A member of a new Picornaviridae genus is shed in pig feces

Abstract

During a study of the fecal microbiomes from two healthy piglets using high-throughput sequencing (HTS), we identified a viral genome containing an open reading frame encoding a predicted polyprotein of 2,133 amino acids. This novel viral genome displayed the typical organization of picornaviruses, containing three structural proteins (VP0, VP3, and VP1), followed by seven nonstructural proteins (2A, 2B, 2C, 3A, 3B, 3C(pro), and 3D(pol)). Given its particular relationship with Parechovirus, we propose to name it "Pasivirus" for Parecho sister clade virus, with "Swine pasivirus 1" (SPaV1) as the type species. Fecal samples collected at an industrial farm from healthy sows and piglets from the same herd (25 and 75, respectively) with ages ranging from 4 to 28 weeks were analyzed for the presence of SPaV1 by one-step reverse transcription (RT)-PCR targeting a 3D region of 151 bp. SPaV1 was detected in fecal samples from 51/75 healthy piglets (68% of the animals) and in none of the 25 fecal samples from healthy sows, indicating that SPaV1 circulates through enteric infection of healthy piglets. We propose that SPaV1 represents the first member of a novel Picornaviridae genus related to parechoviruses.

Fig 1

Schematic representation of predicted SPaV1 genome organization, including 5′ UTR, 3′ UTR, P1, P2, and P3 regions. Primer pairs designed from contigs and used to generate overlapping PCR products are distributed along the nucleotide sequence. Conserved motifs and predicted cleavage sites are indicated along the polyprotein.

Fig 2

Two-dimensional structure predictions of the capsid proteins, VP0 (2A), VP3 (2B), and VP1 (2C), of SPaV1 aligned with representatives of parechoviruses (HPeV1 and HPeV3 and American [LV64-7855] and Swedish [LV87-012, 174F, and 145SL] strains of LV) performed with Jalview 11.0. Predicted α-helices and β-strands in SPaVL1 capsid proteins are represented by red and green arrows, respectively. The positions of BC and EF loops are noted above the alignments. (A) The double-headed arrow indicates the shorter N-terminal extremity of VP0. (B) The conserved KXKXXRXK motif of VP3 is boxed. (C) VP1 showing the two N-terminal amino acid insertions (line with solid circles) and the C-terminal amino acid extension (dashed double-headed arrow).

Fig 2

Two-dimensional structure predictions of the capsid proteins, VP0 (2A), VP3 (2B), and VP1 (2C), of SPaV1 aligned with representatives of parechoviruses (HPeV1 and HPeV3 and American [LV64-7855] and Swedish [LV87-012, 174F, and 145SL] strains of LV) performed with Jalview 11.0. Predicted α-helices and β-strands in SPaVL1 capsid proteins are represented by red and green arrows, respectively. The positions of BC and EF loops are noted above the alignments. (A) The double-headed arrow indicates the shorter N-terminal extremity of VP0. (B) The conserved KXKXXRXK motif of VP3 is boxed. (C) VP1 showing the two N-terminal amino acid insertions (line with solid circles) and the C-terminal amino acid extension (dashed double-headed arrow).

Fig 3

Phylogenetic analysis of complete VP0 (B), VP1 (C), and 3D (A) nucleotide sequences under a GTR+G model and a relaxed uncorrelated clock implemented in the BEAST package. The scale bars are expressed in numbers of substitutions per site. Posterior probabilities are reported at the nodes, and most supported nodes are highlighted in red.

Fig 3

Phylogenetic analysis of complete VP0 (B), VP1 (C), and 3D (A) nucleotide sequences under a GTR+G model and a relaxed uncorrelated clock implemented in the BEAST package. The scale bars are expressed in numbers of substitutions per site. Posterior probabilities are reported at the nodes, and most supported nodes are highlighted in red.

Fig 3

Phylogenetic analysis of complete VP0 (B), VP1 (C), and 3D (A) nucleotide sequences under a GTR+G model and a relaxed uncorrelated clock implemented in the BEAST package. The scale bars are expressed in numbers of substitutions per site. Posterior probabilities are reported at the nodes, and most supported nodes are highlighted in red.

Fig 4

Prevalence of SPaV1 in fecal samples from 25 healthy sows and 75 healthy piglets ranging from 4 to 28 weeks old. The hatched bars represent weakly positive animals.