Astroviruses are small, non-enveloped, positive-stranded RNA viruses. Previously studied mammalian astroviruses have been associated with diarrhoeal disease. Knowledge of astrovirus diversity is very limited, with only six officially recognized astrovirus species from mammalian hosts and, in addition, one human and some bat astroviruses were recently described. We used consensus PCR techniques for initial identification of five astroviruses of marine mammals: three from California sea lions (), one from a Steller sea lion () and one from a bottlenose dolphin (). Bayesian and maximum-likelihood phylogenetic analysis found that these viruses showed significant diversity at a level consistent with novel species. Astroviruses that we identified from marine mammals were found across the mamastrovirus tree and did not form a monophyletic group. Recombination analysis found that a recombination event may have occurred between a human and a California sea lion astrovirus, suggesting that both lineages may have been capable of infecting the same host at one point. The diversity found amongst marine mammal astroviruses and their similarity to terrestrial astroviruses suggests that the marine environment plays an important role in astrovirus ecology.


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  1. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J.(1997). Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25, 3389–3402.[CrossRef] [Google Scholar]
  2. Atkins, A., Wellehan, J. F. X., Jr, Childress, A. L., Archer, L. L., Fraser, W. A. & Citino, S. B.(2009). Characterization of an outbreak of astroviral diarrhea in a group of cheetahs (Acinonyx jubatus). Vet Microbiol 136, 160–165.[CrossRef] [Google Scholar]
  3. Boni, M. F., Posada, D. & Feldman, M. W.(2007). An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics 176, 1035–1047. [Google Scholar]
  4. Caballero, S., Guix, S., Ribes, E., Bosch, A. & Pinto, R. M.(2004). Structural requirements of astrovirus virus-like particles assembled in insect cells. J Virol 78, 13285–13292.[CrossRef] [Google Scholar]
  5. Chu, D. K., Poon, L. L., Guan, Y. & Peiris, J. S.(2008). Novel astroviruses in insectivorous bats. J Virol 82, 9107–9114.[CrossRef] [Google Scholar]
  6. Dennehy, P. H., Nelson, S. M., Spangenberger, S., Noel, J. S., Monroe, S. S. & Glass, R. I.(2001). A prospective case–control study of the role of astrovirus in acute diarrhea among hospitalized young children. J Infect Dis 184, 10–15.[CrossRef] [Google Scholar]
  7. Edgar, R. C.(2004).muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32, 1792–1797.[CrossRef] [Google Scholar]
  8. Elamri, D. E., Aouni, M., Parnaudeau, S. & Le Guyader, F. S.(2006). Detection of human enteric viruses in shellfish collected in Tunisia. Lett Appl Microbiol 43, 399–404.[CrossRef] [Google Scholar]
  9. Espinosa, A. C., Mazari-Hiriart, M., Espinosa, R., Maruri-Avidal, L., Méndez, E. & Arias, C. F.(2008). Infectivity and genome persistence of rotavirus and astrovirus in groundwater and surface water. Water Res 42, 2618–2628.[CrossRef] [Google Scholar]
  10. Felsenstein, J.(1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef] [Google Scholar]
  11. Felsenstein, J.(1989).phylip – phylogeny inference package (version 3.2). Cladistics 5, 164–166. [Google Scholar]
  12. Finkbeiner, S. R., Kirkwood, C. D. & Wang, D.(2008). Complete genome sequence of a highly divergent astrovirus isolated from a child with acute diarrhea. Virol J 5, 117[CrossRef] [Google Scholar]
  13. Gallimore, C. I., Taylor, C., Gennery, A. R., Cant, A. J., Galloway, A., Lewis, D. & Gray, J. J.(2005). Use of a heminested reverse transcriptase PCR assay for detection of astrovirus in environmental swabs from an outbreak of gastroenteritis in a pediatric primary immunodeficiency unit. J Clin Microbiol 43, 3890–3894.[CrossRef] [Google Scholar]
  14. Gibbs, M. J., Armstrong, J. S. & Gibbs, A. J.(2000). Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16, 573–582.[CrossRef] [Google Scholar]
  15. Gmyl, A. P., Belousov, E. V., Maslova, S. V., Khitrina, E. V., Chetverin, A. B. & Agol, V. I.(1999). Nonreplicative RNA recombination in poliovirus. J Virol 73, 8958–8965. [Google Scholar]
  16. Holmes, E. C., Worobey, M. & Rambaut, A.(1999). Phylogenetic evidence for recombination in dengue virus. Mol Biol Evol 16, 405–409.[CrossRef] [Google Scholar]
  17. Jarvis, T. C. & Kirkegaard, K.(1992). Poliovirus RNA recombination: mechanistic studies in the absence of selection. EMBO J 11, 3135–3145. [Google Scholar]
  18. Jonassen, C. M., Jonassen, T., Saif, Y. M., Snodgrass, D. R., Ushijima, H., Shimizu, M. & Grinde, B.(2001). Comparison of capsid sequences from human and animal astroviruses. J Gen Virol 82, 1061–1067. [Google Scholar]
  19. Jones, D. T., Taylor, W. R. & Thornton, J. M.(1992). The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8, 275–282. [Google Scholar]
  20. Kosiol, C. & Goldman, N.(2005). Different versions of the Dayhoff rate matrix. Mol Biol Evol 22, 193–199. [Google Scholar]
  21. Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A. & other authors(2007).clustalw and clustal_x version 2. Bioinformatics 23, 2947–2948.[CrossRef] [Google Scholar]
  22. Lukashov, V. V. & Goudsmit, J.(2002). Evolutionary relationships among Astroviridae. J Gen Virol 83, 1397–1405. [Google Scholar]
  23. Madeley, C. R. & Cosgrove, B. P.(1975). 28 nm particles in faeces in infantile gastroenteritis. Lancet 2, 451–452. [Google Scholar]
  24. Marshall, J. A., Kennett, M. L., Rodger, S. M., Studdert, M. J., Thompson, W. L. & Gust, I. D.(1987). Virus and virus-like particles in the faeces of cats with and without diarrhoea. Aust Vet J 64, 100–105.[CrossRef] [Google Scholar]
  25. Martin, D. & Rybicki, E.(2000).rdp: detection of recombination amongst aligned sequences. Bioinformatics 16, 562–563.[CrossRef] [Google Scholar]
  26. Martin, D. P., Posada, D., Crandall, K. A. & Williamson, C.(2005a). A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Res Hum Retroviruses 21, 98–102.[CrossRef] [Google Scholar]
  27. Martin, D. P., Williamson, C. & Posada, D.(2005b).rdp2: recombination detection and analysis from sequence alignments. Bioinformatics 21, 260–262.[CrossRef] [Google Scholar]
  28. Maynard Smith, J.(1992). Analyzing the mosaic structure of genes. J Mol Evol 34, 126–129. [Google Scholar]
  29. Monroe, S. S., Carter, M. J., Hermann, J., Mitchell, D. K. & Sanchez-Fauquier, A.(2005).Astroviridae. In Virus Taxonomy: Eighth Report of the International Committee on Taxonomy of Viruses, pp. 859–864. Edited by C. M. Fauquet, M. A. Mayo, J. Maniloff, U. Desselberger & L. A. Ball. San Diego: Academic Press.
  30. Moser, L. A., Carter, M. & Schultz-Cherry, S.(2007). Astrovirus increases epithelial barrier permeability independently of viral replication. J Virol 81, 11937–11945.[CrossRef] [Google Scholar]
  31. Notredame, C., Higgins, D. G. & Heringa, J.(2000). T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 302, 205–217.[CrossRef] [Google Scholar]
  32. Padidam, M., Sawyer, S. & Fauquet, C. M.(1999). Possible emergence of new geminiviruses by frequent recombination. Virology 265, 218–225.[CrossRef] [Google Scholar]
  33. Pantin-Jackwood, M. J., Spackman, E. & Woolcock, P. R.(2006). Phylogenetic analysis of turkey astroviruses reveals evidence of recombination. Virus Genes 32, 187–192.[CrossRef] [Google Scholar]
  34. Posada, D. & Crandall, K. A.(2001). Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci U S A 98, 13757–13762.[CrossRef] [Google Scholar]
  35. Ronquist, F. & Huelsenbeck, J. P.(2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572–1574.[CrossRef] [Google Scholar]
  36. Simmonds, P.(2006). Recombination and selection in the evolution of picornaviruses and other mammalian positive-stranded RNA viruses. J Virol 80, 11124–11140.[CrossRef] [Google Scholar]
  37. Smith, A. W., Skilling, D. E., Cherry, N., Mead, J. H. & Matson, D. O.(1998). Calicivirus emergence from ocean reservoirs: zoonotic and interspecies movements. Emerg Infect Dis 4, 13–20.[CrossRef] [Google Scholar]
  38. Van Hemert, F. J., Lukashov, V. V. & Berkhout, B.(2007). Different rates of (non-)synonymous mutations in astrovirus genes; correlation with gene function. Virol J 4, 25[CrossRef] [Google Scholar]
  39. Veerassamy, S., Smith, A. & Tillier, E. R.(2003). A transition probability model for amino acid substitutions from blocks. J Comput Biol 10, 997–1010.[CrossRef] [Google Scholar]
  40. Whelan, S. & Goldman, N.(2001). A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 18, 691–699.[CrossRef] [Google Scholar]
  41. Woolhouse, M. E. & Gowtage-Sequeria, S.(2005). Host range and emerging and reemerging pathogens. Emerg Infect Dis 11, 1842–1847.[CrossRef] [Google Scholar]
  42. Zhu, H. C., Chu, D. K., Liu, W., Dong, B. Q., Zhang, S. Y., Zhang, J. X., Li, L. F., Vijaykrishna, D., Smith, G. J. & other authors(2009). Detection of diverse astroviruses from bats in China. J Gen Virol 90, 883–887.[CrossRef] [Google Scholar]

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