Khare, S. et al. GISAID’s role in pandemic response. China CDC Wkly 3, 1049–1051 (2021).

Article  PubMed  PubMed Central  Google Scholar 

Pybus, O. G. & Rambaut, A. Evolutionary analysis of the dynamics of viral infectious disease. Nat. Rev. Genet. 10, 540–550 (2009).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Volz, E. et al. Evaluating the effects of SARS-CoV-2 spike mutation D614G on transmissibility and pathogenicity. Cell 184, 64–75.e11 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Clarke, D. K. et al. Genetic bottlenecks and population passages cause profound fitness differences in RNA viruses. J. Virol. 67, 222–228 (1993).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sanjuán, R., Nebot, M. R., Chirico, N., Mansky, L. M. & Belshaw, R. Viral mutation rates. J. Virol. 84, 9733–9748 (2010).

Article  PubMed  PubMed Central  Google Scholar 

Sanjuán, R. & Domingo-Calap, P. Mechanisms of viral mutation. Cell. Mol. Life Sci. 73, 4433–4448 (2016).

Article  PubMed  PubMed Central  Google Scholar 

Loewe, L. & Hill, W. L. The population genetics of mutations: good, bad and indifferent. Philos. Trans. R. Soc. Lond. B Biol. Sci. 365, 1153–1167 (2010).

Article  PubMed  PubMed Central  Google Scholar 

Fehr, A. R. & Perlman, S. Coronaviruses: an overview of their replication and pathogenesis. Methods Mol. Biol. 1282, 1–23 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Amicone, M. et al. Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution. Evol. Med. Public Health 10, 142–155 (2022).

Article  PubMed  PubMed Central  Google Scholar 

Minskaia, E., Hertzig, T., Gorbalenya, A. E. & Ziebuhr, J. Discovery of an RNA virus 3′→5′ exoribonuclease that is critically involved in coronavirus RNA synthesis. Proc. Natl Acad. Sci. USA 103, 5108–5113 (2006).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ribeiro, R. M. et al. Quantifying the diversification of hepatitis C virus (HCV) during primary infection: estimates of the in vivo mutation rate. PLoS Pathog. 8, e1002880 (2012).

Article  PubMed  PubMed Central  Google Scholar 

Rawson, J. M. O., Landman, S. R., Reilly, C. S. & Mansky, L. M. HIV-1 and HIV-2 exhibit similar mutation frequencies and spectra in the absence of G-to-A hypermutation. Retrovirology 12, 60 (2015).

Article  PubMed  PubMed Central  Google Scholar 

Meng, B. et al. Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. Cell Rep. 35, 109292 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Malim, M. H. APOBEC proteins and intrinsic resistance to HIV-1 infection. Philos. Trans. R. Soc. Lond. B Biol. Sci. 364, 675–687 (2009).

Article  CAS  PubMed  Google Scholar 

Jarmuz, A. et al. An anthropoid-specific locus of orphan C to U RNA-editing enzymes on chromosome 22. Genomics 79, 285–296 (2002).

Article  CAS  PubMed  Google Scholar 

Rogozin, I. B., Basu, M. K., Jordan, I. K., Pavlov, Y. I. & Koonin, E. V. APOBEC4, a new member of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases predicted by computational analysis. Cell Cycle 4, 1281–1285 (2005).

Article  CAS  PubMed  Google Scholar 

Simmonds, P. & Ansari, M. A. Extensive C→U transition biases in the genomes of a wide range of mammalian RNA viruses; potential associations with transcriptional mutations, damage- or host-mediated editing of viral RNA. PLoS Pathog. 17, e1009596 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Klimczak, L. J., Randall, T. A., Saini, N., Li, J.-L. & Gordenin, D. A. Similarity between mutation spectra in hypermutated genomes of rubella virus and in SARS-CoV-2 genomes accumulated during the COVID-19 pandemic. PLoS ONE 15, e0237689 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Kim, K. et al. The roles of APOBEC-mediated RNA editing in SARS-CoV-2 mutations, replication and fitness. Sci. Rep. 12, 14972 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Simmonds, P. 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. mSphere 5, e00408–e00420 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Di Giorgio, S., Martignano, F., Torcia, M. G., Mattiuz, G. & Conticello, S. G. Evidence for host-dependent RNA editing in the transcriptome of SARS-CoV-2. Sci. Adv. 6, eabb5813 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ringlander, J., Fingal, J., Kann, H. & Kann, M. Impact of ADAR-induced editing of minor viral RNA populations on replication and transmission of SARS-CoV-2. Proc. Natl Acad. Sci. USA 119, e2112663119 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

van Dorp, L. et al. Emergence of genomic diversity and recurrent mutations in SARS-CoV-2. Infect. Genet. Evol. 83, 104351 (2020).

Article  PubMed  PubMed Central  Google Scholar 

van Dorp, L. et al. No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2. Nat. Commun. 11, 5986 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Belshaw, R., Sanjuán, R. & Pybus, O. G. Viral mutation and substitution: units and levels. Curr. Opin. Virol. 1, 430–435 (2011).

Article  CAS  PubMed  Google Scholar 

Rambaout, A. Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies. Bioinformatics 16, 395–399 (2000).

Article  Google Scholar 

Drummond, A. Nicholls, G. K., Rodrigo, A. G. & Solomon, W. in Tools for Constructing Chronologies: Crossing Disciplinary Boundaries Vol. 177 (eds Buck, C.E. & Maillard, A.R.) 149–171 (Springer-Verlag, 2004).

Duchene, S. et al. Temporal signal and the phylodynamic threshold of SARS-CoV-2. Virus Evol. 6, veaa061 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Ghafari, M. et al. Purifying selection determines the short-term time dependency of evolutionary rates in SARS-CoV-2 and pH1N1 influenza. Mol. Biol. Evol. 39, msac009 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jackson, B. et al. Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic. Cell 184, 5179–5188 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Boni, M. F. et al. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Nat. Microbiol. 5, 1408–1417 (2020).

Article  CAS  PubMed  Google Scholar 

Lai, M. M. & Cavanagh, D. The molecular biology of corona viruses. Adv. Virus Res. 48, 1–100 (1997).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rambaut, A. et al. Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations. Virological https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563/1 (2020).

O’Toole, Á. et al. Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with Grinch. Wellcome Open Res. 6, 121 (2021).

PubMed  PubMed Central  Google Scholar 

Sekizuka, T. et al. Genome recombination between the Delta and Alpha variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Jpn J. Infect. Dis. 75, 415–418 (2022).

Article  CAS  PubMed  Google Scholar 

UK Health Security Agency (UKHSA). SARS-CoV-2 variants of concern and variants under investigation in England — Technical Briefing 39. GOV.UK https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1063424/Tech-Briefing-39-25March2022_FINAL.pdf (2022).

UK Health Security Agency (UKHSA). SARS-CoV-2 variants of public health interest: 28 October 2022. GOV.UK https://www.gov.uk/government/publications/sars-cov-2-variants-of-public-health-interest/sars-cov-2-variants-of-public-health-interest-28-october-2022 (2022).

Rhee, C., Kanjilal, S., Baker, M. & Klompas, M. Duration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectivity: when is it safe to discontinue isolation? Clin. Infect. Dis. 72, 1467–1474 (2021).

Article  CAS  PubMed  Google Scholar 

Bullard, J. et al. Predicting infectious severe acute respiratory syndrome coronavirus 2 from diagnostic samples. Clin. Infect. Dis. 71, 2663–2666 (2020).

Article  CAS