Discovery of diverse polyomaviruses in bats and the evolutionary history of the Polyomaviridae

Journal of General Virology

Volumn 94, Issue PART4, 2013, Pages 738-748

  Tao, Ying ^a   Shi, Mang ^b   Conrardy, Christina ^a   Kuzmin, Ivan V ^c   Recuenco, Sergio ^c   Agwanda, Bernard ^d   Alvarez, Danilo A ^e   Ellison, James A ^c   Gilbert, Amy T ^c   Moran, David ^e   Niezgoda, Michael ^c   Lindblade, Kim A ^a   Holmes, Edward C ^b,f   Breiman, Robert F ^g   Rupprecht, Charles E ^c   Tong, Suxiang ^a  

^a CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

^b UNIVERSITY OF SYDNEY   (Australia)

^c NATIONAL CENTER FOR EMERGING AND ZOONOTIC INFECTIOUS DISEASES   (United States)

^d KENYA WILDLIFE SERVICE   (Kenya)

^e UNIVERSIDAD DEL VALLE DE GUATEMALA   (Guatemala)

^f NATIONAL INSTITUTES OF HEALTH   (United States)

^g Centers for Disease Control and Prevention Kenya   (Kenya)

Author keywords

[No Author keywords available]

Indexed keywords

CAPSID PROTEIN; VIRUS DNA;

ARTICLE; BAT; CARDIODERMA POLYOMA VIRUS; CHAEREPHON POLYOMA VIRUS 1; CHAEREPHON POLYOMA VIRUS 2; DNA SEQUENCE; EIDOLON POLYOMA VIRUS 1; EIDOLON POLYOMA VIRUS 2; EVOLUTION; GENE SEQUENCE; GENETIC HETEROGENEITY; GENETIC RECOMBINATION; GENETIC VARIABILITY; GENOME; GUATEMALA; KENYA; MAMMAL; MASTOMYS POLYOMA VIRUS; MINIOPTERUS POLYOMA VIRUS; MYOTIS POLYOMA VIRUS; NONHUMAN; OTOMOPS POLYOMA VIRUS 1; OTOMOPS POLYOMA VIRUS 2; OTOMOPS POLYOMA VIRUS 3; PARAPHYLY; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYOMA VIRUS; PRIORITY JOURNAL; PTERONOTUS POLYOMA VIRUS; ROUSETTUS POLYOMA VIRUS 1; ROUSETTUS POLYOMA VIRUS 2; VIRUS CELL INTERACTION; VIRUS CLASSIFICATION; VIRUS DETECTION;

EID: 84875682552     PISSN: 00221317     EISSN: 14652099     Source Type: Journal    
DOI: 10.1099/vir.0.047928-0     Document Type: Article

References (40)

1. Allander, T., Andreasson, K., Gupta, S., Bjerkner, A., Bogdanovic, G., Persson, M. A., Dalianis, T., Ramqvist, T. & Andersson, B. (2007). Identification of a third human polyomavirus. J Virol 81, 4130-4136.
2. Bergsten, J. (2005). A review of long-branch attraction. Cladistics 21, 163-193.
3. Cantalupo, P., Doering, A., Sullivan, C. S., Pal, A., Peden, K. W., Lewis, A. M. & Pipas, J. M. (2005). Complete nucleotide sequence of polyomavirus SA12. J Virol 79, 13094-13104.
4. Charleston, M. A. (1998). Jungles: a new solution to the host/parasite phylogeny reconciliation problem. Math Biosci 149, 191-223.
5. Charleston, M. A. & Robertson, D. L. (2002). Preferential host switching by primate lentiviruses can account for phylogenetic similarity with the primate phylogeny. Syst Biol 51, 528-535.
6. Cui, J., Han, N., Streicker, D., Li, G., Tang, X., Shi, Z., Hu, Z., Zhao, G., Fontanet, A. & other authors (2007). Evolutionary relationships between bat coronaviruses and their hosts. Emerg Infect Dis 13, 1526-1532.
7. Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32, 1792-1797.
8. Fagrouch, Z., Sarwari, R., Lavergne, A., Delaval, M., de Thoisy, B., Lacoste, V. & Verschoor, E. J. (2012). Novel polyomaviruses in South American bats and their relationship to other members of the family Polyomaviridae. J Gen Virol 93, 2652-2657.
9. Fourment, M. & Gibbs, M. J. (2006). PATRISTIC: a program for calculating patristic distances and graphically comparing the components of genetic change. BMC Evol Biol 6, 1.
10. Gaynor, A. M., Nissen, M. D., Whiley, D. M., Mackay, I. M., Lambert, S. B., Wu, G., Brennan, D. C., Storch, G. A., Sloots, T. P. & Wang, D. (2007). Identification of a novel polyomavirus from patients with acute respiratory tract infections. PLoS Pathog 3, e64.
11. Hatwell, J. N. & Sharp, P. M. (2000). Evolution of human polyomavirus JC. J Gen Virol 81, 1191-1200.
12. Hebert, P. D. N., Cywinska, A., Ball, S. L. & deWaard, J. R. (2003). Biological identifications through DNA barcodes. Proc Biol Sci 270, 313-321.
13. Jiang, M., Abend, J. R., Johnson, S. F. & Imperiale, M. J. (2009). The role of polyomaviruses in human disease. Virology 384, 266-273.
14. Jobes, D. V., Chima, S. C., Ryschkewitsch, C. F. & Stoner, G. L. (1998). Phylogenetic analysis of 22 complete genomes of the human polyomavirus JC virus. J Gen Virol 79, 2491-2498.
15. Johne, R., Wittig, W., Fernández-de-Luco, D., Hofle, U. & Muller, H. (2006). Characterization of two novel polyomaviruses of birds by using multiply primed rolling-circle amplification of their genomes. J Virol 80, 3523-3531.
16. Johne, R., Buck, C. B., Allander, T., Atwood, W. J., Garcea, R. L., Imperiale, M. J., Major, E. O., Ramqvist, T. & Norkin, L. C. (2011). Taxonomical developments in the family Polyomaviridae. Arch Virol 156, 1627-1634.
17. Khalili, K., White, M. K., Sawa, H., Nagashima, K. & Safak, M. (2005). The agnoprotein of polyomaviruses: a multifunctional auxiliary protein. J Cell Physiol 204, 1-7.
18. Krumbholz, A., Bininda-Emonds, O. R., Wutzler, P. & Zell, R. (2009). Phylogenetics, evolution, and medical importance of polyomaviruses. Infect Genet Evol 9, 784-799.
19. Kuzmin, I. V., Bozick, B., Guagliardo, S. A., Kunkel, R., Shak, J. R., Tong, S. & Rupprecht, C. E. (2011). Bats, emerging infectious diseases, and the rabies paradigm revisited. Emerging Health Threats Journal 4, 7159.
20. Legendre, P., Desdevises, Y. & Bazin, E. (2002). A statistical test for host-parasite coevolution. Syst Biol 51, 217-234.
21. Longdon, B., Hadfield, J. D., Webster, C. L., Obbard, D. J. & Jiggins, F. M. (2011). Host phylogeny determines viral persistence and replication in novel hosts. PLoS Pathog 7, e1002260.
22. Martin, D. P., Lemey, P., Lott, M., Moulton, V., Posada, D. & Lefeuvre, P. (2010). RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26, 2462-2463.
23. Meier-Kolthoff, J. P., Auch, A. F., Huson, D. H. & Goker, M. (2007). COPYCAT: cophylogenetic analysis tool. Bioinformatics 23, 898-900.
24. Misra, V., Dumonceaux, T., Dubois, J., Willis, C., Nadin-Davis, S., Severini, A., Wandeler, A., Lindsay, R. & Artsob, H. (2009). Detection of polyoma and corona viruses in bats of Canada. J Gen Virol 90, 2015-2022.
25. Norkin, L. C., Allander, T., Atwood, W. J., Buck, C. B., Garcea, R. L., Imperiale, M. J., Johne, R., Major, E. O., Pipas, J. M. & Ramqvist, T. (2011). Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses. Oxford: Elsevier.
26. Pérez-Losada, M., Christensen, R. G., McClellan, D. A., Adams, B. J., Viscidi, R. P., Demma, J. C. & Crandall, K. A. (2006). Comparing phylogenetic codivergence between polyomaviruses and their hosts. J Virol 80, 5663-5669.
27. Pipas, J. M. (1992). Common and unique features of T antigens encoded by the polyomavirus group. J Virol 66, 3979-3985.
28. Ramsden, C., Holmes, E. C. & Charleston, M. A. (2009). Hantavirus evolution in relation to its rodent and insectivore hosts: no evidence for codivergence. Mol Biol Evol 26, 143-153.
29. Renshaw, R. W., Wise, A. G., Maes, R. K. & Dubovi, E. J. (2012). Complete genome sequence of a polyomavirus isolated from horses. J Virol 86, 8903.
30. Ronquist, F. & Huelsenbeck, J. P. (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574.
31. Schowalter, R. M., Pastrana, D. V., Pumphrey, K. A., Moyer, A. L. & Buck, C. B. (2010). Merkel cell polyomavirus and two previously unknown polyomaviruses are chronically shed from human skin. Cell Host Microbe 7, 509-515.
32. Shadan, F. F. & Villarreal, L. P. (1993). Coevolution of persistently infecting small DNA viruses and their hosts linked to host-interactive regulatory domains. Proc Natl Acad Sci U S A 90, 4117-4121.
33. Siebrasse, E. A., Reyes, A., Lim, E. S., Zhao, G., Mkakosya, R. S., Manary, M. J., Gordon, J. I. & Wang, D. (2012). Identification of MW polyomavirus, a novel polyomavirus in human stool. J Virol 86, 10321-10326.
34. Soeda, E., Maruyama, T., Arrand, J. R. & Griffin, B. E. (1980). Host dependent evolution of three papova viruses. Nature 285, 165-167.
35. Streicker, D. G., Turmelle, A. S., Vonhof, M. J., Kuzmin, I. V., McCracken, G. F. & Rupprecht, C. E. (2010). Host phylogeny constrains cross-species emergence and establishment of rabies virus in bats. Science 329, 676-679.
36. Talavera, G. & Castresana, J. (2007). Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56, 564-577.
37. Tong, S., Conrardy, C., Ruone, S., Kuzmin, I. V., Guo, X., Tao, Y., Niezgoda, M., Haynes, L., Agwanda, B. & other authors (2009). Detection of novel SARS-like and other coronaviruses in bats from Kenya. Emerg Infect Dis 15, 482-485.
38. Tong, S., Li, Y., Rivailler, P., Conrardy, C., Castillo, D. A., Chen, L. M., Recuenco, S., Ellison, J. A., Davis, C. T. & other authors (2012). A distinct lineage of influenza A virus from bats. Proc Natl Acad Sci USA 109, 4269-4274.
39. Van Ghelue, M., Khan, M. T., Ehlers, B. & Moens, U. (2012). Genome analysis of the new human polyomaviruses. Rev Med Virol 22, 354-377.
40. White, M. K., Safak, M. & Khalili, K. (2009). Regulation of gene expression in primate polyomaviruses. J Virol 83, 10846-10856.