RESUMO
Two and three genotypes of enterovirus G (EV-G) carrying a papain-like cysteine protease (PL-CP) sequence were detected on two pig farms and classified into genotypes G1 and G10, and G1, G8, and G17, respectively, based on VP1 sequences. A G10 EV-G virus bearing a PL-CP sequence was detected for the first time. Phylogenetic analysis of the P2 and P3 regions grouped the viruses by farm with high sequence similarity. Furthermore, clear recombination break points were detected in the 2A region, suggesting that PL-CP EV-G-containing strains gained sequence diversity through recombination events among the multiple circulating EV-G genotypes on the farms.
Assuntos
Cisteína Proteases/genética , Infecções por Enterovirus/veterinária , Enterovirus Suínos/genética , Genoma Viral , Recombinação Genética , Animais , Proteínas do Capsídeo/genética , Infecções por Enterovirus/epidemiologia , Infecções por Enterovirus/virologia , Enterovirus Suínos/enzimologia , Fezes/virologia , Variação Genética , Genótipo , Japão , Filogenia , Análise de Sequência de DNA , Sus scrofa , Proteínas Virais/genéticaRESUMO
To study the genetic diversity of enterovirus G (EV-G) among Japanese pigs, metagenomics sequencing was performed on fecal samples from pigs with or without diarrhea, collected between 2014 and 2016. Fifty-nine EV-G sequences, which were >5,000 nucleotides long, were obtained. By complete VP1 sequence analysis, Japanese EV-G isolates were classified into G1 (17 strains), G2 (four strains), G3 (22 strains), G4 (two strains), G6 (two strains), G9 (six strains), G10 (five strains), and a new genotype (one strain). Remarkably, 16 G1 and one G2 strain identified in diarrheic (23.5%; four strains) or normal (76.5%; 13 strains) fecal samples possessed a papain-like cysteine protease (PL-CP) sequence, which was recently found in the USA and Belgium in the EV-G genome, at the 2C-3A junction site. This paper presents the first report of the high prevalence of viruses carrying PL-CP in the EV-G population. Furthermore, possible inter- and intragenotype recombination events were found among EV-G strains, including G1-PL-CP strains. Our findings may advance the understanding of the molecular epidemiology and genetic evolution of EV-Gs.
Assuntos
Infecções por Enterovirus/virologia , Enterovirus Suínos/genética , Variação Genética , Recombinação Genética , Animais , Proteínas do Capsídeo/genética , Cisteína Proteases/genética , Infecções por Enterovirus/epidemiologia , Enterovirus Suínos/enzimologia , Fezes/virologia , Japão , Metagenoma , Filogenia , Prevalência , Sus scrofaRESUMO
Identification of unknown pathogens in pigs displaying enteric illness is difficult due to the large diversity of bacterial and viral species found within faecal samples. Current methods often require bacterial or viral isolation, or testing only a limited number of known species using quantitative PCR analysis. Herein, faeces from two 25-day-old piglets with diarrhoea from Texas, USA, were analysed by metagenomic next-generation sequencing to rapidly identify possible pathogens. Our analysis included a bioinformatics pipeline of rapid short-read classification and de novo genome assembly which resulted in the identification of a porcine enterovirus G (EV-G), a complete genome with substantial nucleotide differences (>30â%) among current sequences, and a novel non-structural protein similar in sequence to the Torovirus papain-like cysteine protease (PLpro). This discovery led to the identification and circulation of an EV-G with a novel PLpro in the USA that has not been previously reported.
Assuntos
Cisteína Proteases/genética , Diarreia/veterinária , Infecções por Enterovirus/veterinária , Enterovirus Suínos/classificação , Enterovirus Suínos/enzimologia , Fezes/virologia , Doenças dos Suínos/virologia , Animais , Análise por Conglomerados , Biologia Computacional , Diarreia/virologia , Infecções por Enterovirus/virologia , Enterovirus Suínos/genética , Enterovirus Suínos/isolamento & purificação , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala , Filogenia , Análise de Sequência de DNA , Suínos , TexasRESUMO
The genetic diversity of porcine teschoviruses (PTVs; previously named porcine enterovirus 1) and most serotypes of porcine enteroviruses (PEVs) was studied. Following the determination of the major portion of the genomic sequence of PTV reference strain Talfan, the nucleotide and derived amino acid sequences of the RNA-dependent RNA polymerase (RdRp) region, the capsid VP2 region and the 3' non-translated region (3'-NTR) were compared among PTVs and PEVs and with other picornaviruses. The sequences were obtained by RT-PCR and 3'-RACE with primers based on the sequences of Talfan and available PEV strains. Phylogenetic analysis of RdRp/VP2 and analysis of the predicted RNA secondary structure of the 3'-NTR indicated that PEVs should be reclassified genetically into at least three groups, one that should be assigned to PTVs and two PEV subspecies represented by strain PEV-8 V13 and strain PEV-9 UKG410/73.
