The genomic constellation of a novel avian orthoreovirus strain associated with runting-stunting syndrome in broilers

Diagnostic investigation of avian reovirus field variants circulating in broiler chickens in Pennsylvania of United States between 2017 and 2022

Avian reovirus (ARV) has been continuously affecting the poultry industry in Pennsylvania (PA) in recent years. This report provides our diagnostic investigation on monitoring ARV field variants from broiler chickens in Pennsylvania. Genomic characterization findings of 72 ARV field isolates obtained from broiler cases during the last 6 years indicated that six distinct cluster variant strains (genotype I-VI), which were genetically diverse and distant from the vaccine and vaccine-related field strains, continuously circulated in PA poultry. Most of the variants clustered within genotype V (24/72, 33.3%), followed by genotype II (16/72, 22.2%), genotype IV (13/72, 18.1%), genotype III (13/72, 18.1%), genotype VI (05/72, 6.94%), and genotype I (1/72, 1.38%). The amino acid identity between 72 field variants and the vaccine strains (1133, 1733, 2408, 2177) varied from 45.3% to 99.7%, while the difference in amino acid counts ranged from 1-164. Among the field variants, the amino acid identity and count difference ranged from 43.3% to 100% and 0 to 170, respectively. Variants within genotype V had maximum amino acid identity (94.7-100%), whereas none of the variants within genotypes II and VI were alike. These findings indicate the continuing occurrence of multiple ARV genotypes in the environment.

Advancement of Autogenous Vaccines in the Poultry Industry

Autogenous vaccines, also known as "custom" vaccines, have become an essential instrument in the production veterinarian's toolbox for the control of emerging and evolving diseases. Autogenous vaccines require a reduced burden of U.S. Department of Agriculture licensing, making them rapidly accessible. Autogenous vaccines have made significant advancements in the ability to reduce disease within the poultry industry from a combination of several different advancements in regulation requirements, rapid and accurate diagnostic assessments, and improvements in manufacturing. The use of autogenous vaccines by poultry health professionals has also increased, and these custom-made products have been instrumental in combating diseases resulting from antigenic variants such as salmonellosis, colibacillosis, infectious coryza, infectious bursal disease, inclusion body hepatitis, viral enteritis, and viral arthritis and tenosynovitis.

Co-circulation of multiple genotypes of ARV in poultry in Anhui, China

ABSTRACTPoultry production in China has been experiencing a high incidence of broiler arthritis /tenosynovitis caused by avian orthoreovirus (ARV) since 2013. In the spring of 2020 severe arthritis cases from broiler flocks were identified in a large-scale commercial poultry company in Anhui Province, China. Diseased organs from dead birds were sent for diagnosis to our laboratory. ARVs, including seven broiler-isolates and two breeder-isolates, were successfully harvested and sequenced. Interestingly, the genotypes of ARVs isolated from infected chickens were inconsistent between different flocks, or even between different houses on the same flocks. Pathogenicity testing in chicks confirmed that the seven broiler-isolates were pathogenic strains, which could cause arthritis in infected chickens. Subsequently, a total of 89.66% serum samples collected from apparently healthy adult broiler flocks not vaccinated against ARV tested positive for ARV antibodies, suggesting that low and high virulence reovirus strains may be co-circulating in the farm. To this end, we collected dead embryos of unhatched chicken eggs for pathogen tracing, and the two ARV breeder-isolates isolated indicated that vertical transmission from breeders to progeny should not be underestimated for the prevalence of ARV within broiler flocks. The findings have implications for the evidenced-based formulation of prevention and control strategies.

Whole Genomic Constellation of Avian Reovirus Strains Isolated from Broilers with Arthritis in North Carolina, USA

Avian reovirus (ARV) is an emerging pathogen which causes significant economic challenges to the chicken and turkey industry in the USA and globally, yet the molecular characterization of most ARV strains is restricted to a single particular gene, the sigma C gene. The genome of arthrogenic reovirus field isolates (R18-37308 and R18-38167), isolated from broiler chickens in North Carolina (NC), USA in 2018, was sequenced using long-read next-generation sequencing (NGS). The isolates were genotyped based on the amino acid sequence of sigma C (σC) followed by phylogenetic and amino acid analyses of the other 11 genomically encoded proteins for whole genomic constellation and genetic variation detection. The genomic length of the NC field strains was 23,494 bp, with 10 dsRNA segments ranging from 3959 bp (L1) to 1192 bp (S4), and the 5' and 3' untranslated regions (UTRs) of all the segments were found to be conserved. R18-37308 and R18-38167 were found to belong to genotype (G) VI based on the σC analysis and showed nucleotide and amino acid sequence identity ranging from 84.91-98.47% and 83.43-98.46%, respectively, with G VI strains. Phylogenetic analyses of individual genes of the NC strains did not define a single common ancestor among the available completely sequenced ARV strains. Nevertheless, most sequences supported the Chinese strain LY383 as a probable ancestor of these isolates. Moreover, amino acid analysis revealed multiple amino acid substitution events along the entirety of the genes, some of which were unique to each strain, which suggests significant divergence owing to the accumulation of point mutations. All genes from R18-37308 and R18-38167 were found to be clustered within genotypic clusters that included only ARVs of chicken origin, which negates the possibility of genetic pooling or host variation. Collectively, this study revealed sequence divergence between the NC field strains and reference ARV strains, including the currently used vaccine strains could help updating the vaccination regime through the inclusion of these highly divergent circulating indigenous field isolates.

A Novel Variant of Avian Reovirus Is Pathogenic to Vaccinated Chickens

Avian reovirus (ARV) infections, characterized by severe arthritis, tenosynovitis, pericarditis, and poor weight gain, have become increasingly serious in recent years. The economic impact is significant as it causes growth inhibition and immunosuppression. Some commercial poultry in China have been widely vaccinated with available ARV vaccines; however, infections continue to occur even after vaccination. This study aimed to isolate a novel variant, ARV-SD19/11103, from the joint tissues of infected broiler chickens vaccinated with ARV vaccines in Shandong Province. Genetic evolution analysis of the major protective antigen σC gene in ARVs showed that ARV-SD19/11103 was located in the genotype cluster I but not in the same sub-cluster as the S1133 vaccine strain. The amino acid sequence similarity between SD19/11103 and vaccine strains S1133, 1733, and 2408 was <80%. After analyzing the amino acid sequences of the σC protein, 33 amino acid differences were found between the new variant isolate and the vaccine strains. This novel variant showed obvious pathogenicity in specific pathogen-free chicken embryos and chicks and could cause serious disease in chickens vaccinated with commercially available ARV vaccines. Cross-neutralization experiments further demonstrated a significant antigenic difference between the novel variant and genotype cluster I ARV strains. The novel variant strain isolated in this study provides an important theoretical basis for understanding the prevalence and genetic evolutionary characteristics of ARV variant strains in our country. This study identified the causes of ARVs circulating and emphasizes the needs for developing new vaccines against novel ARV variants.

Molecular characterization of emerging chicken and turkey parvovirus variants and novel strains in Guangxi, China

Avian parvoviruses cause several enteric poultry diseases that have been increasingly diagnosed in Guangxi, China, since 2014. In this study, the whole-genome sequences of 32 strains of chicken parvovirus (ChPV) and 3 strains of turkey parvovirus (TuPV) were obtained by traditional PCR techniques. Phylogenetic analyses of 3 genes and full genome sequences were carried out, and 35 of the Guangxi ChPV/TuPV field strains were genetically different from 17 classic ChPV/TuPV reference strains. The nucleotide sequence alignment between ChPVs/TuPVs from Guangxi and other countries revealed 85.2-99.9% similarity, and the amino acid sequences showed 87.8-100% identity. The phylogenetic tree of these sequences could be divided into 6 distinct ChPV/TuPV groups. More importantly, 3 novel ChPV/TuPV groups were identified for the first time. Recombination analysis with RDP 5.0 revealed 15 recombinants in 35 ChPV/TuPV isolates. These recombination events were further confirmed by Simplot 3.5.1 analysis. Phylogenetic analysis based on full genomes showed that Guangxi ChPV/TuPV strains did not cluster according to their geographic origin, and the identified Guangxi ChPV/TuPV strains differed from the reference strains. Overall, whole-genome characterizations of emerging Guangxi ChPV and TuPV field strains will provide more detailed insights into ChPV/TuPV mutations and recombination and their relationships with molecular epidemiological features.

Genetic diversity among reptilian orthoreoviruses isolated from pet snakes and lizards

Reovirus infections in reptiles are frequently detected and associated with various clinical diseases; yet, our knowledge about their genetic diversity and evolutionary relationships remains limited. In this study, we characterize at the genomic level five reptile origin orthoreovirus strains isolated from exotic snakes and lizards in Hungary and Germany. The genomic organization of the study strains was similar to that of the representative strains of reptile origin reoviruses belonging to species Reptilian orthoreovirus and Testudine orthoreovirus. Additionally, all five study strains clustered with the bush viper origin reference Reptilian orthoreovirus strain, 47/02. The nucleotide sequence divergence among strains fell from 56.64 to 99.36%. Based on genome segment constellations two well separated groups were observed, which may represent two genetic lineages of reptilian orthoreoviruses we tentatively referred here as genogroups, classifying two squamata origin strains with available whole genome sequences into genogroup I (GGI) and four strains into genogroup II (GGII). The representative GGI and GGII Reptilian orthoreovirus strains are characterized by moderate-to-high nucleotide and amino acid similarities within genogroups (range, 69.45 to 99.36% and 74.64 to 100.00%), whereas lower nucleotide and amino acid similarities (range, 56.64 to 77.24% and 54.53 to 93.85%) and different structures of the bicistronic S1 segment were found between genogroups. Further studies are needed to explore the genomic diversity among reptilian reoviruses of squamata origin; this would be critical to establish a robust classification system for these viruses and to see if interaction among members of distinct lineages may result in viable progenies with novel genetic features.

Identification of the main genetic clusters of avian reoviruses from a global strain collection

Introduction

Avian reoviruses (ARV), an important pathogen of poultry, have received increasing interest lately due to their widespread occurrence, recognized genetic diversity, and association to defined disease conditions or being present as co-infecting agents. The efficient control measures require the characterization of the available virus strains.

Methods

The present study describes an ARV collection comprising over 200 isolates from diagnostic samples collected over a decade from 34 countries worldwide. One hundred and thirty-six ARV isolates were characterized based on σC sequences.

Results and discussion

The samples represented not only arthritis/tenosynovitis and runting-stunting syndrome, but also respiratory symptoms, egg production problems, and undefined disease conditions accompanied with increased mortality, and were obtained from broiler, layer or breeder flocks. In 31 percent of the cases other viral or bacterial agents were demonstrated besides ARV. The most frequent co-infectious agent was infectious bronchitis virus followed by infectious bursal disease virus and adenoviruses. All isolates could be classified in one of the major genetic clusters, although we observed marked discrepancies in the genotyping systems currently in use, a finding that made genotype assignment challenging. Reovirus related clinical symptoms could not be unequivocally connected to any particular virus strains belonging to a specific genetic group, suggesting the lack of strict association between disease forms of ARV infection and the investigated genetic features of ARV strains. Also, large genetic differences were seen between field and vaccine strains. The presented findings reinforce the need to establish a uniform, widely accepted molecular classification scheme for ARV and further, highlight the need for ARV strain identification to support more efficient control measures.

Molecular and pathological investigation of avian reovirus (ARV) in Egypt with the assessment of the genetic variability of field strains compared to vaccine strains

Avian orthoreovirus (ARV) is among the important viruses that cause drastic economic losses in the Egyptian poultry industry. Despite regular vaccination of breeder birds, a high prevalence of ARV infection in broilers has been noted in recent years. However, no reports have revealed the genetic and antigenic characteristics of Egyptian field ARV and vaccines used against it. Thus, this study was conducted to detect the molecular nature of emerging ARV strains in broiler chickens suffering from arthritis and tenosynovitis in comparison to vaccine strains. Synovial fluid samples (n = 400) were collected from 40 commercial broiler flocks in the Gharbia governorate, Egypt, and then pooled to obtain 40 samples, which were then used to screen ARV using reverse transcriptase polymerase chain reaction (RT-PCR) with the partial amplification of ARV sigma C gene. The obtained RT-PCR products were then sequenced, and their nucleotide and deduced amino acid sequences were analyzed together with other ARV field and vaccine strains from GenBank. RT-PCR successfully amplified the predicted 940 bp PCR products from all tested samples. The phylogenetic tree revealed that the analyzed ARV strains were clustered into six genotypic clusters and six protein clusters, with high antigenic diversity between the genotypic clusters. Surprisingly, our isolates were genetically different from vaccine strains, which aligned in genotypic cluster I/protein cluster I, while our strains were aligned in genotypic cluster V/protein cluster V. More importantly, our strains were highly divergent from vaccine strains used in Egypt, with 55.09-56.23% diversity. Sequence analysis using BioEdit software revealed high genetic and protein diversity between our isolates and vaccine strains (397/797 nucleotide substitutions and 148-149/265 amino acid substitutions). This high genetic diversity explains the vaccination failure and recurrent circulation of ARV in Egypt. The present data highlight the need to formulate a new effective vaccine from locally isolated ARV strains after a thorough screening of the molecular nature of circulating ARV in Egypt.

Isolation and Molecular Characteristics of a Novel Recombinant Avian Orthoreovirus From Chickens in China

In recent years, the emergence of avian orthoreovirus (ARV) has caused significant losses to the poultry industry worldwide. In this study, a novel ARV isolate, designated as AHZJ19, was isolated and identified from domestic chicken with viral arthritis syndrome in China. AHZJ19 can cause typical syncytial cytopathic effect in the chicken hepatocellular carcinoma cell line, LMH. High-throughput sequencing using Illumina technology revealed that the genome size of AHZJ19 is about 23,230 bp, which codes 12 major proteins. Phylogenetic tree analysis found that AHZJ19 was possibly originated from a recombination among Hungarian strains, North American strains, and Chinese strains based on the sequences of the 12 proteins. Notably, the σC protein of AHZJ19 shared only about 50% homology with that of the vaccine strains S1133 and 1733, which also significantly differed from other reported Chinese ARV strains. The isolation and molecular characteristics of AHZJ19 provided novel insights into the molecular epidemiology of ARV and laid the foundation for developing efficient strategies for control of ARV in China.

Metagenomic sequencing determines complete infectious bronchitis virus (avian Gammacoronavirus) vaccine strain genomes and associated viromes in chicken clinical samples

Infectious bronchitis virus (IBV, genus Gammacoronavirus) causes an economically important and highly contagious disease in chicken. Random primed RNA sequencing was applied to two IBV positive clinical samples and one in ovo-passaged virus. The virome of a cloacal swab pool was dominated by IBV (82% of viral reads) allowing de novo assembly of a GI-13 lineage complete genome with 99.95% nucleotide identity to vaccine strain 793B. In addition, substantial read counts (16% of viral reads) allowed the assembly of a near-complete chicken astrovirus genome, while lower read counts identified the presence of chicken calicivirus and avian leucosis virus. Viral reads in a respiratory/intestinal tissue pool were distributed between IBV (22.53%), Sicinivirus (Picornaviridae, 24%), and avian leucosis virus (37.04%). A complete IBV genome with 99.95% nucleotide identity to vaccine strain H120 (lineage GI-1), as well as a near-complete avian leucosis virus genome and a partial Sicinivirus genome were assembled from the tissue sample data. Lower read counts identified chicken calicivirus, Avibirnavirus (infectious bursal disease virus, assembling to 98.85% of segment A and 69.66% of segment B closely related to D3976/1 from Germany, 2017) and avian orthoreovirus, while three avian orthoavulavirus 1 reads confirmed prior real-time RT-PCR result. IBV sequence variation analysis identified both fixed and minor frequency variations in the tissue sample compared to its in ovo-passaged virus. Metagenomic methods allow the determination of complete coronavirus genomes from clinical chicken samples while providing additional insights in RNA virus sequence diversity and coinfecting viruses potentially contributing to pathogenicity.

Seroprevalence and risk factors of avian reovirus in backyard chickens in different areas of Mymensingh district in Bangladesh

Objective:

The present study estimated the seroprevalence of avian reovirus (ARV) infections in backyard chickens of the Mymensingh district in Bangladesh.

Materials and Methods:

Considering several risk factors, a total of 460 serum samples were collected from backyard chickens from eight Upazilas of the Mymensingh district in Bangladesh. Blood samples were taken from the wing vein using 3-ml sterile syringes and kept at room temperature for clotting in a slanting position and then transported to the laboratory maintaining the cool chain. Subsequently, the prepared sera were harvested and stored at −20°C until used. Finally, an indirect enzyme-linked immunosorbent assay (ELISA) was performed to detect ARVspecific antibodies using a commercial ARV antibody detection ELISA test kit.

Results:

The results revealed high prevalence rates of ARV antibodies, with a total seroprevalence of 69.78% (321/460). Area-wise, 74.55% (82/110) seroprevalence was recorded as the highest in Mymensingh Sadar, whereas 64% (32/50) was the lowest in Gauripur Upazila. With regard to sex, female chickens showed a significantly higher (p < 0.05) seroprevalence as 90.33% (271/300) compared to male chickens 31.25% (50/160). With regard to age groups, the seroprevalence of ARV infection was 59.33% (89/150) within 2–8 weeks, 82% (205/250) within 9–16 weeks, and 45% (27/60) within 17–20 weeks, respectively. Based on hygienic conditions, the highest seroprevalence of ARV was noted in backyard chickens housed in poor conditions 80% (120/150) than good conditions 50% (40/80). Backyard chickens reared in free-ranging conditions exhibited a significantly higher seroprevalence 73.33% (220/300) of ARV antibodies compared to rearing in separate houses 63.12% (101/160). The seroprevalence of ARV was higher in crossbreeds 71.67% (43/60), brought from market 76% (38/50), and unhealthy 78.57% (55/70) backyard chickens than non-descriptive indigenous 69.5% (278/400), home-reared 69.02% (283/410), and healthy chickens 68.21% (266/390).

Conclusion:

The high prevalence of ARV antibodies revealed in the current study indicates an extensive exposure of ARV to backyard chickens in Bangladesh that may be transmitted naturally to other chickens, ultimately leading to ominous economic effects on the poultry sector.

Interaction between Translocation-associated membrane protein 1 and σC protein of novel duck reovirus controls virus infectivity

Novel duck reovirus (NDRV), the prototype strain of the species Avian orthoreovirus (ARV), is associated with high mortality in Pekin ducklings. σC is an outer capsid protein encoded by the S1 genome segment of NDRV which mediates attachment to host cells. Our previous studies using immunoprecipitation and mass spectrometry found that σC coprecipitated with some host proteins including Translocation-associated membrane protein 1 (TRAM1). However, the interaction between σC and TRAM1 has not been further confirmed experimentally. In this study, we utilized coimmunoprecipitation assays, glutathione S-transferase pull-down, and confocal microscopy to confirm the interaction between σC and TRAM1. In addition, knockdown of TRAM1 using siRNA and overexpression of TRAM1 gene were conducted to explore its effect on virus replication. The result showed that TRAM1 silencing benefits while overexpression inhibits viral replication. This study confirms the important role TRAM1 during NDRV infection which can help develop new approaches for NDRV disease prevention and control.

Genetic and pathogenic characteristics of newly emerging avian reovirus from infected chickens with clinical arthritis in China

In recent years, emerging avian reovirus (ARV) strains causing viral arthritis have become a challenge to the worldwide chicken industry, and were responsible for significant economic losses. In this study, we characterized emerging variant ARV strains and examined their genetic relationship and pathogenicity variation with reference strains. A total of 18 emerging variant ARV strains were isolated from tendon and capsular synovial fluid of broiler chickens with clinical cases of arthritis/tenosynovitis at commercial farms in China. Comparative analysis based on σC sequence showed that 4/18 isolates were in the same cluster (Cluster 1) as vaccine strains (S1133), whereas 14 of 18 isolates were in Clusters 2, 3, and 6. The field isolates shared a rather low identity (38.1 to 81.9%) with S1133 in Cluster 1, especially for those from Cluster 6 (38.1 to 67.2%). A higher ARV isolation rate was observed in chicken embryos (47/61) compared to cell culture (37/61) through PCR with a detection primer. A total of 3 isolates were selected to infect specific-pathogen-free (SPF) chickens, showing that the tested isolates, especially that from Cluster 6, displayed greater pathogenicity than S1133 strain, characterized by higher incidence. These findings suggest that the virulence of Chinese ARVs has been increasing rapidly in recent years, and the vaccine need to be updated correspondingly.

Genotypic Characterization of Emerging Avian Reovirus Genetic Variants in California

This study focuses on virus isolation of avian reoviruses from a tenosynovitis outbreak between September 2015 and June 2018, the molecular characterization of selected isolates based on partial S1 gene sequences, and the full genome characterization of seven isolates. A total of 265 reoviruses were detected and isolated, 83.3% from tendons and joints, 12.3% from the heart and 3.7% from intestines. Eighty five out of the 150 (56.6%) selected viruses for sequencing and characterization were successfully detected, amplified and sequenced. The characterized reoviruses grouped in six distinct genotypic clusters (GC1 to GC6). The most represented clusters were GC1 (51.8%) and GC6 (24.7%), followed by GC2 (12.9%) and GC4 (7.2%), and less frequent GC5 (2.4%) and GC3 (1.2%). A shift on cluster representation throughout time occurred. A reduction of GC1 and an increase of GC6 classified strains was noticed. The highest homologies to S1133 reovirus strain were detected in GC1 (~77%) while GC2 to GC6 homologies ranged between 58.5 and 54.1%. Over time these homologies have been maintained. Seven selected isolates were full genome sequenced. Results indicated that the L3, S1 and M2 genes, coding for proteins located in the virus capsid accounted for most of the variability of these viruses. The information generated in the present study helps the understanding of the epidemiology of reoviruses in California. In addition, provides insights on how other genes that are not commonly studied add variability to the reovirus genome.

Occurrence of Reovirus (ARV) Infections in Poultry Flocks in Poland in 2010-2017

Introduction

Avian reovirus (ARV) infections in poultry populations are reported worldwide. The reovirus belongs to the genus Orthoreovirus, family Reoviridae. The aim of the study was to evaluate the incidence of ARV infections in the poultry population based on diagnostic tests performed in 2010–2017.

Material and Methods

Samples of the liver and spleen were collected from sick birds suspected of ARV infection and sent for diagnostics. Isolation was performed in 5–7-day-old SPF chicken embryos infected into the yolk sac with homogenates of internal organs of sick birds. Four primer pairs were used to detect the σNS, σC, σA, and μA ARV RNA gene fragments. A nested PCR was used for the detection of the σNS and σC genes.

Results

In 2010–2017, ARV infection was found in birds from 81 flocks of broiler chickens and/or layers, 8 flocks of slaughter turkeys, and in 4 hatchery embryos at 17–20 days of incubation. The primers used in RT-PCR and nested PCR did not allow effective detection of ARV RNA in all virus-positive samples.

Conclusion

The problem of ARV infections in the poultry population in Poland still persist. The primers used for various ARV segments in RT-PCR and nested PCR did not allow effective detection of RNA in the visceral organs of sick birds. The presented results confirm the necessity of using classical diagnostic methods (isolation in chicken embryos, AGID).

Construction and characterization of an infectious molecular clone of novel duck reovirus

Novel duck reovirus (NDRV), the prototype strain of the species Avian orthoreovirus (ARV), is currently an infectious agent for ducks. Studies on NDRV replication and pathogenesis have been hampered by the lack of an available reverse-genetics system. In this study, a plasmid-based reverse-genetics system that is free of helper viruses has been developed. In this system, 10 full-length gene segments of wild-type NDRV TH11 strain are transfected into BSR-T7/5 cells that express bacteriophage T7 RNA polymerase. Production of infectious virus was shown by the inoculation of cell lysate derived from transfected cells into 10-day-old duck embryos. The in vivo growth kinetics and infectivity of the recombinant strains were identical to those of the wild-type strain. These viruses grew well and were genetically stable both in vitro and in vivo. Altogether, these results show the successful production of an infectious clone for NDRV. The infectious clone reported will be further used to elucidate the mechanisms of host tropism, viral replication and pathogenesis, as well as immunological changes induced by NDRV.

Chicken astrovirus as an aetiological agent of runting-stunting syndrome in broiler chickens

Despite descriptions of runting-stunting syndrome (RSS) in broiler chickens dating back over 40 years, the aetiology has not yet been described. A novel chicken astrovirus (CkAstV) was isolated in an LMH liver cell line from the intestines of chickens affected with RSS. Clinical RSS is characterized by retarded growth and cystic crypt lesions in the small intestine. In 1-day-old broiler chickens infected with the CkAstV isolate, virus was only detected in the intestinal epithelial cells during the first few days after infection. Notably, the preferred host cells are the crypt epithelial cells following initial replication in the villous epithelial cells, thus implying viral preference for immature intestinal cells. Nevertheless, the CkAstV isolate did not induce remarkable pathological changes, despite the presence of the virus in situ. Serial chicken-to-chicken passages of the virus induced increased virulence, as displayed by decreased weight gain and the presence of cystic lesions in the small intestine reproducing clinical RSS in chickens. The analysis of the full-length genome sequences from the isolated CkAstV and the CkAstV from the bird-to-bird passages showed >99 % similarity. The data obtained in this study suggest that the CkAstV isolate is capable of inducing RSS following serial bird-to-bird passages in broilers and is as an aetiological agent of the disease.

Detection of Avian Reoviruses in Wild Birds in Poland

Introduction

The purpose of this study was to determine the occurrence of avian reovirus (ARV) infections in wild birds in Poland and attempt to propagate the selected ARV strains in chicken embryo kidney (CEK) cells or chicken SPF embryos.

Material and Methods

The study included 192 wild birds representing 32 species, collected between 2014 and 2016. A part of the S4 segment encoding the σNS protein of avian reoviruses (ARVs) isolated from different species of wild birds from that period was amplified.

Results

The presence of ARV was demonstrated in 58 (30.2%) wild birds belonging to nine orders. The isolated strains were propagated in chicken embryos by yolk sac inoculation, and CPE was induced in the infected CEK monolayer. Agar gel precipitation showed that two ARV isolates from rock pigeon and mute swan shared a common group-specific antigen with chicken reovirus S1133. Specific products of predicted size were found in two ARV isolates from the chicken embryo passage and 13 ARVs isolated from CEK cells.

Conclusion

The study indicates the high prevalence of ARV among wild birds in Poland and its possible transmission to farmed birds.

Lineage diversification, homo- and heterologous reassortment and recombination shape the evolution of chicken orthoreoviruses

The near complete genome sequences of ten field avian orthoreovirus (ARV) strains collected from young chicken between 2002 and 2011 in Hungary have been determined in order to explore the genetic diversity and evolutionary mechanisms affecting ARVs in this region. Sequence analyses and phylogenetic calculations revealed similar geographic distribution and distinct evolution in case of eight studied strains that were closely related to the recently described Hungarian strain T1781. The remaining two strains showed the highest similarity with the US origin AVS-B. The topology of the phylogenetic trees of certain segments was affected by several potential homologous reassortment events between strains of Hungarian, Chinese and US origin. Analyzing the μB gene a possible heterologous reassortment event was identified in three Hungarian strains. Recombination events were detected in as much as a dozen cases implying that beside point mutations and reassorment this mechanism also plays an important role in the diversification of ARVs. All these mechanisms in concert may explain the reduced effectiveness of immunization using commercial vaccine strains.

Genetic and pathogenic characterisation of 11 avian reovirus isolates from northern China suggests continued evolution of virulence

Avian reovirus (ARV) infections characterised by severe arthritis, tenosynovitis, pericarditis, and depressed growth have become increasingly frequent in recent years. In this study, we isolated and identified 11 ARV field strains from chickens with viral arthritis and reduced growth in northern China. Comparative analysis of the σC nucleotide and amino acid sequences demonstrated that all isolates, except LN05 and JS01, were closely related to ARV S1133 and clustered in the first genetic lineage. LN05 and JS01 strains were clustered in the third lineage with the ARV 138 strain. Using S1133 as a reference, five isolates were selected to infect specific-pathogen-free chickens, and we found that the recent isolated Chinese ARV strains had higher replication ability in vivo and caused enhanced mortality than the S1133 strain. These findings suggest that the pathogenicity of Chinese ARVs has been changing in recent years and disease control may become more difficult. This study provides genetic and pathogenic characterisations of ARV strains isolated in northern China and calls for a sustained surveillance of ARV infection in China in order to support a better prevention and control of the disease.

Molecular detection of chicken parvovirus in broilers with enteric disorders presenting curving of duodenal loop, pancreatic atrophy, and mesenteritis

Enteric disorders are an important cause of economic losses in broiler chickens worldwide. Several agents have been associated with enteric problems, such as viruses, bacteria, and parasites. In this study, broiler chickens showing signs of enteric disorders were subjected to molecular diagnosis for several viral agents and also for pathological examination for elucidating this problem. Thus, the chickens were screened for avian nephritis virus (ANV), chicken astrovirus (CAstV), avian rotavirus (ArtV), avian reovirus (AReoV), infectious bronchitis virus (IBV), fowl adenovirus group I (FAdV-1), and chicken parvovirus (ChPV). Postmortem examinations revealed a curving of the duodenal loop (J-like appearance) and intestines filled with liquid and gaseous content. Histopathological analysis of the duodenal loop showed pancreatic atrophy, acute mesenteritis, and enteritis. PCR results showed that ChPV was the sole viral agent detected in samples with lesions such as the curved duodenal loop and pancreatic atrophy. Molecular characterization of the nucleotide and deduced amino acid sequences revealed a high similarity with other strains of ChPV from Brazil, Canada, United States, Europe, and Asia. These findings suggest an association between ChPV and the development of enteritis, pancreatitis, and pancreatic atrophy, which may lead to curling of the duodenal loop. Together, these alterations may disrupt the normal functioning of the digestive system, diminishing digestion and the absorption of dietary nutrients and consequently leading to reduced weight gain, flock impairment, dwarfism, and an elevated feed conversion rate.

Whole genome alignment based one-step real-time RT-PCR for universal detection of avian orthoreoviruses of chicken, pheasant and turkey origins

Newly emerging avian orthoreovirus (ARV) variants have been continuously detected in Pennsylvania poultry since 2011. In this paper, we report our recent diagnostic assay development of one-step real-time RT-PCR (rRT-PCR) for the rapid and universal detection of all ARVs or reference strains of chicken, pheasant and turkey origins and six σC genotypes of the newly emerging field ARV variants in Pennsylvania (PA) poultry. Primers and probes for the rRT-PCR were designed from the conserved region of the M1 genome segment 5' end based on the whole-genome alignment of various ARV strains, including six field variants or novel strains obtained in PA poultry. The detection limit of the newly developed rRT-PCR for ARV was as low as 10 copies/reaction of viral RNA, and 10(0.50)-10(0.88) tissue culture infectious dose (TCID50)/100 μL of viruses. This new rRT-PCR detected all six σC genotypes from the 66 ARV field variant strains and reference strains tested in this study. There were no cross-reactions with other avian viruses. Reproducibility of the assay was confirmed by intra- and inter-assay tests with variability from 0.12% to 2.19%. Sensitivity and specificity of this new rRT-PCR for ARV were achieved at 100% and 88%, respectively, in comparison with virus isolation as the "gold standard" in testing poultry tissue specimen.

Phylogenetic analysis of a novel reassortant orthoreovirus strain detected in partridge (Perdix perdix)

Avian orthoreoviruses cause various diseases in wild birds and domesticated poultry. In this study we report the detection and genomic characterization of a partridge (Perdix perdix) origin reovirus strain, D1007/2008. The virus was isolated on cell culture from acute pneumonia and infra-orbital sinusitis. The 23,497 nucleotide long genome sequence was obtained by combined use of semiconductor and capillary sequencing. Sequence and phylogenetic analyses showed that the partridge reovirus strain was related to orthoreoviruses of gallinaceous birds. In fact, five (λB, λC, μB, σC, σNS) and one (σB) out of 10 genes clustered definitely with turkey or chicken origin orthoreoviruses, respectively, whereas in the λA, μA, μNS and σA phylogenies a more distant genetic relationship was observed. Our data indicate that the identified reovirus strain is composed of a mixture of chicken and turkey orthoreovirus related alleles. This finding implies that partridges may serve as natural reservoirs for orthoreoviruses of domesticated poultry.

Isolation and molecular characterization of newly emerging avian reovirus variants and novel strains in Pennsylvania, USA, 2011-2014

Avian reovirus (ARV) infections of broiler and turkey flocks have caused significant clinical disease and economic losses in Pennsylvania (PA) since 2011. Most of the ARV-infected birds suffered from severe arthritis, tenosynovitis, pericarditis and depressed growth or runting-stunting syndrome (RSS). A high morbidity (up to 20% to 40%) was observed in ARV-affected flocks, and the flock mortality was occasionally as high as 10%. ARV infections in turkeys were diagnosed for the first time in PA in 2011. From 2011 to 2014, a total of 301 ARV isolations were made from affected PA poultry. The molecular characterization of the Sigma C gene of 114 field isolates, representing most ARV outbreaks, revealed that only 21.93% of the 114 sequenced ARV isolates were in the same genotyping cluster (cluster 1) as the ARV vaccine strains (S1133, 1733, and 2048), whereas 78.07% of the sequenced isolates were in genotyping clusters 2, 3, 4, 5, and 6 (which were distinct from the vaccine strains) and represented newly emerging ARV variants. In particular, genotyping cluster 6 was a new ARV genotype that was identified for the first time in 10 novel PA ARV variants of field isolates.

Genotyping and Classification of Tunisian Strains of Avian Reovirus using RT-PCR and RFLP Analysis

Since 1998, avian reovirus (ARV) infection has been detected in broiler and breeding chicken flocks in Tunisia. The genotype of avian reoviruses was established using simple and rapid approaches. Reverse transcription PCR (RT-PCR) on both sigma C (σC) and sigma B (σB)-encoding genes followed by restriction fragment length polymorphism (RFLP) analyses were used to better characterize Tunisian isolated strains. The RT-PCR amplified fragments of 738 and 540 bp for σC- and σB-encoding genes, respectively, of 15 ARV Tunisian strains. DNA fragments amplified from S 1133 vaccine and isolated strains were digested with different restrictions enzymes. RFLP on the σC gene indicated that the field isolates and the S 1133 vaccine strain have identical profiles when separately digested with TaqI, PstI, DdeI, and HincII. Considering the σB gene, RFLP profiles were identical with RsaI, BclI, DpnII, and NciI restriction enzymes for all the strains. However, using MseI and AciI enzymes, it was shown that all tested isolates could be clearly distinguished from the vaccine strain. ARV strains could be classified in groups with strong relatedness. Strain-typing based on cleavage site results are in agreement with ARV clustering based on nucleotide sequences of both the σC and σB genes. RT-PCR-RFLP provides a simple and a rapid approach for genotyping ARV isolates, especially when a large number of isolates are being studied. Additionally, this approach may also determine whether a new variant strain has been introduced into a flock or if a given virus strain is being spread from one flock to another.

Genomic characterization of a turkey reovirus field strain by Next-Generation Sequencing

The genome of a turkey arthritis reovirus (TARV) field strain (Reo/PA/Turkey/22342/13), isolated from a turkey flock in Pennsylvania (PA) in 2013, has been sequenced using Next-Generation Sequencing (NGS) on the Illumina MiSeq platform. The genome of the PA TARV field strain was 23,496bp in length with 10 dsRNA segments encoding 12 viral proteins. The lengths of the genomic segments ranged from 1192bp (S4) to 3959bp (L1). The 5' and 3' conserved terminal sequences of the PA TARV field strain were similar to the two Minnesota (MN) TARVs (MN9 and MN10) published recently and avian orthoreovirus (ARV) reference strains. Phylogenetic analysis of the nucleotide sequences of all 10 genome segments revealed that there was a low to significant nucleotide sequence divergence between the PA TARV field strain and reference TARV and ARV strains. Analysis of the PA TARV sequence indicates that this PA TARV field strain is a unique strain and is different from the TARV MN9 or MN10 in M2 segment genes and ARV S1133 vaccine strain.

Isolation of chicken astrovirus from specific pathogen-free chicken embryonated eggs

Astroviruses have been associated with enteric disorders in many animal species, including chickens. Here, we describe the isolation, propagation, and pathological characteristics of chicken astrovirus (CAstV) in specific pathogen free (SPF) chicken embryonated eggs (CEE) from chickens with diarrhea and runting-stunting syndrome. The CEE were inoculated via the yolk sac route. Viral confirmation was carried out using PCR techniques and transmission electron microscopy negative staining with ammonium molybdate. The intestinal contents were screened for CAstV, and differential diagnostic testing was performed for avian nephritis virus, avian rotavirus, avian reovirus, chicken parvovirus, infectious bronchitis virus, and fowl adenovirus Group I to detect co-infection with other infectious agents. Seven- or 14-day-old CEEs presented with hemorrhages, edema, a gelatinous aspect, deformities, and dwarfism. The supporting membranes did not show any alterations. Here, we have described the isolation of CAstV and its pathological characteristics in SPF CEE.

Phylogenetic analysis, genomic diversity and classification of M class gene segments of turkey reoviruses

From 2011 to 2014, 13 turkey arthritis reoviruses (TARVs) were isolated from cases of swollen hock joints in 2-18-week-old turkeys. In addition, two isolates from similar cases of turkey arthritis were received from another laboratory. Eight turkey enteric reoviruses (TERVs) isolated from fecal samples of turkeys were also used for comparison. The aims of this study were to characterize turkey reovirus (TRV) based on complete M class genome segments and to determine genetic diversity within TARVs in comparison to TERVs and chicken reoviruses (CRVs). Nucleotide (nt) cut off values of 84%, 83% and 85% for the M1, M2 and M3 gene segments were proposed and used for genotype classification, generating 5, 7, and 3 genotypes, respectively. Using these nt cut off values, we propose M class genotype constellations (GCs) for avian reoviruses. Of the seven GCs, GC1 and GC3 were shared between the TARVs and TERVs, indicating possible reassortment between turkey and chicken reoviruses. The TARVs and TERVs were divided into three GCs, and GC2 was unique to TARVs and TERVs. The proposed new GC approach should be useful in identifying reassortant viruses, which may ultimately be used in the design of a universal vaccine against both chicken and turkey reoviruses.

Complete genome analysis identifies Tvärminne avian virus as a candidate new species within the genus Orthoreovirus

Orthoreoviruses have been associated with a variety of diseases in domesticated poultry and wild-living birds. In 2002, a reovirus strain named Tvärminne avian virus (TVAV), was identified in Finland in a crow showing neurological disorders. The objective of this study was the molecular characterization of this novel reovirus strain. Genome sequencing was performed by combining semiconductor sequencing and traditional capillary sequencing. Sequence and phylogenetic analyses showed that TVAV shares low nucleotide sequence identity with other reoviruses (range for each gene, 31–72 %) including strains belonging to the species Avian orthoreovirus. The most closely related reovirus strain was an isolate identified in Steller sea lion. Our data indicate that TVAV is a divergent reovirus of avian origin that may be the first representative of a distinct virus species within the genus Orthoreovirus.

Enteric viruses in turkey enteritis

Gut health is very important to get maximum returns in terms of weight gain and egg production. Enteric diseases such as poult enteritis complex (PEC) in turkeys do not allow their production potential to be achieved to its maximum. A number of viruses, bacteria, and protozoa have been implicated but the primary etiology has not been definitively established. Previously, electron microscopy was used to detect the presence of enteric viruses, which were identified solely on the basis of their morphology. With the advent of rapid molecular diagnostic methods and next generation nucleic acid sequencing, researchers have made long strides in identification and characterization of viruses associated with PEC. The molecular techniques have also helped us in identification of pathogens which were previously not known. Regional and national surveys have revealed the presence of several different enteric viruses in PEC including rotavirus, astrovirus, reovirus and coronavirus either alone or in combination. There may still be unknown pathogens that may directly or indirectly play a role in enteritis in turkeys. This review will focus on the role of turkey coronavirus, rotavirus, reovirus, and astrovirus in turkey enteritis.

Sequencing and phylogenetic analysis of an avian reovirus genome

Avian reovirus infection causes considerable economic loss to the commercial poultry industry. Live-attenuated vaccine strain S1133 (v-S1133, derived from parent strain S1133) is considered the safest and most effective vaccine and is currently used worldwide. To identify the genes responsible for its attenuation, DNA sequences of open reading frames (ORF) of S1133 and its parent strains S1133, 1733, 526, and C78 along with three field isolates (GuangxiR1, GuangxiR2, and GX110058) and one isolate (GX110116) from a vaccinated chicken were performed. The sequence data were compared with available sequences in nucleotide sequence databases of American (AVS-B, 138, 176) and Chinese (C-98 and T-98) origin. Sequence analysis identified that several v-S1133 specific nucleotide substitutions existed in the ORFs of λA, λB, λC, μA, μB, μNS, σA, σB, and σNS genes. The v-S1133 strain could be differentiated from the field-isolated strains based on single nucleotide polymorphisms. Phylogenetic analysis revealed that v-S1133 shared the highest sequence homologies with S1133 and reovirus isolates from China, grouped together in one cluster. Chinese isolates were clearly more distinct from the American reovirus AVS-B strain, which is associated with runting-stunting syndrome in broilers.

Whole-genome sequencing of a green bush viper reovirus reveals a shared evolutionary history between reptilian and unusual mammalian orthoreoviruses

In this study, we sequenced the whole genome of a reovirus isolated from a green bush viper (Atheris squamigera). The bush viper reovirus shared several features with other orthoreoviruses, including its genome organization. In phylogenetic analysis, this strain was monophyletic with Broome virus and baboon orthoreovirus, indicating that these viruses might have originated from a common ancestor. These new molecular data supplement previous information based mainly on biological properties of reptilian reoviruses, confirming their taxonomic position and broadening our knowledge of the evolution of members of the genus Orthoreovirus.

Complete genome sequences of an avian orthoreovirus isolated from guangxi, china

We report the complete genomic sequences of an avian orthoreovirus, strain GuangxiR1, isolated from a chicken flock in Guangxi Province, southern China, in 2000. Phylogenetic analyses suggest that the strain is closely related to the S1133 strain, which is associated with tenosynovitis, but is far different from strain AVS-B, which is associated with runting-stunting syndrome in broilers.

Detection and characterization of a divergent avian reovirus strain from a broiler chicken with central nervous system disease

Avian orthoreoviruses have been associated with a variety of diseases in chickens, including tenosynovitis, runting-stunting syndrome, hepatitis, myocarditis, osteoporosis, respiratory diseases, and central nervous system disease. The primary objective of our study was the molecular characterization of an avian reovirus strain, T1781, which was isolated from a broiler chicken with a central nervous system disorder in Hungary during 2012. The complete genome sequence was determined using a traditional sequencing method after cell culture adaptation of the strain. Sequence and phylogenetic analyses showed that T1781 shared only moderate nucleic acid sequence identity in several genes to previously analyzed reovirus strains from chickens, and each gene formed separate branches in the corresponding phylogenetic trees. The maximum nucleotide sequence identities of strain T1781 genes to reference avian reovirus strains ranged from 79 % to 90 %. Collectively, our analyses indicated that T1781 is a divergent chicken reovirus strain. The genetic background of this and other avian reoviruses associated with various disease manifestations needs further investigation.

Molecular characterization of avian reovirus isolates in Tunisia

BACKGROUND

Genotype analyses of avian reoviruses isolated from organ samples collected from chickens with suspicious clinical symptoms, between 1997-2008, was based on sequences for both σC and σB genes and aligned with those published in the Genbank, making it possible to carry out studies of molecular classification and relationships.

METHODS

The full length of the known variable protein σC and part of the σB encoding genes, were amplified with RT-PCR, using conserved primers. PCR products were sequenced and the sequences were analyzed and aligned with avian reovirus sequences from the Genbank database.

RESULTS

The sequences of σC-encoding genes of all the isolated strains indicated their close relationship with the American, Chinese and Indian strains. Taking the American strain S1133 as a reference, the two Tunisian isolates 97.1 and 97.2 showed some nucleotide substitutions. For isolate 97.1, the substitution was silent whereas for strain 97.2 the mutation was at the first position of the corresponding codon and induced the substitution of the amino acid encoded. For the σB-encoding gene, the sequences of the Tunisian strains showed mutations at positions two or three of the corresponding codons, inducing substitutions of amino acids at these positions. The phylogenic trees based on σC and σB encoding genes indicated closer relationship between Tunisian, American and Taiwanese isolates of genotype I.

CONCLUSION

Our study describes the genotype of avian reoviruses that are not yet well characterized genetically. The characterization and classification of these viruses might be significant for understanding the epidemiology of malabsorption syndrome and viral arthritis, and improving our knowledge of the genotype of strains circulating in Tunisian flocks. Furthermore, the study of their variable pathogenicity could be extremely important in the choice of the appropriate vaccine strain to control disease.