Investigations into Increased Incidence of Severe Gizzard Erosions and Ulcerations in U.S. Commercial Broilers.

During a series of pathology surveys in four production complexes of a U.S. broiler integrator, the technical services veterinarians of an animal health company noted a high incidence of severe gizzard erosions and ulcerations (GEU), prompting further clinical investigation and a battery trial. No growth-promoting antibiotics or ionophore coccidiostats were used during the period of these surveys. All used tribasic copper chloride (TBCC) at ≤120 ppm added copper in broiler rations. Clostridium perfringens was isolated from 83% and 67% of gizzard lesions cultured in two complexes, and cecal C. perfringens most probable number determinations were higher in severely affected than in mildly affected or unaffected birds. Histopathology revealed both acellular koilin fusion defects characteristic of copper toxicity, as well as inflammatory cell infiltrates. Intralesional bacilli suggestive of C. perfringens were noted in 78% of affected flocks examined. Species E Aviadenovirus was isolated from one bird in one complex, and that bird had a single intranuclear inclusion body; no other flocks had Adenoviruses isolated or detected on PCR, nor any inclusion bodies. Other viruses detected were thought to be incidental. A pilot study using feed with supplemental copper from TBCC or copper sulfate and challenge with one of the isolated C. perfringens strains reproduced the lesions. A battery study was conducted with an unchallenged negative control group fed a diet with 16 ppm added copper, a group fed the control diet and orally challenged with 108 organisms of a field strain of C. perfringens at 21 and 22 days, and a group treated with the same diet containing 250 ppm added copper from TBCC and orally challenged with C. perfringens. Birds were necropsied at 23 and 28 days. All challenged groups developed lesions, with those receiving both TBCC and C. perfringens having significantly higher gross and histopathological lesion scores than the unchallenged negative controls. Lesions were qualitatively similar to those in the field and contained suspected C. perfringens bacilli. Because the levels of TBCC used in the commercial birds and in the battery trial generally have been considered safe, and because C. perfringens is usually regarded as a pathogen of the lower GI tract, the possible association of these two agents with GEU is a novel observation and warrants further investigation.

Investigaciones sobre el aumento de la incidencia de erosiones y ulceraciones severas en la molleja en pollos de engorde comerciales en los Estados Unidos. Durante una serie de estudios de patología en cuatro complejos de producción de un integrador de pollos de engorde de los Estados Unidos, veterinarios de servicio técnico de una empresa de salud animal observaron una alta incidencia de erosiones y ulceraciones severas de la molleja (GEU), lo que motivó una mayor investigación clínica y un estudio en batería. Durante el período de estas encuestas no se utilizaron antibióticos promotores del crecimiento ni coccidiostáticos ionóforos. Todos utilizaron cloruro de cobre tribásico (TBCC) con un nivel de ≤120 ppm de cobre agregado en raciones para pollos de engorde. Se aisló Clostridium perfringens del 83% y el 67% de las lesiones de molleja cultivadas en dos complejos, y las determinaciones del número más probable de C. perfringens en los sacos ciegos fueron mayores en aves severamente afectadas que en aves levemente afectadas o no afectadas. La histopatología reveló defectos de fusión de la capa córnea acelular característicos de la toxicidad por cobre, así como infiltrados de células inflamatorias. Se observaron bacilos intralesionales sugestivos de C. perfringens en el 78% de las parvadas afectadas examinadas. La especie Aviadenovirus E se aisló de un ave en un complejo, y esa ave tenía un único cuerpo de inclusión intranuclear; en ninguna otra parvada se aislaron o detectaron adenovirus mediante PCR, ni se observaron cuerpos de inclusión. Se pensó que otros virus detectados fueron incidentales. Un estudio piloto que utilizó alimento con cobre suplementario de cloruro de cobre tribásico o sulfato de cobre y con desafío con una de las cepas aisladas de C. perfringens reprodujo las lesiones. Se realizó un estudio de batería con un grupo de control negativo no desafiado alimentado con una dieta con 16 ppm de cobre agregado, un grupo alimentado con la dieta de control y desafiado por vía oral con 108 organismos de una cepa de campo de C. perfringens a los 21 y 22 días, y un grupo tratado con la misma dieta que contenía 250 ppm de cobre agregado de cloruro de cobre tribásico y desafiados por vía oral con C. perfringens. A las aves se les realizó la necropsia a los 23 y 28 días. Todos los grupos desafiados desarrollaron lesiones, y aquellos que recibieron cloruro de cobre tribásico y C. perfringens tuvieron puntuaciones de lesiones macroscópicas e histopatológicas significativamente más altas que los controles negativos no desafiados. Las lesiones eran cualitativamente similares a las del campo y contenían bacilos sospechosos de C. perfringens. Debido a que los niveles de cloruro de cobre tribásico utilizados en las aves comerciales y en el ensayo en batería generalmente se han considerado seguros, y debido a que C. perfringens generalmente se considera un patógeno del tracto gastrointestinal inferior, la posible asociación de estos dos agentes con erosiones y ulceraciones severas de la molleja es una observación reciente y justifica una mayor investigación.

Efficacy of recombinant H5 vaccines delivered in ovo or day of age in commercial broilers against the 2015 U.S. H5N2 clade 2.3.4.4c highly pathogenic avian Influenza virus.

BACKGROUND: Avian influenza is a highly contagious, agriculturally relevant disease that can severely affect the poultry industry and food supply. Eurasian-origin H5Nx highly pathogenic avian influenza viruses (HPAIV) (clade 2.3.4.4) have been circulating globally in wild birds with spill over into commercial poultry operations. The negative impact to commercial poultry renewed interest in the development of vaccines against these viruses to control outbreaks in the U.S. METHODS: The efficacy of three recombinant H5 vaccines delivered in ovo or day of age were evaluated in commercial broilers challenged with the 2015 U.S. H5N2 clade 2.3.4.4c HPAIV. The recombinant vaccines included an alphavirus RNA particle vaccine (RP-H5), an inactivated reverse genetics-derived (RG-H5) and recombinant HVT vaccine (rHVT-AI) expressing H5 hemagglutinin (HA) genes. In the first experiment, in ovo vaccination with RP-H5 or rHVT-AI was tested against HPAI challenge at 3 or 6 weeks of age. In a second experiment, broilers were vaccinated at 1 day of age with a dose of either 107 or 108 RP-H5, or RG-H5 (512 HA units (HAU) per dose). RESULTS: In experiment one, the RP-H5 provided no protection following in ovo application, and shedding titers were similar to sham vaccinated birds. However, when the RP-H5 was delivered in ovo with a boost at 3 weeks, 95% protection was demonstrated at 6 weeks of age. The rHVT-AI vaccine demonstrated 95 and 100% protection at 3 and 6 weeks of age, respectively, of challenged broilers with reduced virus shedding compared to sham vaccinated birds. Finally, when the RP-H5 and rHVT vaccines were co-administered at one day of age, 95% protection was demonstrated with challenge at either 3 or 6 weeks age. In the second experiment, the highest protection (92%) was observed in the 108 RP-H5 vaccinated group. Significant reductions (p < 0.05) in virus shedding were observed in groups of vaccinated birds that were protected from challenge. The RG-H5 provided 62% protection from challenge. In all groups of surviving birds, antibody titers increased following challenge. CONCLUSIONS: Overall, these results demonstrated several strategies that could be considered to protected broiler chickens during a H5 HPAI challenge.

Optimizing the Conditions for Whole-Genome Sequencing of Avian Reoviruses.

Whole-genome sequencing (WGS) is becoming an essential tool to characterize the genomes of avian reovirus (ARV), a viral disease of economic significance to poultry producers. The current strategies and procedures used to obtain the complete genome sequences of ARV isolates are not cost-effective because most of the genetic material data resulting from next-generation sequencing belong to the host and cannot be used to assemble the viral genome. The purpose of this study was to develop a workflow to enrich the ARV genomic content in a sample before subjecting it to next-generation sequencing (NGS). Herein, we compare four different ARV purification and enrichment approaches at the virion, RNA and cDNA levels to determine which treatment or treatment combination would provide a higher proportion of ARV-specific reads after WGS. Seven ARV isolates were subjected to different combinations of virion purification via ultracentrifugation in sucrose density gradient or Capto Core 700 resin with or without a subsequent Benzonase treatment, followed by a chicken rRNA depletion step after RNA extraction and a final ARV cDNA amplification step using a single-primer amplification assay. Our results show that the combination of Capto Core 700 resin, Chicken rRNA depletion and cDNA amplification is the most cost-effective strategy to obtain ARV whole genomes after short-read sequencing.

Presumed Spontaneous Astrocytoma in a Domestic Backyard Chicken.

A cerebral tumor was identified in an adult female domestic chicken (Gallus domesticus). On gross examination, the cut surface of the cerebrum revealed a poorly circumscribed, pale tan soft mass within the thalamus and midbrain. On histologic examination, there was an unencapsulated, multilobulated neoplasm composed of spindle cells on a loose fibrovascular stroma. Neoplastic cells had variably distinct cell borders, abundant fibrillar eosinophilic cytoplasm, oval nuclei with finely stippled chromatin, and 1-2 distinct nucleoli. There was moderate anisocytosis and anisokaryosis with <1 mitoses per 2.37 mm2. The morphologic features of the neoplastic cells were consistent with an astrocytic neoplasm. PCR was performed on formalin-fixed paraffin-embedded sections of brain tissue, which was negative for subgroup A avian leukosis virus. Based on these findings, the tumor was diagnosed as a presumed spontaneous astrocytoma.

Reporte de caso - Presunto astrocitoma espontáneo en un pollo doméstico de traspatio. Se identificó un tumor cerebral en una gallina doméstica adulta (Gallus domesticus). En el examen macroscópico, la superficie de corte del cerebro reveló una masa blanda de color canela pálido mal delimitada dentro del tálamo y el mesencéfalo. En el examen histológico, había una neoplasia multilobulada no encapsulada compuesta de células fusiformes sobre un estroma fibrovascular laxo. Las células neoplásicas tenían bordes celulares diferenciados de forma variable, abundante citoplasma eosinofílico fibrilar, núcleos ovalados con cromatina finamente punteada y 1 o 2 nucléolos distintos. Había anisocitosis moderada y anisocariosis con <1 mitosis por 2.37 mm2. Las características morfológicas de las células neoplásicas eran compatibles con una neoplasia astrocítica. Se realizó una PCR en secciones de tejido cerebral incluidas en parafina y fijadas con formalina, que resultó negativa para el virus de la leucosis aviar del subgrupo A. Con base en estos hallazgos, el tumor se diagnosticó como un presunto astrocitoma espontáneo.

MORBIDITY AND MORTALITY OF HAWAIIAN GEESE (BRANTA SANDVICENSIS) AND LAYSAN ALBATROSS (PHOEBASTRIA IMMUTABILIS) ASSOCIATED WITH RETICULOENDOTHELIOSIS VIRUS.

Only one virus, Avipox, has been documented previously in wild birds in Hawaii. Using immunohistochemistry and PCR, we found that two native threatened Hawaiian Geese (Branta sandvicensis), one with multicentric histiocytoma and the other with toxoplasmosis, and one Laysan Albatross (Phoebastria immutabilis) with avian pox were infected with reticuloendotheliosis virus (REV). The virus was isolated from one of the geese by cell culture. Surveys of other Hawaiian geese with various pathologies, avian pox cases, and pox viral isolates using PCR failed to reveal REV, suggesting that the virus is uncommon, at least in samples examined. The full genome of the Gag, Pol, and Env genes were sequenced for all three infected birds and revealed geographic divergence of the Pol gene, suggesting it to be under strong selective pressure. Our finding of REV in Hawaii makes this only the second virus documented in native Hawaiian birds associated with pathology. Moreover, the presence of REV in a pelagic seabird is unusual. Future surveys should seek the reservoir of the virus in efforts to trace its origins.

Runting Stunting Syndrome in Broiler Chickens Is Associated with Altered Intestinal Stem Cell Morphology and Gene Expression.

Runting stunting syndrome (RSS) in broiler chickens is characterized by altered intestinal morphology and gene expression and stunted growth. The objective of this study was to conduct a retrospective study of gene expression in stem and differentiated cells in the small intestine of RSS chicks. Two different models of RSS were analyzed: broiler chicks that were experimentally infected and broiler chicks that were naturally infected. Experimentally infected chicks were exposed to litter from infected flocks (RSS-litter chicks) or infected with astrovirus (RSS-astrovirus chicks). Intestinal samples from naturally infected chicks showing clinical signs of RSS were acquired from commercial farms in Georgia and were brought into a poultry diagnostic lab (RSS-clinical-GA) and from farms in Brazil that had a history of RSS (RSS-clinical-BR). The RSS-clinical-BR chicks were separated into those that were positive or negative for gallivirus based on DNA sequencing. Intestinal morphology and intestinal cell type were identified in archived formalin-fixed, paraffin-embedded tissues. In situ hybridization for cell-specific mRNA was used to identify intestinal stem cells expressing olfactomedin 4 (Olfm4), proliferating cells expressing Ki67, absorptive cells expressing sodium glucose cotransporter 1 (SGLT1) and peptide transporter 1 (PepT1), and goblet cells expressing mucin 2 (Muc2). RSS-litter and RSS-clinical-GA chicks showed 4% to 7.5% cystic crypts, while gallivirus-positive RSS-clinical-BR chicks showed 11.7% cystic crypts. RSS-astrovirus and gallivirus-negative RSS-clinical-BR chicks showed few cystic crypts. RSS-litter and gallivirus-positive RSS-clinical-BR chicks showed an increase in crypt depth compared to control or gallivirus-negative chicks, respectively. There was no expression of Olfm4 mRNA in the stem cells of RSS-litter and RSS-clinical-GA chicks, in contrast to the normal expression of Olfm4 mRNA in RSS-astrovirus and RSS-clinical-BR chicks. All chicks regardless of infection status showed normal expression of Ki67 mRNA in crypt cells, Muc2 mRNA in goblet cells, and SGLT1 or PepT1 mRNA in enterocytes. These results demonstrate that RSS, which can be induced by different etiologies, can show differences in the expression of the stem cell marker Olfm4.

El síndrome del enanismo infeccioso en pollos de engorde se asocia con alteración de la morfología de las células madre intestinales y la expresión de genes. El síndrome del enanismo infeccioso (con las siglas en inglés RSS) en pollos de engorde se caracteriza por alteraciones en la morfología intestinal y en la expresión de genes, además de retraso en el crecimiento. El objetivo de este estudio fue realizar un estudio retrospectivo de la expresión genética en células madre y células diferenciadas en el intestino delgado de pollitos con el síndrome del enanismo infeccioso. Se analizaron dos modelos diferentes del síndrome del enanismo infeccioso: en pollos de engorde que fueron infectados experimentalmente y en pollos de engorde infectados naturalmente. Los pollitos infectados experimentalmente se expusieron a la cama de parvadas infectadas (RSS-litter chicks), o infectados con astrovirus (RSS-astrovirus chicks). Se adquirieron muestras intestinales de pollitos infectados naturalmente que mostraban signos clínicos del síndrome del enanismo infeccioso de granjas comerciales en Georgia y se llevaron a un laboratorio de diagnóstico avícola (RSS-Clinical-GA) y de granjas en Brasil que tenían antecedentes del síndrome del enanismo infeccioso (RSS-Clinical-BR). Los pollitos de granjas de Brasil (RSS-Clinical-BR) se separaron en aquellos que fueron positivos o negativos para gallivirus de acuerdo con la secuenciación del ADN. Se identificaron la morfología intestinal y el tipo de células intestinales en tejidos archivados fijados con formalina e incluidos en parafina. La hibridación in situ para ARNm específico de células se utilizó para identificar células madre intestinales que expresan olfactomedina 4 (Olfm4), células en proliferación que expresaban Ki67, células absorbentes que expresan el cotransportador 1 de glucosa y sodio (SGLT1) y el transportador de péptidos 1 (PepT1), y células caliciformes que expresan mucina 2 (Muc2). Los pollos expuestos a cama infectada (RSS-litter) y los infectados naturalmente de Georgia (RSS-clinical-GA) mostraron entre un 4% y un 7.5% de criptas quísticas, mientras que los pollos infectados de granjas de Brasil (RSS-clinical-BR) que eran positivos para gallivirus mostraron un 11.7% de criptas quísticas. Los pollos infectados con astrovirus (RSS-astrovirus chicks) y los pollos de Brasil (RSS-clinical-BR) que eran negativos para gallivirus mostraron pocas criptas quísticas. Los pollos expuestos a cama infectada (RSS-litter chicks) y los pollos infectados de Brasil (RSS-clinical-BR) que eran positivos para gallivirus mostraron un aumento en la profundidad de las criptas en comparación con los pollos control o negativos para el gallivirus, respectivamente. No se observó expresión de ARNm de Olfm4 en las células madre de pollitos expuestos a cama infectada (RSS-litter chicks) ni en pollos infectados de Georgia (RSS-clinical-GA), en contraste con la expresión normal de ARNm de Olfm4 en pollitos infectados con astrovirus (RSS-astrovirus chicks) y en pollitos infectados de Brasil (RSS-clinical-BR). Todos los pollos, independientemente del estado de infección, mostraron una expresión normal de ARNm para Ki67 en las células de la cripta, de ARNm para Muc2 en las células caliciformes y ARNm de SGLT1 o PepT1 en los enterocitos. Estos resultados demuestran que el síndrome del enanismo infeccioso, que puede ser inducido por diferentes etiologías, puede mostrar diferencias en la expresión del marcador para células madre Olfm4.

Avian Reoviruses from Clinical Cases of Tenosynovitis: An Overview of Diagnostic Approaches and 10-Year Review of Isolations and Genetic Characterization.

Reoviral-induced tenosynovitis/viral arthritis is an economically significant disease of poultry. Affected birds present with lameness, unilateral or bilateral swollen hock joints or shanks, and/or reluctance to move. In severe cases, rupture of the gastrocnemius or digital flexor tendons may occur, and significant culling may be necessary. Historically, vaccination with a combination of modified live and inactivated vaccines has successfully controlled disease. Proper vaccination reduced vertical transmission and provided maternal-derived antibodies to progeny to protect against disease, at an age when they were most susceptible. Starting in 2011-2012, an increased incidence of tenosynovitis/viral arthritis was observed in chickens and turkeys. In chickens, progeny from reovirus-vaccinated breeders were affected, suggesting commercial vaccines did not provide adequate protection against disease. In turkeys, clinical disease was primarily in males, although females can also be affected. The most significant signs were observed around 14-16 wks of age and include reluctance to move, lameness, and limping on one or both legs. The incidence of tenosynovitis/viral arthritis presently remains high. Reoviruses isolated from clinical cases are genetically and antigenically characterized as variants, meaning they are different from vaccine strains. Characterization of the field isolates reveals multiple new genotypes and serotypes that are significantly different from commercial vaccines and each other. In 2012, a single prevalent virus was isolated from a majority of the cases submitted to the Poultry Diagnostic and Research Center at the University of Georgia. Genetic characterization of the σC protein revealed the early isolates belonged to genetic cluster (GC) 5. Soon after the initial identification of the GC5 variant reovirus, many broiler companies incorporated these isolates from their farms into their autogenous vaccines and continue to do so today. The incidence of GC5 field isolates has decreased significantly, likely because of the widespread use of the isolates in autogenous vaccines. Unfortunately, variant reoviruses belonging to multiple GCs have emerged, despite inclusion of these isolates in autogenous vaccines. In this review, an overview of nomenclature, sample collection, and diagnostic testing will be covered, and a summary of variant reoviruses isolated from clinical cases of tenosynovitis/viral arthritis over the past 10 yrs will be provided.

Estudio recapitulativo- Reovirus aviares de casos clínicos de tenosinovitis: una descripción general de los enfoques de diagnóstico y una revisión de 10 años de aislamientos y caracterización genética. La tenosinovitis/artritis viral inducida por reovirus es una enfermedad económicamente significativa de la avicultura. Las aves afectadas presentan cojera, articulaciones de corvejones o patas inflamadas unilateral o bilateralmente y/o renuencia a moverse. En casos severos, puede ocurrir la ruptura de los tendones del gastrocnemio o del flexor digital, y puede ser necesario una eliminación de aves afectadas significativa. Históricamente, la vacunación con una combinación de vacunas vivas modificadas e inactivadas ha controlado con éxito la enfermedad. La vacunación adecuada redujo la transmisión vertical y proporcionó anticuerpos derivados de las reproductoras a la progenie para protegerlos contra la enfermedad, a una edad en la que eran más susceptibles. A partir de los años 2011-2012, se observó una mayor incidencia de tenosinovitis/artritis viral en pollos y pavos. En los pollos, la progenie de reproductores vacunados con reovirus se vio afectada, lo que sugiere que las vacunas comerciales no brindaron una protección adecuada contra la enfermedad. En pavos, la enfermedad clínica fue principalmente en machos, aunque las hembras también pueden verse afectadas. Los signos más significativos se observaron alrededor de las 14 a 16 semanas de edad e incluyen renuencia a moverse y cojera en una o ambas piernas. La incidencia de tenosinovitis/artritis viral actualmente sigue siendo alta. Los reovirus aislados de casos clínicos se caracterizan genética y antigénicamente como variantes, lo que significa que son diferentes de las cepas vacunales. La caracterización de los aislamientos de campo revela múltiples genotipos y serotipos nuevos que son significativamente diferentes de las vacunas comerciales y entre sí. En 2012, se aisló un solo virus prevalente de la mayoría de los casos presentados al Centro de Investigación y Diagnóstico Avícola de la Universidad de Georgia. La caracterización genética de la proteína sigma C reveló que los primeros aislamientos pertenecían al grupo genético 5 (GC5). Poco después de la identificación inicial de la variante GC5 del reovirus, muchas empresas de pollos de engorde incorporaron estos aislamientos de sus granjas en sus vacunas autógenas y continúan haciéndolo en la actualidad. La incidencia de aislamientos de campo de GC5 ha disminuido significativamente, probablemente debido al uso generalizado de los aislamientos en vacunas autógenas. Desafortunadamente, han surgido variantes de reovirus que pertenecen a múltiples grupos genéticos, a pesar de la inclusión de estos aislados en vacunas autógenas. En esta revisión, se cubrirá una descripción general de la nomenclatura, la recolección de muestras y las pruebas de diagnóstico, y se brindará un resumen de las variantes de reovirus aisladas de casos clínicos de tenosinovitis/artritis viral durante los últimos 10 años.

Field Control of Avian Reoviruses in Commercial Broiler Production.

Prevention of tenosynovitis/viral arthritis caused by variant avian reoviruses within commercial broiler production has become increasingly more challenging because of the lack of protection afforded by the current commercially available vaccines. Avian reoviruses isolated from clinical cases of tenosynovitis/viral arthritis in recent years are antigenically distinct from nearly all of the commercially licensed modified live and inactivated biologics available in the United States. The emergence of new variants is likely shaped by a lack of homologous protection coupled with selection pressure influences and results in antigenically diverse populations of avian reoviruses. One tool available to the poultry industry is the use of autogenous (custom) vaccines. Although these can be effective, isolation, characterization, and screening of isolates from clinical cases is paramount for the selection of isolates to include in these vaccines. With no treatment options, control can only be attained via prevention of infection. To achieve this goal, commercially licensed products with antigenic applicability and broadly cross-protective vaccine strains are needed.

Estudio recapitulativo- Control de campo de los reovirus aviares en la producción comercial de pollos de engorde. La prevención de la tenosinovitis/artritis viral causada por variantes de reovirus aviares dentro de la producción comercial de pollos de engorde se ha vuelto cada vez más difícil debido a la falta de protección que brindan las vacunas disponibles comercialmente en la actualidad. Los reovirus aviares aislados de casos clínicos de tenosinovitis/artritis viral en los últimos años son antigénicamente distintos de casi todos los biológicos vivos modificados e inactivados con licencia y disponibles comercialmente en los Estados Unidos. La aparición de nuevas variantes probablemente se deba a la falta de protección homóloga junto con las influencias de la presión de selección y da como resultado poblaciones antigénicamente diversas de reovirus aviares. Una herramienta disponible para la industria avícola es el uso de vacunas autógenas (elaboradas de acuerdo a los virus de cada compañía). Si bien estos pueden ser efectivos, el aislamiento, la caracterización y la detección de aislamientos de casos clínicos son de suma importancia para la selección de aislamientos para incluir en estas vacunas. Sin opciones de tratamiento, el control solo se puede lograr a través de la prevención de la infección. Para lograr este objetivo, se necesitan productos comercialmente autorizados con aplicabilidad antigénica y cepas de vacunas que induzcan protección cruzada amplia.

A Universal, Single-Primer Amplification Protocol to Perform Whole-Genome Sequencing of Segmented dsRNA Avian Orthoreoviruses.

The Reoviridae family represents the largest family of double-stranded RNA viruses, and members have been isolated from a wide range of mammals, birds, reptiles, fishes, insects, and plants. Orthoreoviruses, one of the 15 recognized genera in the Reoviridae family, can infect humans and nearly all mammals and birds. Genomic characterization of reoviruses has not been adopted on a large scale because of the complexity of obtaining sequences for all 10 segments. In this study, we develop a time-efficient and practical method to enrich reovirus sequencing reads from isolates that allows for full-genome recovery using a single-primer amplification method coupled with next-generation sequencing. We refer to this protocol as reovirus-single-primer amplification (R-SPA). Our results demonstrate that most of the genes are covered with at least 500 reads per base space. Furthermore, R-SPA covers both the 5' and 3' ends of each reovirus genes. In summary, this study presents a universal and fast amplification protocol that yields sufficient double-stranded cDNA and facilitates and expedites the whole-genome sequencing of reoviruses.

Protocolo universal de amplificación con un iniciador único para realizar la secuenciación del genoma completo de orthoreovirus aviares con ARN de doble cadena y segmentados La familia Reoviridae representa la familia más grande de virus de ARN de doble cadena y se han aislado miembros de una amplia variedad de mamíferos, aves, reptiles, peces, insectos y plantas. El género Orthoreovirus, uno de los 15 géneros reconocidos en la familia Reoviridae, pueden infectar a humanos y a casi todos los mamíferos y aves. La caracterización genómica de los reovirus no se ha adoptado a gran escala debido a la complejidad de obtener secuencias para los 10 segmentos. En este estudio, desarrollamos un método práctico y eficiente para enriquecer las lecturas de secuenciación de reovirus a partir de aislamientos que permite la recuperación del genoma completo utilizando un método de amplificación con un iniciador único junto con la secuenciación de próxima generación. Nos referimos a este protocolo como amplificación de un solo iniciador de reovirus (R-SPA). Estos resultados demuestran que la mayoría de los genes están cubiertos con al menos 500 lecturas por espacio base. Además, el método R-SPA cubre los extremos 5' y 3' de cada gene de reovirus. En resumen, este estudio presenta un protocolo de amplificación rápido y universal que produce suficiente ADN complementario de doble cadena y facilita y acelera la secuenciación del genoma completo de los reovirus.

Randomly primed, strand-switching, MinION-based sequencing for the detection and characterization of cultured RNA viruses.

RNA viruses rapidly mutate, which can result in increased virulence, increased escape from vaccine protection, and false-negative detection results. Targeted detection methods have a limited ability to detect unknown viruses and often provide insufficient data to detect coinfections or identify antigenic variants. Random, deep sequencing is a method that can more fully detect and characterize RNA viruses and is often coupled with molecular techniques or culture methods for viral enrichment. We tested viral culture coupled with third-generation sequencing for the ability to detect and characterize RNA viruses. Cultures of bovine viral diarrhea virus, canine distemper virus (CDV), epizootic hemorrhagic disease virus, infectious bronchitis virus, 2 influenza A viruses, and porcine respiratory and reproductive syndrome virus were sequenced on the MinION platform using a random, reverse primer in a strand-switching reaction, coupled with PCR-based barcoding. Reads were taxonomically classified and used for reference-based sequence building using a stock personal computer. This method accurately detected and identified complete coding sequence genomes with a minimum of 20× coverage depth for all 7 viruses, including a sample containing 2 viruses. Each lineage-typing region had at least 26× coverage depth for all viruses. Furthermore, analyzing the CDV sample through a pipeline devoid of CDV reference sequences modeled the ability of this protocol to detect unknown viruses. Our results show the ability of this technique to detect and characterize dsRNA, negative- and positive-sense ssRNA, and nonsegmented and segmented RNA viruses.

Real-time, MinION-based, amplicon sequencing for lineage typing of infectious bronchitis virus from upper respiratory samples.

Infectious bronchitis (IB) causes significant economic losses in the global poultry industry. Control of IB is hindered by the genetic diversity of the causative agent, infectious bronchitis virus (IBV), which has led to the emergence of several serotypes that lack complete serologic cross-protection. Although serotyping requires immunologic characterization, genotyping is an efficient means to identify IBVs detected in samples. Sanger sequencing of the S1 subunit of the spike gene is currently used to genotype IBV; however, the universal S1 PCR was created to work from cultured IBV, and it is inefficient at detecting multiple viruses in a single sample. We describe herein a MinION-based, amplicon-based sequencing (AmpSeq) method that genetically categorized IBV from clinical samples, including samples with multiple IBVs. Total RNA was extracted from 15 tracheal scrapings and choanal cleft swab samples, randomly reverse transcribed, and PCR amplified using modified S1-targeted primers. Amplicons were barcoded to allow for pooling of samples, processed per manufacturer's instructions into a 1D MinION sequencing library, and then sequenced on the MinION. The AmpSeq method detected IBV in 13 of 14 IBV-positive samples. AmpSeq accurately detected and genotyped both IBV lineages in 3 of 5 samples containing 2 IBV lineages. Additionally, 1 sample contained 3 IBV lineages, and AmpSeq accurately detected 2 of the 3 lineages. Strain identification, including detection of different IBVs from the same lineage, was also possible with this AmpSeq method. Our results demonstrate the feasibility of using MinION-based AmpSeq for rapid and accurate identification and lineage typing of IBV from oral swab samples.

Multicentric Round Cell Neoplasms and Their Viral Associations in Wild Turkeys (Meleagris gallopavo) in the Southeastern United States.

Multiple oncogenic viruses, including lymphoproliferative disease virus (LPDV) and reticuloendotheliosis virus (REV), have been detected in wild turkeys (Meleagris gallopavo). The prevalence of infection with these viruses appears to be more common than overt disease; thus, data on the manifestation of associated disease in wild turkeys are scarce. Diagnostic records from wild turkeys submitted to the Southeastern Cooperative Wildlife Disease Study from 1980 to 2017 were reviewed to identify cases of neoplasia. Neoplasia was reported in 59 of 851 (6.9%) wild turkeys submitted. Of the cases of neoplasia tested by polymerase chain reaction, LPDV was detected in 34 of 58 (59%), REV in 10 of 39 (26%), both viruses in 3 of 39 (8%), and no retroviruses detected in 5 of 39 (13%) turkeys. The most common gross lesions observed among turkeys with neoplasms were emaciation (30/40; 75%); nodules in the skin (26/59; 44%), liver (17/59; 29%), or spleen (9/59; 15%); and splenomegaly (14/59; 24%). Microscopically, nodules were composed of pleomorphic round cells with large eccentric nuclei and prominent nucleoli resembling lymphocytes or lymphoblasts (57/59; 97%) except for 2 cases, one of myeloid cell origin and the other with primarily spindloid cells. This study indicates the need to characterize the pathogenesis and potential health threat posed by REV and LPDV to wild turkeys. Experimental infection studies and the development of additional diagnostic tests to confirm the role of retroviruses in lymphoproliferative disease are warranted.

Semi-Quantification of Total Campylobacter and Salmonella During Egg Incubations Using a Combination of 16S rDNA and Specific Pathogen Primers for qPCR.

Rapid molecular techniques that evaluate eggs for the presence of foodborne pathogens is an essential component to poultry food safety monitoring. Interestingly, it is not just table eggs that contribute to outbreaks of foodborne disease. Broiler layer production actively contributes to sustaining of foodborne pathogens within a flock. The surface contamination of production eggs with invasive pathogens such as Salmonella enterica, Campylobacter jejuni, and Listeria monocytogenes during embryogenesis results in gastrointestinal tract (GIT) colonization. Pathogens that secure a niche within the GIT during embryonic development are nearly impossible to eradicate from the food chain. Therefore, current monitoring paradigms are not comprehensive because they fail to capture the presence of invasive pathogens within the embryonic GIT rapidly. By developing tools to recognize the pathogens' presence in the GIT during embryogenesis, producers are then able to spot evaluate broiler eggs for their potential risk as carriers of foodborne pathogens. In this study a novel qPCR assay was developed to semi-quantify pathogen load relative to total bacterial burden. Eggs sampled from three independent production broiler flocks of different ages were assayed for S. enterica (invA), C. jejuni (HipO), and L. monocytogenes (HlyA) against total microbial load (16s). The eggs were sampled at 1-day post-set within each flock, 2 weeks post-set, after vaccination (at 2.5 weeks) and 1-day post-hatch. The eggs were washed, and the yolk and embryonic chick GIT were collected. The DNA was extracted and subjected to a qPCR assay. The results confirm a novel technique for pathogen monitoring relative to total bacterial load and a unique method for monitoring the dynamics of foodborne pathogen invasion throughout broiler egg production.

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.

Current limitations in control of viral arthritis and tenosynovitis caused by avian reoviruses in commercial poultry.

Avian reoviruses are the causative agent of viral arthritis/tenosynovitis in chickens and turkeys. Clinical signs of disease include swelling of the hock joints accompanied by lesions in the gastrocnemius and digital flexor tendons causing lameness in addition to hydropericardium. The economic impact is significant as it results in poor weight gain, increased feed conversion ratios and condemnations at the processing plant. Vaccination with both live attenuated and inactivated oil emulsion vaccines have been used successfully for decades to control the disease. Current commercial vaccine strains belong to the same serotype and are antigenically and serologically distinct from circulating variant field viruses isolated from clinical cases of tenosynovitis. Since 2012, there has been a dramatic increase in the number of clinical cases of tenosynovitis in commercial poultry and commercial vaccines are unable to provide adequate levels of protection against disease. Producers have elected to use custom inactivated vaccines in the absence of any commercially available homologous vaccines. Identification and selection of field isolates for use in autogenous vaccines can be difficult especially when multiple reoviruses are co-circulating among flocks. In addition, field data suggests that in some cases the custom vaccines are providing adequate protection against disease but as new genetic variants emerge, new vaccines are needed.

rpoS-Regulated core genes involved in the competitive fitness of Salmonella enterica Serovar Kentucky in the intestines of chickens.

Salmonella enterica serovar Kentucky has become the most frequently isolated serovar from poultry in the United States over the past decade. Despite its prevalence in poultry, it causes few human illnesses in the United States. The dominance of S. Kentucky in poultry does not appear to be due to single introduction of a clonal strain, and its reduced virulence appears to correlate with the absence of virulence genes grvA, sseI, sopE, and sodC1. S. Kentucky's prevalence in poultry is possibly attributable to its metabolic adaptation to the chicken cecum. While there were no difference in the growth rate of S. Kentucky and S. Typhimurium grown microaerophilically in cecal contents, S. Kentucky persisted longer when chickens were coinfected with S. Typhimurium. The in vivo advantage that S. Kentucky has over S. Typhimurium appears to be due to differential regulation of core Salmonella genes via the stationary-phase sigma factor rpoS. Microarray analysis of Salmonella grown in cecal contents in vitro identified several metabolic genes and motility and adherence genes that are differentially activated in S. Kentucky. The contributions of four of these operons (mgl, prp, nar, and csg) to Salmonella colonization in chickens were assessed. Deletion of mgl and csg reduced S. Kentucky persistence in competition studies in chickens infected with wild-type or mutant strains. Subtle mutations affecting differential regulation of core Salmonella genes appear to be important in Salmonella's adaptation to its animal host and especially for S. Kentucky's emergence as the dominant serovar in poultry.

Biological specimen collection and processing for molecular analysis.

This chapter provides a standardized best practice approach to sample collection and handling for the purpose of nucleic acid (NA) extraction and PCR. These methods are described through text and clearly illustrated figures. Furthermore, for those cases in which transportation of samples cannot be accomplished due to the inability to maintain the cold chain or limitations on the import of live disease agents in diagnostic samples, the chapter describes the use of FTA cards for collection transport and NA preparation of samples for PCR. This chapter also makes emphasis in the best safety practices for handling of samples/tissues to avoid unnecessary disease exposures to laboratory personnel. Finally, NA extraction best practices and methods will be briefly outlined.

Tribasic copper chloride toxicosis in commercial broiler chicks.

Two broiler chicken houses containing 17,500 chicks each experienced an extreme elevation in chick mortality beginning on day 3 after placement. Clinical signs observed upon farm visit included numerous small chicks for their age; depressed, lethargic, and comatose chicks; and chicks huddling near feed pans and under heaters. Necropsied chicks were markedly pale and had atrophy of the thymus and bursa, swollen and edematous proventriculus, erosions in the koilin and in the proventricular-ventricular junction, pale kidneys, and yellowish to brownish-orange liver often with linear pale areas. The chicks had watery blood and hematocrits measured from 9.5% to 18%. Chicken infectious anemia was initially suspected based on the clinical signs and gross lesions. Histopathology revealed multifocal acute hepatic degeneration and necrosis with golden-brown pigment in the cytoplasm of hepatocytes and Kupffer cells, moderate to severe koilin degeneration and fragmentation, multifocal mild to moderate proventricular necrosis, mild to moderate necrosis and loss of enterocytes, blunting of small intestinal villi, lymphoid depletion in the thymus and bursa, erythrophagocytosis in the liver and spleen, and acute renal tubular degeneration and necrosis. Special stains revealed mild to abundant accumulation of copper pigment in the cytoplasm of hepatocytes and iron pigment in the cytoplasm of Kupffer cells. Feed analysis revealed 2140 to 2393 parts per million of copper in the starter ration, and heavy metal analysis detected markedly elevated copper levels in formalin-fixed samples of the liver. Excessive amounts of tribasic copper chloride in the starter ration caused copper toxicosis in these chicks. Similar clinical signs and lesions were reproduced when the suspect feed was used in an experimental pen trial.

An in vivo experimental model to determine antigenic variations among infectious bursal disease viruses.

Infectious bursal disease virus (IBDV) is a double-stranded RNA virus causing infectious bursal disease in chickens. IBDV undergoes antigenic drift, so characterizing the antigenicity of IBDV plays an important role for identification and selection of vaccine candidates. In this study, an in vivo experimental model was developed to differentiate a new antigenic variant of IBDV. To this end, a hyper-immune serum to IBDV E/Del-type virus was generated in specific pathogen-free chickens and a standard volume of the hyper-immune serum was serially diluted and injected in specific pathogen-free birds via intravenous, subcutaneous, or intramuscular routes. The chickens were bled at different time points in order to evaluate the dynamics of virus neutralization titres. Based on the results, chickens were injected with different serum dilutions by the subcutaneous route. Twenty-four hours later, chickens were bled and then challenged with 100 median chicken infectious doses of the E/Del virus and a new IBDV variant. Chickens were euthanized at 7 days post infection and the bursa of Fabricius was removed for microscopic evaluation to determine the bursal lesion score. The determined virus neutralization titre along with the bursal lesion score was used to determine the breakthrough titre in the in vivo chicken model. Based on the data obtained, an antigenic subtype of IBDV was identified and determined to be different from E/Del. This model is a sensitive model for determination of IBDV antigenicity of non-tissue culture adapted IBDV.

Comparing presence of avian paramyxovirus-1 through immunohistochemistry in tracheas of experimentally and naturally infected chickens.

Tracheas from chickens infected both in the field and experimentally with lentogenic Newcastle disease virus (also known as avian paramyxovirus-1 [APMV-1] and referred to here as "lentogenic NDV") were examined histopathologically to score degree of pathologic changes and by immunohistochemistry to determine presence of viral protein. In the field cases there was often a striking lack of correlation between severity of tracheal lesions and amount of immunohistochemical signal for APMV-1 protein. Experimental cases had minimal pathologic changes and also minimal immunohistochemical signal. Positive cells were often associated with surface deciliation. It may be that lentogenic NDV has only a minor role as a respiratory pathogen, merely compromising the mucosa to allow other respiratory pathogens to infect and worsen the clinical and pathologic presentation.