A Member of a New Picornaviridae Genus Is Shed in Pig Feces

Institut Pasteur, Laboratory for Urgent Responses to Biological Threats, Paris, France.
Journal of Virology (Impact Factor: 4.44). 07/2012; 86(18):10036-46. DOI: 10.1128/JVI.00046-12
Source: PubMed


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, 3Cpro, and 3Dpol). 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.

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    • "However, both studies indicated that a virus of this genus was common in piglets worldwide. To-date, viruses in the seven Picornaviridae genera have been related to pig disease [20]. Although PLV-CHN and SPaV-1 have a high prevalence in healthy piglets, their pathogenicity remains unknown. "
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    ABSTRACT: In this study, we describe a novel porcine parechovirus-like virus (tentatively named PLV-CHN) from healthy piglets in China using 454 high-throughput sequencing. The complete genome of the virus comprises 6832 bp, encoding a predicted polyprotein of 2132 amino acids that is most similar to Ljungan virus (32% identity). A similar virus that belongs to a novel Picornaviridae genus, named swine pasivirus 1 (SPaV-1), was reported during the preparation of this paper. Sequence analysis revealed that PLV-CHN and SPaV1 shared 82% nucleotide identity and 89% amino acid identity. Further genomic and phylogenetic analyses suggested that both SPaV1 and PLV-CHN shared similar genomic characteristics and belong to the same novel Picornaviridae genus. A total of 36 (20.0%) fecal samples from 180 healthy piglets were positive for PLV-CHN by RT-PCR, while no fecal samples from 100 healthy children and 100 children with diarrhea, and no cerebrospinal fluid samples from 196 children with suspected viral encephalitis, was positive for the virus. However, Western blot and enzyme-linked immunosorbent assays using recombinant PLV-CHN VP1 polypeptide as an antigen showed a high seroprevalence of 63.5% in the healthy population. When grouped by age, the antibody-positivity rates showed that the majority of children under 12 years of age have been infected by the virus. It was suggested that PLV-CHN, SPaV1, or an as-yet-uncharacterized virus can infect humans early in life. Thus, investigation of the role of this novel virus is vital.
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    • "members of the genera Aphthovirus, Cardiovirus, Avihepatovirus , Erbovirus, Senecavirus and Teschovirus and a number of recently identified picornaviruses e.g. 'Hungarovirus', 'Aquamavirus' and 'Pasivirus' (Knowles et al., 2012; Reuter et al., 2012, Kapoor et al., 2008b; Sauvage et al., 2012). "
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    ABSTRACT: This study reports the metagenomic detection and complete genome characterization of a novel turkey picornavirus from fecal samples of healthy (1/3) and affected (6/8) commercial turkeys with enteric and/or stunting syndrome in Hungary. The virus was detected in seven of the eight farms examined. The turkey/M176-TuASV/2011/HUN genome (KC465954) was genetically different from the currently known picornaviruses of turkey origin (megriviruses and galliviruses), and showed distant phylogenetic relationship and common genomic features (e.g. uncleaved VP0 and three predicted and unrelated 2A polypeptides) to duck hepatitis A virus (DHAV) of the genus Avihepatovirus. The complete genome analysis revealed multiple distinct genome features like the presence of two in-tandem aphthovirus 2A-like sequence repeat with DxExNPG/P 'ribosome-skipping' sites (76%, 23/30 amino acid identical), with the first aphthovirus 2A-like sequence being located at the end of VP1 capsid protein (VP1/2A1 'ribosome-skipping' site). The phylogenetic analyses, low sequence identity (33%, 32% and 36% aa in P1, P2, and P3 regions) to DHAV, and the type II-like IRES suggests that this turkey picornavirus is related to, but distinct from the genus Avihepatovirus and it could be the founding member of a novel Avihepatovirus sister-clade genus. This is the third, taxonomically highly distinct picornavirus clade identified from turkeys exhibiting varied symptoms. The possible contribution of these picornaviruses to the development of stunting syndrome and/or poultry enteritis complex as a single infection or part of co-infections or with other pathogens, as well as their world-wide distribution remains unknown and should be investigated.
    Full-text · Article · Apr 2013 · Journal of General Virology
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    ABSTRACT: We determined the genomic features and the taxonomic classification of Sebokele virus 1 (SEBV1), a previously unclassified arbovirus isolated in 1972 from rodents collected in Botambi, Central African Republic. The complete genome sequence was obtained using a deep sequencing approach (Illumina technology) and dedicated bioinformatics workflows for data analysis. Molecular analysis identified SEBV1 as a picornavirus, most closely related to Ljungan viruses of the genus Parechovirus. The genome has a typical Ljungan virus-like organization, including the presence of two unrelated 2A protein motifs. Phylogenetic analysis confirmed that SEBV1 belongs to the parechovirus phylogroup and was most closely related to the Ljungan virus species. However, it appeared clearly distinct from all members of this phylogroup, suggesting that it represents a novel species of the genus Parechovirus.
    Preview · Article · Apr 2013 · Journal of General Virology
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