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The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages
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Abstract
The independent emergence late in 2020 of the B.1.1.7, B.1.351, and P.1 lineages of SARS-CoV-2 prompted renewed concerns about the evolutionary capacity of this virus to overcome public health interventions and rising population immunity. Here, by examining patterns of synonymous and non-synonymous mutations that have accumulated in SARS-CoV-2 genomes since the pandemic began, we find that the emergence of these three “501Y lineages” coincided with a major global shift in the selective forces acting on various SARS-CoV-2 genes. Following their emergence, the adaptive evolution of 501Y lineage viruses has involved repeated selectively favored convergent mutations at 35 genome sites, mutations we refer to as the 501Y meta-signature. The ongoing convergence of viruses in many other lineages on this meta-signature suggests that it includes multiple mutation combinations capable of promoting the persistence of diverse SARS-CoV-2 lineages in the face of mounting host immune recognition.
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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
Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England
Davies, N. G., Abbott, S., Barnard, R. C., Jarvis, C. I., Kucharski, A. J., Munday, J. D., Pearson, C. A. B., Russell, T. W., Tully, D. C., Washburne, A. D., et al. (2020) · doi:10.1101/2020.12.24.20248822 · Cited by 2,557
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
Detection of a SARS-CoV-2 variant of concern in South Africa
Tegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., Doolabh, D., Pillay, S., San, E. J., Msomi, N., et al. (2021) · Nature · doi:10.1038/s41586-021-03402-9 · Cited by 2,510
Self-citationAntibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7
Wang, P., Nair, M. S., Liu, L., Iketani, S., Luo, Y., Guo, Y., Wang, M., Yu, J., Zhang, B., Kwong, P. D., et al. (2021) · Nature · doi:10.1038/s41586-021-03398-2 · Cited by 2,312
Data, disease and diplomacy: GISAID's innovative contribution to global health
Elbe, S., & Buckland‐Merrett, G. (2017) · Global Challenges · doi:10.1002/gch2.1018 · Cited by 1,928
Detecting Individual Sites Subject to Episodic Diversifying Selection
Murrell, B., Wertheim, J. O., Moola, S., Weighill, T., Scheffler, K., & Kosakovsky Pond, S. L. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002764 · Cited by 1,811
Self-citationEvolution of antibody immunity to SARS-CoV-2
Gaebler, C., Wang, Z., Lorenzi, J. C. C., Muecksch, F., Finkin, S., Tokuyama, M., Cho, A., Jankovic, M., Schaefer-Babajew, D., Oliveira, T. Y., et al. (2021) · Nature · doi:10.1038/s41586-021-03207-w · Cited by 1,674
Self-citationAssessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England
The COVID-19 Genomics UK (COG-UK) consortium, Volz, E., Mishra, S., Chand, M., Barrett, J. C., Johnson, R., Geidelberg, L., Hinsley, W. R., Laydon, D. J., Dabrera, G., et al. (2021) · Nature · doi:10.1038/s41586-021-03470-x · Cited by 1,611
Spike mutation D614G alters SARS-CoV-2 fitness
Plante, J. A., Liu, Y., Liu, J., Xia, H., Johnson, B. A., Lokugamage, K. G., Zhang, X., Muruato, A. E., Zou, J., Fontes-Garfias, C. R., et al. (2021) · Nature · doi:10.1038/s41586-020-2895-3 · Cited by 1,558
Self-citation
Research works printed but not linked: 30
- Althaus, 2021, A tale of two variants: Spread of SARS-CoV-2 variants Alpha in Geneva, Switzerland, and Beta in South Africa, MedRxiv
- Annavajhala, 2021, A Novel SARS-CoV-2 Variant of Concern, B.1.526, Identified in New York, MedRxiv
- Campbell, 2020, Prediction of SARS-CoV-2 epitopes across 9360 HLA class I alleles, BioRxiv
- Cottam, 2011, Coronavirus nsp6 proteins generate autophagosomes from the endoplasmic reticulum via an omegasome intermediate, Autophagy, 7, 1335, 10.4161/auto.7.11.16642 · DOI · Paper page
- de Oliveira, 2021, A novel variant of interest of SARS-CoV-2 with multiple spike mutations is identified from travel surveillance in Africa, MedRxiv
- Dearlove, 2020, A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants, Proc. Natl. Acad. Sci. USA, 117, 23652, 10.1073/pnas.2008281117 · DOI · Paper page
- Garvin, 2020, Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models, Genome Biol., 21, 304, 10.1186/s13059-020-02191-0 · DOI
- Guo, 2021, Interferon Resistance of Emerging SARS-CoV-2 Variants, BioRxiv
- Katoh, 2002, MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform, Nucleic Acids Res., 30, 3059, 10.1093/nar/gkf436 · DOI · Paper page
- Kosakovsky Pond, 2005, Not so different after all: a comparison of methods for detecting amino acid sites under selection, Mol. Biol. Evol., 22, 1208, 10.1093/molbev/msi105 · DOI · Paper page
- Kosakovsky Pond, 2018, HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens, Mol. Biol. Evol., 35, 1812, 10.1093/molbev/msy016 · DOI · Paper page
- Kosakovsky Pond, 2020, HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies, Mol. Biol. Evol., 37, 295, 10.1093/molbev/msz197 · DOI · Paper page
- Kozlov, 2019, RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference, Bioinformatics, 35, 4453, 10.1093/bioinformatics/btz305 · DOI · Paper page
- Lau, 2020, Attenuated SARS-CoV-2 variants with deletions at the S1/S2 junction, Emerg. Microbes Infect., 9, 837, 10.1080/22221751.2020.1756700 · DOI · Paper page
- Lubinski, 2021, Functional evaluation of proteolytic activation for the SARS-CoV-2 variant B.1.1.7: role of the P681H mutation, BioRxiv
- MacLean, 2021, Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen, PLoS Biol., 19, e3001115, 10.1371/journal.pbio.3001115 · DOI · Paper page
- Miorin, 2020, SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling, Proc. Natl. Acad. Sci. USA, 117, 28344, 10.1073/pnas.2016650117 · DOI · Paper page
- Murrell, 2013, FUBAR: a fast, unconstrained bayesian approximation for inferring selection, Mol. Biol. Evol., 30, 1196, 10.1093/molbev/mst030 · DOI · Paper page
- Murrell, 2015, Gene-wide identification of episodic selection, Mol. Biol. Evol., 32, 1365, 10.1093/molbev/msv035 · DOI · Paper page
- Nelson, 2021, BioRxiv
- Nguyen, 2021, Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus), Sci. Rep., 11, 3487, 10.1038/s41598-021-83105-3 · DOI
- Nickle, 2007, HIV-specific probabilistic models of protein evolution, PLoS ONE, 2, e503, 10.1371/journal.pone.0000503 · DOI
- Peacock, 2021, SARS-CoV-2 one year on: evidence for ongoing viral adaptation, J. Gen. Virol., 102, 001584, 10.1099/jgv.0.001584 · DOI
- Pearson, 2021, Estimates of severity and transmissibility of novel SARS-CoV-2 variant 501Y.V2 in South Africa | CMMID Repository, MedRxiv
- Poon, 2007, An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope, PLoS Comput. Biol., 3, e231, 10.1371/journal.pcbi.0030231 · DOI
- Pybus, 2007, Phylogenetic evidence for deleterious mutation load in RNA viruses and its contribution to viral evolution, Mol. Biol. Evol., 24, 845, 10.1093/molbev/msm001 · DOI · Paper page
- Rhee, 2019, National and International Dimensions of Human Immunodeficiency Virus-1 Sequence Clusters in a Northern California Clinical Cohort, Open Forum Infect. Dis., 6, ofz135, 10.1093/ofid/ofz135 · DOI
- Scheffler, 2014, On the validity of evolutionary models with site-specific parameters, PLoS ONE, 9, e94534, 10.1371/journal.pone.0094534 · DOI · Paper page
- Starr, 2020, Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding, Cell, 182, 1295, 10.1016/j.cell.2020.08.012 · DOI · Paper page
- Zhang, 2020, SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity, Nat. Commun., 11, 6013, 10.1038/s41467-020-19808-4 · DOI · Paper page
Cited by
SARS-CoV-2 variants, spike mutations and immune escape
Harvey, W. T., Carabelli, A. M., Jackson, B., Gupta, R. K., Thomson, E. C., Harrison, E. M., Ludden, C., Reeve, R., Rambaut, A., COVID-19 Genomics UK (COG-UK) Consortium, et al. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00573-0 · Cited by 3,528
Self-citationThe 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
Self-citationZehr, J. D., Kosakovsky Pond, S. L., Millet, J. K., Olarte-Castillo, X. A., Lucaci, A. G., Shank, S. D., Ceres, K. M., Choi, A., Whittaker, G. R., Goodman, L. B., et al. (2023) · Virus Evolution · doi:10.1093/ve/vead019 · Cited by 30
Self-citationAccurate detection of convergent mutations in large protein alignments with ConDor
Morel, M., Zhukova, A., Lemoine, F., & Gascuel, O. (2024) · Genome Biology and Evolution · doi:10.1093/gbe/evae040 · Cited by 3
RASCL: Rapid Assessment Of SARS-CoV-2 Clades Through Molecular Sequence Analysis
Lucaci, A. G., Zehr, J. D., Shank, S. D., Bouvier, D., Mei, H., Nekrutenko, A., Martin, D. P., & Kosakovsky Pond, S. L. (2022) · doi:10.1101/2022.01.15.476448 · Cited by 2
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Metadata
- Authors
- Martin, D. P., Weaver, S., Tegally, H., San, J. E., Shank, S. D., Wilkinson, E., Lucaci, A. G., Giandhari, J., Naidoo, S., Pillay, Y., Singh, L., Lessells, R. J., Gupta, R. K., Wertheim, J. O., Nekturenko, A., Murrell, B., Harkins, G. W., Lemey, P., MacLean, O. A., Robertson, D. L., de Oliveira, T., & Kosakovsky Pond, S. L.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2021-09
- Volume
- 184
- Issue
- 20
- Pages
- 5189-5200.e7
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W3198909684
- Cited by
- 291
- References
- 37
- FWCI
- 18.80
- Type
- journal article
- Language
- en
- Open access
- bronze
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 394 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
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- Martin, D. P., Weaver, S., Tegally, H., San, J. E., Shank, S. D., Wilkinson, E., Lucaci, A. G., Giandhari, J., Naidoo, S., Pillay, Y., Singh, L., Lessells, R. J., Gupta, R. K., Wertheim, J. O., Nekturenko, A., Murrell, B., Harkins, G. W., Lemey, P., MacLean, O. A., . . . Kosakovsky Pond, S. L. (2021). The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. Cell. https://doi.org/10.1016/j.cell.2021.09.003
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