Viral load and histological distribution of atypical porcine pestivirus in different tissues of naturally infected piglets Abstract A newly identified atypical porcine pestivirus (APPV) associated with congenital tremors in newborn piglets has been shown to have a worldwide geographic distribution. In view of the function of Erns in pestivirus infection and replication, the viral load and histological distribution of APPV in different tissues of naturally infected piglets were analyzed by quantitative RT-PCR and immunohistochemical detection using Erns as the target. The results showed that the viral copy number was higher in the cerebellum, submandibular lymph nodes, and thymus than in other tissues, indicating that these are important target organs of APPV. The histological distribution of APPV was mainly in the matrix and nerve fiber in nervous tissues, endothelial cells in lymphoid tissues, and epithelial cells in other tissues, suggesting that these cells were target cells of APPV. The results will provide basic data for elucidating the pathogenesis and deepening the understanding of this newly discovered pathogen.

Molecular characterization of a new badnavirus infecting green Sichuan pepper ( Zanthoxylum schinifolium ) Abstract A new virus with a circular double-stranded DNA genome was discovered in green Sichuan pepper with vein clearing symptoms. Its complete genome of 8,014 bp contains three open reading frames (ORF) on the plus strand, which is typical of members of the genus Badnavirus in the family Caulimoviridae. Sequence comparisons revealed that the new virus has the highest nucleotide sequence identity with grapevine vein-clearing virus (GVCV). In particular, the identity of the two viruses in the ORF3 RT-RNase H region is 71.9%, which is below the species demarcation cutoff of 80% for badnaviruses. Phylogenetic analysis also placed the new virus with GVCV in a cluster. The virus was tentatively named “green Sichuan pepper vein clearing-associated virus” (GSPVCaV). The geographical distribution and genetic diversity of GSPVCaV were studied. Another isolate was found to be highly divergent.

The complete genome sequence of apple rootstock virus A, a novel nucleorhabdovirus identified in apple rootstocks Abstract We report the complete genome sequence of a novel nucleorhabdovirus, apple rootstock virus A (ApRVA), isolated from Malus spp. in South Korea. ApRVA has a 14,043-nt single-stranded negative-sense RNA genome. In the antigenome sense, it contains seven open reading frames, encoding the putative nucleocapsid protein, phosphoprotein, cell-to-cell movement protein, matrix protein, glycoprotein, RNA-dependent RNA polymerase, and an additional hypothetical protein, the gene for which is located between the genes for the matrix protein and glycoprotein. The complete genome sequence of ApRVA showed 47.45% nucleotide sequence identity to that of black currant-associated rhabdovirus 1. The genome organization, phylogenetic relationships, and sequence similarities to other nucleorhabdoviruses suggest that ApRVA is a new member of the genus Nucleorhabdovirus.

Complete genome sequence and analysis of a new lethal arterivirus, Trionyx sinensis hemorrhagic syndrome virus (TSHSV), amplified from an infected Chinese softshell turtle Abstract Trionyx sinensis hemorrhagic syndrome virus (TSHSV) is a newly discovered lethal arterivirus that causes serious disease in Trionyx sinensis in China. In this study, the complete genome sequence of TSHSV was determined by RACE cloning, and the functions of the predicted proteins were predicted. The complete genome of TSHSV was found to be 17,875 bp in length, and a 3’-end poly(A) tail was detected. Eight TSHSV hypothetical proteins (TSHSV-HPs) were predicted by gene model identification. TSHSV-HP2, 3 and 4 were associated with replicase activity, since papain-like protease (PLPs), serine-type endopeptidase, P-loop-containing nucleoside triphosphate hydrolase, and EndoU-like endoribonuclease motifs were detected. Phylogenetic analysis showed that TSHSV clusters with an arterivirus from a Chinese broad-headed pond turtle.

A novel ourmia-like mycovirus isolated from the plant pathogenic fungus Colletotrichum gloeosporioides Abstract In this study, a novel mycovirus designed Colletotrichum gloeosporioides ourmia-like virus 1 (CgOLV1) was isolated from a filamentous phytopathogenic fungus, Colletotrichum gloeosporioides. The virus has a genome of 2,516 nucleotides and contains a large open reading frame (ORF) encoding an RNA-dependent RNA polymerase (RdRp). Phylogenetic analysis indicated that CgOLV1 is located in the ourmia-like mycovirus clade, whose members are related to plant ourmiaviruses. To the best of our knowledge, this is the first report of an ourmia-like mycovirus in C. gloeosporioides.

Molecular characterization of a new trichovirus from peach in Mexico Abstract The complete genome sequence of a trichovirus was obtained from peach samples collected from Mexico and found to be 7985 nucleotides long, excluding the poly(A) tail. Phylogenetic analysis using the complete nucleotide sequence revealed that the virus is a member of the genus Trichovirus and is closely related to peach mosaic virus (PcMV) and cherry mottle leaf virus (CMLV). The highest nucleotide sequence identity was 70% to both PcMV and CMLV, indicating that this virus, which we have tentatively named “peach virus M” (PeVM) should be considered a member of a new trichovirus species. We determined, for the first time, the initiation sites of the subgenomic RNAs (sgRNA) of a trichovirus. The sgRNAs for the movement and coat proteins started with the sequence ‘GAA’, while the smallest one, coding for the nucleotide-binding protein, started with the nucleotides ‘GU’. In all cases, the sgRNAs leader ranged between 113 and 121 nt in length.

Complete genome analysis of the novel Enterococcus faecalis phage vB_EfaS_AL3 Abstract This work describes the characterization and genome annotation of a new lytic Enterococcus faecalis siphovirus, vB_EfaS_AL3 (referred to as AL3), isolated from wastewater samples collected in Liaoning Province, China. The genome of phage AL3 is composed of linear double-stranded DNA that is 40,789 bp in length with a G + C content of 34.84% and 61 putative protein-coding genes. Phylogenetic and comparative genomic analyses indicate that phage AL3 should be considered a novel phage.

Molecular characterization of a new vitivirus discovered in a blueberry plant with green mosaic symptoms Abstract A new virus belonging to the genus Vitivirus in the family Betaflexiviridae was identified by next-generation sequencing of a blueberry plant showing green mosaic symptoms. The genome organization of the virus, which is tentatively named “blueberry green mosaic-associated virus” (BGMaV), is typical of vitiviruses, with five open reading frames (ORFs) and a polyadenylated 3’ terminus. The ORFs code for the viral replicase, a 16K protein of unknown function, a movement protein, a coat protein (CP), and a nucleic acid binding protein. Phylogenetic analyses based on the deduced amino acid sequence of the CP and conserved motifs of the RNA-dependent RNA polymerase confirmed the taxonomic placement of BGMaV in the genus Vitivirus.

Raoultella bacteriophage RP180, a new member of the genus Kagunavirus , subfamily Guernseyvirinae Abstract A novel lytic Raoultella phage, RP180, was isolated and characterized. The RP180 genome has 44,851 base pairs and contains 65 putative genes, 35 of them encoding proteins whose functions were predicted based on sequence similarity to known proteins. The RP180 genome possesses a gene synteny typical of members of the subfamily Guernseyvirinae. Phylogenetic analysis of the RP180 genome and similar phage genomes revealed that phage RP180 is the first member of the genus Kagunavirus, subfamily Guernseyvirinae, that is specific for Raoultella sp. The genome of RP180 encodes a putative protein with similarity to CRISPR-like Cas4 nucleases, which belong to the pfam12705/PDDEXK_1 family. Cas4-like proteins of this family have been shown to interfere with the bacterial host type II-C CRISPR-Cas system.

A mycoparasitic and opportunistic fungus is inhabited by a mycovirus Abstract A novel bisegmented double-stranded RNA virus was identified in the mycoparasitic and opportunistic fungus Hypomyces chrysospermus. The RNA1 genome segment comprises 1866 bp and encodes an RNA-dependent RNA polymerase (RdRp). The RNA2 segment comprises 1822 bp and encodes a capsid protein. Phylogenetic analysis of the RdRp protein indicated that this virus is a new member of genus Alphapartitivirus in the family Partitiviridae. We have designated this mycovirus as “Hypomyces chrysospermus partitivirus 1” (HcPV1). HcPV1 is highly transmissible with aleurioconidia and is present in large amounts within growing mycelium in comparison to the GAPDH reference gene.