Short communicationWhole genomic analysis of a porcine G6P[13] rotavirus strain
Introduction
Rotavirus-A (RVA) are a major cause of severe diarrhea in piglets (Estes and Greenberg, 2013). To date, RVAs have been classified into at least 27 G- and 37 P-genotypes based on differences in the nucleotide sequences of their outer capsid proteins VP7- and VP4-encoding genes, respectively (Matthijnssens et al., 2011, Trojnar et al., 2013). Among them, G3–G5, G9 or G11 genotypes in combination with P[6] or P[7] are commonly found in porcine RVAs (Papp et al., 2013). In addition, several other VP7- (G1, G2, G6, G8, G10, G12 and G26) and VP4- (P[5], P[8], P[11], P[13], P[14], P[19], P[23], P[26], P[27], P[32] and P[34]) genotypes have also been detected in pigs, albeit at lower frequencies (Ghosh and Kobayashi, 2014, Papp et al., 2013).
Although RVA strains possessing bovine RVA-like VP7- (G6, G8 and G10) and/or VP4- (P[1], P[5] and P[11]) genotypes have been detected in pigs, the whole genomes of only a few of the atypical porcine strains have been analyzed so far (Ghosh and Kobayashi, 2014, Papp et al., 2013). Among them, strain RVA/Pig-tc/KOR/174-1/2006/G8P[7]) was found to possess two bovine RVA-like gene segments (VP3 and VP7) and nine porcine RVA-like gene segments, whilst strains RVA/Pig-tc/VEN/A131/1998/G3P9[7] and RVA/Pig-wt/VEN/A253/1998/G11P9[7] possessed a bovine RVA-like VP2 gene on a porcine RVA genetic backbone (Table 1) (Matthijnssens et al., 2008a, Matthijnssens et al., 2008b, Park et al., 2014).
In the present study, we report whole genomic analysis of an atypical porcine G6P[13] strain, RVA/Pig-wt/IND/HP113/2002/G6P[13], detected in a diarrheic piglet on a pig farm in eastern India (Ghosh et al., 2007). The nucleotide sequences of the VP4, VP6, VP7, NSP4 and NSP5 genes of strain HP113 have been determined previously (Ghosh et al., 2007). Since whole genomic analyses of RVAs provide important information on the complex origin of atypical RVA strains, the nearly full-length nucleotide sequences of the remaining six gene segments (VP1–VP3 and NSP1–NSP3 genes) of HP113 were obtained in the present study.
In the previous study (Ghosh et al., 2007), phylogenetic analyses of the VP4, VP6, VP7 and NSP4 genes of HP113 were based on deduced amino acid sequences, and only a small number of RVA gene sequences were available in the GenBank database for comparison. On the other hand, the whole genome-based RVA genotyping scheme that offers a uniform platform to study the evolutionary patterns of all the 11 gene segments of RVAs is based on nucleotide sequences (Matthijnssens et al., 2008a, Matthijnssens et al., 2008b). Moreover, recently, there has been a significant increase in the volume of RVA whole genome sequence data, inclusion of which in phylogenetic analyses have redefined the origin of several RVA strains (Ghosh and Kobayashi, 2011, Matthijnssens et al., 2008a, Matthijnssens et al., 2008b). Therefore, the nucleotide sequences of all the 11 gene segments of atypical porcine RVA strain HP113 were subjected to detailed phylogenetic analysis in the present study.
Section snippets
Viruses
Porcine RVA strain HP113 was detected in a diarrheic fecal sample collected from a month-old piglet on a pig farm located near the city of Kolkata, eastern India, in 2002 (Ghosh et al., 2007).
RT-PCR and nucleotide sequencing
For RT-PCR, viral RNA was extracted from fecal sample using the QIAamp Viral RNA Mini kit (Qiagen Sciences, MD, USA). Primers used for the amplification of the VP1–VP3 and NSP1–NSP3 gene segments of strain HP113 have been described previously (Ghosh et al., 2012a, Ghosh et al., 2012b, Wang et al., 2010).
Results and discussion
Whole genomic analysis of porcine RVA strain HP113 revealed a G6-P[13]-I2-R1-C1-M1-A1-N1-T7-E1-H1 genotype constellation, not reported previously (Table 1; Fig. 1A–K). Therefore, HP113 was found to possess a common bovine-like (G6), typical porcine-like (P[13], T7) and a DS-1-like (I2) genotypes on a Wa-like genotype backbone. The genotype constellation of HP113 indicated complex origin of the strain, necessitating detailed phylogenetic studies.
Recently, the nucleotide sequences of VP7 and VP6
Acknowledgement
This study was supported by a Grant-in-Aid for Scientific Research (KAKENHI) (No. 25305022) from Japan Society for Promotion of Science (JSPS).
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