High prevalence of four novel astrovirus genotype species identified from rodents in China

Journal of General Virology

Volumn 98, Issue 5, 2017, Pages 1004-1015

  To, Kelvin K W ^a,b,c   Chan, Wan Mui ^a   Li, Kenneth S M ^a   Lam, Carol S F ^a   Chen, Zhiwei ^a,b,c   Tse, Herman ^a,b,c   Lau, Susanna K P ^a,b,c   Woo, Patrick C Y ^a,b,c   Yuen, Kwok Yung ^a,b,c  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b THE UNIVERSITY OF HONG KONG   (Hong Kong)

^c UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

Astrovirus; Genotype; Phylogenetic tree; Rodents; Virus discovery; Whole genome

Indexed keywords

AMINO ACID DERIVATIVE; RNA DIRECTED RNA POLYMERASE;

ARTICLE; ASTROVIRIDAE; BANDICOTA; BANDICOTA INDICA; GENE CLUSTER; GENETIC DISTANCE; GENOME ANALYSIS; GENOTYPE; GUANGXI; HONG KONG; NIVIVENTER COXINGI; NIVIVENTER FULVESCENS; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; RATTUS ANDAMANENSIS; RATTUS NORVEGICUS; RATTUS RATTUS; RODENT; VIRUS DETECTION; WHOLE GENOME SEQUENCING; ANIMAL; ASTROVIRIDAE INFECTIONS; CLASSIFICATION; CLUSTER ANALYSIS; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; PREVALENCE; RECTUM; RODENT DISEASES; SEQUENCE HOMOLOGY; VETERINARY; VIROLOGY; VIRUS GENOME;

ANIMALS; ASTROVIRIDAE; ASTROVIRIDAE INFECTIONS; CLUSTER ANALYSIS; GENOME, VIRAL; GENOTYPE; HONG KONG; PHYLOGENY; PREVALENCE; RECTUM; RNA REPLICASE; RODENT DISEASES; RODENTIA; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY;

EID: 85020426685     PISSN: 00221317     EISSN: 14652099     Source Type: Journal    
DOI: 10.1099/jgv.0.000766     Document Type: Article

References (50)

1. Madeley CR, Cosgrove BP. Letter: 28 nm particles in faeces in infantile gastroenteritis. Lancet 1975;2:451-452.
2. Grytdal SP, Debess E, Lee LE, Blythe D, Ryan P et al. Incidence of Norovirus and other viral pathogens that cause acute gastroenteritis (AGE) among Kaiser Permanente member populations in the United States, 2012-2013. PLoS One 2016;11:e0148395.
3. Chau ML, Hartantyo SH, Yap M, Kang JS, Aung KT et al. Diarrheagenic pathogens in adults attending a hospital in Singapore. BMC Infect Dis 2016;16:32.
4. Yuen KY, Woo PC, Liang RH, Chiu EK, Chen FF et al. Clinical significance of alimentary tract microbes in bone marrow transplant recipients. Diagn Microbiol Infect Dis 1998;30:75-81.
5. Liu J, Platts-Mills JA, Juma J, Kabir F, Nkeze J et al. Use of quantitative molecular diagnostic methods to identify causes of diarrhoea in children: a reanalysis of the GEMS case-control study. Lancet 2016;388:1291-1301.
6. Bosch A, Pintó RM, Guix S. Human astroviruses. Clin Microbiol Rev 2014;27:1048-1074.
7. Kurtz JB, Lee TW, Craig JW, Reed SE. Astrovirus infection in volunteers. J Med Virol 1979;3:221-230.
8. Lum SH, Turner A, Guiver M, Bonney D, Martland T et al. An emerging opportunistic infection: fatal astrovirus (VA1/HMO-C) encephalitis in a pediatric stem cell transplant recipient. Transpl Infect Dis 2016;18:960-964.
9. Brown JR, Morfopoulou S, Hubb J, Emmett WA, Ip W et al. Astrovirus VA1/HMO-C: an increasingly recognized neurotropic pathogen in immunocompromised patients. Clin Infect Dis 201560: 881-888.
10. Quan PL, Wagner TA, Briese T, Torgerson TR, Hornig M et al. Astrovirus encephalitis in boy with X-linked agammaglobulinemia. Emerg Infect Dis 2010;16:918-925.
11. Selimovic-Hamza S, Bouzalas IG, Vandevelde M, Oevermann A, Seuberlich T. Detection of astrovirus in historical cases of European sporadic bovine encephalitis, Switzerland 1958-1976. Front Vet Sci 2016;3:91.
12. Bouzalas IG, Wüthrich D, Walland J, Drögemüller C, Zurbriggen A et al. Neurotropic astrovirus in cattle with nonsuppurative encephalitis in Europe. J Clin Microbiol 2014;52:3318-3324.
13. Li L, Diab S, McGraw S, Barr B, Traslavina R et al. Divergent astrovirus associated with neurologic disease in cattle. Emerg Infect Dis 2013;19:1385-1392.
14. Zhou N, Lin X, Wang S, Wang H, Li W et al. Environmental surveillance for human astrovirus in Shandong Province, China in 2013. Sci Rep 2014;4:7539.
15. Zhou N, Lin X, Wang S, Wang H, Bi Z et al. Molecular characterization of classic human astrovirus in eastern China, as revealed by environmental sewage surveillance. J Appl Microbiol 2016;120: 1436-1444.
16. Koci MD, Schultz-Cherry S. Avian astroviruses. Avian Pathol 2002; 31:213-227.
17. Woo PC, Lau SK, Teng JL, Tsang AK, Joseph S et al. A novel astrovirus from dromedaries in the Middle East. J Gen Virol 2015; 96:2697-2707.
18. Tse H, Chan WM, Tsoi HW, Fan RY, Lau CC et al. Rediscovery and genomic characterization of bovine astroviruses. J Gen Virol 2011; 92:1888-1898.
19. Lau SK, Woo PC, Yip CC, Bai R, Wu Y et al. Complete genome sequence of a novel feline astrovirus from a domestic cat in Hong Kong. Genome Announc 2013;1:e00708-13.
20. Mendenhall IH, Smith GJ, Vijaykrishna D. Ecological drivers of virus evolution: astrovirus as a case study. J Virol 2015;89:6978-6981.
21. Atkins A, Wellehan JF, Childress AL, Archer LL, Fraser WA et al. Characterization of an outbreak of astroviral diarrhea in a group of cheetahs (Acinonyx jubatus). Vet Microbiol 2009;136:160-165.
22. Chu DK, Chin AW, Smith GJ, Chan KH, Guan Y et al. Detection of novel astroviruses in urban brown rats and previously known astroviruses in humans. J Gen Virol 2010;91:2457-2462.
23. Chu DK, Poon LL, Guan Y, Peiris JS. Novel astroviruses in insectivorous bats. J Virol 2008;82:9107-9114.
24. Finkbeiner SR, Allred AF, Tarr PI, Klein EJ, Kirkwood CD et al. Metagenomic analysis of human diarrhea: viral detection and discovery. PLoS Pathog 2008;4:e1000011.
25. Hu B, Chmura AA, Li J, Zhu G, Desmond JS et al. Detection of diverse novel astroviruses from small mammals in China. J Gen Virol 2014;95:2442-2449.
26. Kapoor A, Li L, Victoria J, Oderinde B, Mason C et al. Multiple novel astrovirus species in human stool. J Gen Virol 2009;90: 2965-2972.
27. Luo Z, Roi S, Dastor M, Gallice E, Laurin MA et al. Multiple novel and prevalent astroviruses in pigs. Vet Microbiol 2011;149:316-323.
28. Martella V, Moschidou P, Lorusso E, Mari V, Camero M et al. Detection and characterization of canine astroviruses. J Gen Virol 2011;92:1880-1887.
29. Martella V, Moschidou P, Pinto P, Catella C, Desario C et al. Astroviruses in rabbits. Emerg Infect Dis 2011;17:2287-2293.
30. Phan TG, Kapusinszky B, Wang C, Rose RK, Lipton HL et al. The fecal viral flora of wild rodents. PLoS Pathog 2011;7:e1002218.
31. Rivera R, Nollens HH, Venn-Watson S, Gulland FM, Wellehan JF. Characterization of phylogenetically diverse astroviruses of marine mammals. J Gen Virol 2010;91:166-173.
32. Smits SL, van Leeuwen M, Kuiken T, Hammer AS, Simon JH et al. Identification and characterization of deer astroviruses. J Gen Virol 2010;91:2719-2722.
33. Stenglein MD, Velazquez E, Greenacre C, Wilkes RP, Ruby JG et al. Complete genome sequence of an astrovirus identified in a domestic rabbit (Oryctolagus cuniculus) with gastroenteritis. Virol J 2012;9:216.
34. Guix S, Bosch A, Pinto RM. Astrovirus taxonomy. In: Schultz-Cherry S (editor). Astrovirus Research. New York: Springer; 2013. pp. 97-118.
35. Karlsson EA, Small CT, Freiden P, Feeroz MM, Matsen FA et al. Non-Human primates harbor diverse mammalian and avian astroviruses including those associated with human infections. PLoS Pathog 2015;11:e1005225.
36. Mihalov-Kovács E, Martella V, Lanave G, Bodnar L, Fehér E et al. Genome analysis of canine astroviruses reveals genetic heterogeneity and suggests possible inter-species transmission. Virus Res 2017;232:162-170.
37. Pankovics P, Boros Á, Kiss T, Delwart E, Reuter G. Detection of a mammalian-like astrovirus in bird, European roller (Coracias garrulus). Infect Genet Evol 2015;34:114-121.
38. Bosch A, Guix S, Krishna NK, Méndez E, Ms S et al. 2010. Nineteen new species in the genus Mamastrovirus in the astroviridae family. http://ictvonline.org/proposals/2010.018a-cV.A.v4.Mamastrovirus.pdf [accessed on 16 December 2016].
39. Meerburg BG, Singleton GR, Kijlstra A. Rodent-borne diseases and their risks for public health. Crit Rev Microbiol 2009;35:221-270.
40. Bordes F, Blasdell K, Morand S. Transmission ecology of rodent-borne diseases: new frontiers. Integr Zool 2015;10:424-435.
41. Ng TF, Kondov NO, Hayashimoto N, Uchida R, Cha Y et al. Identification of an astrovirus commonly infecting laboratory mice in the US and Japan. PLoS One 2013;8:e66937.
42. Yokoyama CC, Loh J, Zhao G, Stappenbeck TS, Wang D et al. Adaptive immunity restricts replication of novel murine astroviruses. J Virol 2012;86:12262-12270.
43. Farkas T, Fey B, Keller G, Martella V, Egyed L. Molecular detection of novel astroviruses in wild and laboratory mice. Virus Genes 2012;45:518-525.
44. Kjeldsberg E, Hem A. Detection of astroviruses in gut contents of nude and normal mice. Brief report. Arch Virol 1985;84:135-140.
45. Anthony SJ, Islam A, Johnson C, Navarrete-Macias I, Liang E et al. Non-random patterns in viral diversity. Nat Commun 2015;6: 8147.
46. Shan T, Li L, Simmonds P, Wang C, Moeser A et al. The fecal virome of pigs on a high-density farm. J Virol 2011;85:11697-11708.
47. Lau SK, Woo PC, Li KS, Zhang HJ, Fan RY et al. Identification of novel Rosavirus species that infects diverse rodent species and causes multisystemic dissemination in mouse model. PLoS Pathog 2016;12:e1005911.
48. To KK, Tse H, Chan WM, Choi GK, Zhang AJ et al. A novel psittacine adenovirus identified during an outbreak of avian chlamydiosis and human psittacosis: zoonosis associated with virus-bacterium coinfection in birds. PLoS Negl Trop Dis 2014;8: e3318.
49. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013;30:2725-2729.
50. Sonnhammer EL, von Heijne G, Krogh A. A hidden Markov model for predicting transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Biol 1998;6:175-182.