PREVALENCE AND GENETIC DIVERSITY OF GROUP A AND NON-GROUP A PORCINE ROTAVIRUSES IN SELECTED FARMS IN THE US
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Fecal samples collected in different seasons of 2004 and 2011 from diarrheic and healthy nursing piglets from 5 selected swine farms in the US were screened for group (Gp) A, B and C rotaviruses (RVs) using RT-PCR. RVs were identified in 27.4% (65/237) of the samples, with 7.6%, 1.3% and 21.5% positive for Gp A, B and C RVs, respectively. An increased prevalence of Gp A and C RVs was observed between 2004 (18%) and 2011 (37%), with the highest increase for Gp C (from 11.9% to 31.1%). Seasonal effects on the prevalence of Gp A and C RVs were observed within and between the 2 years with the highest in summer (35.2%) followed by winter (27.4%). The prevalence varied among the farms and since none of them used Gp A RV vaccines, we concluded that differences in management may influence RV prevalence. Partial sequencing and phylogenetic analysis of the VP6 gene of selected Gp C RVs from different farms revealed high nucleotide sequence identity with reference human (82.5-86%) and porcine (86.2-97.2%) Gp C RVs. Historic (2004) and recent (2011) Gp C strains from two farms shared high nucleotide identity between each other (97.2-99.5%) and clustered (>92% identity) with recent Korean (2009, G6 serotype) and Brazilian strains, however, a recent Gp C RV strain from another farm was distant from Cowden, Brazilian and Korean strains or the strains from other farms. Our preliminary data on Gp A RV genotyping (VP7 gene) indicate that there are multiple genotypes of Gp A RVs currently circulating in US swine. In conclusion, our study demonstrates that infection with distinct Gp C RVs is more frequent among nursing piglets than Gp A and B RV infections.