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Forni, D., Cagliani, R., Clerici, M. & Sironi, M. Molecular evolution of human coronavirus genomes. Trends Microbiol. 25, 35–48 (2017).
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Source: https://www.nature.com/articles/s41467-020-17687-3
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Original Text (This is the original text for your reference.)
- 1.
Forni, D., Cagliani, R., Clerici, M. & Sironi, M. Molecular evolution of human coronavirus genomes. Trends Microbiol. 25, 35–48 (2017).
- 2.
Tao, Y. et al. Surveillance of bat coronaviruses in Kenya identifies relatives of human coronaviruses NL63 and 229E and their recombination history. J. Virol. 91, e01953–16 (2017).
- 3.
Graham, R. L. & Baric, R. S. Recombination, reservoirs, and the modular spike: mechanisms of coronavirus cross-species transmission. J. Virol. 84, 3134–3146 (2010).
- 4.
Vijgen, L. et al. Evolutionary history of the closely related group 2 coronaviruses: porcine hemagglutinating encephalomyelitis virus, bovine coronavirus, and human coronavirus OC43. J. Virol. 80, 7270–7274 (2006).
- 5.
Zhang, X. et al. Quasispecies of bovine enteric and respiratory coronaviruses based on complete genome sequences and genetic changes after tissue culture adaptation. Virology 363, 1–10 (2007).
- 6.
Parrish, C. R. et al. Cross-species virus transmission and the emergence of new epidemic diseases. Microbiol. Mol. Biol. Rev. 72, 457–470 (2008).
- 7.
Li, D. L. et al. Molecular evolution of porcine epidemic diarrhea virus and porcine deltacoronavirus strains in Central China. Res. Vet. Sci. 120, 63–69 (2018).
- 8.
Cui, J., Li, F. & Shi, Z.-L. Origin and evolution of pathogenic coronaviruses. Nat. Rev. Microbiol. 17, 181–192 (2019).
- 9.
Lau, S. K. P. & Chan, J. F. W. Coronaviruses: emerging and re-emerging pathogens in humans and animals. Virol. J. 12, 209 (2015).
- 10.
Drosten, C. et al. Identification of a novel coronavirus in patients with severe acute respiratory syndrome. N. Engl. J. Med. 348, 1967–1976 (2003).
- 11.
Heymann, D. L. The international response to the outbreak of SARS in 2003. Philos. Trans. R. Soc. Lond. Ser. B 359, 1127–1129 (2004).
- 12.
World Health Organization. Summary of Probable SARS Cases with Onset of Illness from 1 November 2002 to 31 July 2003, Vol. 2019 (World Health Organization, 2004).
- 13.
Ge, X.-Y. et al. Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature 503, 535–538 (2013).
- 14.
Li, W. et al. Bats are natural reservoirs of SARS-like coronaviruses. Science 310, 676–679 (2005).
- 15.
Lau, S. K. P. et al. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. Proc. Natl Acad. Sci. USA 102, 14040–14045 (2005).
- 16.
Hu, B. et al. Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus. PLoS Pathog. 13, e1006698 (2017).
- 17.
Zhou, P. et al. Fatal swine acute diarrhoea syndrome caused by an HKU2-related coronavirus of bat origin. Nature 556, 255–258 (2018).
- 18.
Gong, L. et al. A new bat-HKU2-like coronavirus in swine, China, 2017. Emerg. Infect. Dis. 23, 1607–1609 (2017).
- 19.
Pan, Y. et al. Discovery of a novel swine enteric alphacoronavirus (SeACoV) in southern China. Vet. Microbiol. 211, 15–21 (2017).
- 20.
Zhou, P. et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579, 270–273 (2020).
- 21.
Zhou, H. et al. A novel bat coronavirus closely related to SARS-CoV-2 contains natural insertions at the S1/S2 cleavage site of the spike protein. Curr. Biol. 30, 2196–2203.e3 (2020).
- 22.
Lam, T. T.-Y. et al. Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins. Nature 583, 282–285 (2020).
- 23.
Xiao, K. et al. Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins. Nature 583, 286–289 (2020).
- 24.
Corman, V. M. et al. Rooting the phylogenetic tree of Middle East respiratory syndrome coronavirus by characterization of a conspecific virus from an African bat. J. Virol. 88, 11297–11303 (2014).
- 25.
Anthony, S. J. et al. Further evidence for bats as the evolutionary source of Middle East respiratory syndrome coronavirus. mBio 8, e00373–17 (2017).
- 26.
Lau, S. K. P. et al. Receptor usage of a novel bat lineage c betacoronavirus reveals evolution of Middle East respiratory syndrome-related coronavirus spike proteins for human dipeptidyl peptidase 4 binding. J. Infect. Dis. https://doi.org/10.1093/infdis/jiy018 (2018).
- 27.
Corman, V. M. et al. Evidence for an ancestral association of human coronavirus 229E with bats. J. Virol. 89, 11858–11870 (2015).
- 28.
Huynh, J. et al. Evidence supporting a zoonotic origin of human coronavirus strain NL63. J. Virol. 86, 12816–12825 (2012).
- 29.
Lu, R. et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet 395, 565–574 (2020).
- 30.
Wong, A. C. P., Li, X., Lau, S. K. P. & Woo, P. C. Y. Global epidemiology of bat coronaviruses. Viruses 11, 174 (2019).
- 31.
Drexler, J. F., Corman, V. M. & Drosten, C. Ecology, evolution and classification of bat coronaviruses in the aftermath of SARS. Antivir. Res. 101, 45–56 (2014).
- 32.
Anthony, S. J. et al. Global patterns in coronavirus diversity. Virus Evol. 3, vex012–vex012 (2017).
- 33.
Leopardi, S. et al. Interplay between co-divergence and cross-species transmission in the evolutionary history of bat coronaviruses. Infect. Genet. Evol. 58, 279–289 (2018).
- 34.
Cui, J. et al. Evolutionary relationships between bat coronaviruses and their hosts. Emerg. Infect. Dis. 13, 1526–1532 (2007).
- 35.
Smith, A. T. & Xie, Y. A Guide to the Mammals of China (Princeton University Press, Princeton, 2008).
- 36.
Lin, X.-D. et al. Extensive diversity of coronaviruses in bats from China. Virology 507, 1–10 (2017).
- 37.
Ge, X.-Y. et al. Coexistence of multiple coronaviruses in several bat colonies in an abandoned mineshaft. Virol. Sin. 31, 31–40 (2016).
- 38.
Woo, P. C. Y. et al. Molecular diversity of coronaviruses in bats. Virology 351, 180–187 (2006).
- 39.
Wu, Z. et al. Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases. ISME J. 10, 609–620 (2016).
- 40.
Tang, X. C. et al. Prevalence and genetic diversity of coronaviruses in bats from China. J. Virol. 80, 7481–7490 (2006).
- 41.
Woo, P. C. Y. et al. Comparative analysis of twelve genomes of three novel group 2c and group 2d coronaviruses reveals unique group and subgroup features. J. Virol. 81, 1574–1585 (2007).
- 42.
Ge, X. et al. Metagenomic analysis of viruses from bat fecal samples reveals many novel viruses in insectivorous bats in China. J. Virol. 86, 4620–4630 (2012).
- 43.
Xu, L. et al. Detection and characterization of diverse alpha- and betacoronaviruses from bats in China. Virol. Sin. 31, 69–77 (2016).
- 44.
Luo, Y. et al. Longitudinal surveillance of betacoronaviruses in fruit bats in Yunnan Province, China During 2009–2016. Virol. Sin. 33, 87–95 (2018).
- 45.
Legendre, P. & Legendre, L. F. Numerical Ecology (Elsevier, 2012).
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Drummond, A. J., Suchard, M. A., Xie, D. & Rambaut, A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969–1973 (2012).
- 47.
Lemey, P., Rambaut, A., Drummond, A. J. & Suchard, M. A. Bayesian phylogeography finds its roots. PLoS Comput. Biol. 5, e1000520 (2009).
- 48.
Minin, V. N. & Suchard, M. A. Counting labeled transitions in continuous-time Markov models of evolution. J. Math. Biol. 56, 391–412 (2008).
- 49.
O’Brien, J. D., Minin, V. N. & Suchard, M. A. Learning to count: robust estimates for labeled distances between molecular sequences. Mol. Biol. Evol. 26, 801–814 (2009).
- 50.
Webb, C. O., Ackerly, D. D., McPeek, M. A. & Donoghue, M. J. Phylogenies community ecology. Annu. Rev. Ecol. Syst. 33, 475–505 (2002).
- 51.
Simmons, N. B. Mammal Species of the World: A Taxonomic and Geographic Reference (eds Wilson, D. E. & Reeder, D. M.) 312–529 (Johns Hopkins Univ. Press, 2005).
- 52.
Teeling, E. C. et al. A molecular phylogeny for bats illuminates biogeography and the fossil record. Science 307, 580–584 (2005).
- 53.
Stoffberg, S., Jacobs, D. S., Mackie, I. J. & Matthee, C. A. Molecular phylogenetics and historical biogeography of Rhinolophus bats. Mol. Phylogenet. Evol. 54, 1–9 (2010).
- 54.
Foley, N. M. et al. How and why overcome the impediments to resolution: lessons from rhinolophid and hipposiderid bats. Mol. Biol. Evol. 32, 313–333 (2014).
- 55.
Eick, G. N., Jacobs, D. S. & Matthee, C. A. A nuclear DNA phylogenetic perspective on the evolution of echolocation and historical biogeography of extant bats (Chiroptera). Mol. Biol. Evol. 22, 1869–1886 (2005).
- 56.
Ravel, A., Marivaux, L., Qi, T., Wang, Y.-Q. & Beard, K. C. New chiropterans from the middle Eocene of Shanghuang (Jiangsu Province, Coastal China): new insight into the dawn horseshoe bats (Rhinolophidae) in Asia. Zool. Scr. 43, 1–23 (2014).
- 57.
Luo, J. et al. Bat conservation in China: should protection of subterranean habitats be a priority? Oryx 47, 526–531 (2013).
- 58.
Willoughby, A. R., Phelps, K. L., Consortium, P. & Olival, K. J. A comparative analysis of viral richness and viral sharing in cave-roosting bats. Diversity 9, 35 (2017).
- 59.
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