The DOI matches its Crossref record; 17 of the 17 references it cites were found in a registry or an index.
A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants
Open accessPublished version of a preprint
Abstract
Significance: The rapid spread of the virus causing COVID-19, SARS-CoV-2, raises questions about the possibility of a universally effective vaccine. The virus can mutate in a given individual, and these variants can be propagated across populations and time. To understand this process, we analyze 18,514 SARS-CoV-2 sequences sampled since December 2019. We find that neutral evolution, rather than adaptive selection, can explain the rare mutations seen across SARS-CoV-2 genomes. In the immunogenic Spike protein, the D614G mutation has become consensus, yet there is no evidence of mutations affecting binding to the ACE2 receptor. Our results suggest that, to date, the limited diversity seen in SARS-CoV-2 should not preclude a single vaccine from providing global protection.
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.
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
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209
ModelFinder: fast model selection for accurate phylogenetic estimates
Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A., & Jermiin, L. S. (2017) · Nature Methods · doi:10.1038/nmeth.4285 · Cited by 18,449
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
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009490 · Cited by 14,894
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
An interactive web-based dashboard to track COVID-19 in real time
Dong, E., Du, H., & Gardner, L. (2020) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(20)30120-1 · Cited by 10,048
Korber, B., Fischer, W. M., Gnanakaran, S., Yoon, H., Theiler, J., Abfalterer, W., Hengartner, N., Giorgi, E. E., Bhattacharya, T., Foley, B., et al. (2020) · Cell · doi:10.1016/j.cell.2020.06.043 · Cited by 4,281
Ou, X., Liu, Y., Lei, X., Li, P., Mi, D., Ren, L., Guo, L., Guo, R., Chen, T., Hu, J., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15562-9 · Cited by 3,097
Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period
Kissler, S. M., Tedijanto, C., Goldstein, E., Grad, Y. H., & Lipsitch, M. (2020) · Science · doi:10.1126/science.abb5793 · Cited by 2,611
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology
Rambaut, A., Holmes, E. C., O’Toole, Á., Hill, V., McCrone, J. T., Ruis, C., du Plessis, L., & Pybus, O. G. (2020) · Nature Microbiology · doi:10.1038/s41564-020-0770-5 · Cited by 2,543
Research works printed but not linked: 47
- F. Wu . Neutralizing antibody responses to SARS-CoV-2 in a COVID-19 recovered patient cohort and their implications. medRxiv:10.1101/2020.03.30.20047365 (20 April 2020). · DOI · Paper page
- 10.1016/j.celrep.2020.107725 · DOI · Paper page
- 10.1038/s41586-020-2012-7 · DOI · Paper page
- 10.1001/jama.2020.2648 · DOI · Paper page
- A. Latinne . Origin and cross-species transmission of bat coronaviruses in China. bioRxiv:10.1101/2020.05.31.116061 (31 May 2020). · DOI
- 10.1016/j.cub.2020.05.023 · DOI · Paper page
- 10.1038/s41586-020-2169-0 · DOI · Paper page
- 10.1038/s41586-020-2313-x · DOI · Paper page
- S. Duchene . Temporal signal and the phylodynamic threshold of SARS-CoV-2. bioRxiv:10.1101/2020.05.04.077735 (4 May 2020). · DOI
- 10.1038/nrg2323 · DOI · Paper page
- 10.1098/rspb.2014.0732 · DOI · Paper page
- 10.1038/nature13087 · DOI · Paper page
- 10.1016/j.cell.2015.07.020 · DOI · Paper page
- 10.1016/j.cell.2015.06.007 · DOI · Paper page
- M. Worobey . The emergence of SARS-CoV-2 in Europe and the US. bioRxiv:10.1101/2020.05.21.109322 (23 May 2020). · DOI
- L. Zhang . The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity. bioRxiv:10.1101/2020.06.12.148726 (12 June 2020). · DOI
- S. Ozono . Naturally mutated spike proteins of SARS-CoV-2 variants show differential levels of cell entry. bioRxiv:10.1101/2020.06.15.151779 (26 June 2020). · DOI
- J. Hu . D614G mutation of SARS-CoV-2 spike protein enhances viral infectivity. bioRxiv:10.1101/2020.06.20.161323 (6 July 2020). · DOI
- 10.1073/pnas.70.12.3321 · DOI · Paper page
- 10.1111/j.1365-294X.2008.03887.x · DOI · Paper page
- 10.1111/j.1755-0998.2012.03174.x · DOI · Paper page
- 10.7554/eLife.03568 · DOI · Paper page
- 10.1371/journal.pcbi.1004312 · DOI
- 10.1093/sysbio/syx046 · DOI
- 10.1093/sysbio/syv116 · DOI
- 10.1093/ve/vez044 · DOI
- 10.1126/science.1070441 · DOI · Paper page
- 10.1016/j.cell.2020.02.058 · doi:10.1016/j.cell.2020.02.058 · Paper page
- 10.1586/erv.09.43 · DOI · Paper page
- 10.1128/JVI.02002-17 · DOI · Paper page
- 10.1126/science.1256427 · DOI · Paper page
- 10.7554/eLife.49324 · DOI
- 10.1016/j.chom.2017.02.002 · DOI
- 10.1111/gtc.12463 · DOI
- 10.1128/JVI.01913-16 · DOI
- G. Wong ., Naturally occurring single mutations in Ebola virus observably impact infectivity. J. Virol. 93, e01098-18 (2018).
- 10.1016/j.celrep.2018.04.027 · DOI
- 10.1093/ve/vew007 · DOI · Paper page
- 10.1093/bioinformatics/bty633 · DOI · Paper page
- 10.1093/molbev/msy194 · DOI · Paper page
- 10.1093/molbev/msu300 · DOI · Paper page
- 10.1093/molbev/msi105 · DOI · Paper page
- 10.1111/j.1365-294X.2010.04996.x · DOI · Paper page
- 10.1111/2041-210X.12526 · DOI · Paper page
- 10.1093/oxfordjournals.molbev.a026369 · DOI · Paper page
- 10.1093/nar/gkaa379 · DOI · Paper page
- 10.1111/tan.13811 · DOI · Paper page
Cited by
Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants
Weisblum, Y., Schmidt, F., Zhang, F., DaSilva, J., Poston, D., Lorenzi, J. C., Muecksch, F., Rutkowska, M., Hoffmann, H.-H., Michailidis, E., et al. (2020) · eLife · doi:10.7554/elife.61312 · Cited by 1,308
Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity
Volz, E., Hill, V., McCrone, J. T., Price, A., Jorgensen, D., O’Toole, Á., Southgate, J., Johnson, R., Jackson, B., Nascimento, F. F., et al. (2021) · Cell · doi:10.1016/j.cell.2020.11.020 · Cited by 1,006
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
Emergence of genomic diversity and recurrent mutations in SARS-CoV-2
van Dorp, L., Acman, M., Richard, D., Shaw, L. P., Ford, C. E., Ormond, L., Owen, C. J., Pang, J., Tan, C. C. S., Boshier, F. A. T., et al. (2020) · Infection, Genetics and Evolution · doi:10.1016/j.meegid.2020.104351 · Cited by 774
Thomson, E. C., Rosen, L. E., Shepherd, J. G., Spreafico, R., da Silva Filipe, A., Wojcechowskyj, J. A., Davis, C., Piccoli, L., Pascall, D. J., Dillen, J., et al. (2021) · Cell · doi:10.1016/j.cell.2021.01.037 · Cited by 606
Metadata
- Authors
- Dearlove, B., Lewitus, E., Bai, H., Li, Y., Reeves, D. B., Joyce, M. G., Scott, P. T., Amare, M. F., Vasan, S., Michael, N. L., Modjarrad, K., & Rolland, M.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2020-08-31
- Volume
- 117
- Issue
- 38
- Pages
- 23652-23662
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W3082387069
- Cited by
- 200
- References
- 17
- FWCI
- 5.73
- Type
- journal article
- Language
- en
- Open access
- hybrid
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
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. https://app.cochat.ai/papers/10.1073/pnas.2008281117
- The paper
- Dearlove, B., Lewitus, E., Bai, H., Li, Y., Reeves, D. B., Joyce, M. G., Scott, P. T., Amare, M. F., Vasan, S., Michael, N. L., Modjarrad, K., & Rolland, M. (2020). A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2008281117
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.