Molecular characterization of a new porcine rotavirus P genotype found in an asymptomatic pig in Slovenia

Abstract

Rotaviral RNA was detected in the stool sample of an asymptomatic fattening pig at a Slovenian pig farm. To characterize the rotavirus, RT-PCR was used, employing primers specific for the VP7, VP4 and NSP4 genes. Specific products were purified and the sequencing reaction was performed for the molecular analysis of amplified genes. Nucleotide and amino acid sequences of the VP7 gene were found highly identical (85.3-88.1% and 90.7-91.6%) to G1 genotype strains. Phylogenetic and molecular analyses of the VP7 antigen regions revealed the sample to be from a new lineage of G1 genotype. In the molecular analysis of the VP4 gene, only 70.9% nucleotide (76.2% amino acid) identity was found with the most related rotavirus VP4 gene from GenBank. Following this, the NSP4 gene was also analyzed. After the phylogenetic analysis, it clustered with the NSP4 B genotype, but also seemed to represent a new lineage of this genotype. This new rotavirus strain, named P21-5, differed greatly from all rotaviruses characterized so far in all three genes analyzed. The virulence of this strain is not clear yet and has to be investigated.

Human, porcine and bovine rotaviruses in Slovenia: evidence of interspecies transmission and genome reassortment

“…We detected the recently described new rotavirus genotype P[27] in 11.1 % of all positive samples. It is interesting that, in this and other studies, the P[27] genotype was found in four G/P combinations: G1, G2-like, G4 (this study) and G5 (Khamrin et al, 2007;Martella et al, 2007;Steyer et al, 2007a). The rotavirus P[27] genotype strains (CMP034, 344/04-1 and P21-5) independently detected by these three author groups showed high genetic variability, as they shared only 89-90.8 % VP4 amino acid sequence identity within this genotype.…”

“…The most prevalent rotavirus genotypes in pigs were G3P[6] (15 samples, 18.5 %), G4P[6] (ten samples, 12.3 %) and G5P [7] (11 samples, 13.6 %). The recently recognized rotavirus genotype P[27] (Khamrin et al, 2007;Martella et al, 2007;Steyer et al, 2007a) was found in nine (11.1 %) samples and was combined with three different G types: G1, G2 and G4 (Table 4).…”

“…As both epitopes are important for host immunity, eliciting neutralizing antibodies, a dual classification system for rotaviruses is used. To date at least 15 G and 27 P genotypes have been characterized using molecular techniques (Estes, 2001;Hoshino et al, 2002;Khamrin et al, 2007;Liprandi et al, 2003;Martella et al, 2003Martella et al, , 2006aMartella et al, , 2007McNeal et al, 2005;Rahman et al, 2005;Rao et al, 2000;Steyer et al, 2007a). Some of these genotypes have been found only in certain animal species or in humans and appear to be host-restricted.…”

Unexpected detection of porcine rotavirus C strains carrying human origin VP6 gene

“…Hitherto reports mention co-infection of different RV genotypes in pigs (Nyaga et al 2015). Hence, a chance for re-assortment in swine cannot be overlooked until the extensive screening of pig population for the presence of re-assorted or new RV types across the globe (Steyer et al 2007;Medici et al 2011;Sharma et al 2013;Navarro et al 2017).…”

Novel Nonstructural Protein 4 Genetic Group in Rotavirus of Porcine Origin

“…In our study, the virus carried a novel NSP4 genetic group that has been isolated from a diarrheic piglet in Thailand. The NSP4 sequence analysis of our CMP034 strain revealed a PoRV strain closely related genetically to the NSP4 gene sequence of PoRV strain P21-5 isolated in Slovenia (9). PoRV strains CMP034 and P21-5 shared the same VP4 genotype as P[27] with over 90% aa sequence identity.…”