Complete genome sequence of an isolate of duck enteritis virus from China.

Here, we present the complete genomic sequence of duck enteritis virus (DEV) strain SD, isolated in China in 2012. The virus was virulent in experimentally infected 2-month-old ducks. The DEV SD genome is 160,945 base pairs (bp) in length. The viral genome sequence, when compared to that of strain DEV CSC, which was isolated in 1962, showed three discontinuous deletions of 101 bp, 48 bp and 417 bp within the inverted repeats. A comparison of the amino acid (aa) sequences of all ORFs of the CSC and SD isolates demonstrated an11-aa deletion, two single-aa deletions, and one single-aa deletion in LORF3, UL47, UL4, respectively. Moreover, 38 single aa variations were also detected in 24 different ORFs. These results will further advance our understanding of the genetic variations involved in evolution.

Detection and genomic characterization of new avian-like hepatitis E virus in a sparrow in the United States.

Hepatitis E virus (HEV) is a nonenveloped, positive-sense, single-stranded RNA virus that has been detected in a wide variety of animals. In 2017, an avian-like HEV was identified in sparrow feces sampled from around a pig farm in the midwestern United States. Sequence analysis revealed that the sparrow isolate represents a novel HEV that is distantly related to chicken and little egret HEVs.

Porcine Astrovirus Type 3 in Central Nervous System of Swine with Polioencephalomyelitis.

Using next-generation sequencing, we identified and genetically characterized a porcine astrovirus type 3 strain found in tissues from the central nervous system of 1 piglet and 3 sows with neurologic signs and nonsuppurative polioencephalomyelitis. Further studies are needed to understand the potential for cross-species transmission and clinical impact.

Construction of a recombinant duck enteritis virus vaccine expressing hemagglutinin of H9N2 avian influenza virus and evaluation of its efficacy in ducks.

H9 subtype avian influenza viruses (AIVs) remain a significant burden in the poultry industry and are considered to be one of the most likely causes of any new influenza pandemic in humans. As ducks play an important role in the maintenance of H9 viruses in nature, successful control of the spread of H9 AIVs in ducks will have significant beneficial effects on public health. Duck enteritis virus (DEV) may be a promising candidate viral vector for aquatic poultry vaccination. In this study, we constructed a recombinant DEV, rDEV-∆UL2-HA, inserting the hemagglutinin (HA) gene from duck-origin H9N2 AIV into the UL2 gene by homologous recombination. One-step growth analyses showed that the HA gene insertion had no effect on viral replication and suggested that the UL2 gene was nonessential for virus growth in vitro. In vivo tests further showed that the insertion of the HA gene in place of the UL2 gene did not affect the immunogenicity of the virus. Moreover, a single dose of 103 TCID50 of rDEV-∆UL2-HA induced solid protection against lethal DEV challenge and completely prevented H9N2 AIV viral shedding. To our knowledge, this is the first report of a DEV-vectored vaccine providing robust protection against both DEV and H9N2 AIV virus infections in ducks.

Complete genomic sequence of a duck enteritis virus attenuated via serial passage in chick embryos.

Here, we present the complete genomic sequence of an attenuated duck enteritis virus (DEV). The Chinese standard challenge strain of DEV (DEV CSC) was serially passaged 20 times in chick embryo fibroblasts and then 85 times in chick embryos. The virus was attenuated and was avirulent to 2-month-old ducks. The attenuated DEV genome is 162,131 base pairs (bp) in length and as long as the parental genomic sequence. There are only 22 nucleotide substitutions, resulting in single amino acid changes in open reading frames LORF5, LORF4, UL41, UL39, UL32, UL13, UL10, UL3, US3, US4 and US7. The genome sequence has been deposited in the GenBank database under accession number KU216226. This study provides genetic information about DEV attenuation and further advances our understanding of the molecular basis of DEV pathogenesis.

Biological properties of a duck enteritis virus attenuated via serial passaging in chick embryo fibroblasts.

To gain a better understanding of the genetic changes required for attenuation of duck enteritis virus (DEV), the Chinese standard challenge strain of DEV (DEV CSC) was serially passaged 80 times in chick embryo fibroblasts. We plaque-purified the virus after the 25th passage (DEV p25) and the 80th passage (DEV p80) and investigated its in vitro and in vivo properties. Average plaque sizes for DEV p25 and p80 were significantly smaller than those for their parental DEV CSC. The results from an in vivo experiment revealed that DEV p25 and p80 were avirulent in ducks and protected them from virulent DEV challenge. The complete genome sequence of DEV p80 was determined and compared with that of the parent virus. An 1801-bp deletion was identified in the genome of DEV p80, which affected the genes encoding gI and gE. Moreover, there were 11 base substitutions, which led to seven amino acid changes in open reading frames LORF9, UL51, UL9, UL7, UL4, ICP4 and US3. Further DNA sequence analysis showed that the 1801-bp deletion was also present in DEV p25. Our findings suggest that DEV gE and/or gI are nonessential for virus growth and might, as with other herpesviruses, play an important role in cell-to-cell spread and virulence. Our experiments provide more genetic information about DEV attenuation and further advance our understanding of the molecular basis of DEV pathogenesis.

Isolation, identification, and whole genome sequencing of reticuloendotheliosis virus from a vaccine against Marek's disease.

According to the requirements of the Ministry of Agriculture of China, all vaccines must be screened for exogenous virus contamination before commercialization. A freeze-dried vaccine against Marek's disease was used to inoculate specific pathogen-free chickens, from which serum samples were collected after 42 days. The results were positive for reticuloendotheliosis virus antibody, which was indicative of reticuloendotheliosis virus contamination. After neutralization with serum positive for Marek's disease virus, chicken embryo fibroblasts were inoculated with the vaccine. Afterward, viral isolation and identification were performed. One reticuloendotheliosis virus strain (MD-2) was isolated and verified using an immunofluorescence assay. Polymerase chain reaction amplification of the provirus MD-2 genome was performed using seven overlapping fragments as primers. The amplified products were sequenced and spliced to obtain the whole MD-2 genome sequence. The full genome length of MD-2 was 8,284 bp, which had an identity greater than 99% with the prairie chicken isolate APC-566 from the US, the goose-derived isolate 3410/06 from Taiwan, and the chicken-derived reticuloendotheliosis virus isolate HLJR0901 from Heilongjiang Province, China. The MD-2 was phylogenetically close to these isolates. The identity with REV isolate HA9901 from Jiangsu Province of China was 96.7%. The MD-2 had the lowest identity with duck-derived Sin Nombre virus from the United States, with the value of only 93.5%. The main difference lay in the U3 region of the long terminal repeat. The present research indicated that some vaccines produced during specific periods in China might be contaminated by reticuloendotheliosis virus. The reticuloendotheliosis virus strain isolated from the vaccine was phylogenetically close to the prevalent strain, with only minor variations.

Comparative genomic sequence analysis between a standard challenge strain and a vaccine strain of duck enteritis virus in China.

Here, we present the complete genomic sequence of the Chinese standard challenge strain (CSC) of duck enteritis virus (DEV), which was isolated in China in 1962. The DEV CSC genome is 162,131 bp long and contains 78 predicted open reading frames (ORFs). Comparison of the genomic sequences of DEV CSC and DEV live vaccine strain K at passage 63 (DEV K p63) revealed that the DEV CSC genome is 4,040 bp longer than the DEV K p63 genome, mainly because of 3,513-bp and 528-bp insertions at the 5' and 3' ends of the unique long segment, respectively. At the nucleotide level, 63 of the 76 ORFs in the DEV CSC genome were 100 % identical to the ORFs in the DEV K p63 genome. Two ORFs (UL56 and US10) had frameshift mutations in the C-terminal regions, while LORF5 was unique to the DEV K p63 genome. It is difficult to assign attenuated virulence to changes in specific genes. However, the complete DEV CSC genome will further advance our understanding of the genes involved in virulence and evolution. The DEV CSC genome sequence has been deposited in GenBank under accession number JQ673560.

Functional divergence of oligoadenylate synthetase 1 (OAS1) proteins in Tetrapods.

OASs play critical roles in immune response against virus infection by polymerizing ATP into 2-5As, which initiate the classical OAS/RNase L pathway and induce degradation of viral RNA. OAS members are functionally diverged in four known innate immune pathways (OAS/RNase L, OASL/IRF7, OASL/RIG-I, and OASL/cGAS), but how they functionally diverged is unclear. Here, we focus on evolutionary patterns and explore the link between evolutionary processes and functional divergence of Tetrapod OAS1. We show that Palaeognathae and Primate OAS1 genes are conserved in genomic and protein structures but differ in function. The former (i.e., ostrich) efficiently synthesized long 2-5A and activated RNase L, while the latter (i.e., human) synthesized short 2-5A and did not activate RNase L. We predicted and verified that two in-frame indels and one positively selected site in the active site pocket contributed to the functional divergence of Palaeognathae and Primate OAS1. Moreover, we discovered and validated that an in-frame indel in the C-terminus of Palaeognathae OAS1 affected the binding affinity of dsRNA and enzymatic activity, and contributed to the functional divergence of Palaeognathae OAS1 proteins. Our findings unravel the molecular mechanism for functional divergence and give insights into the emergence of novel functions in Tetrapod OAS1.

Comparative efficacy evaluation of different CSF vaccines in pigs with CSF maternally derived antibodies.

Classical swine fever (CSF) is a highly contagious and important swine disease in China. Sporadic outbreaks with mild clinical signs are still being reported despite massive vaccination with the CSF C-strain vaccine. One possible reason for vaccine failure could be interference from maternally derived antibodies (MDAs) during vaccination in the field. The aim of this study was to evaluate the efficacy of different CSF vaccines in the presence of MDAs and to assess the different vaccination schemes in the field. The results demonstrated that vaccination with a single dose of C-strain-PK vaccine protected pigs against severe clinical signs and significantly reduced viremia. The impact of MDAs was negligible. The interference was also mild during a prime and boost vaccination scheme using the C-strain-ST vaccine. In contrast, a significant influence of MDAs on the efficacy of the subunit E2 vaccine in a one-dose vaccination scheme was observed, with pigs showing severe clinical signs, CSF-associated death, typical pathological lesions and a high level of viremia after challenge, despite robust E2 antibody induction. A field vaccination and challenge study further confirmed the superior effectiveness of a single dose of C-strain-PK vaccine in the presence of MDAs in comparison to a routine prime and boost vaccination scheme applied in the field, with pigs having fever, chronic signs, significant viremia and shedding after challenge. Delaying the vaccination time from the age of 28 days to 45 days, when MDA was low, was beneficial for improving the clinical protection and immunity induced by vaccines. Altogether, the results presented here emphasize that a high-quality vaccine and a scientific design of the vaccination scheme based on serological surveillance are essential pillars to control and eliminate CSF in China.

The whole genome analysis for the first human infection with H10N3 influenza virus in China.

A strain of H10N3 influenza virus, A/Jiangsu/428/2021/H10N3, was isolated from patient in Jiangsu province, eastern China. Phylogenetic analysis illustrated this human H10N3 virus was a low pathogenic avian-origin recombinant virus with HA and NA genes from H10N3 viruses and the other six internal genes from H9N2 viruses. To date, this is the first report of interspecies transmission of an avian H10N3 influenza virus to human.

Case Report and Genomic Characterization of a Novel Porcine Nodavirus in the United States.

Nodaviruses are small bisegmented RNA viruses belonging to the family Nodaviridae. Nodaviruses have been identified in different hosts, including insects, fishes, shrimps, prawns, dogs, and bats. A novel porcine nodavirus was first identified in the United States by applying next-generation sequencing on brain tissues of pigs with neurological signs, including uncontrollable shaking. RNA1 of the porcine nodavirus had the highest nucleotide identity (51.1%) to the Flock House virus, whereas its RNA2 shared the highest nucleotide identity (48%) with the RNA2 segment of caninovirus (Canine nodavirus). Genetic characterization classified porcine nodavirus as a new species under the genus Alphanodavirus. Further studies are needed to understand the pathogenicity and clinical impacts of this virus.

Different clinical presentations of subgenotype 2.1 strain of classical swine fever infection in weaned piglets and adults, and long-term cross-protection conferred by a C-strain vaccine.

Classical swine fever is an important swine disease in China, and sporadic outbreaks with mild clinical signs despite compulsory vaccination have raised questions about the virulence and pathogenicity of prevalent subgenotype 2.1 strains, and the ability of C-strain vaccines to cross-protect against them. To investigate this, three field isolates were evaluated in experimentally infected piglets and compared with the highly virulent reference Shimen strain. Clinical signs for the field strains ranged from mild to severe, and mortality ranged from 0 to 80 %. These data show differences in virulence among the subgenotype 2.1 field isolates and support the use of field strain GD191 as a genotype 2 challenge virus to assess efficacy of C-strain vaccines. In contrast to the historical genotype 1 strain, which caused acute infection with significant virus shedding in non-vaccinated animals, the subgenotype 2.1 GD191 strain produced different clinical manifestations in weaned piglets and adults. Adult pigs showed subclinical infection with viral shedding, whereas weaned piglets showed overt signs of infection. Efficacy of, and duration of immunity conferred by a C-strain vaccine were assessed using the reference Shimen strain and field isolate GD191 at 12 and 15 months after vaccination. A robust antibody response and sterilising protection were seen in all vaccinated animals and lasted up to 15 months post-vaccination. This study confirms that C-strain vaccines confer both clinical and virological protection against the historical genotype 1 Shimen strain and cross-protection against the prevalent genotype 2 field strain.

Preparation and Application of Organic-Inorganic Nanocomposite Materials in Stretched Organic Thin Film Transistors.

High-transparency soluble polyimide with COOH and fluorine functional groups and TiO2-SiO2 composite inorganic nanoparticles with high dielectric constants were synthesized in this study. The polyimide and inorganic composite nanoparticles were further applied in the preparation of organic-inorganic hybrid high dielectric materials as the gate dielectric for a stretchable transistor. The optimal ratio of organic and inorganic components in the hybrid films was investigated. In addition, Jeffamine D2000 and polyurethane were added to the gate dielectric to improve the tensile properties of the organic thin film transistor (OTFT) device. PffBT4T-2OD was used as the semiconductor layer material and indium gallium liquid alloy as the upper electrode. Electrical property analysis demonstrated that the mobility could reach 0.242 cm2·V-1·s-1 at an inorganic content of 30 wt.%, and the switching current ratio was 9.04 × 103. After Jeffamine D2000 and polyurethane additives were added, the mobility and switching current could be increased to 0.817 cm2·V-1·s-1 and 4.27 × 105 for Jeffamine D2000 and 0.562 cm2·V-1·s-1 and 2.04 × 105 for polyurethane, respectively. Additives also improved the respective mechanical properties. The stretching test indicated that the addition of polyurethane allowed the OTFT device to be stretched to 50%, and the electrical properties could be maintained after stretching 150 cycles.

Identification, Genetic Analysis, and Pathogenicity of Classical Swine H1N1 and Human-Swine Reassortant H1N1 Influenza Viruses from Pigs in China.

Swine influenza virus causes a substantial disease burden to swine populations worldwide and poses an imminent threat to the swine industry and humans. Given its importance, we characterized two swine influenza viruses isolated from Shandong, China. The homology and phylogenetic analyses showed that all eight gene segments of A/swine/Shandong/AV1522/2011(H1N1) were closely related to A/Maryland/12/1991(H1N1) circulating in North America. The HA, NA, M, and NS genes of the isolate were also confirmed to have a high homology to A/swine/Hubei/02/2008(H1N1) which appeared in China in 2008, and the virus was clustered into the classical swine lineage. The gene segments of A/swine/Shandong/AV1523/2011(H1N1) were highly homologous to the early human H1N1 and H2N2 influenza viruses, except for the HA gene, and the virus was a reassortant H1N1 virus containing genes from the classical swine (HA) and human (NA, PB2, PB1, PA, NP, M, and NS) lineages. Both the viruses could cause lethal infection and replicate efficiently in the lungs, brains, spleens, and kidneys of mice. Histopathological examinations showed that AV1522 and AV1523 viruses caused a spectrum of marked pneumonia and meningoencephalitis according to the duration of infection, demonstrating a progression of respiratory disease and neurological disease over the course of infection that ultimately resulted in lethality for the infected mice. The changes in the pathogenicity of swine influenza viruses to mammals, accompanied with the continuous reassortment and evolution of the viruses, highlights the importance of ongoing epidemiological investigation.

Genetic Characteristics and Pathogenicity Analysis in Chickens and Mice of Three H9N2 Avian Influenza Viruses.

H9N2 avian influenza is a remarkable disease that has circulated in domestic poultry in large regions of China and posed a serious threat to the poultry industry. The H9N2 virus can not only infect mammals directly, but also provide gene segments to generate novel, but lethal human reassortants. Therefore, it is important to study the evolution, pathogenicity, and transmission of the H9N2 virus. In this study, three H9N2 viruses isolated from chickens in different layer farms were identified. Phylogenetic analysis revealed that these H9N2 viruses were all multiple genotype reassortants, with genes originating from Y280-like, F/98-like, and G1-like viruses. Animal studies indicated that the AV1535 and AV1548 viruses replicated efficiently in the lungs, tracheas, spleens, kidneys, and brains of chickens; the viruses shed for at least 11 days post-inoculation (DPI) and were transmitted efficiently among contact chickens. The AV1534 virus replicated poorly in chickens, shed for 7 DPI, and were not transmitted efficiently among contact chickens. The AV1534 virus replicated well in mice lungs and caused about 2% weight loss. The AV1535 and AV1548 viruses were not able to replicate in the lungs of mice. Our results indicate that we should pay attention to H9N2 avian influenza virus surveillance in poultry and changes in the pathogenicity of them to mammals.

Phylogeny, Pathogenicity, Transmission, and Host Immune Responses of Four H5N6 Avian Influenza Viruses in Chickens and Mice.

H5Nx viruses have continuously emerged in the world, causing poultry industry losses and posing a potential public health risk. Here, we studied the phylogeny, pathogenicity, transmission, and immune response of four H5N6 avian influenza viruses in chickens and mice, which were isolated from waterfowl between 2013 and 2014. Their HA genes belong to Clade 2.3.4.4, circulated in China since 2008. Their NA genes fall into N6-like/Eurasian sublineage. Their internal genes originated from different H5N1 viruses. The results suggested that the four H5N6 viruses were reassortants of the H5N1 and H6N6 viruses. They cause lethal infection with high transmission capability in chickens. They also cause mild to severe pathogenicity in mice and can spread to the brain through the blood-brain barrier. During the infection, the viruses result in the up-regulation of PRRs and cytokine in brains and lungs of chickens and mice. Our results suggested that the high viral loads of several organs may result in disease severity in chickens and mice; there were varying levels of cytokines induced by the H5N6 viruses with different pathogenicity in chickens and mice.

Development of a Hemagglutination Inhibition Assay for Duck Tembusu Virus.

The HB strain of duck Tembusu virus (DTMUV) propagated in the brains of newborn mice was used to prepare antigens for use in the hemagglutination inhibition (HI) test. Results showed that such prepared antigens are highly specific to the serum samples derived from DTMUV-infected animals. No spurious hemagglutination reactions against serum samples specific to avian influenza virus H5, H7, H9 subtypes, Newcastle disease virus, egg drop syndrome virus, duck plague virus, and duck hepatitis A virus were observed. The HI test can detect specific antibodies in the serum samples as early as day 4 after experimental infection of ducks with DTMUV. When compared to a virus neutralization test, the sensitivity is 100%. Overall, the HI test developed is highly specific to DTMUV and can be used in clinical diagnosis of diseases and in vaccine studies to monitor the kinetics of antibody response.

Desarrollo de un ensayo de inhibición de la hemaglutinación para el virus Tembusu del pato. La cepa HB del virus Tembusu del pato (DTMUV) propagada en el cerebro de ratones recién nacidos se usó para preparar antígenos para su uso en la prueba de inhibición de la hemaglutinación (HI). Los resultados mostraron que tales antígenos preparados son altamente específicos para las muestras de suero derivadas de animales infectados con el virus Tembusu del pato. No se observaron reacciones inespecíficas de hemaglutinación con muestras de suero específicas para el virus de la influenza aviar subtipos H5, H7 y H9, virus de la enfermedad de Newcastle, virus del síndrome de baja de postura, virus de la enteritis viral del pato y virus de la hepatitis A del pato. La prueba de inhibición de la hemaglutinación puede detectar anticuerpos específicos en las muestras de suero desde el día cuatro después de la infección experimental de patos con el virus Tembusu. Cuando se comparó con una prueba de neutralización viral, la sensibilidad es del 100%. En general, la prueba de inhibición de la hemaglutinación desarrollada es altamente específica para el virus Tembusu y se puede utilizar en el diagnóstico clínico de enfermedades y en estudios de vacunas para controlar la cinética de la respuesta de anticuerpos.

Broad-spectrum antiviral functions of duck interferon-induced protein with tetratricopeptide repeats (AvIFIT).

Mammalian interferon-induced proteins with tetratricopeptide repeats (IFITs) play important roles in many cellular processes and host innate immune response to viruses. However, the functions of IFIT proteins in birds are largely unknown. Here, we first describe that the only one avian IFIT protein is orthologous to ancestor of mammalian IFITs. We find that the predicted structure of duck AvIFIT protein is similar to that of human IFIT5. We also find that duck AvIFIT protein shows antiviral activity to a broad range of specific RNA and DNA viruses like mammalian IFIT proteins. Further analysis indicates that overexpression of duck AvIFIT protein in DF1 cells leads to a remarkable accumulation of cells at G1/S transition associated with growth arrest and may promote apoptosis. Moreover, duck AvIFIT binds to nucleoprotein (NP) of H5N1 influenza virus and upregulates the expression of genes involving the IFN pathway in DF1 cells. In summary, our findings support that duck AvIFIT protein plays critical role in host immune response to viruses, at least H5N1 virus, through affecting function of viral NP protein, magnifying the IFN signaling and arresting cell growth.

Molecular Mechanisms for the Adaptive Switching Between the OAS/RNase L and OASL/RIG-I Pathways in Birds and Mammals.

Host cells develop the OAS/RNase L [2'-5'-oligoadenylate synthetase (OAS)/ribonuclease L] system to degrade cellular and viral RNA, and/or the OASL/RIG-I (2'-5'-OAS like/retinoic acid inducible protein I) system to enhance RIG-I-mediated IFN induction, thus providing the first line of defense against viral infection. The 2'-5'-OAS-like (OASL) protein may activate the OAS/RNase L system using its typical OAS-like domain (OLD) or mimic the K63-linked pUb to enhance antiviral activity of the OASL/RIG-I system using its two tandem ubiquitin-like domains (UBLs). We first describe that divergent avian (duck and ostrich) OASL inhibit the replication of a broad range of RNA viruses by activating and magnifying the OAS/RNase L pathway in a UBL-dependent manner. This is in sharp contrast to mammalian enzymatic OASL, which activates and magnifies the OAS/RNase L pathway in a UBL-independent manner, similar to 2'-5'-oligoadenylate synthetase 1 (OAS1). We further show that both avian and mammalian OASL can reversibly exchange to activate and magnify the OAS/RNase L and OASL/RIG-I system by introducing only three key residues, suggesting that ancient OASL possess 2-5A [px5'A(2'p5'A)n; x = 1-3; n ≥ 2] activity and has functionally switched to the OASL/RIG-I pathway recently. Our findings indicate the molecular mechanisms involved in the switching of avian and mammalian OASL molecules to activate and enhance the OAS/RNase L and OASL/RIG-I pathways in response to infection by RNA viruses.