, 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


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.


Rotavirus Porcine Epidemiology Sequencing Phylogenetic analysis VP6 gene Genotyping India 



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.


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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

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