1887

Abstract

The yak () is an iconic symbol in the high-altitude region of the Qinghai–Tibetan Plateau. Diarrhoea is a common disease in yaks, resulting in major economic losses. To investigate the diversity of viral species, we reported the metagenomics-derived virome in a pooled faecal sample of 20 diarrhoeic yaks. The nine viruses found in the pooled diarrhoeic samples, in order of abundance of nucleic acid sequence, were influenza A virus, bovine viral diarrhoea virus (BVDV), rotavirus, ungulate tetraparvovirus 1 (bovine hokovirus), astrovirus (AstV), bovine enterovirus, hepatitis E virus, kobuvirus and woodchuck hepatitis virus. Compared with healthy yaks, only AstV had a significantly higher prevalence rate in diarrhoeal samples, indicating a correlation with the clinical symptoms of diarrhoea in yaks. To further investigate the molecular characterization of yak AstV, a near-full genome was obtained from a diarrhoeic sample. It was 6243 bp in length and shared 46.4–66.2 % similarity with other related bovine AstVs from faeces. Phylogenetic analysis of the genome demonstrated that the yak AstV fell within the bovine AstVs cluster, but was located in a unique lineage, suggesting a novel AstV species was identified in yaks. Interestingly, the ORF2 region of yak AstV had closer similarity and genetically relationship with deer AstV strain CcAstV-2 than that of the bovine AstVs. Further analysis showed that one possible interspecies recombination event occurred in ORF2. In summary, this study expanded our understanding of the viral communities of diarrhoeal yaks and identified a novel AstV that was associated with diarrhoea in yaks.

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2015-12-01
2024-03-28
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References

  1. Al Mawly J., Grinberg A., Prattley D., Moffat J., French N. 2015; Prevalence of endemic enteropathogens of calves in New Zealand dairy farms. N Z Vet J 63:147–152 [CrossRef]
    [Google Scholar]
  2. Belliot G., Laveran H., Monroe S. S. 1997; Detection and genetic differentiation of human astroviruses: phylogenetic grouping varies by coding region. Arch Virol 142:1323–1334 [View Article][PubMed]
    [Google Scholar]
  3. Blanchard P. C. 2012; Diagnostics of dairy and beef cattle diarrhoea. Vet Clin North Am Food Anim Pract 28:443–464 [View Article][PubMed]
    [Google Scholar]
  4. Brnić D., Jemeršić L., Keros T., Prpić J. 2014; High prevalence and genetic heterogeneity of porcine astroviruses in domestic pigs. Vet J 202:390–392 [View Article][PubMed]
    [Google Scholar]
  5. Candido M., Alencar A. L., Almeida-Queiroz S. R., Buzinaro M. G., Munin F. S., de Godoy S. H., Livonesi M. C., Fernandes A. M., de Sousa R. L. 2015; Molecular detection and phylogenetic analysis of bovine astrovirus in Brazil. Arch Virol 160:1519–1525 [View Article][PubMed]
    [Google Scholar]
  6. Cattoli G., De Battisti C., Toffan A., Salviato A., Lavazza A., Cerioli M., Capua I. 2007; Co-circulation of distinct genetic lineages of astroviruses in turkeys and guinea fowl. Arch Virol 152:595–602 [View Article][PubMed]
    [Google Scholar]
  7. Cho Y. I., Yoon K. J. 2014; An overview of calf diarrhoea – infectious etiology, diagnosis, and intervention. J Vet Sci 15:1–17 [View Article][PubMed]
    [Google Scholar]
  8. Chu D. K., Chin A. W., Smith G. J., Chan K. H., Guan Y., Peiris J. S., Poon L. L. 2010; Detection of novel astroviruses in urban brown rats and previously known astroviruses in humans. J Gen Virol 91:2457–2462 [View Article][PubMed]
    [Google Scholar]
  9. De Benedictis P., Schultz-Cherry S., Burnham A., Cattoli G. 2011; Astrovirus infections in humans and animals – molecular biology, genetic diversity, and interspecies transmissions. Infect Genet Evol 11:1529–1544 [View Article][PubMed]
    [Google Scholar]
  10. Dhama K., Chauhan R. S., Mahendran M., Malik S. V. 2009; Rotavirus diarrhoea in bovines and other domestic animals. Vet Res Commun 33:1–23 [View Article][PubMed]
    [Google Scholar]
  11. Finkbeiner S. R., Allred A. F., Tarr P. I., Klein E. J., Kirkwood C. D., Wang D. 2008; Metagenomic analysis of human diarrhoea: viral detection and discovery. PLoS Pathog 4:e1000011 [View Article][PubMed]
    [Google Scholar]
  12. Foster D. M., Smith G. W. 2009; Pathophysiology of diarrhoea in calves. Vet Clin North Am Food Anim Pract 25:13–36 [CrossRef]
    [Google Scholar]
  13. Fu M., Chen Y., Xiong X., Lan D., Li J. 2014; Establishment of mammary gland model in vitro: culture and evaluation of a yak mammary epithelial cell line. PLoS One 9:e113669 [View Article][PubMed]
    [Google Scholar]
  14. Harp J. A., Goff J. P. 1998; Strategies for the control of Cryptosporidium parvum infection in calves. J Dairy Sci 81:289–294 [View Article][PubMed]
    [Google Scholar]
  15. Hu Q., Ma T., Wang K., Xu T., Liu J., Qiu Q. 2012; The Yak genome database: an integrative database for studying yak biology and high-altitude adaption. BMC Genomics 13:600 [View Article][PubMed]
    [Google Scholar]
  16. Kaplon J., Guenau E., Asdrubal P., Pothier P., Ambert-Balay K. 2011; Possible novel nebovirus genotype in cattle, France. Emerg Infect Dis 17:1120–1123 [View Article][PubMed]
    [Google Scholar]
  17. Kosakovsky Pond S. L., Posada D., Gravenor M. B., Woelk C. H., Frost S. D. 2006; gard: a genetic algorithm for recombination detection. Bioinformatics 22:3096–3098 [CrossRef]
    [Google Scholar]
  18. Lan D., Xiong X., Wei Y., Xu T., Zhong J., Zhi X., Wang Y., Li J. 2014; RNA-Seq analysis of yak ovary: improving yak gene structure information and mining reproduction-related genes. Sci China Life Sci 57:925–935 [View Article][PubMed]
    [Google Scholar]
  19. Laureyns J., Ribbens S., de Kruif A. 2010; Control of bovine virus diarrhoea at the herd level: reducing the risk of false negatives in the detection of persistently infected cattle. Vet J 184:21–26 [View Article][PubMed]
    [Google Scholar]
  20. Li J., Suolang S., Gong G., Daba C. 2012; [Prevention and treatment of infectious diseases and parasitic in yak and its prospects]. Chin Dairy Cattle 1:30–33 (in Chinese).
    [Google Scholar]
  21. Li L., Diab S., McGraw S., Barr B., Traslavina R., Higgins R., Talbot T., Blanchard P., Rimoldi G., other authors. 2013; Divergent astrovirus associated with neurologic disease in cattle. Emerg Infect Dis 19:1385–1392 [View Article][PubMed]
    [Google Scholar]
  22. Liu C., Liu Q., Chen X., Zeng X., Zhang W., Liu D., Xu W. 1986; [Investigation of the yak diarrhoeal pathogen – rotavirus]. Chin J Vet Sci Technol 10:19–21 (in Chinese).
    [Google Scholar]
  23. Marczinke B., Bloys A. J., Brown T. D., Willcocks M. M., Carter M. J., Brierley I. 1994; The human astrovirus RNA-dependent RNA polymerase coding region is expressed by ribosomal frameshifting. J Virol 68:5588–5595
    [Google Scholar]
  24. Mi R., Wang X., Li C., Huang Y., Zhou P., Li Z., Lei M., Cai J., Chen Z. 2013; Prevalence and genetic characterization of Cryptosporidium in yaks in Qinghai Province of China. PLoS One 8:e74985 [View Article][PubMed]
    [Google Scholar]
  25. Mokili J. L., Rohwer F., Dutilh B. E. 2012; Metagenomics and future perspectives in virus discovery. Curr Opin Virol 2:63–77 [View Article][PubMed]
    [Google Scholar]
  26. Moser L. A., Schultz-Cherry S. 2005; Pathogenesis of astrovirus infection. Viral Immunol 18:4–10 [View Article][PubMed]
    [Google Scholar]
  27. Nogueira J. S., Asano K. M., de Souza S. P., Brandão P. E., Richtzenhain L. J. 2013; First detection and molecular diversity of Brazilian bovine torovirus (BToV) strains from young and adult cattle. Res Vet Sci 95:799–801 [View Article][PubMed]
    [Google Scholar]
  28. Oem J. K., An D. J. 2014; Phylogenetic analysis of bovine astrovirus in Korean cattle. Virus Genes 48:372–375 [View Article][PubMed]
    [Google Scholar]
  29. Qiu Q., Zhang G., Ma T., Qian W., Wang J., Ye Z., Cao C., Hu Q., Kim J., other authors. 2012; The yak genome and adaptation to life at high altitude. Nat Genet 44:946–949 [View Article][PubMed]
    [Google Scholar]
  30. Rosario K., Breitbart M. 2011; Exploring the viral world through metagenomics. Curr Opin Virol 1:289–297 [View Article][PubMed]
    [Google Scholar]
  31. Shan T., Li L., Simmonds P., Wang C., Moeser A., Delwart E. 2011; The fecal virome of pigs on a high-density farm. J Virol 85:11697–11708 [View Article][PubMed]
    [Google Scholar]
  32. Smits S. L., van Leeuwen M., Kuiken T., Hammer A. S., Simon J. H., Osterhaus A. D. 2010; Identification and characterization of deer astroviruses. J Gen Virol 91:2719–2722 [View Article][PubMed]
    [Google Scholar]
  33. Tse H., Chan W. M., Tsoi H. W., Fan R. Y., Lau C. C., Lau S. K., Woo P. C., Yuen K. Y. 2011; Rediscovery and genomic characterization of bovine astroviruses. J Gen Virol 92:1888–1898 [View Article][PubMed]
    [Google Scholar]
  34. Woode G. N., Bridger J. C. 1978; Isolation of small viruses resembling astroviruses and caliciviruses from acute enteritis of calves. J Med Microbiol 11:441–452 [View Article][PubMed]
    [Google Scholar]
  35. Woode G. N., Pohlenz J. F., Gourley N. E., Fagerland J. A. 1984; Astrovirus and Breda virus infections of dome cell epithelium of bovine ileum. J Clin Microbiol 19:623–630
    [Google Scholar]
  36. Woode G. N., Gourley N. E., Pohlenz J. F., Liebler E. M., Mathews S. L., Hutchinson M. P. 1985; Serotypes of bovine astrovirus. J Clin Microbiol 22:668–670
    [Google Scholar]
  37. 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 [View Article][PubMed]
    [Google Scholar]
  38. Yamashita T., Ito M., Kabashima Y., Tsuzuki H., Fujiura A., Sakae K. 2003; Isolation and characterization of a new species of kobuvirus associated with cattle. J Gen Virol 84:3069–3077 [View Article][PubMed]
    [Google Scholar]
  39. Zhang F., Wang G., Zhang F., Gong X., Zhou J., Wu R., Qiu C. 2011; [Isolation and identification of a bovine viral diarrhoea virus isolate from yak in Qinghai Province]. Chin Vet Sci 41:1101–1105 (in Chinese).
    [Google Scholar]
  40. Zhang B., Tang C., Yue H., Ren Y., Song Z. 2014; Viral metagenomics analysis demonstrates the diversity of viral flora in piglet diarrhoeic faeces in China. J Gen Virol 95:1603–1611 [View Article][PubMed]
    [Google Scholar]
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