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

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.