Table 1.
Primers based on:
Table 2.
Pairwise amino acid sequence identities of Sicinivirus Strain JSY (KP779642) compared to other representative members.
Fig 1.
Sequence classification of obtained reads based on BLASTx.
Percentages of reads with similarity to those of eukaryotes, bacteria, phages, viruses, unclassifiable sequences (other, including plasmid vector sequences) and to unknown sequences (Left). Percentages of viral sequence reads are classified by viral types (Right).
Fig 2.
Genome organization and the conserved picornaviral motifs.
(A) Predicted genome organization possesses conserved picornaviral motifs of Sicinivirus JSY (KP779642), ChPV1 100C (KF979332), ChPV1 55C (NC_024765), Sicinivirus 1 UCC001 (NC_023861) and Sicinivirus UCC1 (KF366619); the predicted cleavage sites of Sicinivirus JSY are indicated above the junction region. (B) Amino acid sequence alignment of Sicinivirus, Turdivirus 1 (NC_014411), Turkey gallivirus (NC_018400), Feline sakobuvirus A isolate FFUP1 (NC_022802), Aichi virus (NC_001918) and Salivirus A isolate 02394–01 (NC_012986), the identified motifs are indicated with jacinth boxes.
Fig 3.
Predicted RNA secondary structure of the Sicinivirus JSY 5' UTR as determined by Mfold and RNAfold.
The complete structure of the 5'UTR (A to L, indicates the type II IRES) has been annotated (inset). Two GNRA motifs and the pyrimidine-rich region are illustrated with gray background boxes.
Fig 4.
Predicted RNA secondary structure and the conserved 3' UTR motifs.
(A) Complete structure of the 3'UTR of Sicinivirus JSY (KP779642), the Poly(Y) tract and the 'barbell-like' structure are illustrated with gray background boxes. (B) Nucleotide sequence alignment of Sicinivirus, Turdivirus 1 (NC_014411), Turkey gallivirus (NC_018400), Feline sakobuvirus A isolate FFUP1 (NC_022802), Aichi virus (NC_001918) and Salivirus A isolate 02394–01 (NC_012986), the conserved regions are indicated with jacinth boxes.
Fig 5.
Amino acid sequence alignment of VP1 polypeptide of the five Sicinivirus.
Drug-binding pocket sites of Sicinivirus JSY (KP779642), ChPV1 100C (KF979332), ChPV1 55C (NC_024765), Sicinivirus 1 UCC001 (NC_023861) and Sicinivirus UCC1 (KF366619) are illustrated with jacinth frames, I118 and L120 positions are labeled with jacinth frames in bold. rhv_like capsid domain (cd00205) in Sicinivirus JSY (KP779642) is indicated with yellow background.
Fig 6.
Phylogenetic analyses of the Sicinivirus strain JSY.
Phylogenetic relationship between Sicinivirus strain JSY and the representative members of the 29 officially recognized genera based upon the complete amino acid sequences of picornavirus P1, 2C, and 3D coding regions. The phylogenetic tree was constructed using the Molecular Evolutionary Genetics Analysis (MEGA) [17] applying the maximum-likelihood method based on the JTT matrix-based model [18], the robustness of the phylogenetic constructions was evaluated by bootstrapping with 1,000 replicates, initial trees for the heuristic search were obtained automatically by applying neighbour-join and BioNJ algorithms.
Fig 7.
Detection of Sicinivirus in clinical stool samples by RT-PCR.
M, Molecular marker D2000; Lanes 1–9, stool samples from farm A; Lanes 10–14, stool samples from farm B; Lanes 15–17, stool samples from farm C; Lanes 18, negative control. The fecal sample that was used to perform the metagenomic analysis is indicated with an orangey-red asterisk (Lane 4).