Shixing Yang

Virome comparisons in wild-diseased and healthy captive giant pandas

BackgroundThe 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.MethodsUsing 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.ResultsThe 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.ConclusionThis 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.

Genotype 4 Hepatitis E Virus Prevalent in Eastern China Shows Diverse Subtypes

Background: Hepatitis E Virus (HEV), a zoonotic pathogen, uses several species of animal as reservoirs. Swine is considered as the major reservoir for HEV infection in humans. Genotype 4 HEV is the dominant cause of hepatitis E disease in humans in China. Objectives: Although many researches revealed that genotype 4 HEV is the main genotype that prevalent in eastern China, few researches have done to study the subtype of HEV in this area. Thus, this study aimed to investigate the subtype of HEV prevalent in eastern China. Materials and Methods: A total of 125 anti-HEV IgM positive human serum and 290 swine fecal samples were subjected to reverse transcription polymerase chain reaction (RT-PCR) screening of HEV RNA. Positive PCR products were sequenced and phylogenetically analyzed. Results: From a total of 125 human serum samples, 19.2% (24.125) were positive, while 9.66% (28.290) of the 290 swine fecal samples were positive for HEV RNA. Phylogenetic analysis based on partial capsid gene showed that the 51 HEV strains in the current study all belonged to genotype 4, clustering into 6 different subtypes. Our results also revealed that some of HEV isolates prevalent in the human and swine populations were classified into the same clusters. Conclusions: Genotype 4 HEV in eastern China shows subtype diversity and some HEV isolates are involved in cross-species transmission.

Plasma virome of cattle from forest region revealed diverse small circular ssDNA viral genomes

BackgroundFree-range cattle are common in the Northeast China area, which have close contact with farmers and may carry virus threatening to cattle and farmers.MethodsUsing viral metagenomics we analyzed the virome in plasma samples collected from 80 cattle from the forested region of Northeast China.ResultsThe 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.ConclusionThe 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.

Recombinant porcine norovirus identified from piglet with diarrhea

BackgroundNoroviruses (NoVs) are members of the family Caliciviridae and are emerging enteric pathogens of humans and animals. Some porcine NoVs are genetically similar to human strains and are classified into GII, like most epidemic human NoVs. So far, PoNoV have been exclusively detected in fecal samples of adult pig without clinical signs.ResultsResult showed that 2 of the 12 evaluated fecal samples were positive for PoNoVs, one of which was positive for PoNoV alone, and the other was coinfected with porcine circovirus and PoNoV. Phylogenetic and recombination analysis showed that the PoNoV positive alone strain was a recombinant new genotype strain. Experimental infection of miniature pigs with fecal suspensions confirmed that this strain can cause gastroenteritis in piglets.ConclusionThis is the first report that recombinant new genotype PoNoV exised in pig herd of China, which cause diarrhea in pigs in nature condition. This find raised questions about the putative epidemiologic role of PoNoV.

Changes in the cellular proteins of A549 infected with Hepatitis E virus by proteomics analysis

BackgroundOur understanding of Hepatitis E virus (HEV) has changed enormously over the past 30 years, from a waterborne infection causing outbreaks of acute hepatitis in developing countries to an infection of global distribution causing a range of hepatic and extra-hepatic illness. However, the key proteins playing important parts in the virus infection were still unknown. Understanding the changes of cellular proteins in these cells exposed to HEV is helpful for elucidating molecular mechanisms associated with function alterations of HEV-infected susceptible cells. In the present study, a comparative gel-based proteomic analysis was employed to study the changes in cellular proteins of A549 exposed to HEV in vitro to provide novel information for understanding the functional alterations of A549 induced by HEV infection.ResultOf 2 585-3 152 protein spots visualized on each gel using silver staining, a total of 31 protein spots were found to be differentially expressed in HEV-infected A549 cells compared with mock-infected A549, including 10 significantly up-regulated protein spots and 21 significantly down-regulated protein spots.ConclusionOur work is the first time regarding the proteomic analysis on the cellular responses to HEV infection. This work is helpful for investigating the molecular basis associated with the interaction between HEV and the host cells although more efforts should be required to discover the mechanisms.

Complete genomes of three human bocavirus strains from children with gastroenteritis and respiratory tract illnesses in Jiangsu, China.

ABSTRACT Human bocavirus (HBoV) is a newly discovered parvovirus associated with acute respiratory tract illness (ARTI) and gastrointestinal illness. No previous reports indicated the presence of HBoV infection in Jiangsu Province, China. Here we report three complete genomic sequences of HBoV strains from children with gastroenteritis and respiratory tract illnesses in Jiangsu, China. Phylogenetic analysis indicated that the three HBoV strains in the present study belong to the HBoV1 lineage, where jz-42 clustered separately, forming a single branch, while zj-68 and zj-92 existed in two separate branches, clustering with several other Chinese HBoV1 strains.

Viral metagenomics of fecal samples from non-human primates revealed human astrovirus in a chimpanzee, China

BackgroundHuman astroviruses (HAstVs) are commonly identified worldwide as important aetiological agents of acute gastroenteritis in all age groups. More and more evidences challenged the paradigm that AstV infections are species-specific. Yet to date, AstVs associated with human infections have not been detected in any animal hosts.ResultsViral metagenomics methods were used to detect viral nucleic acids in fecal samples from 69 captive non-human primates (NHPs) from three zoos in China. Sequence reads showing high similarity to astrovirus MLB2 were found in feces from a chimpanzee with diarrhea. The complete genome of this astrovirus was determined and deposited in the GenBank under accession number KX273058 (named SAstV-nj). Phylogenetic analysis based on complete genomes revealed that SAstV-nj was closely related to and shared >98% nucleotide sequence identity with the previous human astrovirus MLB2 strains.ConclusionsThis study suggested that MLB2-related astroviruses might have the potential of cross-species transmission between human and NHP.

Full-length and defective enterovirus G genomes with distinct torovirus protease insertions are highly prevalent on a Chinese pig farm

Recombination occurs frequently between enteroviruses (EVs) which are classified within the same species of the Picornaviridae family. Here, using viral metagenomics, the genomes of two recombinant EV-Gs (strains EVG 01/NC_CHI/2014 and EVG 02/NC_CHI/2014) found in the feces of pigs from a swine farm in China are described. The two strains are characterized by distinct insertion of a papain-like protease gene from toroviruses classified within the Coronaviridae family. According to recent reports the site of the torovirus protease insertion was located at the 2C/3A junction region in EVG 02/NC_CHI/2014. For the other variant EVG 01/NC_CHI/2014, the inserted protease sequence replaced the entire viral capsid protein region up to the VP1/2A junction. These two EV-G strains were highly prevalent in the same pig farm with all animals shedding the full-length genome (EVG 02/NC_CHI/2014) while 65% also shed the capsid deletion mutant (EVG 01/NC_CHI/2014). A helper-defective virus relationship between the two co-circulating EV-G recombinants is hypothesized.

Viral metagenomics analysis of feces from coronary heart disease patients reveals the genetic diversity of the Microviridae

Recent studies have declared that members of the ssDNA virus family Microviridae play an important role in multiple environments, as they have been found taking a dominant position in the human gut. The aim of this study was to analyze the overall composition of the gut virome in coronary heart disease (CHD) patients, and try to discover the potential link between the human gut virome and CHD. Viral metagenomics methods were performed to detect the viral sequences in fecal samples collected from CHD inpatients and healthy persons as controls. We present the analysis of the virome composition in these CHD patients and controls. Our data shows that the virome composition may be linked to daily living habits and the medical therapy of CHD. Virgaviridae and Microviridae were the two dominant types of viruses found in the enteric virome of CHD patients. Fourteen divergent viruses belonging to the family Microviridae were found, twelve of which were grouped into the subfamily Gokushovirinae, while the remaining two strains might represent two new subfamilies within Microviridae, according to the phylogenetic analysis. In addition, the genomic organization of these viruses has been characterized.

A novel cardiovirus in wild rats

BackgroundCardioviruses cause severe illnesses in rodents and humans. In recent years, novel cardioviruses have been frequently found, which promoted further studies of the genetic diversity of cardioviruses. Using viral metagenomics, we genetically characterized a novel cardiovirus (named SX1) from wild rat feces. The genomic structure of SX1 shared similar features with those of the Theiler’s murine encephalomyelitis viruses, including a leader protein, four structural proteins and seven non-structural proteins. Phylogenetic analysis based on both structural proteins and non-structural proteins coding regions showed that SX1 was formed into a separate branch, being located between the branches of Theiler’s murine encephalomyelitis viruses and Thera viruses. Variable resides presented in the Ser/Thr rich domain of L protein, VP1 loops, and VP2 puffs distinguished SX1 from Theiler’s murine encephalomyelitis viruses, suggesting the different antigenicity and pathogenicity of SX1.