Prevalence and genetic heterogeneity of porcine group C rotaviruses in nursing and weaned piglets in Ohio, USA and identification of a potential new VP4 genotype

Abstract

Swine fecal samples collected from seven farms were screened for group C rotaviruses (RVCs) using a reverse transcription-polymerase chain reaction assay. A total of 380 samples were tested and 19.5% were positive. Of the 128 samples collected in 2012, 23.5% from nursing piglets and 8.5% from weaned piglets were RVC positive, with a higher RVC frequency in diarrheic (28.4%) than in non-diarrheic (6.6%) piglets. Two strains (RVC/Pig-wt/USA/RV0104/2011/G3PX and RVC/Pig-wt/USA/RV0143/2012/G6Px) from two different farms were characterized genetically to gain information on virus diversity based on full length sequences of the inner capsid VP6, enterotoxin NSP4 and the outer capsid VP7 and VP4 (partial for RV0104) genes. The VP6 gene of the two strains showed high (99%) nucleotide identity to one another, 84-91% identity to other porcine RVCstrains and 81-82% identity to human and bovine RVC strains. The NSP4 gene analysis revealed that RVC/Pig-wt/USA/RV0104/2011/G3PX and RVC/Pig-wt/USA/RV0143/2012/G6Px strains were not closely related to each other (87% identity), but shared higher identity with prototype RVC/Pig-wt/USA/Cowden/1980/G1Px strain (93% and 89%, respectively) and were more distantly related to human strains (72-76% identity). The VP7 gene analysis indicated that the two strains were distantly related to one another (72% identity). RVC/Pig-wt/USA/RV0143/2012/G6Px was most closely related to porcine RVC G6 strains (82-86% identity), whereas RVC/Pig-wt/USA/RV0104/2011/G3PX was most closely related to porcine HF (G3) strain (94% identity). Analysis of the full length nucleotide sequence of the VP4 gene revealed that RVC/Pig-wt/USA/RV0143/2012/G6Px was distantly related to porcine (75%), bovine (74%) and human (70%) strains. The deduced amino acid identities (69.5-75.6%) of VP4 between RVC/Pig-wt/USA/RV0143/2012/G6Px and other RVCs were low; hence, we propose that this strain comprises a new VP4 genotype. Our results indicate high genetic heterogeneity in RVCs genes and the concurrent co-circulation of different genotypes at the same time. Our findings are useful for the development of more accurate diagnostic tools, for basic research to understand gene function and to provide information for RVC diversity germane to vaccine development.

Fig. 1

Prevalence of RVCs between and within surveyed farms and years. In 2004, Farms 1 and 3 were sampled once, Farm 2 was sampled twice; in 2011, Farms 4, 5 and 6 were each sampled once and Farm 2 was sampled twice; in 2012, Farms 6 and 7 were sampled once and Farm 2 was sampled 3 times.

Fig. 2

Annual and seasonal variability of RVC prevalence within and among the 3 years. Only Farms 2 and 6 were sampled repeatedly in different years: Farm 2 (July and December, 2004; July and December, 2011; January, March and May, 2012); Farm 6 (November, 2011; January, 2012). Farms 1, 3, 4 and 5 were each sampled just once in April, 2004, June, 2011, April, 2011, and May, 2012, respectively.

Fig. 3

Phylogenetic dendrogram of RVC full-length VP7 gene of selected divergent field strains and Lab adapted RVC/Pig-wt/USA/Cowden/1980/G1Px strain (bold, dots) compared with VP7 gene sequences for human, bovine and porcine RVCs available in GenBank.

Fig. 4

Phylogenetic dendrogram of RVC partial VP4 gene (VP8*) of selected divergent field strains (bold, dots) compared with VP4 gene sequences for human, bovine and porcine RVCs available in GenBank.

Fig. 5

Phylogenetic dendrogram of RVC full length VP4 gene of RVC/PIG-WT/USA/RV0143/2012 strain compared with VP4 gene sequences for human, bovine and porcine RVCs available in GenBank.