Elsevier

Veterinary Microbiology

Volume 180, Issues 3–4, 18 November 2015, Pages 286-298
Veterinary Microbiology

Short communication
Whole genomic analysis of a porcine G6P[13] rotavirus strain

https://doi.org/10.1016/j.vetmic.2015.09.017Get rights and content

Highlights

  • First report on whole genome of a porcine G6P[13] rotavirus-A (RVA) strain, HP113.

  • The VP6 and VP7 genes of HP113 were derived from bovine RVAs.

  • Identification of a new lineage within the VP7-G6 genotype.

  • The NSP2 gene of HP113 shared a more common origin with several Wa-like human RVAs.

  • Remaining genes of HP113 were closely related to porcine or porcine-like human RVAs.

Abstract

We report here the whole genomic analysis of an unusual porcine G6P[13] rotavirus-A (RVA) strain, RVA/Pig-wt/IND/HP113/2002/G6P[13], detected from a diarrheic piglet in eastern India in 2002. Strain HP113 exhibited a G6-P[13]-I2-R1-C1-M1-A1-N1-T7-E1-H1 genotype constellation, not reported previously. The VP1, VP3, VP4, NSP1 and NSP3–NSP5 genes of RVA strain HP113 were found to be closely related to those of porcine and/or porcine-like human RVAs. On the other hand, the NSP2 gene of HP113 was found to share a more common origin with those of several recent and archival human Wa-like RVA strains than those of other RVAs, whilst its VP6 and VP7 genes appeared to be derived from co-circulating bovine RVAs from India. Within the VP7-G6 genotype, strain HP113 and the Indian bovine RVAs appeared to constitute a new G6 lineage, tentatively designated as G6 lineage-VI. Based on the available data, it was difficult to pinpoint the porcine or human origin of VP2 gene of HP113. Taken together, whole genomic analysis of strain HP113 revealed important insights into the complex evolutionary patterns of atypical porcine RVAs, providing evidence for reassortment events involving strains from different host species and evolutionary relationships between porcine and human RVAs. To our knowledge, this is the first report on whole genomic analysis of a G6P[13] RVA 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).

References (17)

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