VirusDisease

, Volume 29, Issue 1, pp 96–102 | Cite as

Frequency distribution of porcine rotavirus-A and capsid protein gene based sequence and phylogenetic analysis indicating marked heterogeneity among prevailing strains, India

  • Jobin Jose Kattoor
  • Sharad Saurabh
  • Shubhankar Sircar
  • Obli Rajendran Vinodhkumar
  • Ujjwal Kumar De
  • Kuldeep Dhama
  • Souvik Ghosh
  • Raj Kumar Singh
  • Yashpal Singh Malik
Original Article
  • 44 Downloads

Abstract

Rotavirus (RV), is an etiological agent of acute infantile diarrhea in both humans and animals including poultry. Among the eight accepted species/types of RVs, RV-A is genetically and antigenically the most diverse. RV-A associated enteritis is a major problem in the weaning and post-weaning piglets. Due to high genetic variability in the antigenic regions, RV-A is thought to have high interspecies jumping probability. In this study, comparatively a large sized sample (n = 757) was screened, where the samples were collected from diarrheic porcine population of north (Uttar Pradesh), North eastern (Assam, Nagaland, Meghalaya, Tripura, Manipur, Mizoram and Arunachal Pradesh) and Southern states of India (Kerala, Karnataka and Tamil Nadu). The VP6 gene based reverse-transcription (RT)-PCR based screening of the samples for RV-A identified 42.4% (321/757) positivity, where highest identification was from Uttar Pradesh 119 (37.07%), followed by 74 (23.05%), 34 (10.6%), 31 (9.65%), 21 (6.54%), 15 (4.67%), 11 (3.43%), 8 (2.49%), 3 (0.93%), 3 (0.93%) and 2 (0.62%) from Assam, Nagaland, Meghalaya, Tripura, Kerala, Manipur, Mizoram, Arunachal Pradesh, Karnataka and Tamil Nadu, respectively. Percentage identity calculation of the VP6 gene sequences from different porcine RV-A revealed 77.1–97.3% identity within the Indian porcine RV-A strains of the current study. Phylodendrogram and percent identity based analysis of the amplified and sequenced full length VP6 gene confirmed the presence of new VP6 genotypes (I1 and I5). Although, there are reports of detection of porcine RV-A based on VP6 gene from India, no lineage/genotype based characterization is available for the target gene. Till date, only a single VP6 type (I2) has been confirmed from pig population of India. Here, the findings confirm the circulation of diverse RV-A strains in porcine population in India.

Keywords

Rotavirus Porcine Epidemiology Sequencing Phylogenetic analysis VP6 gene Genotyping India 

Notes

Acknowledgements

The authors of the manuscript are thankful to authority of ICAR-Indian Veterinary Research Institute, Bareilly, India, for providing infrastructure facilities. Kattoor JJ and Malik YS acknowledges Indian Council of Medical Research, India, for junior research fellowship and Indian Council of Agricultural Research, India, for National Fellowship, respectively.

References

  1. 1.
    19th Livestock census-2012 All India report. 2014. Department of Animal Husbandry Diarying and Fisheries. Krishibhavan, New Delhi. 2014; p. 75–76.Google Scholar
  2. 2.
    Anh PH, Carrique-Mas JJ, Van Cuong N, Hoa NT, Anh NL, Hien VB, et al. The prevalence and genetic diversity of group A rotaviruses on pig farms in the Mekong Delta region of Vietnam. Vet Microbiol. 2014;170(3):258–65.Google Scholar
  3. 3.
    Awang A, Yap K. Group A rotavirus infection in animals from an animal house and in wild-caught monkeys. J Diarrh Dis Res. 1990;8(3):82–6.Google Scholar
  4. 4.
    Bányai K, Kemenesi G, Budinski I, Földes F, Zana B, Marton S, et al. Candidate new rotavirus species in Schreiber’s bats, Serbia. Infect Genet Evol. 2017;48:19–26.CrossRefPubMedGoogle Scholar
  5. 5.
    Barman N, Sharma D, Penseart M. Detection of swine rotavirus and transmissible gastroenteritis virus in piglets with diarrhoea by sandwich ELISA. Indian J Anim Sci. 1998;68(9):886–7.Google Scholar
  6. 6.
    Bohl E, Theil K, Saif LJ. Isolation and serotyping of porcine rotaviruses and antigenic comparison with other rotaviruses. J Clin Microbiol. 1984;19(2):105–11.PubMedPubMedCentralGoogle Scholar
  7. 7.
    Burns JW, Krishnaney AA, Vo PT, Rouse RV, Anderson LJ, Greenberg HB. Analyses of homologous rotavirus infection in the mouse model. Virology. 1995;207(1):143–53.CrossRefPubMedGoogle Scholar
  8. 8.
    Chandler-Bostock R, Hancox LR, Payne H, Iturriza-Gomara M, Daly JM, Mellits KH. Diversity of group A rotavirus on a UK pig farm. Vet Microbiol. 2015;180(3):205–11.CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Conner ME, Estes M, Graham D. Rabbit model of rotavirus infection. J Virol. 1988;62(5):1625–33.PubMedPubMedCentralGoogle Scholar
  10. 10.
    Das S, Handique P. Detection of porcine rotaviruses group A in free ranging and farm pig population of North East India. J Biotechnol Biochem. 2016;2(1):62–6.Google Scholar
  11. 11.
    Desselberger U. Rotaviruses. Virus Res. 2014;190:75–96.CrossRefPubMedGoogle Scholar
  12. 12.
    Dubal ZB, Bhilegaonkar KN, Barbuddhe SB, Kolhe RP, Kaur S, Rawat S, et al. Prevalence and genotypic (G and P) determination of porcine group A rotaviruses from different regions of India. Trop Anim Health Prod. 2013;45(2):609–15.CrossRefPubMedGoogle Scholar
  13. 13.
    Estes M, Kapikian A. Rotaviruses. In: Knipe DM, Howley PM, editors. Fields virology. Philadelphia: Lippincott Williams & Wilkins; 2007. p. 1917–74.Google Scholar
  14. 14.
    Eugster A, Sidwa T. Rotaviruses in diarrheic feces of a dog. VM SAC Vet Med Small Anim Clin. 1979.Google Scholar
  15. 15.
    Garam G, Bora D, Borah B, Bora M, Das S. Seroprevalence of Rotavirus infection in pig population of Arunachal Pradesh. Vet World. 2016;9(11):1300–4.CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Ghosh S, Navarro R, Malik YS, Willingham AL, Kobayashi N. Whole genomic analysis of a porcine G6P [13] rotavirus strain. Vet Microbiol. 2015;180(3):286–98.CrossRefPubMedGoogle Scholar
  17. 17.
    Kapikian A. Overview of viral gastroenteritis. In: Viral gastroenteritis. Springer; 1996. p. 7–19.Google Scholar
  18. 18.
    Kapikian AZ, Chanock RM. Rotaviruses. In: Fields BN, Knipe DM, Howley PM, editors. Fields virology. Philadelphia: Lippincott Raven; 1996. p. 1657–708.Google Scholar
  19. 19.
    Kelkar S. Development of indigenous ELISA for rotavirus diagnosis & its comparison with commercial kit. Indian J Med Res. 1993;97:93–101.PubMedGoogle Scholar
  20. 20.
    Kerin TK, Kane EM, Glass RI, Gentsch JR. Characterization of VP6 genes from rotavirus strains collected in the United States from 1996–2002. Virus Genes. 2007;35(3):489–95.CrossRefPubMedGoogle Scholar
  21. 21.
    Kraft LM. Studies on the etiology and transmission of epidemic diarrhea of infant mice. J Exp Med. 1957;106(5):743–55.CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Martella V, Ciarlet M, Banyai K, Lorusso E, Arista S, Lavazza A, et al. Identification of group A porcine rotavirus strains bearing a novel VP4 (P) genotype in Italian swine herds. J Clin Microbiol. 2007;45(2):577–80.CrossRefPubMedGoogle Scholar
  23. 23.
    Martella V, Bányai K, Matthijnssens J, Buonavoglia C, Ciarlet M. Zoonotic aspects of rotaviruses. Vet Microbiol. 2010;140(3):246–55.CrossRefPubMedGoogle Scholar
  24. 24.
    Matthijnssens J, Desselberger U. Genome diversity and evolution of rotaviruses. In: Genome plasticity and infectious diseases. American Society of Microbiology; 2012. p. 214–41.Google Scholar
  25. 25.
    Matthijnssens J, Ciarlet M, Heiman E, Arijs I, Delbeke T, McDonald SM, et al. Full genome-based classification of rotaviruses reveals a common origin between human Wa-Like and porcine rotavirus strains and human DS-1-like and bovine rotavirus strains. J Virol. 2008;82(7):3204–19.CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Mihalov-Kovács E, Gellért Á, Marton S, Farkas SL, Fehér E, Oldal M, et al. Candidate new rotavirus species in sheltered dogs, Hungary. Emerg Infect Dis. 2015;21(4):660–3.CrossRefPubMedPubMedCentralGoogle Scholar
  27. 27.
    Molinari BL, Lorenzetti E, Otonel RA, Alfieri AF, Alfieri AA. Species H rotavirus detected in piglets with diarrhea, Brazil, 2012. Emerg Infect Dis. 2014;20(6):1019–22.CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Mondal A, Sharma K, Malik YS, Joardar SN. Detection of Group A rotavirus in faeces of diarrhoeic bovine porcine and human population from eastern india by reverse transcriptase–polymerase chain reaction. Adv Anim Vet Sci. 2013;1(1S):18–9.Google Scholar
  29. 29.
    Ntafis V, Fragkiadaki E, Xylouri E, Omirou A, Lavazza A, Martella V. Rotavirus-associated diarrhoea in foals in Greece. Vet Microbiol. 2010;144(3):461–5.CrossRefPubMedGoogle Scholar
  30. 30.
    Okitsu S, Khamrin P, Thongprachum A, Kongkaew A, Maneekarn N, Mizuguchi M, et al. Whole-genomic analysis of G3P [23], G9P [23] and G3P [13] rotavirus strains isolated from piglets with diarrhea in Thailand, 2006–2008. Infect Genet Evol. 2013;18:74–86.CrossRefPubMedGoogle Scholar
  31. 31.
    Papp H, László B, Jakab F, Ganesh B, De Grazia S, Matthijnssens J, et al. Review of group A rotavirus strains reported in swine and cattle. Vet Microbiol. 2013;165(3):190–9.CrossRefPubMedGoogle Scholar
  32. 32.
    Phan TG, Leutenegger CM, Chan R, Delwart E. Rotavirus I in feces of a cat with diarrhea. Virus Genes. 2017;53(3):487–90.CrossRefPubMedGoogle Scholar
  33. 33.
    Saif L, Jiang B. Nongroup A rotaviruses of humans and animals. Curr Top Microbiol Immunol. 1994;185:339–71.PubMedGoogle Scholar
  34. 34.
    Saif L, editor. Immunodiagnosis of enteric viral infections application of electron microscopy and monoclonal antibodies. In: Proceedings 38th Western Poultry Disease Conference, Tempe, Ariz; 1989.Google Scholar
  35. 35.
    Snodgrass D, Angus K, Gray E. A rotavirus from kittens. Vet Rec. 1979;104(10):222–3.CrossRefPubMedGoogle Scholar
  36. 36.
    Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30(12):2725–9.CrossRefPubMedPubMedCentralGoogle Scholar
  37. 37.
    Trojnar E, Otto P, Roth B, Reetz J, Johne R. The genome segments of a group D rotavirus possess group A-like conserved termini but encode group-specific proteins. J Virol. 2010;84(19):10254–65.CrossRefPubMedPubMedCentralGoogle Scholar
  38. 38.
    Trojnar E, Sachsenröder J, Twardziok S, Reetz J, Otto PH, Johne R. Identification of an avian group A rotavirus containing a novel VP4 gene with a close relationship to those of mammalian rotaviruses. J Gen Virol. 2013;94(1):136–42.CrossRefPubMedGoogle Scholar

Copyright information

© Indian Virological Society 2018

Authors and Affiliations

  • Jobin Jose Kattoor
    • 1
  • Sharad Saurabh
    • 1
    • 7
  • Shubhankar Sircar
    • 1
  • Obli Rajendran Vinodhkumar
    • 2
  • Ujjwal Kumar De
    • 3
  • Kuldeep Dhama
    • 4
  • Souvik Ghosh
    • 5
  • Raj Kumar Singh
    • 6
  • Yashpal Singh Malik
    • 1
  1. 1.Division of Biological StandardizationICAR-Indian Veterinary Research InstituteIzatnagar, BareillyIndia
  2. 2.Division of Veterinary EpidemiologyICAR-Indian Veterinary Research InstituteIzatnagar, BareillyIndia
  3. 3.Division of MedicineICAR-Indian Veterinary Research InstituteIzatnagar, BareillyIndia
  4. 4.Division of PathologyICAR-Indian Veterinary Research InstituteIzatnagar, BareillyIndia
  5. 5.Department of Biomedical Sciences, One Health Center for Zoonoses and Tropical Veterinary MedicineRoss University School of Veterinary MedicineBasseterreSt. Kitts and Nevis
  6. 6.ICAR-Indian Veterinary Research InstituteIzatnagar, BareillyIndia
  7. 7.Department of Molecular and Structural BiologyCSIR-Central Institute of Medicinal and Aromatic PlantsLucknowIndia

Personalised recommendations