Whole-genomic analysis of 12 porcine group A rotaviruses isolated from symptomatic piglets in Brazil during the years of 2012–2013

Abstract

Group A rotaviruses (RVAs) are leading causes of viral diarrhea in children and in the young of many animal species, particularly swine. In the current study, porcine RVAs were found in fecal specimens from symptomatic piglets on 4 farms in Brazil during the years of 2012-2013. Using RT-PCR, Sanger nucleotide sequencing, and phylogenetic analyses, the whole genomes of 12 Brazilian porcine RVA strains were analyzed. Specifically, the full-length open reading frame (ORF) sequences were determined for the NSP2-, NSP3-, and VP6-coding genes, and partial ORF sequences were determined for the VP1-, VP2-, VP3-, VP4-, VP7-, NSP1-, NSP4-, and NSP5/6-coding genes. The results indicate that all 12 strains had an overall porcine-RVA-like backbone with most segments being designated as genotype 1, with the exception of the VP6- and NSP1-coding genes, which were genotypes I5 and A8, respectively. These results add to our growing understanding of porcine RVA genetic diversity and will provide a platform for monitoring the role of animals as genetic reservoirs of emerging human RVAs strains.

Distinguishing the genotype 1 genes and proteins of human Wa-like rotaviruses vs. porcine rotaviruses

“…2), we confirmed previous reports that the most divergent genes are those encoding outer capsid proteins VP7 and VP4, the intermediate capsid protein VP6, and the nonstructural innate immune antagonist protein NSP1 (Kim et al, 2012; Martel-Paradis et al, 2013; Monini et al, 2014; Nagai et al, 2015; Okitsu et al, 2013; Silva et al, 2015; Theuns et al, 2015). Indeed, human Wa-like RVAs and porcine RVAs usually exhibit different genotypes for these four genes, which by definition share <85% nucleotide sequence identity (Matthijnssens et al, 2008).…”

“…These strains were considered to be wildtype porcine RVAs because they had G/P-genotypes normally associated with porcine RVAs and they were found in the feces of diarrheic or non-diarrheic piglets during the years of 2006–2014. The porcine RVAs were also from various geographical locations: Brazil (strains ROTA01-10, ROTA24-25, ROTA27, and ROTA30-31), Belgium (strains 12R022, 12R002, 12R006, 12R005, 12R041, and 12R046), Italy (strains 3BS, 2CR, and 7RE), Thailand (strains CMP45, CMP29, CMP40, and CMP48), Korea (strains PRG921, PRG9121, PRG9235, and PRG942), Canada (strains F8-4 and F7-4), and Japan (strains BU8 and BU2) (Kim et al, 2012; Martel-Paradis et al, 2013; Monini et al, 2014; Nagai et al, 2015; Okitsu et al, 2013; Silva et al, 2015; Theuns et al, 2015). We also included the gene sequences of several atypical strains (Fig.…”

“…In fact, prior to 2015, <20 complete/near-complete genome sequences had been reported for wildtype porcine RVAs (i.e., those found in the feces of symptomatic piglets), whereas >300 wildtype human Wa-like RVA genome sequences existed. Recently, we described the near-complete genome sequencing and analysis of 12 Brazilian porcine RVAs isolated in 2012–2013 (Silva et al, 2015). Here, we report an additional 11 near-complete genome sequences of porcine RVAs from this same sample collection, thereby adding significantly to the number of wildtype porcine RVA sequences available in GenBank.…”

“…Near-complete genome nucleotide sequences were determined for 11 porcine RVAs (ROTA02, ROTA03, ROTA04, ROTA05, ROTA13, ROTA16, ROTA18, ROTA25, ROTA27, ROTA30, and ROTA31) using the same approach described in Silva et al, 2015 (Silva et al, 2015). These porcine strains are considered to represent typical modern isolates as they were found in fecal specimens collected from diarrheic nursing and suckling piglets (<60 days of age) on various Brazilian farms during the years of 2012–2013.…”

“…Human RVAs with this genotype constellation are referred to as “Wa-like” because they are genetically similar to the archival reference strain Wa (Wyatt et al, 1980). While fewer porcine RVAs have been sequenced to date (n = 33), the available data suggests that these strains typically exhibit the genotype constellation G3/5/9/11-P[6]/[7]/[13]/[19]/[23]-I5-R1-C1-M1-A8-N1-T1/7-E1-H1 (Kim et al, 2012; Martel-Paradis et al, 2013; Matthijnssens et al, 2008; Monini et al, 2014; Nagai et al, 2015; Okitsu et al, 2013; Silva et al, 2015; Theuns et al, 2015). Thus, it seems that while human Wa-like RVAs and porcine RVAs differ in their VP7, VP4, VP6, and NSP1 gene genotypes, they tend to have similar genotype 1 VP1-VP3 and NSP2-NSP5/6 genes.…”