Abstract
A viral metagenomics approach was used to investigate fecal samples of Japanese calves with and without diarrhea. Of the different viral pathogens detected, read counts gave nearly complete astrovirus-related RNA sequences in 15 of the 146 fecal samples collected in three distinct areas (Hokkaido, Ishikawa, and Kagoshima Prefectures) between 2009 and 2015. Due to the lack of genetic information about bovine astroviruses (BoAstVs) in Japan, these sequences were analyzed in this study. Nine of the 15 Japanese BoAstVs were closely related to Chinese BoAstVs and clustered into a lineage (tentatively named lineage 1) in all phylogenetic trees. Three of 15 strains were phylogenetically separate from lineage 1, showing low sequence identities, and clustered instead with an American strain isolated from cattle with respiratory disease (tentatively named lineage 2). Interestingly, two of 15 strains clustered with lineage 1 in the open reading frame (ORF)1a and ORF1b regions, while they clustered with lineage 2 in the ORF2 region. Remarkably, one of 15 strains exhibited low amino acid sequence similarity to other BoAstVs and was clustered separately with porcine astrovirus type 5 in all trees, and ovine astrovirus in the ORF2 region, suggesting past interspecies transmission.
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Djikeng A, Halpin R, Kuzmickas R, DePasse J, Feldblyum J, Sengamalay N, Afonso C, Zhang X, Anderson NG, Ghedin E, Spiro DJ (2008) Viral genome sequencing by random primer methods. BMC Genom 9:5
Batty EM, Wong TH, Trebes A, Argoud K, Attar M, Buck D, Ip CL, Golubchik T, Cule M, Bowden R, Manganis C, Klenerman P, Barnes E, Walker AS, Wyllie DH, Wilson DJ, Dingle KE, Peto TE, Crook DW, Piazza P (2013) A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples. PLoS One 8:e66129
Bosch A, Guix S, Krishna NK, Méndez E, Monroe SS, Pantin-Jackwood M, Schultz-Cherry S (2011) Family Astroviridae. In: King AMQ, Lefkowitz E, Adams MJ, Carstens EB (eds) Virus taxonomy: classification and nomenclature of viruses (Ninth Report of the International Committee on the Taxonomy of Viruses). Elsevier Academic Press, New York, pp 953–959
Méndez E, Arias CF (2007) Fields virology. In: Knipe DM, Howley PM, Griffin DE, Lamb RA, Martin MA, Roizman B (eds) Virus taxonomy: classification and nomenclature of viruses (Ninth Report of the International Committee on the Taxonomy of Viruses), 5th edn. Lippincott, Williams & Wilkins, Philadelphia, pp 981–1000
Woode GN, Bridger JC (1978) Isolation of small viruses resembling astroviruses and caliciviruses from acute enteritis of calves. J Med Microbiol 11:441–452
Woode GN, Gourley NE, Pohlenz JF, Liebler EM, Mathews SL, Hutchinson MP (1985) Serotypes of bovine astrovirus. J Clin Microbiol 22:668–670
Glass RI, Noel J, Mitchell D, Herrmann JE, Blacklow NR, Pickering LK, Dennehy P, Ruiz-Palacios G, de Guerrero ML, Monroe SS (1996) The changing epidemiology of astrovirus-associated gastroenteritis: a review. Arch Virol Suppl 12:287–300
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
Li L, Diab S, McGraw S, Barr B, Traslavina R, Higgins R, Talbot T, Blanchard P, Rimoldi G, Fahsbender E, Page B, Phan TG, Wang C, Deng X, Pesavento P, Delwart E (2013) Divergent astrovirus associated with neurologic disease in cattle. Emerg Infect Dis 9:1385–1392
Bouzalas IG, Wüthrich D, Walland J, Drögemüller C, Zurbriggen A, Vandevelde M, Oevermann A, Bruggmann R, Seuberlich T (2014) Neurotropic astrovirus in cattle with nonsuppurative encephalitis in Europe. J Clin Microbiol 52:3318–3324
Snodgrass DR, Gray EW (1977) Detection and transmission of 30 nm virus particles (astroviruses) in faeces of lambs with diarrhoea. Arch Virol 50:287–291
Reuter G, Pankovics P, Delwart E, Boros Á (2012) Identification of a novel astrovirus in domestic sheep in Hungary. Arch Virol 157:323–327
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882
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
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC (1999) Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 73:152–160
Laurin MA, Dastor M, L’homme Y (2011) Detection and genetic characterization of a novel pig astrovirus: relationship to other astroviruses. Arch Virol 156:2095–2099
Tse H, Chan WM, Tsoi HW, Fan RY, Lau CC, Lau SK, Woo PC, Yuen KY (2011) Rediscovery and genomic characterization of bovine astroviruses. J Gen Virol 92:1888–1898
Smits SL, van Leeuwen M, Kuiken T, Hammer AS, Simon JH, Osterhaus AD (2010) Identification and characterization of deer astroviruses. J Gen Virol 91:2719–2722
Ng TF, Kondov NO, Deng X, Van Eenennaam A, Neibergs HL, Delwart E (2015) A metagenomics and case-control study to identify viruses associated with bovine respiratory disease. J Virol 89:5340–5349
Oem JK, An DJ (2014) Phylogenetic analysis of bovine astrovirus in Korean cattle. Virus Genes 48:372–375
Candido M, Alencar AL, Almeida-Queiroz SR, Buzinaro MD, Munin FS, de Godoy SH, Livonesi MC, Fernandes AM, de Sousa RL (2015) Molecular detection and phylogenetic analysis of bovine astrovirus in Brazil. Arch Virol 160:1519–1525
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
Xiao CT, Giménez-Lirola LG, Gerber PF, Jiang YH, Halbur PG, Opriessnig T (2013) Identification and characterization of novel porcine astroviruses (PAstVs) with high prevalence and frequent co-infection of individual pigs with multiple PAstV types. J Gen Virol 94:570–582
Brnić D, Prpić J, Keros T, Roić B, Starešina V, Jemeršić L (2013) Porcine astrovirus viremia and high genetic variability in pigs on large holdings in Croatia. Infect Genet Evol 14:258–264
Ulloa JC, Gutiérrez MF (2010) Genomic analysis of two ORF2 segments of new porcine astrovirus isolates and their close relationship with human astroviruses. Can J Microbiol 56:569–577
Walter JE, Briggs J, Guerrero ML, Matson DO, Pickering LK, Ruiz-Palacios G, Berke T, Mitchell DK (2001) Molecular characterization of a novel recombinant strain of human astrovirus associated with gastroenteritis in children. Arch Virol 146:2357–2367
Wolfaardt M, Kiulia NM, Mwenda JM, Taylor MB (2011) Evidence of a recombinant wild-type human astrovirus strain from a Kenyan child with gastroenteritis. J Clin Microbiol 49:728–731
Acknowledgment
This study was supported by the Research Project for Improving Food Safety and Animal Health of the Ministry of Agriculture, Forestry and Fisheries of Japan.
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M. Nagai and T. Omatsu contributed equally to the work.
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Nagai, M., Omatsu, T., Aoki, H. et al. Full genome analysis of bovine astrovirus from fecal samples of cattle in Japan: identification of possible interspecies transmission of bovine astrovirus. Arch Virol 160, 2491–2501 (2015). https://doi.org/10.1007/s00705-015-2543-7
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DOI: https://doi.org/10.1007/s00705-015-2543-7