Identification of a novel bovine enterovirus possessing highly divergent amino acid sequences in capsid protein

Abstract

BackgroundBovine enterovirus (BEV) belongs to the species Enterovirus E or F, genus Enterovirus and family Picornaviridae. Although numerous studies have identified BEVs in the feces of cattle with diarrhea, the pathogenicity of BEVs remains unclear. Previously, we reported the detection of novel kobu-like virus in calf feces, by metagenomics analysis. In the present study, we identified a novel BEV in diarrheal feces collected for that survey. Complete genome sequences were determined by deep sequencing in feces. Secondary RNA structure analysis of the 5′ untranslated region (UTR), phylogenetic tree construction and pairwise identity analysis were conducted.ResultsThe complete genome sequences of BEV were genetically distant from other EVs and the VP1 coding region contained novel and unique amino acid sequences. We named this strain as BEV AN12/Bos taurus/JPN/2014 (referred to as BEV-AN12). According to genome analysis, the genome length of this virus is 7414 nucleotides excluding the poly (A) tail and its genome consists of a 5′UTR, open reading frame encoding a single polyprotein, and 3′UTR. The results of secondary RNA structure analysis showed that in the 5′UTR, BEV-AN12 had an additional clover leaf structure and small stem loop structure, similarly to other BEVs. In pairwise identity analysis, BEV-AN12 showed high amino acid (aa) identities to Enterovirus F in the polyprotein, P2 and P3 regions (aa identity ≥82.4%). Therefore, BEV-AN12 is closely related to Enterovirus F. However, aa sequences in the capsid protein regions, particularly the VP1 encoding region, showed significantly low aa identity to other viruses in genus Enterovirus (VP1 aa identity ≤58.6%). In addition, BEV-AN12 branched separately from Enterovirus E and F in phylogenetic trees based on the aa sequences of P1 and VP1, although it clustered with Enterovirus F in trees based on sequences in the P2 and P3 genome region.ConclusionsWe identified novel BEV possessing highly divergent aa sequences in the VP1 coding region in Japan. According to species definition, we proposed naming this strain as “Enterovirus K”, which is a novel species within genus Enterovirus. Further genomic studies are needed to understand the pathogenicity of BEVs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-016-0923-0) contains supplementary material, which is available to authorized users.

Emergency Services of Viral RNAs: Repair and Remodeling

“…The indels may not be strictly neutral, but if they are associated with some fitness cost, the detrimental phenotypic changes are likely to be suppressed by some secondsite mutations (see below). In some cases, such indels appeared to even be advantageous, judging by their strong conservation in representatives of a given picornavirus species, as is the case, for example, with the triplication of the VPg gene in the FMDV RNA (276,277) and the duplication of the 5=-terminal cis-element of the bovine enterovirus RNA (278,279). Conserved duplications in untranslated and coding RNA regions of other viruses have been described as well (cf.…”

A novel defective recombinant porcine enterovirus G virus carrying a porcine torovirus papain-like cysteine protease gene and a putative anti-apoptosis gene in place of viral structural protein genes

“…In addition to type 1 recombinant EV-G, second type of recombinant EV-G (we call type 2 recombinant EV-G in this study), which carried the PLCP gene in place of viral structural genes, has been identified in a Chinese pig farm (Wang et al, 2018). The PLCP gene is encoded in the ORF1 of the genome of torovirus, a member of family Coronaviridae, and the order Nidovirales (Conceição-Neto et al, 2017;Knutson et al, 2017;Shang et al, 2017;Tsuchiaka et al, 2017;Wang et al, 2018). The PLCP of nidoviruses serves as a protease to cleave viral gene 1 polyproteins to mature proteins (Mielech et al, 2014).…”

“…By using a metagenomics approach, we have detected the genomes of EV-G1, 2, 3, 4, 6, 9, 10 and a new type of EV-Gs in feces of pigs with or without diarrhea in Japan (Tsuchiaka et al, 2017). Among them, 16 sequences of EV-G1 and one isolate of EV-G2 show an insertion of a papain-like cysteine protease (PLCP) gene from porcine torovirus at the 2C-3A junction sites (Tsuchiaka et al, 2017) (Fig. 1).…”

“…Schematic diagram of the genome organization of EV-G, type 1 and type 2 recombinant EVGs. Genome order of EV-G, type 1 and type 2 recombinant EV-G came from the EVG/Porcine/JPN/Iba464-3-1/2015/G1 (Tsuchiaka et al, 2017), EVG/Porcine/JPN/MoI2-1-1/2015/G1-PL-CP (Tsuchiaka et al, 2018), and a newly identified type 2 EV-G (EVG/Porcine/JPN/MoI2-1-2/2015/type 2) in this study, respectively.…”

Molecular Identification of Enteroviruses from Cattle and Goat Feces and Environment in Thailand

“…VP1 represents a highly variable region in the enteroviral genome; VP1 sequence variations are useful for determining the genotypes of species by use of molecular methods (8,9). On the basis of the sequence analysis of capsid proteins, 5, 7, and 20 genotypes of EV-E (EV-E1 to EV-E5), EV-F (EV-F1 to EV-F7), and EV-G (EV-G1 to EV-G20), respectively, have been identified (1, [10][11][12][13].…”