Genetics-based classification of filoviruses calls for expanded sampling of genomic sequences

Viruses

Volumn 4, Issue 9, 2012, Pages 1425-1437

  Lauber, Chris ^a   Gorbalenya, Alexander E ^a,b  

^a LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^b MOSCOW STATE UNIVERSITY   (Russian Federation)

Author keywords

DEmARC; Ebolavirus; Filoviruses; Genetic diversity; Genetics based classification; Pairwise evolutionary distances; Taxonomy; Virus species

Indexed keywords

GLYCOPROTEIN; METHYLTRANSFERASE; NUCLEOPROTEIN; PROTEIN VP24; PROTEIN VP40; RNA DIRECTED RNA POLYMERASE; SINGLE STRANDED RNA; UNCLASSIFIED DRUG; VIRUS PROTEIN;

ARTICLE; EBOLA VIRUS; FILOVIRUS; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC VARIABILITY; HEMORRHAGIC FEVER; MARBURG VIRUS; NONHUMAN; OPEN READING FRAME; PHENOTYPE; PROTEIN FUNCTION; TAXONOMY; VIRUS GENOME;

CLUSTER ANALYSIS; FILOVIRIDAE; GENETIC VARIATION; GENOME, VIRAL; GENOMICS; PHYLOGENY; VIROLOGY;

EBOLA VIRUS; FILOVIRIDAE; MARBURGVIRUS;

EID: 84866987686     PISSN: 19994915     EISSN: None     Source Type: Journal    
DOI: 10.3390/v4091425     Document Type: Article

References (57)

1. Lauber, C.; Gorbalenya, A.E. Partitioning the genetic diversity of a virus family: Approach and evaluation through a case study of picornaviruses. J. Virol. 2012, 86, 3890-3904.
2. Lauber, C.; Gorbalenya, A.E. Toward genetics-based virus taxonomy: Comparative analysis of a genetics-based classification and the taxonomy of picornaviruses. J. Virol. 2012, 86, 3905-3915.
3. Knowles, N.J.; Hovi, T.; Hyypia, T.; King, A.M.Q.; Lindberg, A.M.; Pallansch, M.A.; Palmenberg, A.C.; Simmonds, P.; Skern, T.; Stanway, G.; et al. Family Picornaviridae. In Virus Taxonomy, Ninth Report of the International Committee on Taxonomy of Viruses; King, A.M.Q., Adams, M.J., Carstens, E.B., Lefkowitz, E.J., Eds.; Elsevier Academic Press: Amsterdam, The Netherlands, 2012; pp. 855-880.
4. Adams, M.J.; Antoniw, J.F.; Bar-Joseph, M.; Brunt, A.A.; Candresse, T.; Foster, G.D.; Martelli, G.P.; Milne, R.G.; Fauquet, C.M. The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation. Arch. Virol. 2004, 149, 1045-1060.
5. Adams, M.J.; Antoniw, J.F.; Fauquet, C.M. Molecular criteria for genus and species discrimination within the family Potyviridae. Arch. Virol. 2005, 150, 459-479.
6. Bao, Y.; Kapustin, Y.; Tatusova, T. Virus classification by Pairwise Sequence Comparison (PASC). In Encyclopedia of Virology; Mahy, B.W.J., van Regenmortel, M.H.V., Eds.; Elsevier: Oxford, UK, 2008; Volume 5: pp. 342-348.
7. Bernard, H.U.; Burk, R.D.; Chen, Z.G.; van Doorslaer, K.; zur Hausen, H.; de Villiers, E.M. Classification of papillomaviruses (PVs) based on 189 PV types and proposal of taxonomic amendments. Virology 2010, 401, 70-79.
8. Chan, Y.F.; Sam, I.C.; Abubakar, S. Phylogenetic designation of enterovirus 71 genotypes and subgenotypes using complete genome sequences. Inf. Genet. Evol. 2010, 10, 404-412.
9. Fauquet, C.M.; Bisaro, D.M.; Briddon, R.W.; Brown, J.K.; Harrison, B.D.; Rybicki, E.P.; Stenger, D.C.; Stanley, J. Revision of taxonomic criteria for species demarcation in the family Geminiviridae, and an updated list of begomovirus species. Arch. Virol. 2003, 148, 405-421.
10. Gonzaalez, J.M.; Gomez-Puertas, P.; Cavanagh, D.; Gorbalenya, A.E.; Enjuanes, L. A comparative sequence analysis to revise the current taxonomy of the family Coronaviridae. Arch. Virol. 2003, 148, 2207-2235.
11. Lefkowitz, E.J.; Wang, C.; Upton, C. Poxviruses: Past, present and future. Virus Res. 2006, 117, 105-118.
12. Maes, P.; Klempa, B.; Clement, J.; Matthijnssens, J.; Gajdusek, D.C.; Kruger, D.H.; van Ranst, M. A proposal for new criteria for the classification of hantaviruses, based on S and M segment protein sequences. Inf. Genet. Evol. 2009, 9, 813-820.
13. Matthijnssens, J.; Ciarlet, M.; Heiman, E.; Arijs, I.; Delbeke, T.; McDonald, S.M.; Palombo, E.A.; Iturriza-Gomara, M.; Maes, P.; Patton, J.T.; et al. Full genome-based classification of rotaviruses reveals a common origin between human Wa-like and porcine rotavirus strains and human DS-1-like and bovine rotavirus strains. J. Virol. 2008, 82, 3204-3219.
14. Oberste, M.S.; Maher, K.; Kilpatrick, D.R.; Pallansch, M.A. Molecular evolution of the human enteroviruses: Correlation of serotype with VP1 sequence and application to picornavirus classification. J. Virol. 1999, 73, 1941-1948.
15. Schuffenecker, I.; Ando, T.; Thouvenot, D.; Lina, B.; Aymard, M. Genetic classification of "Sapporo-like viruses". Arch. Virol. 2001, 146, 2115-2132.
16. Shukla, D.D.; Ward, C.W. Amino-acid sequence homology of coat proteins as a basis for identification and classification of the potyvirus group. J. Gen. Virol. 1988, 69, 2703-2710.
17. Zheng, D.P.; Ando, T.; Fankhauser, R.L.; Beard, R.S.; Glass, R.I.; Monroe, S.S. Norovirus classification and proposed strain nomenclature. Virology 2006, 346, 312-323.
18. De Groot, R.J.; Baker, S.C.; Baric, R.; Enjuanes, L.; Gorbalenya, A.E.; Holmes, K.V.; Perlman, S.; Poon, L.L.; Rottier, P.J.M.; Talbot, P.J.; et al. Family Coronaviridae. In Virus Taxonomy, Ninth Report of the International Committee on Taxonomy of Viruses; King, A.M.Q., Adams, M.J., Carstens, E.B., Lefkowitz, E.J., Eds.; Elsevier Academic Press: Amsterdam, The Netherlands, 2012; pp. 806-828.
19. Nga, P.T.; Parquet, M.D.; Lauber, C.; Parida, M.; Nabeshima, T.; Yu, F.X.; Thuy, N.T.; Inoue, S.; Ito, T.; Okamoto, K.; et al. Discovery of the first insect nidovirus, a missing evolutionary link in the emergence of the largest RNA virus genomes. PLoS Pathog. 2011, 7, e1002215.
20. Zirkel, F.; Kurth, A.; Quan, P.L.; Briese, T.; Ellerbrok, H.; Pauli, G.; Leendertz, F.H.; Lipkin, W.I.; Ziebuhr, J.; Drosten, C.; et al. An insect nidovirus emerging from a primary tropical rainforest. mBio 2011, 2, e00077-11.
21. Lauber, C.; Ziebuhr, J.; Junglen, S.; Drosten, C.; Zirkel, F.; Nga, P.T.; Morita, K.; Snijder, E.J.; Gorbalenya, A.E. Mesoniviridae: A proposed new family in the order Nidovirales formed by a single species of mosquito-borne viruses. Arch. Virol. 2012, doi:10.1007/s00705-012-1295-x.
22. Easton, A.J.; Pringle, C.R. Order Mononegavirales. In Virus Taxonomy, Ninth Report of the International Committee on Taxonomy of Viruses; King, A.M.Q., Adams, M.J., Carstens, E.B., Lefkowitz, E.J., Eds.; Elsevier Academic Press: Amsterdam, The Netherlands, 2012; pp. 653-657.
23. Adams, M.J.; Carstens, E.B. Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2012). Arch. Virol. 2012, 157, 1411-1422.
24. Kuhn, J.H.; Becker, S.; Ebihara, H.; Geisbert, T.W.; Johnson, K.M.; Kawaoka, Y.; Lipkin, W.I.; Negredo, A.I.; Netesov, S.V.; Nichol, S.T.; et al. Proposal for a revised taxonomy of the family Filoviridae: Classification, names of taxa and viruses, and virus abbreviations. Arch. Virol. 2010, 155, 2083-2103.
25. Kuhn, J.K.; Becker, S.; Ebihara, H.; Geisbert, T.W.; Jahrling, P.B.; Kawaoka, Y.; Netesov, S.V.; Nichol, S.T.; Peters, C.J.; Volchkov, V.E.; et al. Familiy Filoviridae. In Virus Taxonomy, Ninth Report of the International Committee on Taxonomy of Viruses; King, A.M.Q., Adams, M.J., Carstens, E.B., Lefkowitz, E.J., Eds.; Elsevier Academic Press: Amsterdam, The Netherlands, 2012; pp. 665-671.
26. Towner, J.S.; Khristova, M.L.; Sealy, T.K.; Vincent, M.J.; Erickson, B.R.; Bawiec, D.A.; Hartman, A.L.; Comer, J.A.; Zaki, S.R.; Stroher, U.; et al. Marburgvirus Genomics and association with a large hemorrhagic fever outbreak in Angola. J. Virol. 2006, 80, 6497-6516.
27. Towner, J.S.; Sealy, T.K.; Khristova, M.L.; Albarino, C.G.; Conlan, S.; Reeder, S.A.; Quan, P.L.; Lipkin, W.I.; Downing, R.; Tappero, J.W.; et al. Newly Discovered Ebola Virus Associated with Hemorrhagic Fever Outbreak in Uganda. PLoS Pathog. 2008, 4, e1000212.
28. Ferron, F.; Longhi, S.; Henrissat, B.; Canard, B. Viral RNA-polymerases-A predicted 2 '-Oribose methyltransferase domain shared by all Mononegavirales. Trends Biochem. Sci. 2002, 27, 222-224.
29. Feldmann, H.; Muhlberger, E.; Randolf, A.; Will, C.; Kiley, M.P.; Sanchez, A.; Klenk, H.D. Marburg Virus, A Filovirus-Messenger-RNAs, gene order, and regulatory elements of the replication cycle. Virus Res. 1992, 24, 1-19.
30. Negredo, A.; Palacios, G.; Vazquez-Moron, S.; Gonzalez, F.; Dopazo, H.; Molero, F.; Juste, J.; Quetglas, J.; Savji, N.; Martinez, M.D.; et al. Discovery of an ebolavirus-like filovirus in Europe. PLoS Pathog. 2011, 7, e1002304.
31. Sanchez, A.; Trappier, S.G.; Mahy, B.W.J.; Peters, C.J.; Nichol, S.T. The virion glycoproteins of Ebola viruses are encoded in two reading frames and are expressed through transcriptional editing. Proc. Natl. Acad. Sci. U. S. A. 1996, 93, 3602-3607.
32. Volchkov, V.E.; Becker, S.; Volchkova, V.A.; Ternovoj, V.A.; Kotov, A.N.; Netesov, S.V.; Klenk, H.D. GP mRNA of Ebola virus is edited by the Ebola virus polymerase and by T7 and vaccinia virus polymerases. Virology 1995, 214, 421-430.
33. Volchkova, V.A.; Klenk, H.D.; Volchkov, V.E. Delta-peptide is the carboxy-terminal cleavage fragment of the nonstructural small glycoprotein sGP of Ebola virus. Virology 1999, 265, 164-171.
34. Leroy, E.M.; Kumulungui, B.; Pourrut, X.; Rouquet, P.; Hassanin, A.; Yaba, P.; Delicat, A.; Paweska, J.T.; Gonzalez, J.P.; Swanepoel, R. Fruit bats as reservoirs of Ebola virus. Nature 2005, 438, 575-576.
35. Miranda, M.E.; Ksiazek, T.G.; Retuya, T.J.; Khan, A.S.; Sanchez, A.; Fulhorst, C.F.; Rollin, P.E.; Calaor, A.B.; Manalo, D.L.; Roces, M.C.; et al. Epidemiology of Ebola (subtype Reston) virus in the Philippines, 1996. J. Infect. Dis. 1999, 179, S115-S119.
36. Gorbalenya, A.E.; Lieutaud, P.; Harris, M.R.; Coutard, B.; Canard, B.; Kleywegt, G.J.; Kravchenko, A.A.; Samborskiy, D.V.; Sidorov, I.A.; Leontovich, A.M.; et al. Practical application of bioinformatics by the multidisciplinary VIZIER consortium. Antivir. Res. 2010, 87, 95-110.
37. Lauber, C.; Gorbalenya, A.E. Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands. Geneticsbased classification of coronaviruses. Unpublished work, to be submitted for publication, 2012.
38. Van Regenmortel, M.H.V. Virus species and virus identification: Past and current controversies. Inf. Genet. Evol. 2007, 7, 133-144.
39. Mayo, M.A.; Pringle, C.R. Virus taxonomy-1997. J. Gen. Virol. 1998, 79, 649-657.
40. Dimmic, M.W.; Rest, J.S.; Mindell, D.P.; Goldstein, R.A. rtREV: An amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny. J. Mol. Evol. 2002, 55, 65-73.
41. Hraber, P.; Kuiken, C.; Waugh, M.; Geer, S.; Bruno, W.J.; Leitner, T. Classification of hepatitis C virus and human immunodeficiency virus-1 sequences with the branching index. J. Gen. Virol. 2008, 89, 2098-2107.
42. Pons, J.; Barraclough, T.G.; Gomez-Zurita, J.; Cardoso, A.; Duran, D.P.; Hazell, S.; Kamoun, S.; Sumlin, W.D.; Vogler, A.P. Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Syst. Biol. 2006, 55, 595-609.
43. Jiang, P.; Faase, J.A.J.; Toyoda, H.; Paul, A.; Wimmer, E.; Gorbalenya, A.E. Evidence for emergence of diverse polioviruses from C-cluster coxsackie A viruses and implications for global poliovirus eradication. Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 9457-9462.
44. Lukashev, A.N. Recombination among picornaviruses. Rev. Med. Virol. 2010, 20, 327-337.
45. Chare, E.R.; Gould, E.A.; Holmes, E.C. Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses. J. Gen. Virol. 2003, 84, 2691-2703.
46. Holmes, E.C. The evolutionary genetics of emerging viruses. Annu. Rev. Ecol. Evol. Systemat. 2009, 40, 353-372.
47. Archer, A.M.; Rico-Hesse, R. High genetic divergence and recombination in arenaviruses from the Americas. Virology 2002, 304, 274-281.
48. Charrel, R.N.; Feldmann, H.; Fulhorst, C.F.; Khelifa, R.; de Chesse, R.; de Lamballerie, X. Phylogeny of New World arenaviruses based on the complete coding sequences of the small genomic segment identified an evolutionary lineage produced by intrasegmental recombination. Biochem. Biophys. Res. Comm. 2002, 296, 1118-1124.
49. Hao, W.L. Evidence of intra-segmental homologous recombination in influenza A virus. Gene 2011, 481, 57-64.
50. Wittmann, T.J.; Biek, R.; Hassanin, A.; Rouquet, P.; Reed, P.; Yaba, P.; Pourrut, X.; Real, L.A.; Gonzalez, J.P.; Leroy, E.M. Isolates of Zaire ebolavirus from wild apes reveal genetic lineage and recombinants. Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 17123-17127.
51. Chare, E.R.; Holmes, E.C. A phylogenetic survey of recombination frequency in plant RNA viruses. Arch. Virol. 2006, 151, 933-946.
52. Edgar, R.C. MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004, 5, 113.
53. Schmidt, H.A.; Strimmer, K.; Vingron, M.; von Haeseler, A. TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 2002, 18, 502-504.
54. Whelan, S.; Goldman, N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol. 2001, 18, 691-699.
55. Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 2000, 17, 540-552.
56. Antonov, I.V.; Leontovich, A.M.; Gorbalenya, A.E. BAGG (Blocks Accepting Gaps Generator). 2008. Available online: http://www.genebee.msu.su/~antonov/bagg/cgi/bagg.cgi (accessed on 16 February 2012).
57. Guindon, S.; Gascuel, O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 2003, 52, 696-704.