The diversity of birds in most parts of the world is very high, and thus, they may carry different types of highly differentiated and unknown viruses. Thanks to advanced sequencing technologies, studies on the diversity of bird-associated viruses have increased over the past few years. In this study, a large-scale viral metagenomics survey was performed on cloacal swabs of 2,990 birds from nine provinces of the Chinese mainland. To detect undescribed RNA viruses in birds, more than 1,800 sequences sharing relatively low (<60%) amino acid sequence identity with the best match in the GenBank database were screened. Potentially novel viruses related to vertebrates have been identified, and several potential recombination signals were found. Additionally, hundreds of RNA viral sequences related to plants, fungi, and insects were detected, including previously unknown viruses. Furthermore, we investigated the novelty, functionality, and classification of the phages examined in this study. These viruses occupied topological positions on the evolutionary trees to a certain extent and might form novel putative families, genera, or species, thus providing information to fill the phylogenetic gaps of related viruses. These findings provided new insights into bird-associated viruses, but the interactions among these viruses remain unknown and require further investigation.IMPORTANCEStudying the diversity of RNA viruses in birds and mammals is crucial due to their potential impact on human health and the global ecosystem. Many RNA viruses, such as influenza and coronaviruses, have been shown to cross the species barrier and cause zoonotic diseases. In this metagenomics study involving 2,990 birds from at least 82 species, we identified over 1,800 RNA sequences with distant relationships to known viruses, some of which are rare in birds. The study highlights the scope and diversity of RNA viruses in birds, providing data to predict disease risks and monitor potential viral threats to wildlife, livestock, and human health. This information can aid in the development of strategies for disease prevention and control.
Most hepatitis E virus (HEV) infections are mild or subclinical, however, the infections are characteristically associated with a high incidence of symptomatic presentation among pregnant women. The aim of this study was to assess the HEV prevalence among pregnant women in Zhenjiang, China. 225 and 208 of serum samples collected from pregnant and healthy nonpregnant women, respectively, were used to detect anti-HEV IgG and IgM levels. IgM positive samples were further tested for HEV RNA by using RT-nested PCR (nPCR) method. Positive PCR products were sequenced and subjected to phylogenetic analysis. 21.8% (49/225) of samples were anti-HEV IgG positive in pregnant women, whereas 7.7% (16/208) of samples were anti-HEV IgG positive in control subjects (P < 0.001). With respect to anti-HEV IgM testing, 3.6% (8/225) and 0.0% (0/208) were positive in pregnant women and control subjects, respectively (P = 0.006 < 0.01). 4 out of 8 IgM positive samples were positive for HEV RNA. Phylogenetic analysis indicated that four HEV strains had distinct nucleotide sequences and clustered into two different sub-genotypes in genotype 4. In the current study, the prevalence of HEV infection with respect to IgG and IgM levels among pregnant women was significantly higher than that in the healthy nonpregnant group. Additionally, all four HEV strains belonged to genotype 4 implying that genotype 4 is the predominant genotype in the area.
The pangolin is the only scaly mammal in the world and also an important reservoir of pathogenic viruses. Habitat loss and poaching have been shrinking the survival range of pangolins. More information on pangolin virus populations is needed to better understand and assess potential disease risks. In this study, viral metagenomic data were used to reinvestigate the virome in pangolin lung tissue. Complete genome sequences of two novel anelloviruses were acquired and clustered with the referenced feline strains belonging to genus Tettorquevirus and genus Etatorquevirus, respectively. Two genomes belonging to the genus Gemykibivirus, and species Bat-associated cyclovirus 9 were detected, respectively. One genome with a large contig belonging to the genus Senecavirus were also characterized, according to phylogenetic analysis, which can be presumed to be a novel species. In addition, a full genome of endogenous retroviruse (ERV) was assembled from the lungs of pangolin, and this virus may have the possibility of cross-species transmission during the evolution. This virological investigation has increased our understanding of the virome carried by pangolins and provided a reference baseline for possible zoonotic infectious diseases in the future.
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.
Highly pathogenic coronaviruses have caused significant outbreaks in humans and animals, posing a serious threat to public health. The rapid global spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has resulted in millions of infections and deaths. However, the mechanisms through which coronaviruses evade a host’s antiviral immune system are not well understood. Liquid–liquid phase separation (LLPS) is a recently discovered mechanism that can selectively isolate cellular components to regulate biological processes, including host antiviral innate immune signal transduction pathways. This review focuses on the mechanism of coronavirus-induced LLPS and strategies for utilizing LLPS to evade the host antiviral innate immune response, along with potential antiviral therapeutic drugs and methods. It aims to provide a more comprehensive understanding and novel insights for researchers studying LLPS induced by pandemic viruses.
Hepatitis E virus (HEV) and caliciviruses are enteric pathogens of humans and animals, and pigs have been considered an important reservoir of these viruses.The aim of this study is to determine the infection rates of HEV and caliciviruses (sapovirus [SaV] and norovirus [NoV]) in different age groups of pigs in Guizhou province, China, and characterize the strains that are prevalent in this mountainous area.A total of 209 stool samples from healthy pigs of different ages were collected from 6 pig farms in Guizhou province from May to June 2009 and tested for HEV, SaV, and NoV by reverse-transcription polymerase chain reaction (RT-PCR).The overall prevalence of porcine HEV and porcine SaV was 6.7% (15/209) and 1.0% (2/209), respectively. No NoV was detected. The prevalence rates of porcine HEV infection were 15.4% in piglets aged < 1 mon (4/26), 6.8% in piglets aged between 1 and 4 mon (3/44), 12.5% in piglets aged ≈ 4 mon (6/48), and 1.1% in sows aged between 6 and 14 mon (2/91). Porcine SaV was detected only in piglets (7.7%, 2/26). All 10 HEV isolates belonged to genotype 4, clustering with a human HEV strain (AF103940) from an adjacent province.This is the first report on the existence of porcine SaV in swine in Guizhou province, China. The clustering of the porcine HEV isolates with a human strain suggests cross-species transmission between swine and humans in this area.
The members of the family Circoviridae are considered to be the smallest autonomously replicating viruses, including two genera, Circovirus and Cyclovirus . Circoviruses have been found in a variety of vertebrates, but whether they infect endangered protected animals has not been studied in much detail. Here, viral metagenomics and reserve PCR methods were used to detected and verified viral nucleic acid in the blood samples from giant pandas. According to these methods, the complete genome sequence of a novel circovirus, the Giant panda associated circovirus (GPCV) from the blood sample of three giant panda was identified. The GPCV genome is 2,090 bp in size and reveals two putative ambisense open-reading frames, encoding the major structural capsid protein and the replication associated protein, respectively, the latter having two predicted introns. Pairwise sequence comparison and phylogenetic analyses indicated GPCV was a putative new species within genus Circovirus based on the species demarcation criteria of the International Committee on the Taxonomy of Viruses. It is the first time that circovirus has been identified from blood samples of giant pandas. These efforts will contribute to future analyses to illuminate the evolutionary relationships between classified and newly identified members of the family Circoviridae .
Abstract Fecal microbiota transplantation (FMT) by manual preparation has been applied to treat diseases for thousands of years. However, this method still endures safety risks and challenges the psychological endurance and acceptance of doctors, patients and donors. Population evidence showed the washed microbiota preparation with microfiltration based on an automatic purification system followed by repeated centrifugation plus suspension for three times significantly reduced FMT-related adverse events. This washing preparation makes delivering a precise dose of the enriched microbiota feasible, instead of using the weight of stool. Intraperitoneal injection in mice with the fecal microbiota supernatant obtained after repeated centrifugation plus suspension for three times induced less toxic reaction than that by the first centrifugation following the microfiltration. The toxic reactions that include death, the change in the level of peripheral white blood cells, and the proliferation of germinal center in secondary lymphoid follicles in spleen were noted. The metagenomic next-generation sequencing (NGS) indicated the increasing types and amount of viruses could be washed out during the washing process. Metabolomics analysis indicated metabolites with pro-inflammatory effects in the fecal microbiota supernatant such as leukotriene B4, corticosterone, and prostaglandin G2 could be removed by repeated washing. Near-infrared absorption spectroscopy could be served as a rapid detection method to control the quality of the washing-process. In conclusion, this study for the first time provides evidence linking clinical findings and animal experiments to support that washed microbiota transplantation (WMT) is safer, more precise and more quality-controllable than the crude FMT by manual.
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