.1602-1603.2004 · DOI
- 10.1016/0042-6822(92)91195-z · DOI
- 10.1128/JVI.79.5.3223-3225.2005 · DOI
- 10.1016/j.meegid.2018.04.031 · DOI
- 10.1016/j.prevetmed.2015.11.001 · DOI
- 10.1128/mBio.01062-13 · DOI
- 10.1016/j.virol.2007.08.010 · DOI
- 10.1186/1471-2164-14-610 · DOI
- 10.1186/s13059-019-1659-6 · DOI
- 10.1016/j.virol.2010.12.004 · DOI
- 10.1038/nature01707 · DOI
- 10.1016/s0092-8674(03)00423-9 · DOI
- 10.1073/pnas.91.8.3092 · DOI
- 10.1016/j.virol.2015.03.012 · DOI · Paper page
- 10.1186/1471-2148-12-71 · DOI
- 10.1371/journal.pone.0030036 · DOI
- 10.1074/jbc.M602367200 · DOI
- 10.1126/science.1100658 · DOI
- 10.1099/vir.0.038919-0 · DOI
- 10.1016/j.antiviral.2019.03.005 · DOI
- 10.1038/s41598-018-24448-2 · DOI
- 10.1038/ncomms7881 · DOI · Paper page
- 10.1186/s13059-019-1651-1 · DOI
- 10.1038/srep39100 · DOI · Paper page
- 10.1093/nar/gkz1164 · DOI
- 10.1126/sciadv.abb5813 · DOI · Paper page
- 10.1016/j.virusres.2014.11.031 · DOI
- 10.1111/j.1863-2378.2012.01528.x · DOI
- 10.1016/bs.aivir.2018.01.001 · DOI
- 10.1186/1756-0500-5-50 · DOI
- 10.1093/molbev/mst197 · DOI
Cited by
Sorted by citations
Markov, P. V., Ghafari, M., Beer, M., Lythgoe, K., Simmonds, P., Stilianakis, N. I., & Katzourakis, A. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-023-00878-2 · Cited by 1,179
The biological and clinical significance of emerging SARS-CoV-2 variants
Tao, K., Tzou, P. L., Nouhin, J., Gupta, R. K., de Oliveira, T., Kosakovsky Pond, S. L., Fera, D., & Shafer, R. W. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00408-x · Cited by 1,009
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
Gupta, M., Azumaya, C. M., Moritz, M., Pourmal, S., Diallo, A., Merz, G. E., Jang, G., Bouhaddou, M., Fossati, A., Brilot, A. F., et al. (2021) · doi:10.1101/2021.05.10.443524 · Cited by 89
Metadata
- Authors
- Simmonds, P.
- Affiliations
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- ORCID
- Simmonds, P.
- Venue
- mSphere
- Publisher
- American Society for Microbiology
- Published
- 2020-06-24
- Volume
- 5
- Issue
- 3
- ISSN
- 2379-5042
- PMC
- PMC7316492
- Cited by
- 245
- References
- 5
- Language
- en
- Funders
- Wellcome Trust (WT103767MA)
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
