Improving virus taxonomy by recontextualizing sequence-based classification with biologically relevant data: The case of the Alphacoronavirus 1 species

mSphere

Volumn 3, Issue 1, 2018, Pages

  Whittaker, Gary R ^a   André, Nicole M ^a   Milleta, Jean Kaoru ^a  

^a Department of Molecular Biology and Genetics   (United States)

Author keywords

Alphacoronavirus; Alphacoronavirus 1; Biotype; Canine coronavirus; Clade; Classification; Coronavirus; Feline coronavirus; Serotype; Transmissible gastroenteritis virus

Indexed keywords

EID: 85041529916     PISSN: None     EISSN: 23795042     Source Type: Journal    
DOI: 10.1128/mSphere.00463-17     Document Type: Article

References (25)

1. Simmonds P, Adams MJ, Benko M, Breitbart M, Brister JR, Carstens EB, Davison AJ, Delwart E, Gorbalenya AE, Harrach B, Hull R, King AM, Koonin EV, Krupovic M, Kuhn JH, Lefkowitz EJ, Nibert ML, Orton R, Roossinck MJ, Sabanadzovic S, Sullivan MB, Suttle CA, Tesh RB, van der Vlugt RA, Varsani A, Zerbini FM. 2017. Consensus statement: virus taxonomy in the age of metagenomics. Nat Rev Microbiol 15:161-168. https://doi.org/10 .1038/nrmicro.2016.177
2. de Groot RJ, Cowley JA, Enjuanes L, Faaberg KS, Perlman S, Rottier PJM, Snijder EJ, Ziebuhr J, Gorbalenya AE. 2012. Order-Nidovirales, p 784-794. In King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (ed), Virus taxonomy. Elsevier, San Diego, CA
3. Lauber C, Ziebuhr J, Junglen S, Drosten C, Zirkel F, Nga PT, Morita K, Snijder EJ, Gorbalenya AE. 2012. Mesoniviridae: a proposed new family in the order Nidovirales formed by a single species of mosquito-borne viruses. Arch Virol 157:1623-1628. https://doi.org/10.1007/s00705-012-1295-x
4. Woo PCY, Lau SKP, Lam CSF, Lau CCY, Tsang AKL, Lau JHN, Bai R, Teng JLL, Tsang CCC, Wang M, Zheng BJ, Chan KH, Yuen KY. 2012. Discovery of seven novel mammalian and avian coronaviruses in the genus Deltacoronavirus supports bat coronaviruses as the gene source of Alphacoronavirus and Betacoronavirus and avian coronaviruses as the gene source of Gammacoronavirus and Deltacoronavirus. J Virol 86: 3995-4008. https://doi.org/10.1128/JVI.06540-11
5. Carstens EB. 2010. Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2009). Arch Virol 155:133-146. https://doi.org/10.1007/s00705-009-0547-x
6. Haijema BJ, Rottier P, de Groot RP. 2007. Feline coronaviruses: a tale of two-faced types, p 183-204. In Thiel V (ed), Coronaviruses: molecular and cellular Biology. Caister Academic Press, Poole, United Kingdom
7. Vennema H, Poland A, Foley J, Pedersen NC. 1998. Feline infectious peritonitis viruses arise by mutation from endemic feline enteric coronaviruses. Virology 243:150-157. https://doi.org/10.1006/viro.1998.9045
8. Garner MM, Ramsell K, Morera N, Juan-Sallés C, Jiménez J, Ardiaca M, Montesinos A, Teifke JP, Löhr CV, Evermann JF, Baszler TV, Nordhausen RW, Wise AG, Maes RK, Kiupel M. 2008. Clinicopathologic features of a systemic coronavirus-associated disease resembling feline infectious peritonitis in the domestic ferret (Mustela putorius). Vet Pathol 45: 236-246. https://doi.org/10.1354/vp.45-2-236
9. Licitra BN, Duhamel GE, Whittaker GR. 2014. Canine enteric coronaviruses: emerging viral pathogens with distinct recombinant spike proteins. Viruses 6:3363-3376. https://doi.org/10.3390/v6083363
10. Belouzard S, Millet JK, Licitra BN, Whittaker GR. 2012. Mechanisms of coronavirus cell entry mediated by the viral spike protein. Viruses 4:1011-1033. https://doi.org/10.3390/v4061011
11. Millet JK, Whittaker GR. 2015. Host cell proteases: critical determinants of coronavirus tropism and pathogenesis. Virus Res 202:120-134. https:// doi.org/10.1016/j.virusres.2014.11.021
12. Pedersen NC, Black JW, Boyle JF, Evermann JF, McKeirnan AJ, Ott RL. 1984. Pathogenic differences between various feline coronavirus isolates, p 365-380. In Rottier PJM, van der Zeijst BAM, Spaan WJM, Horzinek MC (ed), Molecular biology and pathogenesis of coronaviruses. Springer, Boston, MA
13. Hohdatsu T, Okada S, Koyama H. 1991. Characterization of monoclonal antibodies against feline infectious peritonitis virus type II and antigenic relationship between feline, porcine, and canine coronaviruses. Arch Virol 117:85-95. https://doi.org/10.1007/BF01310494
14. Decaro N, Buonavoglia C. 2008. An update on canine coronaviruses: viral evolution and pathobiology. Vet Microbiol 132:221-234. https://doi.org/ 10.1016/j.vetmic.2008.06.007
15. Hohdatsu T, Izumiya Y, Yokoyama Y, Kida K, Koyama H. 1998. Differences in virus receptor for type I and type II feline infectious peritonitis virus. Arch Virol 143:839-850. https://doi.org/10.1007/s007050050336
16. Dye C, Temperton N, Siddell SG. 2007. Type I feline coronavirus spike glycoprotein fails to recognize aminopeptidase N as a functional receptor on feline cell lines. J Gen Virol 88:1753-1760. https://doi.org/10.1099/ vir.0.82666-0
17. Decaro N, Martella V, Elia G, Campolo M, Desario C, Cirone F, Tempesta M, Buonavoglia C. 2007. Molecular characterisation of the virulent canine coronavirus CB/05 strain. Virus Res 125:54-60. https://doi.org/10 .1016/j.virusres.2006.12.006
18. Herrewegh AA, Smeenk I, Horzinek MC, Rottier PJ, de Groot RJ. 1998. Feline coronavirus type II strains 79-1683 and 79-1146 originate from a double recombination between feline coronavirus type I and canine coronavirus. J Virol 72:4508-4514
19. Regan AD, Millet JK, Tse LP, Chillag Z, Rinaldi VD, Licitra BN, Dubovi EJ, Town CD, Whittaker GR. 2012. Characterization of a recombinant canine coronavirus with a distinct receptor-binding (S1) domain. Virology 430: 90-99. https://doi.org/10.1016/j.virol.2012.04.013
20. Graham RL, Baric RS. 2010. Recombination, reservoirs, and the modular spike: mechanisms of coronavirus cross-species transmission. J Virol 84:3134-3146. https://doi.org/10.1128/JVI.01394-09
21. Licitra BN, Millet JK, Regan AD, Hamilton BS, Rinaldi VD, Duhamel GE, Whittaker GR. 2013. Mutation in spike protein cleavage site and pathogenesis of feline coronavirus. Emerg Infect Dis 19:1066-1073. https:// doi.org/10.3201/eid1907.121094
22. de Haan CAM, Haijema BJ, Schellen P, Wichgers Schreur P, te Lintelo E, Vennema H, Rottier PJM. 2008. Cleavage of group 1 coronavirus spike proteins: how furin cleavage is traded off against heparan sulfate binding upon cell culture adaptation. J Virol 82:6078-6083. https://doi.org/ 10.1128/JVI.00074-08
23. Lamers MM, Smits SL, Hundie GB, Provacia LB, Koopmans MP, Osterhaus AD, Haagmans BL, Raj VS. 2016. Naturally occurring recombination in ferret coronaviruses revealed by complete genome characterization. J Gen Virol 97:2180-2186. https://doi.org/10.1099/jgv.0.000520
24. World Health Organization/World Organisation for Animal Health/ Food and Agriculture Organization (WHO/OIE/FAO) H5N1 Evolution Working Group. 2014. Revised and updated nomenclature for highly pathogenic avian influenza A (H5N1) viruses. Influenza Other Respir Viruses 8:384-388. https://doi.org/10.1111/irv.12230
25. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59: 307-321. https://doi.org/10.1093/sysbio/syq010