Energy level measurement for organic semiconductors.

Along with the miniaturization and versatility of organic optoelectronic devices, it is desired to achieve a profound comprehension of the charge transport mechanism and even the basic device physics. The basis of these studies is the acquisition of relevant information about energy levels. This review provides a comprehensive analysis of five commonly-used techniques, including cyclic voltammetry, ultraviolet electron spectroscopy, inverse photoemission electron spectroscopy, low energy inverse photoemission spectroscopy and hot electron spectroscopy. According to the advantages and disadvantages, working mechanism, and application conditions, researchers will screen out a reliable and suitable characterization method, quickly and accurately. This should be beneficial for the efficient promotion of organic electronics and save valuable time for the related research studies.

Development of a label-free photoelectrochemical immunosensor for novel astrovirus detection.

Since 2017, an infectious goose gout disease characterized by urate precipitation in viscera, mainly caused by novel goose astrovirus (GoAstV) infection, has emerged in the main goose-producing region of China. The current challenge in managing goose gout disease is largely due to the absence of a rapid and efficient detection method for the GoAstV pathogen. Notably, the potential application of immunosensors in detecting GoAstV has not yet been explored. Herein, a label-free PEC immunosensor was fabricated by using purchased TiO2 as the photoactive material and antibody against GoAstV P2 proteins as the specific recognition element. First, we successfully expressed the capsid spike domain P2 protein of ORF2 from GoAstV CHSH01 by using the pET prokaryotic expression system. Meanwhile, the polyclonal antibody against GoAstV capsid P2 protein was produced by purified protein. To our knowledge, this is the first establishment and preliminary application of the label-free photoelectrochemical immunosensor method in the detection of AstV. The PEC immunosensor had a linear range of 1.83 fg mL-1 to 3.02 ng mL-1, and the limit of detection (LOD) was as low as 0.61 fg mL-1. This immunosensor exhibited high sensitivity, great specificity, and good stability in detecting GoAstV P2 proteins. To evaluate the practical application of the immunosensor in real-world sample detection, allantoic fluid from goose embryos was collected as test samples. The results indicated that of the eight positive samples, one false negative result was detected, while both negative samples were accurately detected, suggesting that the constructed PEC immunosensor had good applicability and practical application value, providing a platform for the qualitative detection of GoAstV.

Metagenomic analysis of herbivorous mammalian viral communities in the Northwest Plateau.

BACKGROUND: Mammals are potential hosts for many infectious diseases. However, studies on the viral communities of herbivorous mammals in the Northwest Plateau are limited. Here, we studied the viral communities of herbivorous mammals in the Northwest Plateau using virus metagenomic analysis to analyze and compare the viral community composition of seven animal species. RESULTS: By library construction and next-generation sequencing, contigs and singlets reads with similar viral sequences were classified into 24 viral families. Analyzed from the perspective of sampling areas, the virus community composition was relatively similar in two areas of Wuwei and Jinchang, Gansu Province. Analyzed from the perspective of seven animal species, the viral reads of seven animal species were mostly ssDNA and dominated by CRESS-DNA viruses. Phylogenetic analysis based on viral marker genes indicated that CRESS-DNA viruses and microviruses have high genetic diversity. In addition to DNA viruses, nodaviruses, pepper mild mottle viruses and picornaviruses were RNA viruses that we performed by phylogenetic analysis. The CRESS-DNA viruses and nodaviruses are believed to infect plants and insects, and microviruses can infect bacteria, identifying that they were likely from the diet of herbivorous mammals. Notably, two picornaviruses were identified from red deer and wild horse, showing that the picornavirus found in red deer had the relatively high similarity with human hepatitis A virus, and the picornavirus carried by wild horse could potentially form a new species within the Picornaviridae family. CONCLUSIONS: This study explored the herbivorous mammalian virus community in the Northwest Plateau and the genetic characteristics of viruses that potentially threaten human health. It reveals the diversity and stability of herbivorous mammalian virus communities in the Northwest Plateau and helps to expand our knowledge of various herbivorous mammalian potentially pathogenic viruses.

Comparison of gut viral communities in children under 5 years old and newborns.

OBJECTIVES: The gut virome of humans is mainly composed of bacteriophages and their role in shaping the gut microbiome and influencing human health is increasingly recognized. However, little is known about the dynamic changes of the gut virome in children and its role in growth and development. In this study, we collected fecal samples from newborns and children under 5 years old from the same area during the same time period to investigate the gut viral community using viral metagenomic technique. METHODS: We used viral metagenomics to compare the gut bacteriophage composition between newborns and children under 5 years of age. We collected fecal samples from 45 newborns who were born at the Affiliated Hospital of Jiangsu University and 45 healthy children who were examined at the same hospital. The two groups were classified as the newborn group and the children group. RESULTS: Our sequencing analysis showed that the number of seqeunce reads of the children group were more than that of the newborn group. The results of alpha diversity and beta diversity both indicated that the diversity of the children group was significantly higher than that of the newborn group and the children group is different from the newborn group. The abundance of gut virome in the children group was also higher than that in the newborn group. The analysis of the genetic characteristics of the viruses showed that the phage genome was scattered and clustered with specificity. CONCLUSION: Our findings indicate that the gut bacteriophage communities undergo changes over time, presenting diversity and dynamic characteristics. We characterized the composition of gut virome in children and newborns in this region. However, further research is needed to investigate the function of bacteriophages in the ecology of the gastrointestinal tract.

Virome of wild rats (Rattus norvegicus) captured far from pig farms in Jiangsu province of China reveals novel porcine circovirus type 2d (PCV2d) sequences.

BACKGROUND: Porcine circovirus type 2 (PCV2) has caused great economic losses in the global pig industry. There have been published records of wild rats acting as the reservoirs of PCV2 (only PCV2a and PCV2b), but almost all of which were related to the PCV2-infected swine herds. RESULTS: In this study, we carried out the detection, amplification, and characterization of novel PCV2 strains in wild rats that were captured far from pig farms. Nested PCR assay demonstrated that the kidney, heart, lung, liver, pancreas, and large and small intestines of rats were screened positive for PCV2. We subsequently sequenced two full genomes of PCV2 in positive sample pools, designated as js2021-Rt001 and js2021-Rt002. Genome sequence analysis indicated that they had the highest similarity to nucleotide sequences of porcine-origin PCV2 isolates in Vietnam. Phylogenetically, js2021-Rt001 and js2021-Rt002 were a part of the PCV2d genotype cluster, which is a predominant genotype circulating worldwide in recent years. The antibody recognition regions, immunodominant decoy epitope, and heparin sulfate binding motif of the two complete genome sequences coincided with those previously reported. CONCLUSIONS: Our research reported the genomic characterization of two novel PCV2 strains (js2021-Rt001 and js2021-Rt002) and provided the first supported evidence that PCV2d could naturally infect wild rats in China. However, whether the newly identified strains have potential for circulating in nature in vertical and horizontal transmission or inter-species jumping between rats and pigs needs further research.

Identification of avihepadnaviruses and circoviruses in an unexplained death event in farmed ducks.

Research into disease pathogens can greatly benefit from viral metagenomics technology. Using this technique, we investigated potential disease pathogens that resulted in the death of many ducks on a duck farm. Two duck circoviruses (DuCV) and one duck hepatitis B virus (DHBV) were detected and identified, and all three strains were closely related to avian-associated viruses. Two duck circoviruses had 81.64%-97.65% genome-wide sequence identity to some reference strains, and duck hepatitis B virus shared 75.85%-98.92% identity with other strains. Clinical characteristics of the diseased ducks, including ruffled feathers, lethargy, and weight loss, were comparable to those observed in cases of DuCV infection. Further research is needed to determine whether coinfection with DHBV leads to liver damage and exacerbation of the disease.

Molecular detection and characterization of three novel parvoviruses belonging to two different subfamilies in zoo birds.

Birds carry a large number of viruses that may cause diseases in animals or humans. At present, information about the virome of zoo birds is limited. In this study, using viral metagenomics, we investigated the fecal virome of zoo birds collected from a zoo in Nanjing, Jiangsu Province, China. Three novel parvoviruses were obtained and characterized. The genomes of the three viruses are 5,909, 4,411, and 4,233 nt in length, respectively, and contain four or five ORFs. Phylogenetic analysis showed that these three novel parvoviruses clustered with other strains and formed three different clades. Pairwise comparison of NS1 amino acid sequences showed that Bir-01-1 shared 44.30-74.92% aa sequence identity with other parvoviruses belonging to the genus Aveparvovirus, while Bir-03-1 and Bir-04-1 shared less than 66.87% and 53.09% aa sequence identity, respectively, with other parvoviruses belonging to the genus Chaphamaparvovirus. Each of these three viruses was identified as a member of a novel species based on the species demarcation criteria for parvoviruses. These findings broaden our knowledge of the genetic diversity of parvoviruses and provide epidemiological data regarding potential outbreaks of parvovirus disease in birds.

Dynamic alterations of the mice gut virome after Coxsackievirus B3 infection.

The gut microbiome plays an essential role in the human health and dysbiosis has been implicated in numerous diseases. Coxsackievirus B3 infects millions of humans yearly and yet limited research has explored dynamic alterations of the gut virome after infection. Here, we established the mouse model of Coxsackievirus B3 infection and collected fecal samples at several time points to investigate alterations of the gut virome using viral metagenomic analysis. We found that the mice virome was dominated by Caudovirales and Microviridae, and phylogenetic analyses showed that both Caudovirales and Microviridae had high diversity. The gut virome had significant variations with the increase of Caudovirales and the decrease of Microviridae after infection. We proposed that Caudovirales and Microviridae may be biomarkers for the Coxsackievirus infection process. This study provides a reference for the dynamic changes of the gut virome after human Enterovirus infection, which may help guide the rational drug use in clinical treatment and provide new ideas for preventing Enterovirus infection.

Novel putative pathogenic viruses identified in pangolins by mining metagenomic data.

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.

Identification and genome characterization of novel parechovirus sequences from Hipposideros armiger in China.

BACKGROUND: Bats were identified as a natural reservoir of emerging and re-emerging infectious pathogens threatening human health and life. METHODS: This study collected 21 fecal samples of Hipposideros armiger in Mengla County of Xishuangbanna Prefecture Yunnan Province to combine one pool for viral metagenomic sequencing. RESULTS: Two nearly complete genomes of parechoviruses, BPeV11 and BPeV20, were sequenced. Genome analysis revealed that BPeV11 and BPeV20 follow a 3-3-4 genome layout: 5' UTR-VP0-VP3-VP1-2A-2B-2C-3A-3B-3C-3D-3' UTR. The prevalence of BPev11 and BPev20 by Nested-PCR showed that 1 of 21 fecal samples was positive. Based on amino acid identity comparison and phylogenetic analysis of P1, 2C, and 3D, BPeV11 and BPeV20 were closely related to but distinct from FPeVs. CONCLUSION: It was probably proposed to be a novel species in the genus Parechovirus of the family Picornaviridae. The isolation of BPev11 and BPev20 from H. armiger in China is the first complete genome of parechovirus isolations from bat feces of the genus Hipposideros.

Identification and characterization of a novel bocaparvovirus in tufted deer (Elaphodus cephalophus) in China.

We used viral metagenomics and next-generation sequencing to identify a novel strain of bocaparvovirus in the intestinal tract of tufted deer (Elaphodus cephalophus), tentatively named "Elaphodus cephalophus bocaparvovirus" (ECBOV). A nearly complete genome sequence of 5,354 nucleotides was obtained, which had the typical genome organization and protein motifs of a bocaparvovirus. Sequence comparisons and phylogenetic analysis revealed that ECBOV may be a new ungulate bocaparvovirus. The identification and characterization of viruses in wildlife will facilitate our understanding of genetic evolution and cross-species transmission and thus further reduce the potential threat to human and animal health.

Multiple novel smaco-like viruses identified in chicken cloaca swabs.

Viral metagenomics has been used in numerous animal virus discoveries. Recently, an unprecedented diversity of CRESS DNA viruses was identified using this method, and this has expanded our understanding of the environmental distribution and host range of CRESS DNA viruses. In this study, using an unbiased viral metagenomics approach, we investigated the fecal virome of chickens collected from two farms of Anhui Province, China. Five novel CRESS DNA viruses were obtained and characterized. The genome of the five viruses is 2,401-2,742 bp in length, containing two ORFs in the same orientation. Phylogenetic analysis indicated that all five viruses have a closer genetic relationship to smacoviruses than to other viruses in the order Cremevirales. Pairwise comparison of Rep amino acid sequences showed that these five viruses had only low amino acid sequence identity (8.9%-30.6%) to members of the family Smacoviridae, and the sequence identity among the five smaco-like viruses and other unclassified smacovirus strains was 70.3-95.8%. These findings broaden our knowledge of the genetic diversity of CRESS DNA viruses and provide a basis for classification of unclassified smacoviruses.

Comparison of gut viral communities in diarrhoea and healthy dairy calves.

Calf diarrhoea has been a major cause of economic losses in the global dairy industry. Many factors, including multiple pathogen infections, can directly or indirectly cause calf diarrhoea. This study compared the faecal virome between 15 healthy calves and 15 calves with diarrhoea. Significantly lower diversity of viruses was found in samples from animals with diarrhoea than those in the healthy ones, and this feature may also be related to the age of the calves. Viruses belonging to the families Astroviridae and Caliciviridae that may cause diarrhoea in dairy calves have been characterized, which revealed that reads of caliciviruses and astroviruses in diarrhoea calves were much higher than those in healthy calves. Five complete genomic sequences closely related to Smacoviridae have been identified, which may participate in the regulation of the gut virus community ecology of healthy hosts together with bacteriophages. This research provides a theoretical basis for further understanding of known or potential enteric pathogens related to calf diarrhoea.

Viral metagenomic identification of a novel anellovirus in blood sample of a child with atopic dermatitis.

Here, using viral metagenomics, a novel anellovirus with strain name HuAV-zj-ad1 was detected in blood sample from a child with atopic dermatitis. The complete genome sequence of HuAV-zj-ad1 was determined and fully characterized. The circular genome of HuAV-zj-ad1 is 2841 nt in length and includes four polyprotein ORFs. Phylogenetic analysis and pairwise sequence comparisons based on the amino acid sequences of ORF1, ORF2, ORF3, ORF4 indicated that HuAV-zj-ad1 belonged to a novel species within the genus Betatorquevirus. Polymerase chain reaction screening results showed this anellovirus was not present 50 blood samples from normal children. Whether this novel species of anellovirus has association with a certain disease needs further study.

Digging metagenomic data of pangolins revealed SARS-CoV-2 related viruses and other significant viruses.

Pangolin metagenomic data obtained from public databases were used to assemble partial or complete viral genomes showing genetic relationship to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Sendai virus, flavivirus, picornavirus, parvovirus, and genomovirus, respectively. Most of these virus genomes showed genomic recombination signals. Phylogeny based on the SARS-CoV-2-related virus sequences assembled in this study and those recently published indicated that pangolin SARS-CoV-2-related viruses were clustered into two sub-lineages according to geographic sampling sites. These findings suggest the need for further pangolin samples, from different countries, to be collected and analyzed for coronavirus to elucidate whether pangolins are intermittent hosts for SARS-CoV-2.

Multiple novel filamentous phages detected in the cloacal swab samples of birds using viral metagenomics approach.

Members of the family Inoviridae (inoviruses) are characterized by their unique filamentous morphology and infection cycle. The viral genome of inovirus is able to integrate into the host genome and continuously releases virions without lysing the host, establishing chronic infection. A large number of inoviruses have been obtained from microbial genomes and metagenomes recently, but putative novel inoviruses remaining to be identified. Here, using viral metagenomics, we identified four novel inoviruses from cloacal swab samples of wild and breeding birds. The circular genome of those four inoviruses are 6732 to 7709 nt in length with 51.4% to 56.5% GC content and encodes 9 to 13 open reading frames, respectively. The zonula occludens toxin gene implicated in the virulence of pathogenic host bacteria were identified in all four inoviruses and shared the highest amino acid sequences identity (< 37.3%) to other reference strains belonging to different genera of the family Inoviridae and among themselves. Phylogenetic analysis indicated that all the four inoviruses were genetically far away from other strains belonging to the family Inoviridae and formed an independent clade. According to the genetic distance-based criteria, all the four inoviruses identified in the present study respectively belong to four novel putative genera in the family Inoviridae.

Virome analysis of ticks in a forest region of Liaoning, China: characterization of a novel hepe-like virus sequence.

BACKGROUND: Ticks (class Arachnida, subclass Acari) are vectors of transmitting a broad range of pathogenic microorganisms, protozoa, and viruses affecting humans and animals. Liaoning Province is rich in forests where different animals and, abundant Haemaphysalis longicornis ticks exist. METHODS: Using viral metagenomics, we analyzed the virome in 300 Haemaphysalis longicornis ticks collected from June to August 2015 in the forested region of Liaoning Province, China. RESULTS: From the 300 ticks, 1,218,388 high-quality reads were generated, of which 5643 (0.463%) reads showed significant sequence identity to known viruses. Sequence and phylogenetic analysis revealed that viral sequences showing a close relationship with Dabieshan tick virus, Aleutian mink disease virus, adeno-associated virus, Gokushovirus, avian gyrovirus 2 were present in the virome of these ticks. However, the significance of these viruses to human and animal health requires further investigation. Notably, an hepe-like virus, named tick-borne hepe-like virus sequence, was obtained and was highly prevalent in these ticks with a rate of 50%. Nevertheless, one constraint of our study was the limited geographical distribution of the sampled ticks. CONCLUSION: Our study offers an overview of the virome in ticks from a forest region of Liaoning Province and provides further awareness of the viral diversity of ticks.

A novel anellovirus from hospitalized neonates.

Here, using viral metagenomics combined with conventional PCR, the complete genome sequence of a novel anellovirus (named anel-ch-zj and GenBank no. MT157223) from nasopharynx secretion specimens from hospitalized neonates was determined, and the deduced amino acid sequence of its ODF1 protein was found to be only 33.19%-39.33% identical to those of related anelloviruses with sequences available in the GenBank database, suggesting that it represents a putative new genus within the family Anelloviridae. PCR screening of 135 samples (including 45 nasopharynx secretion, 45 blood, and 45 fecal specimens collected from 45 individual hospitalized neonates) indicated that two nasopharynx secretion, two blood, and four fecal samples were positive for anel-ch-zj. Further PCR screening of 50 blood samples, 115 fecal samples, and 396 nasopharynx secretions collected from hospitalized children 1-5 years old did not yield any positive results. Whether this novel anellovirus detected in neonates is associated with specific diseases needs future investigation.

Genomic organization of a Gamma-6 papillomavirus metagenomic discovered from vaginal swab samples of Chinese pregnant women.

A complete genome sequence of human papillomaviruses (HPV) named as HPV-ujs-21015 was determined by viral metagenomic and PCR methods. The complete genome is 7354 bp in length with GC content of 41.7%, of which the genome was predicted to contain six ORFs (Open Reading Frame, ORF) coding for four early proteins (E7, E1, E4, and E2) and two late proteins (L1 and L2). Phylogenetic analysis based on the complete genome and the L1 protein showed that HPV-ujs-21015 belongs to a type 214 member within genus Gamma-6 papillomavirus. It is the first complete genome of Gamma-6 papillomavirus discovered from pregnant women in China.

Viral metagenomics revealed diverse CRESS-DNA virus genomes in faeces of forest musk deer.

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.