Skip to main content
NCBI home page
Springer Nature - PMC COVID-19 Collection logoLink to Springer Nature - PMC COVID-19 Collection
. 2006 Mar 30;151(9):1749–1759. doi: 10.1007/s00705-006-0750-y

Genetic analysis of calicivirus genomes detected in intestinal contents of piglets in Japan

Y Yin 1, Y Tohya 1, Y Ogawa 1, D Numazawa 1, K Kato 1, H Akashi 1
PMCID: PMC7087045  PMID: 16575478

Summary.

Enteric caliciviruses, noroviruses, and sapoviruses are emerging path- ogens responsible for diarrhea or gastroenteritis in their respective hosts. In this study, swine enteric caliciviruses were detected in ten samples of intestinal contents from 24 piglets in Japan by reverse transcription-polymerase chain reaction using a broadly reactive primer pair (P290/289) that targeted the highly conserved RNA polymerase regions of the enteric caliciviruses. From the positive samples, the entire viral genome of strain K7/JP and 3′-end parts of the genomes of strains K5/JP and K10/JP were cloned and sequenced. K7/JP had an RNA genome of 7144 bases, excluding its 3′ poly (A) tail. The K7/JP genome possessed two open reading frames and characteristics common to sapoviruses. In phylogenetic analysis using amino acid sequences of VP1, K5/JP was demonstrated to be close to the noroviruses previously detected in pigs, and K7/JP and K10/JP were considered to be classified as a new genogroup of sapoviruses.

Keywords: Intestinal Content, Sapovirus, Abridge Anchor Primer, Entire Viral Genome, Human Caliciviruses

References

  1. Ando T, Noel JS, Fankhauser RL. Genetic classification of “Norwalk-like viruses.”. J Infect Dis. 2000;181([Suppl 2]):S336–S348. doi: 10.1086/315589. [DOI] [PubMed] [Google Scholar]
  2. Atmar RL, Estes MK. Diagnosis of noncultivatable gastroenteritis viruses, the human caliciviruses. Clin Microbiol Rev. 2001;14:15–37. doi: 10.1128/CMR.14.1.15-37.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Dastjerdi AM, Green J, Gallimore CI, Brown DWG, Bridger JC. The bovine newbury agent-2 is genetically more closely related to human SRSVs than to animal caliciviruses. Virology. 1999;254:1–5. doi: 10.1006/viro.1998.9514. [DOI] [PubMed] [Google Scholar]
  4. Deng Y, Batten CA, Liu BL, Lambden PR, Elschner M, Gunther H, Otto P, Schnurch P, Eichhorn W, Herbst W, Clarke IN. Studies of epidemiology and seroprevalence of bovine noroviruses in Germany. J Clin Microbiol. 2003;41:2300–2305. doi: 10.1128/JCM.41.6.2300-2305.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Farkas T, Jiang X, Guerrero ML, Zhong W, Wilton N, Berke T, Matson DO, Pickering LK, Ruiz-Palacios G. Prevalence and genetic diversity of human caliciviruses (HuCVs) in Mexican children. J Med Virol. 2000;62:217–223. doi: 10.1002/1096-9071(200010)62:2<217::AID-JMV13>3.0.CO;2-F. [DOI] [PubMed] [Google Scholar]
  6. Farkas T, Nakajima S, Sugieda M, Deng X, Zhong W, Jiang X. Seroprevalence of noroviruses in swine. J Clin Microbiol. 2005;43:657–661. doi: 10.1128/JCM.43.2.657-661.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Farkas T, Zhong WM, Jing Y, Huang PW, Espinosa SM, Martinez N, Morrow AL, Ruiz-Palacios GM, Pickering LK, Jiang X. Genetic diversity among sapoviruses. Arch Virol. 2004;149:1309–1323. doi: 10.1007/s00705-004-0296-9. [DOI] [PubMed] [Google Scholar]
  8. Glass RI, Noel J, Ando T, Fankhauser R, Belliot G, Mounts A, Parashar UD, Bresee JS, Monroe SS. The epidemiology of enteric caliciviruses from humans: a reassessment using new diagnostics. J Infect Dis. 2000;181([Suppl 2]):S254–S261. doi: 10.1086/315588. [DOI] [PubMed] [Google Scholar]
  9. Green KY, Ando T, Balayan MS, Berke T, Clarke IN, Estes MK, Matson DO, Nakata S, Neill JD, Studdert MJ, Thiel HJ. Taxonomy of the caliciviruses. J Infect Dis. 2000;181([Suppl 2]):S322–S330. doi: 10.1086/315591. [DOI] [PubMed] [Google Scholar]
  10. Green KY, Chanock RM, Kapikian AZ. Human caliciviruses. In: Knipe DM, Howley PM, editors. Fields virology. 4. Philadelphia: Lippincott & Wilkins; 2001. pp. 841–874. [Google Scholar]
  11. Guo M, Chang KO, Hardy ME, Zhang Q, Parwani AV, Saif LJ. Molecular characterization of a porcine enteric calicivirus genetically related to Sapporo-like human caliciviruses. J Virol. 1999;73:9625–9631. doi: 10.1128/jvi.73.11.9625-9631.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Guo M, Evermann JF, Saif LJ. Detection and molecular characterization of cultivable caliciviruses from clinically normal mink and enteric caliciviruses associated with diarrhea in mink. Arch Virol. 2001;146:479–493. doi: 10.1007/s007050170157. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Jiang X, Graham DY, Wang K, Estes MK. Norwalk virus genome cloning and characterization. Science. 1990;250:1580–1583. doi: 10.1126/science.2177224. [DOI] [PubMed] [Google Scholar]
  14. Jiang X, Huang PW, Zhong WM, Farkas T, Cubitt DW, Matson DO. Design and evaluation of a primer pair that detects both Norwalk- and Sapporo-like caliciviruses by RT-PCR. J Virol Methods. 1999;83:145–154. doi: 10.1016/S0166-0934(99)00114-7. [DOI] [PubMed] [Google Scholar]
  15. Karst SM, Wobus CE, Lay M, Davidson J, Virgin HWIV. STAT1-dependent innate immunity to a Norwalk-like virus. Science. 2003;299:1575–1578. doi: 10.1126/science.1077905. [DOI] [PubMed] [Google Scholar]
  16. Kozak M. Structural features in eukaryotic mRNAs that modulate the initiation of translation. J Biol Chem. 1991;266:19867–19870. [PubMed] [Google Scholar]
  17. Liu BL, Clarke IN, Caul EO, Lambden PR. Human enteric caliciviruses have a unique genome structure and are distinct from the Norwalk-like viruses. Arch Virol. 1995;140:1345–1356. doi: 10.1007/BF01322662. [DOI] [PubMed] [Google Scholar]
  18. Liu BL, Lambden PR, Gunther H, Otto P, Elschner M, Clarke IN. Molecular characterization of a bovine enteric calicivirus: relationship to the Norwalk-like viruses. J Virol. 1999;73:819–825. doi: 10.1128/jvi.73.1.819-825.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Nakata S, Chiba S, Terashima H, Sakuma Y, Kogasaka R, Nakao T. Microtiter solid-phase radioimmunoassay for detection of human calicivirus in stools. J Clin Microbiol. 1983;17:198–201. doi: 10.1128/jcm.17.2.198-201.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Neill JD. Nucleotide sequence of a region of the feline calicivirus genome which encodes picornavirus-like RNA-dependent RNA polymerase, cysteine protease and 2C polypeptides. Virus Res. 1990;17:145–160. doi: 10.1016/0168-1702(90)90061-F. [DOI] [PubMed] [Google Scholar]
  21. Noel JS, Liu BL, Humphrey CD, Rodriguez EM, Lambden PR, Clarke IN, Dwyer DM, Ando T, Glass RI, Monroe SS. Parkville virus: a novel genetic variant of human calicivirus in the Sapporo virus clade, associated with an outbreak of gastroenteritis in adults. J Med Virol. 1997;52:173–178. doi: 10.1002/(SICI)1096-9071(199706)52:2<173::AID-JMV10>3.0.CO;2-M. [DOI] [PubMed] [Google Scholar]
  22. Pang XL, Honma SJ, Nakata SJ, Vesikari T. Human caliciviruses in acute gastroenteritis of young children in the community. J Infect Dis. 2000;181([Suppl 2]):S288–S294. doi: 10.1086/315590. [DOI] [PubMed] [Google Scholar]
  23. Parwani AV, Saif LJ, Kang SY. Biochemical characterization of porcine enteric calicivirus: analysis of structural and non-structural viral proteins. Arch Virol. 1990;112:41–53. doi: 10.1007/BF01348984. [DOI] [PubMed] [Google Scholar]
  24. Saif LJ, Bohl EH, Theil KW, Cross RF, House JA. Rotavirus-like, calicivirus-like, and 23-nm virus-like particles associated with diarrhea in young pigs. J Clin Microbiol. 1980;12:105–111. doi: 10.1128/jcm.12.1.105-111.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Schuffenecker I, Ando T, Thouvenot D, Lina B, Aymard M. Genetic classification of “Sapporo-like viruses”. Arch Virol. 2001;146:2115–2132. doi: 10.1007/s007050170024. [DOI] [PubMed] [Google Scholar]
  26. Shirai J, Shimizu M, Fukusho A. Coronavirus-, calicivirus-, and astrovirus-like particles associated with acute porcine gastroenteritis. Jpn J Vet Sci. 1985;47:1023–1026. doi: 10.1292/jvms1939.47.1023. [DOI] [PubMed] [Google Scholar]
  27. Smiley JR, Hoet AE, Traven M, Tsunemitsu H, Saif LJ. Reverse transcription-PCR assays for detection of bovine enteric caliciviruses (BEC) and analysis of the genetic relationships among BEC and human caliciviruses. J Clin Microbiol. 2003;41:3089–3099. doi: 10.1128/JCM.41.7.3089-3099.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Sugieda M, Nagaoka H, Kakishima Y, Ohshita T, Nakamura S, Nakajima S. Detection of Norwalk-like virus genes in the caecum contents of pigs. Arch Virol. 1998;143:1215–1221. doi: 10.1007/s007050050369. [DOI] [PubMed] [Google Scholar]
  29. Sugieda M, Nakajima S. Viruses detected in the caecum contents of healthy pigs representing a new genetic cluster in genogroup II of the genus ‘Norwalk-like viruses’. Virus Res. 2002;87:165–172. doi: 10.1016/S0168-1702(02)00107-7. [DOI] [PubMed] [Google Scholar]
  30. van der Poel WHM, Vinje J, van der Heide R, Herrera MI, Vivo A, Koopmans MPG. Norwalk-like calicivirus genes in farm animals. Emerg Infect Dis. 2000;6:36–41. doi: 10.3201/eid0601.000106. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. van der Poel WHM, van der Heide R, Vershoor F, Gelderblom H, Vinje J, Koopmans MPG. Epidemiology of Norwalk-like virus infections in cattle in The Netherlands. Vet Microbiol. 2003;92:297–309. doi: 10.1016/S0378-1135(02)00421-2. [DOI] [PubMed] [Google Scholar]

Articles from Archives of Virology are provided here courtesy of Nature Publishing Group

RESOURCES