Discovery of novel virus sequences in an isolated and threatened bat species, the New Ze aland lesser short-tailed bat (Mystacina tuberculata)

Journal of General Virology

Volumn 96, Issue 8, 2015, Pages 2442-2452

  Wang, Jing ^a   Moore, Nicole E ^a   Murray, Zak L ^a   McInnes, Kate ^b   White, Daniel J ^c   Tompkins, Daniel M ^c   Hall, Richard J ^a  

^a INSTITUTE OF ENVIRONMENTAL SCIENCE AND RESEARCH   (New Zealand)

^b DEPARTMENT OF CONSERVATION   (New Zealand)

^c LANDCARE RESEARCH   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BAT; CALICIVIRIDAE; HEPEVIRUS; HOST; METAGENOMICS; MYSTACINA TUBERCULATA; NEW ZEALAND; NONHUMAN; PAPILLOMAVIRIDAE; POLYMERASE CHAIN REACTION; POLYOMAVIRUS; PRIORITY JOURNAL; VIRUS IDENTIFICATION; VIRUS ISOLATION; ANIMAL; CLASSIFICATION; ENDANGERED SPECIES; GENETICS; ISOLATION AND PURIFICATION; MOLECULAR GENETICS; PHYLOGENY; VIROLOGY; VIRUS; VIRUS GENOME;

CALICIVIRIDAE; CHALINOLOBUS TUBERCULATUS; HEPEVIRUS; MAMMALIA; MYSTACINA TUBERCULATA; PAPILLOMAVIRIDAE; POLYOMAVIRUS; VERTEBRATA;

VIRUS PROTEIN;

ANIMALS; CHIROPTERA; ENDANGERED SPECIES; GENOME, VIRAL; METAGENOMICS; MOLECULAR SEQUENCE DATA; NEW ZEALAND; PHYLOGENY; VIRAL PROTEINS; VIRUSES;

EID: 84940182267     PISSN: 00221317     EISSN: 14652099     Source Type: Journal    
DOI: 10.1099/vir.0.000158     Document Type: Article

References (57)

1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990). Basic local alignment search tool. J Mol Biol 215, 403-410
2. Andrews, S. (2010). FastQC: A quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
3. Anthony, S. J., Epstein, J. H., Murray, K. A., Navarrete-Macias, I., Zambrana-Torrelio, C. M., Solovyov, A., Ojeda-Flores, R., Arrigo, N. C., Islam, A. & other authors (2013). A strategy to estimate unknown viral diversity in mammals. MBio 4, e00598-e00e13
4. Baker, K. S., Leggett, R. M., Bexfield, N. H., Alston, M., Daly, G., Todd, S., Tachedjian, M., Holmes, C. E. G., Crameri, S. & other authors (2013). Metagenomic study of the viruses of African straw-coloured fruit bats: detection of a chiropteran poxvirus and isolation of a novel adenovirus. Virology 441, 95-106
5. Batts, W., Yun, S., Hedrick, R. & Winton, J. (2011). A novel member of the family Hepeviridae from cutthroat trout (Oncorhynchus clarkii). Virus Res 158, 116-123
6. Berke, T. & Matson, D. O. (2000). Reclassification of the Caliciviridae into distinct genera and exclusion of hepatitis E virus from the family on the basis of comparative phylogenetic analysis. Arch Virol 145, 1421-1436
7. Berke, T., Golding, B., Jiang, X., Cubitt, D. W., Wolfaardt, M., Smith, A. W. & Matson, D. O. (1997). Phylogenetic analysis of the caliciviruses. J Med Virol 52, 419-424
8. Calisher, C. H., Childs, J. E., Field, H. E., Holmes, K. V. & Schountz, T. (2006). Bats: important reservoir hosts of emerging viruses. Clin Microbiol Rev 19, 531-545
9. Chan, J. F.-W., To, K. K.-W., Tse, H., Jin, D.-Y. & Yuen, K.-Y. (2013a). Interspecies transmission and emergence of novel viruses: lessons from bats and birds. Trends Microbiol 21, 544-555
10. Chan, J. F. W., Lau, S. K. P. & Woo, P. C. Y. (2013b). The emerging novel Middle East respiratory syndrome coronavirus: the ‘‘knowns’’ and ‘‘unknowns’’. J Formos Med Assoc 112, 372-381
11. Chua, K. B., Bellini, W. J., Rota, P. A., Harcourt, B. H., Tamin, A., Lam, S. K., Ksiazek, T. G., Rollin, P. E., Zaki, S. R. & other authors (2000). Nipah virus: a recently emergent deadly paramyxovirus. Science 288, 1432-1435
12. Daly, G. M., Bexfield, N., Heaney, J., Stubbs, S., Mayer, A. P., Palser, A., Kellam, P., Drou, N., Caccamo, M. & other authors (2011). A viral discovery methodology for clinical biopsy samples utilising massively parallel next generation sequencing. PLoS One 6, e28879
13. Drexler, J. F., Corman, V. M., Wegner, T., Tateno, A. F., Zerbinati, R. M., Gloza-Rausch, F., Seebens, A., Muller, M. A. & Drosten, C. (2011). Amplification of emerging viruses in a bat colony. Emerg Infect Dis 17, 449-456.
14. Drexler, J. F., Seelen, A., Corman, V. M., Fumie Tateno, A., Cottontail, V., Melim Zerbinati, R., Gloza-Rausch, F., Klose, S. M., Adu- Sarkodie, Y. & other authors (2012). Bats worldwide carry hepatitis e virus-related viruses that form a putative novel genus within the family Hepeviridae. J Virol 86, 9134-9147
15. 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 Polyomaviridae. J Gen Virol 93, 2652-2657
16. Ge, X., Li, Y., Yang, X., Zhang, H., Zhou, P., Zhang, Y. & Shi, Z. (2012). Metagenomic analysis of viruses from bat fecal samples reveals many novel viruses in insectivorous bats in China. J Virol 86, 4620-4630
17. Ge, X. Y., Li, J. L., Yang, X. L., Chmura, A. A., Zhu, G., Epstein, J. H., Mazet, J. K., Hu, B., Zhang, W. & other authors (2013). Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature 503, 535-538
18. Green, K. Y., Ando, T., Balayan, M. S., Berke, T., Clarke, I. N., Estes, M. K., Matson, D. O., Nakata, S., Neill, J. D. & other authors (2000). Taxonomy of the caliciviruses. J Infect Dis 181 (Suppl. 2), S322-S330
19. Hall, R. J., Wang, J., Peacey, M., Moore, N. E., McInnes, K. & Tompkins, D. M. (2014a). New alphacoronavirus in Mystacina tuberculata bats, New Zealand. Emerg Infect Dis 20, 697-700
20. Hall, R. J., Wang, J., Todd, A. K., Bissielo, A. B., Yen, S., Strydom, H., Moore, N. E., Ren, X., Huang, Q. S. & other authors (2014b). Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery. J Virol Methods 195, 194-204
21. Hand, S. J., Worthy, T. H., Archer, M., Worthy, J. P., Tennyson, A. J. D. & Schofield, R. P. (2013). Miocene Mystacinids (Chiroptera, Noctilionoidea) indicate a long history for endemic bats in New Zealand. J Vertebr Paleontol 33, 1442-1448
22. He, B., Li, Z., Yang, F., Zheng, J., Feng, Y., Guo, H., Li, Y., Wang, Y., Su, N. & other authors (2013). Virome profiling of bats from Myanmar by metagenomic analysis of tissue samples reveals more novel mammalian viruses. PLOS ONE 8, e61950
23. Hickman, A. B. & Dyda, F. (2005). Binding and unwinding: SF3 viral helicases. Curr Opin Struct Biol 15, 77-85
24. Huson, D. H. & Mitra, S. (2012). Introduction to the analysis of environmental sequences: metagenomics with megan. Methods Mol Biol 856, 415-429
25. Huson, D. H., Auch, A. F., Qi, J. & Schuster, S. C. (2007). MEGAN analysis of metagenomic data. Genome Res 17, 377-386
26. Jones, K. E., Patel, N. G., Levy, M. A., Storeygard, A., Balk, D., Gittleman, J. L. & Daszak, P. (2008). Global trends in emerging infectious diseases. Nature 451, 990-993.
27. King, C. M. (2005). The Handbook of New Zealand Mammals. Melbourne: Oxford University Press
28. Lau, S. K. P., Woo, P. C. Y., Li, K. S. M., Huang, Y., Tsoi, H.-W., Wong, B. H. L., Wong, S. S. Y., Leung, S.-Y., Chan, K.-H. & Yuen, K.-Y. (2005). Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. Proc Natl Acad Sci U S A 102, 14040-14045
29. Leroy, E. M., Kumulungui, B., Pourrut, X., Rouquet, P., Hassanin, A., Yaba, P., Délicat, A., Paweska, J. T., Gonzalez, J. -P. & Swanepoel, R. (2005). Fruit bats as reservoirs of Ebola virus. Nature 438, 575-576
30. Li, W., Shi, Z., Yu, M., Ren, W., Smith, C., Epstein, J. H., Wang, H., Crameri, G., Hu, Z. & other authors (2005). Bats are natural reservoirs of SARS-like coronaviruses. Science 310, 676-679
31. Li, L., Victoria, J. G., Wang, C., Jones, M., Fellers, G. M., Kunz, T. H. & Delwart, E. (2010a). Bat guano virome: predominance of dietary viruses from insects and plants plus novel mammalian viruses. J Virol 84, 6955-6965
32. Li, Y., Ge, X., Zhang, H., Zhou, P., Zhu, Y., Zhang, Y., Yuan, J., Wang, L.-F. & Shi, Z. (2010b). Host range, prevalence, and genetic diversity of adenoviruses in bats. J Virol 84, 3889-3897
33. Liu, H., Fu, Y., Xie, J., Cheng, J., Ghabrial, S. A., Li, G., Peng, Y., Yi, X. & Jiang, D. (2011). Widespread endogenization of densoviruses and parvoviruses in animal and human genomes. J Virol 85, 9863-9876
34. Luis, A. D., Hayman, D. T. S., O’Shea, T. J., Cryan, P. M., Gilbert, A. T., Pulliam, J. R. C., Mills, J. N., Timonin, M. E., Willis, C. K. R. & other authors (2013). A comparison of bats and rodents as reservoirs of zoonotic viruses: are bats special? Proc Biol Sci 280, 20122753
35. Memish, Z. A., Mishra, N., Olival, K. J., Fagbo, S. F., Kapoor, V., Epstein, J. H., Alhakeem, R., Durosinloun, A., Al Asmari, M. & other authors (2013). Middle East respiratory syndrome coronavirus in bats, Saudi Arabia. Emerg Infect Dis 19, 1819-1823
36. Milne-Price, S., Miazgowicz, K. L. & Munster, V. J. (2014). The emergence of the Middle East respiratory syndrome coronavirus. Pathog Dis 71, 121-136
37. Murray, K., Selleck, P., Hooper, P., Hyatt, A., Gould, A., Gleeson, L., Westbury, H., Hiley, L., Selvey, L. & other authors (1995). A morbillivirus that caused fatal disease in horses and humans. Science 268, 94-97
38. Naccache, S. N., Hackett, J. Jr, Delwart, E. L. & Chiu, C. Y. (2014). Concerns over the origin of NIH-CQV, a novel virus discovered in Chinese patients with seronegative hepatitis. Proc Natl Acad Sci USA111,E976
39. O’Donnell, C. F. J. (2001). Advances in New Zealand mammalogy 1990-2000: long-tailed bat. J Roy Soc NZ 31, 43-57
40. O’Shea, T. J., Cryan, P. M., Cunningham, A. A., Fooks, A. R., Hayman, D. T., Luis, A. D., Peel, A. J., Plowright, R. K. & Wood, J. L. (2014). Bat flight and zoonotic viruses. Emerg Infect Dis 20, 741-745
41. Phan, T. G., Kapusinszky, B., Wang, C., Rose, R. K., Lipton, H. L. & Delwart, E. L. (2011). The fecal viral flora of wild rodents. PLoS Pathog 7, e1002218
42. Rosseel, T., Pardon, B., De Clercq, K., Ozhelvaci, O. & Van Borm, S. (2014). False-positive results in metagenomic virus discovery: a strong case for follow-up diagnosis. Transbound Emerg Dis 61, 293-299
43. Selvey, L. A., Wells, R. M., McCormack, J. G., Ansford, A. J., Murray, K., Rogers, R. J., Lavercombe, P. S., Selleck, P. & Sheridan, J. W. (1995). Infection of humans and horses by a newly described morbillivirus. Med J Aust 162, 642-645
44. Simmons, N. B. (2005). Order Chiroptera. In Mammal Species of the World: a Taxonomic and Geographic Reference, pp. 312-529. Edited by D. E. Wilson. Reeder. Baltimore, MD: Johns Hopkins University Press
45. Smith, I. & Wang, L. F. (2013). Bats and their virome: an important source of emerging viruses capable of infecting humans. Curr Opin Virol 3, 84-91
46. Smith, D. B., Purdy, M. A. & Simmonds, P. (2013). Genetic variability and the classification of hepatitis E virus. J Virol 87, 4161-4169
47. Sonntag, M., Muhldorfer, K., Speck, S., Wibbelt, G. & Kurth, A. (2009). New adenovirus in bats, Germany. Emerg Infect Dis 15, 2052-2055
48. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. & Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28, 2731-2739
49. Tse, H., Chan, W. M., Li, K. S. M., Lau, S. K. P., Woo, P. C. Y. & Yuen, K. Y. (2012a). Discovery and genomic characterization of a novel bat sapovirus with unusual genomic features and phylogenetic position. PLOS ONE 7, e34987
50. Tse, H., Tsang, A. K. L., Tsoi, H. W., Leung, A. S. P., Ho, C. C., Lau, S. K. P., Woo, P. C. Y. & Yuen, K. Y. (2012b). Identification of a novel bat papillomavirus by metagenomics. PLOS ONE 7, e43986
51. Wang, L.-F., Shi, Z., Zhang, S., Field, H., Daszak, P. & Eaton, B. T. (2006). Review of bats and SARS. Emerg Infect Dis 12, 1834-1840
52. Warrilow, D. (2005). Australian bat lyssavirus: a recently discovered new rhabdovirus. Curr Top Microbiol Immunol 292, 25-44
53. Wertheim, J. O., Chu, D. K. W., Peiris, J. S. M., Kosakovsky Pond, S. L. & Poon, L. L. M. (2013). A case for the ancient origin of coronaviruses. J Virol 87, 7039-7045
54. Woo, P. C., Lau, S. K., Lam, C. S., Lau, C. C., Tsang, A. K., Lau, J. H., Bai, R., Teng, J. L., Tsang, C. C. & other authors (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
55. Wu, Z., Ren, X., Yang, L., Hu, Y., Yang, J., He, G., Zhang, J., Dong, J., Sun, L. & other authors (2012). Virome analysis for identification of novel mammalian viruses in bat species from Chinese provinces. J Virol 86, 10999-11012
56. Ye, Y., Choi, J.-H. & Tang, H. (2011). RAPSearch: a fast protein similarity search tool for short reads. BMC Bioinformatics 12, 159
57. Zhao, Y., Tang, H. & Ye, Y. (2012). RAPSearch2: a fast and memory- efficient protein similarity search tool for next-generation sequencing data. Bioinformatics 28, 125-126