A porcine enterovirus G associated with enteric disease contains a novel papain-like cysteine protease

Knutson, Todd P.; Velayudhan, Binu T.; Marthaler, Douglas

doi:10.1099/jgv.0.000799

Cited by 48 publications

(53 citation statements)

References 30 publications

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“…Enteroviruses have been more generally linked to neurological disorders in pigs, although they are commonly found in feces as well 11,12,[32][33][34] . In a study from Vietnam, no significant correlation was found between diarrhea status and presence of enterovirus G in feces 35 .…”

Section: Discussionmentioning

confidence: 99%

Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus

Theuns

Vanmechelen

Bernaert

et al. 2018

Sci Rep

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Enteric diseases in swine are often caused by different pathogens and thus metagenomics are a useful tool for diagnostics. The capacities of nanopore sequencing for viral diagnostics were investigated here. First, cell culture-grown porcine epidemic diarrhea virus and rotavirus A were pooled and sequenced on a MinION. Reads were already detected at 7 seconds after start of sequencing, resulting in high sequencing depths (19.2 to 103.5X) after 3 h. Next, diarrheic feces of a one-week-old piglet was analyzed. Almost all reads (99%) belonged to bacteriophages, which may have reshaped the piglet’s microbiome. Contigs matched Bacteroides, Escherichia and Enterococcus phages. Moreover, porcine kobuvirus was discovered in the feces for the first time in Belgium. Suckling piglets shed kobuvirus from one week of age, but an association between peak of viral shedding (106.42–107.01 copies/swab) and diarrheic signs was not observed during a follow-up study. Retrospective analysis showed the widespread (n = 25, 56.8% positive) of genetically moderately related kobuviruses among Belgian diarrheic piglets. MinION enables rapid detection of enteric viruses. Such new methodologies will change diagnostics, but more extensive validations should be conducted. The true enteric pathogenicity of porcine kobuvirus should be questioned, while its subclinical importance cannot be excluded.

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Section: Discussionmentioning

confidence: 99%

Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus

Theuns

Vanmechelen

Bernaert

et al. 2018

Sci Rep

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“…The samples from these two cases were processed and submitted for library preparation and NGS on the Illumina MiSeq platform, using previously described methods (Jarvis et al., ). The raw data were analysed using in‐house NGS pipeline with custom bioinformatics tools (Knutson, Velayudhan, & Marthaler, ). Nucleotide and amino acid alignments were constructed using MAFFT in Geneious v9.1.8, and phylogenetic trees were built using PMYML with a GTR substitution model and bootstrapped with 500 replicates.…”

Section: Methodsmentioning

confidence: 99%

Semi‐quantitative duplex RT ‐ PCR reveals the low occurrence of Porcine Pegivirus and Atypical Porcine Pestivirus in diagnostic samples from the United States

Chen

Knutson

Braun

et al. 2019

Transbound Emerg Dis

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SummaryPorcine Pegivirus (PPgV) and Atypical Porcine Pestivirus (APPV) are two recently identified porcine viruses. In this study, the identification of two viruses by metagenomic sequencing, and a duplex semi‐quantitative RT‐PCR was developed to detect these pathogens simultaneously. The PPgV strain Minnesota‐1/2016 had a 95.5%–96.3% nucleotide identity and clustered with the recently identified US PPgV strains, which is a distant clade from the German PPgV strains. The APPV strain Minnesota‐1/2016 shared an 87.3%–92.0% nucleotide identity with the other global APPV strains identity but only shared an 82.8%–83.0% nucleotide identity with clade II consisting of strain identified in China. Detection of both PPgV and APPV was 9.0% of the diagnostic cases. Co‐infection of PPgV and APPV was identified in 7.5% of the diagnostic cases. The occurrence and genetic characterization of PPgV and APPV further enhance our knowledge regarding these new pathogens in the United States.

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“…Furthermore, a previous study using reverse genetics revealed that the US EV‐G17‐PLCP strain functionally produces the exogenous PLCP gene in virus‐infected cells, demonstrating its own ALFQ↓GPPV and AEFQ↓GPPT sequences as the putative cleavage sites (Shang et al., ). Considering the sequence similarity of the putative cleavage sites including GPPT−ALFQ, GPPA−ALFQ, and GPPE−ALPQ among global strains (Conceição‐Neto et al., ; Knutson et al., ; Tsuchiaka et al., ), therefore, the cleavage of the inserted PLCP gene appears to be guaranteed using each corresponding cleavage sequence. Consistently, the recombinant ToV‐PLCP of the EV‐G KNU‐1811 strain is bordered by two analogous predicted 3C pro cleavage sites, ALFQ↓GPPV and AVFQ↓GPPT, at its N and C termini, respectively, indicating its proteolytic processing by 3C pro into a functional product (Figure a).…”

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confidence: 99%

First detection of novel enterovirus G recombining a torovirus papain‐like protease gene associated with diarrhoea in swine in South Korea

Lee

2018

Transbound Emerg Dis

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Enterovirus species G (EV‐G) comprises a highly diversity of 20 genotypes that is prevalent in pig populations, with or without diarrhoea. In the present study, a novel EV‐G strain (KOR/KNU‐1811/2018) that resulted from cross‐order recombination was discovered in diagnostic faecal samples from neonatal pigs with diarrhoea that were negative for swine enteric coronaviruses and rotavirus. The recombinant EV‐G genome possessed an exogenous 594‐nucleotide (198‐amino acid) sequence, flanked by two viral 3Cpro cleavage sites at the 5′ and 3′ ends in its 2C/3A junction region. This insertion encoded a predicted protease similar to the porcine torovirus papain‐like cysteine protease (PLCP), which was recently found in the EV‐G1, ‐G2, and ‐G17 genomes. The complete KNU‐1811 genome shared 73.7% nucleotide identity with a prototype EV‐G1 strain, but had 83.9%–86.7% sequence homology with the global EV‐G1‐PLCP strains. Genetic and phylogenetic analyses demonstrated that the Korean recombinant EV‐G's own VP1 and inserted foreign PLCP genes are most closely related independently to contemporary chimeric G1‐PLCP and G17‐PLCP strains respectively. These results implied that the torovirus‐derived PLCP gene might have undergone continuous nucleotide mutations in the respective EV‐G genome following its independent acquisition through naturally occurring recombination. Our results advance the understanding of the genetic evolution of EV‐G driven by infrequent viral recombination events, by which EV‐G populations laterally gain an exotic gene encoding a virulence factor from heterogeneous virus families, thereby causing clinical disease in swine.

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A porcine enterovirus G associated with enteric disease contains a novel papain-like cysteine protease

Cited by 48 publications

References 30 publications

Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus

Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus

Semi‐quantitative duplex RT ‐ PCR reveals the low occurrence of Porcine Pegivirus and Atypical Porcine Pestivirus in diagnostic samples from the United States

First detection of novel enterovirus G recombining a torovirus papain‐like protease gene associated with diarrhoea in swine in South Korea

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