The giant panda (Ailuropoda melanoleuca) is a vulnerable mammal herbivore living wild in central China. Viral infections have become a potential threat to the health of these endangered animals, but limited information related to these infections is available. Using a viral metagenomic approach, we surveyed viruses in the feces, nasopharyngeal secretions, blood, and different tissues from a wild giant panda that died from an unknown disease, a healthy wild giant panda, and 46 healthy captive animals. The previously uncharacterized complete or near complete genomes of four viruses from three genera in Papillomaviridae family, six viruses in a proposed new Picornaviridae genus (Aimelvirus), two unclassified viruses related to posaviruses in Picornavirales order, 19 anelloviruses in four different clades of Anelloviridae family, four putative circoviruses, and 15 viruses belonging to the recently described Genomoviridae family were sequenced. Reflecting the diet of giant pandas, numerous insect virus sequences related to the families Iflaviridae, Dicistroviridae, Iridoviridae, Baculoviridae, Polydnaviridae, and subfamily Densovirinae and plant viruses sequences related to the families Tombusviridae, Partitiviridae, Secoviridae, Geminiviridae, Luteoviridae, Virgaviridae, and Rhabdoviridae; genus Umbravirus, Alphaflexiviridae, and Phycodnaviridae were also detected in fecal samples. A small number of insect virus sequences were also detected in the nasopharyngeal secretions of healthy giant pandas and lung tissues from the dead wild giant panda. Although the viral families present in the sick giant panda were also detected in the healthy ones, a higher proportion of papillomaviruses, picornaviruses, and anelloviruses reads were detected in the diseased panda. This viral survey increases our understanding of eukaryotic viruses in giant pandas and provides a baseline for comparison to viruses detected in future infectious disease outbreaks. The similar viral families detected in sick and healthy giant pandas indicate that these viruses result in commensal infections in most immuno-competent animals.

Chapparvovirus, a recently determined new genus in the family Parvoviridae, can infect many species of animals including bats, chickens, and pigs. Here, using viral metagenomics method, we identified a novel Chapparvovirus from feces of wild rats and designated it as rat parvovirus 2 (RPV2). The nearly complete genome of RPV2 is 4222-nt long and includes two ORFs encoding a 654-aa nonstructural protein 1 (NS1) and a 472-aa capsid protein (VP), respectively. Phylogenetic analysis over the amino acid sequence of the NS1 showed that RPV2 clustered with Eidolon helvum parvovirus 2 (EHPV2), porcine parvovirus 7 (PPV7), and turkey parvovirus 1 (TP1), forming a separate clade. Sequence analysis indicated that the NS1 protein of RPV2 shared the highest amino acid sequence identity (51 %) with that of EHPV2. According to the genetic distance-based criteria, RPV2 identified here belongs to a novel species of Chapparvovirus.

Bocavirus include bovine parvovirus, minute virus of canine, porcine bocavirus, gorilla bocavirus, and Human bocaviruses 1-4 (HBoVs). Although recent reports showed that recombination happened in bocavirus, no systematical study investigated the recombination of bocavirus. The present study performed the phylogenetic and recombination analysis of bocavirus over the complete genomes available in GenBank. Results confirmed that recombination existed among bocavirus, including the likely inter-genotype recombination between HBoV1 and HBoV4, and intra-genotype recombination among HBoV2 variants. Moreover, it is the first report revealing the recombination that occurred between minute viruses of canine.

Background: Musk deer can produce musk which has high medicinal value and is closely related to human health. Viruses in forest musk deer both threaten the health of forest musk deer and human beings. Methods: Using viral metagenomics we investigated the virome in 85 faeces samples collected from forest musk deer. Results: In this article, eight novel CRESS-DNA viruses were characterized, whole genomes were 2148 nt–3852 nt in length. Phylogenetic analysis indicated that some viral genomes were part of four different groups of CRESS-DNA virus belonging in the unclassified CRESS-DNA virus, Smacoviridae, pCPa-like virus and pPAPh2-like virus. UJSL001 (MN621482), UJSL003 (MN621469) and UJSL017 (MN621476) fall into the branch of unclassified CRESS-DNA virus (CRESSV1–2), UJSL002 (MN621468), UJSL004 (MN621481) and UJSL007 (MN621470) belong to the cluster of Smacoviridae, UJSL005 (MN604398) showing close relationship with pCPa-like (pCRESS4–8) clusters and UJSL006 (MN621480) clustered into the branch of pPAPh2-like (pCRESS9) virus, respectively. Conclusion: The virome in faeces samples of forest musk deer from Chengdu, Sichuan province, China was revealed, which further characterized the diversity of viruses in forest musk deer intestinal tract.

Recombination of Hepatitis E Virus (HEV) has rarely been reported. In the present study, phylogenetic and recombination analyses were performed on 134 complete HEV genomes. Three potentially significant recombination events, including both intra-genotype and one inter-genotype, were identified by recombination detection analysis. Recombination events I and II occurred intra-genotype and inter-genotype, respectively, among three isolates, including the lineage represented by CHN-XJ-SW13 (GU119961, swine isolate), E067-SIJ05C (AB369690, human isolate), and JJT-Kan (AB091394, human isolate), and lead to the recombinant swine isolate swCH31 (DQ450072). Recombination event III occurred between the lineage represented by the NA1 (M73218) and K52-87 (L25595), which resulted in the recombinant Xingjiang-1 (D11092). Our analyses proved that that recombination could occur between human and swine HEV strains, double recombination events existed in HEV, and recombination event could happen within ORF2 region of HEV. These results will provide valuable hints for future research on HEV diversity.

Free-range cattle are common in the Northeast China area, which have close contact with farmers and may carry virus threatening to cattle and farmers. Using viral metagenomics we analyzed the virome in plasma samples collected from 80 cattle from the forested region of Northeast China. The virome of cattle plasma is composed of the viruses belonging to the families including Parvoviridae, Papillomaviridae, Picobirnaviridae, and divergent viral genomes showing sequence similarity to circular Rep-encoding single stranded (CRESS) DNA viruses. Five such CRESS-DNA genomes were full characterized, with Rep sequences related to circovirus and gemycircularvirus. Three bovine parvoviruses belonging to two different genera were also characterized. The virome in plasma samples of cattle from the forested region of Northeast China was revealed, which further characterized the diversity of viruses in cattle plasma.