Variability Assessment of California Infectious Bronchitis Virus Variants.

On the basis of the data from the California Animal Health and Food Safety Laboratory System, 1444 infectious bronchitis (IB) cases were diagnosed between 1997 and 2012. Epidemiologic analyses demonstrated two major IB virus (IBV) outbreak peaks, affecting mainly 35-to-49-day-old broiler chickens. California variant 1737 (CA1737) and California variant 1999 (Cal 99) IBV types were the most prevalent genotypes during the analyzed period. To further understand the increased prevalence of these genotypes, we assessed and compared the variability of the S1 gene hypervariable region of CA1737 and Cal 99 with the variability of IBV strains belonging to the Massachusetts 41 (M41) and Arkansas (Ark) types during serial passages in embryonated chicken eggs. On the basis of the S1 nonsynonymous changes, seven different subpopulations were detected in M41. However, the predominant population of the field strain M41 before passages continued to be predominant throughout the experiment. In contrast, Ark passaging resulted in the detection of 13 different subpopulations, and the field sequence became extinct after the first passage. In IBV Cal 99, eight different subpopulations were detected; one of these became predominant after the second passage. In CA1737, 10 different subpopulations were detected. The field strain major sequence was not detected after the first passage but reappeared after the second passage and remained at low levels throughout the experiment. Compared with M41 and Ark, Cal 99 and CA1737 showed intermediate variability.

Spatial and temporal epidemiology of infectious laryngotracheitis in central California: 2000-2012.

In October of 2005 an outbreak of a vaccine-like strain of infectious laryngotracheitis (ILT), indistinguishable from the chicken embryo origin (CEO)-like vaccine strains, was detected by routine passive surveillance in the Central Valley of California, U. S. A. In response, a highly coordinated industry effort by two companies led to a significant decrease in the incidence of ILT over the same geographic region between 2008-2012. In order to understand the geographic and temporal spread of ILT in California before and after the outbreak, Global Information Systems (GIS) mapping coupled with spatial, temporal, and spatial- temporal statistics were used to identify retrospective and prospective low-rate clustering (i.e., less ILT than statistically expected) and high-rate clustering (i.e., more ILT than statistically expected) of ILT spatially and temporally. Results showed two high-rate retrospective spatial-temporal clusters and one low-rate prospective spatial-temporal cluster which were all statistically significant (P < 0.05). Overall, spatial-temporal clustering accounted for 36.9% of the positive ILT cases, while temporal clustering and spatial clustering done separately each accounted for 0% of the ILT cases, respectively. This demonstrates the utility of combining spatial and temporal clustering for ILT surveillance. Due to the risk of reversion to virulence and spread to immunologically naive broilers, future application of the CEO-based vaccine in the identified high rate spatial-temporal clusters should be avoided and other vaccine alternatives considered in order to avoid repeat outbreaks in those areas. This should especially be followed during the winter months of December, January, and February, which were found to have the highest prevalence of ILT (P < 0.05). Analysis of GIS data within the high-rate clusters showed that wind direction and farm density were minor factors in the spread of ILT. Shared roads may have played a role in the spread of ILT in one of the two high rate spatial-temporal clusters.

Effects of challenge with very virulent infectious bursal disease virus reassortants in commercial chickens.

Pathogenicity and immune responses were characterized in commercial broilers and layers challenged with very virulent infectious bursal disease virus (vvIBDV) reassortants (vvIBDV segment A + serotype 2 segment B and vvIBDV segment A + classic virulent segment B) at 7 days of age. In addition, functional immunosuppression was evaluated after challenge with infectious bronchitis virus (IBV) at 15 days of age. Layers showed higher levels and increased persistence of IBDV- and IBV-specific maternal antibodies than broilers at 1, 13, and 28 days of age. Cytokine gene expression was evaluated, after IBDV challenge, as an indicator of the innate immune function. Similar results were detected between the groups inoculated with vvIBDV reassortants. Interleukin-1ß (IL-1ß) in the bursa of layers demonstrated down-regulation at 1 day postinfection (DPI; 8 days of age), and no changes at 4 DPI (11 days of age) compared with controls. In broilers, IL-6 expression in the bursa was down-regulated 1 DPI (8 days of age) and up-regulated at 4 DPI (11 days of age). A significant lymphoid depletion was detected at 21 DPI (28 days of age) in broilers exposed to a reassortant of vvIBDV segment A and classic virulent IBDV segment B. Finally, reduced specific antibodies against IBV measured 13 days after challenge were detected in layer and broiler chickens inoculated with a reassortant serotype 2 IBDV in segment B, suggesting functional immunosuppression. These results provide evidence indicating that current IBDV vaccination of breeders does not completely protect progeny chickens from challenge with reassortant vvIBDV.

Nephritis associated with infectious bronchitis virus Cal99 variant in game chickens.

Infectious bronchitis virus (IBV) Cal99 variant was isolated from the kidneys of seven 2-5-mo-old game chickens with nephritis and respiratory disease. IBV Cal99 variant is usually associated with respiratory disease in broiler chickens in California. Macroscopically, the majority of the birds had moderately to severely enlarged and mottled pale kidneys, with increased urates in the ureters. Microscopically, most of the birds had acute nephrosis and interstitial nephritis. The birds also had sinusitis, tracheitis, bronchopneumonia, airsacculitis, salivary gland adenitis, and lymphoid depletion in the thymus and bursa of Fabricius. Immunohistochemistry was strongly positive for IBV antigen in the cytoplasm of tubular epithelial cells in the kidneys and also in the epithelium of the respiratory tract, salivary glands, proventriculus, intestine, and bursa of Fabricius. Infectious bronchitis virus was isolated from the trachea, lungs, kidneys, and cecal tonsils. Sequencing of the hypervariable region of the S1 gene of the kidney IBV isolate, designated IBV/CA99variant/07, revealed that the virus was 98% homologous to the Cal99 serotype of IBV.

Unusual pathology of canary poxvirus infection associated with high mortality in young and adult breeder canaries (Serinus canaria).

Mortality in excess of 65% occurred in a flock of 450 canaries (Serinus canaria). Clinical signs in the canaries included severe respiratory distress, loss of feathers and/or scaly skin on the head, neck and back, anorexia, loss of weight and fluffed-up appearance of several days duration before death. Gross pathology in most of the canaries included thickened eye lids and small scab-like nodules on the skin of the head and neck, enlarged thymus, mild to severe consolidation of lungs and exudate in the sinuses and trachea. A few birds also had thickened air sacs and enlarged and pale spleens. Microscopically unusual lesions included severe epithelial proliferation and hypertrophy and mononuclear inflammatory cells containing eosinophilic intracytoplasmic inclusion bodies of poxvirus in the thymus, bursa of Fabricius, spleen, bone marrow, air sac, peritoneum, external and middle ears, and lachrymal gland. Similar inclusion bodies associated with inflammation were also seen in the epidermis, dermis, feather follicles, conjunctivae, sinuses, turbinates, choana, oral mucosa including tongue, oesophagus, larynx, trachea, syrinx and bronchi and parabronchi of lungs. Some of the birds also had concurrent bacterial, mycotic and polyomavirus infections. Poxvirus was isolated from lungs and skin in chicken embryo liver cells and confirmed as avian poxvirus by polymerase chain reaction.

Myocarditis associated with reovirus in turkey poults.

Myocarditis associated with reovirus was diagnosed in 17-day-old, male turkey poults, based on virus isolation, reverse transcriptase-polymerase chain reaction (RT-PCR), demonstration of reovirus antigen in the cytoplasm of mononuclear inflammatory cells and myocytes in the heart by immunohistochemistry (IHC), and reovirus particles in the endoplasmic reticulum of myocytes by transmission electron microscopy (TEM). Clinical signs in the poults included anorexia, growth depression, and increased mortality. Gross lesions in the six poults examined were increased pericardial fluid, mild-to-moderate dilation of right ventricles, pale-yellow myocardium, and ascites. Other lesions in a few birds included mild pulmonary edema, congestion, and pale serosa of the small intestine that had watery contents in their lumens. Microscopically, in the heart, there was mild-to-severe necrosis of myocytes and infiltration of primarily lymphocytes mixed with a few heterophils, macrophages, and occasionally, plasma cells and multinucleated giant cells. There was mild-to-moderate lymphoid depletion in the bursa of Fabricius. Reovirus was isolated from the heart of the turkey poults in chicken-embryo liver cells and was confirmed by RT-PCR, IHC, and TEM. A retrospective search of the laboratory database for cases of myocarditis associated with reovirus in turkeys revealed that this condition has occurred sporadically in California turkey flocks since 1991. This is the first documentation of myocarditis in turkey poults associated with reovirus.

Intervention strategies for laryngotracheitis: impact of extended downtime and enhanced biosecurity auditing.

An outbreak of vaccinal infectious laryngotracheitis (LT) began in 2005 involving 57 ranches of two broiler companies in California. Standard biosecurity, and cleaning and disinfection programs along with vaccination, did not stop the outbreak. Due to the close proximity and number of birds in the same geographic area, the decision was made by both companies to attempt a joint regional and zonal depopulation strategy. The strategy involved extended downtime between flock placements on ranches located within close proximity to one another. This extended downtime on each ranch ranged from 30 to 91 days. An extensive biosecurity audit, with more than 70 items, was implemented. Briefly, this included heating all houses to 37 C for 100 hr, removing the litter, cleaning and disinfecting everything on the ranches, then again heating the houses to 37 C for 100 hr. Used litter was spread on crops away from poultry, or was sent to a litter processor for pasteurization. Extensive surveillance for LT at 28, 35, and 42 days of age was performed on the initial flocks, which had been placed immediately after the extended downtime. Since completion of this plan in early 2008, LT was diagnosed on only two of the previously 57 affected ranches. Those two ranches, and those within close proximity, went through the extended downtime program and biosecurity audit a second time. Currently, both companies are free of LT. This program lends credence to the importance of cooperation between companies to consider all the ranches within close proximity as the population at risk. In the control of LT in broilers, the program also highlights the necessity for extended downtime and enhanced biosecurity auditing of all flocks.

Low-pathogenicity avian influenza virus (H6N2) in chickens in California, 2000-02.

During 2000, 2001, and January 2002, avian influenza virus was isolated from chickens from 12 different locations in California. All the isolates were typed as H6N2 and determined to be of low pathogenicity for chickens. Nine of the isolates came from commercial layer flocks; one from a backyard flock; one from a mixed age flock, where ducks and squabs were also present; and one from a primary broiler breeder. Although a drop in egg production and increased mortality were among the disease signs reported in the layer flocks, the pathological changes observed in the early cases were primarily associated with mild respiratory infections. It was not until August 2001 that yolk peritonitis was observed; this has been a feature of all the remaining cases through 2001 and 2002. All the isolates clustered as a unique group separate from other influenza viruses based upon sequence data of the H6, neuraminidase (N2), and matrix (MA) genes, indicating a common ancestor for these three gene segments. However, sequencing of the nonstructural (NS) gene indicates introductions from two separate origins. With the first isolate CK/CA/431/00 as the index case, the N2, MA, and NS genes are more closely related to North American isolates, as is the NP gene of CK/CA/650/00. In contrast, the H6 gene is more closely related to a Eurasian influenza isolate. Comparison of amino acid sequences of the N2 and MA genes of these isolates with available type A influenza viruses identified two unique changes in the MA gene and nine in the N2 gene, as well as four progressive changes. These results are discussed in relation to available clinical and epidemiological data.

Multiple genotypes of nonpathogenic H6N2 influenza viruses isolated from chickens in California.

From February 2000 through September 2001, a limited number of H6N2 influenza viruses were isolated from chickens in California. This report describes the genetic characterization of nine of these H6N2 viruses. All of the viruses analyzed had phylogenetically similar hemagglutinin (HA) and neuraminidase molecules that suggested the viruses shared a recent common ancestor. The analysis of the HA sequence of these viruses with all available H6 viruses from different hosts and locations showed that these genes do not separate into well-defined North American and Eurasian lineages. The neuraminidase genes of the California viruses contain an 18 amino acid deletion, a possible adaptation to growth in chickens. Analysis of the remaining gene segments of the California viruses revealed that three distinct genotypes of H6N2 viruses were present.

Heterogeneity and seroprevalence of a newly identified avian hepatitis e virus from chickens in the United States.

We recently identified and characterized a novel virus, designated avian hepatitis E virus (avian HEV), from chickens with hepatitis-splenomegaly syndrome (HS syndrome) in the United States. Avian HEV is genetically related to but distinct from human and swine HEVs. To determine the extent of genetic variation and the seroprevalence of avian HEV infection in chicken flocks, we genetically identified and characterized 11 additional avian HEV isolates from chickens with HS syndrome and assessed the prevalence of avian HEV antibodies from a total of 1,276 chickens of different ages and breeds from 76 different flocks in five states (California, Colorado, Connecticut, Virginia, and Wisconsin). An enzyme-linked immunosorbent assay using a truncated recombinant avian HEV ORF2 antigen was developed and used to determine avian HEV seroprevalence. About 71% of chicken flocks and 30% of chickens tested in the study were positive for antibodies to avian HEV. About 17% of chickens younger than 18 weeks were seropositive, whereas about 36% of adult chickens were seropositive. By using a reverse transcription-PCR (RT-PCR) assay, we tested 21 bile samples from chickens with HS syndrome in California, Connecticut, New York, and Wisconsin for the presence of avian HEV RNA. Of the 21 bile samples, 12 were positive for 30- to 35-nm HEV-like virus particles by electron microscopy (EM). A total of 11 of the 12 EM-positive bile samples and 6 of the 9 EM-negative bile samples were positive for avian HEV RNA by RT-PCR. The sequences of a 372-bp region within the helicase gene of 11 avian HEV isolates were determined. Sequence analyses revealed that the 11 field isolates of avian HEV had 78 to 100% nucleotide sequence identities to each other, 79 to 88% identities to the prototype avian HEV, 76 to 80% identities to chicken big liver and spleen disease virus, and 56 to 61% identities to other known strains of human and swine HEV. The data from this study indicated that, like swine and human HEVs, avian HEV isolates are genetically heterogenic and that avian HEV infection is enzoonotic in chicken flocks in the United States.

Turlock-like bunyavirus associated with encephalomyelitis and myocarditis in an ostrich chick.

In the fall of 1995, a 20-day-old female ostrich chick, 1 of a group of 20, was presented live with clinical signs of 2 days duration characterized by unsteady gait, circling to the left, and walking backward. Another bird with similar clinical signs had died and another had recovered. The bird was euthanized and examined at necropsy. Twenty-five milliliters of serous fluid was in the abdominal cavity and there was increased pericardial fluid. Histopathology of the brain revealed mild to moderate nonsuppurative encephalitis characterized by mild multifocal malacia, perivascular cuffing by lymphocytes, and gliosis. The heart had multifocal infiltrations of lymphocytes mixed with macrophages and a few plasma cells throughout the myocardium. Cytopathic effects were observed in primary chicken embryo liver cells following inoculation with a tissue homogenate prepared from the brain of the affected ostrich. Virus particles the size and morphology of the family Bunyaviridae were observed in cell culture lysate by negative-stain electron microscopy. Viral characterization demonstrated that the virus isolate is a previously unknown serotypic variant (subtype) of Turlock virus. Twelve of 65 sera collected over a 3-year period from ostriches aged from 1 month to 4 years were positive for neutralizing antibody to both the Turlock prototype strain and the new subtype of Turlock virus described in this report.

Genetic and antigenic characterization of a poxvirus isolate from ostriches.

Avian poxvirus was isolated from nodules on the heads and conjunctiva of two 3-to-4-wk-old ostrich chicks. The ostriches from which poxvirus was isolated had been placed on premises where turkeys that had shown evidence of poxvirus infection had been raised earlier. Microscopically, the nodules from the ostriches were composed of proliferating and hypertrophic epithelial cells that formed large fronds. Most of the hypertrophic epithelial cells contained large eosinophilic intracytoplasmic inclusion bodies characteristic of poxvirus. Characterization of the avian poxvirus isolated from the cutaneous lesions in ostriches was based on western blotting of virus antigen, restriction fragment length polymorphism of genomic DNA, pathogenesis, and cross-protection studies in chickens. Antigenic and genetic studies did not reveal any significant difference between the poxvirus isolated from ostriches (PVO) and fowl poxvirus (FPV). Further, susceptible chickens immunized with the PVO were protected when challenged with a virulent strain of FPV. Thus, the poxvirus isolated from ostriches had similar antigenic, genetic, and biological properties to FPV.

Isolation from turkey breeder hens of a reassortant H1N2 influenza virus with swine, human, and avian lineage genes.

Type A influenza viruses can infect a wide range of birds and mammals, but influenza in a particular species is usually considered to be species specific. However, infection of turkeys with swine H1N1 viruses has been documented on several occasions. This report documents the isolation of an H1N2 influenza virus from a turkey breeder flock with a sudden drop in egg production. Sequence analysis of the virus showed that it was a complex reassortant virus with a mix of swine-, human-, and avian-origin influenza genes. A swine influenza virus with a similar gene complement was recently reported from pigs in Indiana. Isolation and identification of the virus required the use of nonconventional diagnostic procedures. The virus was isolated in embryonated chicken eggs by the yolk sac route of inoculation rather than by the typical chorioallantoic sac route. Interpretation of hemagglutination-inhibition test results required the use of turkey rather than chicken red blood cells, and identification of the neuraminidase subtype required the use of alternative reference sera in the neuraminidase-inhibition test. This report provides additional evidence that influenza viruses can cross species and cause a disease outbreak, and diagnosticians must be aware that the variability of influenza viruses can complicate the isolation and characterization of new isolates.

Genetic identification and characterization of a novel virus related to human hepatitis E virus from chickens with hepatitis-splenomegaly syndrome in the United States.

Hepatitis-splenomegaly (HS) syndrome is an emerging disease in chickens in North America; the cause of this disease is unknown. In this study, the genetic identification and characterization of a novel virus related to human hepatitis E virus (HEV) isolated from bile samples of chickens with HS syndrome is reported. Based upon the similar genomic organization and significant sequence identity of this virus with HEV, the virus has been tentatively named avian HEV in order to distinguish it from human and swine HEV. Electron microscopy revealed that avian HEV is a non-enveloped virus particle of 30-35 nm in diameter. The sequence of the 3' half of the viral genome ( approximately 4 kb) was determined. Sequence analyses revealed that this genomic region contains the complete 3' non-coding region, the complete genes from open reading frames (ORFs) 2 and 3, the complete RNA-dependent RNA polymerase (RdRp) gene and a partial helicase gene from ORF 1. The helicase gene is the most conserved gene between avian HEV and other HEV strains, displaying 58-61% aa and 57-60% nt sequence identities. The RdRp gene of avian HEV shares 47-50% aa and 52-53% nt sequence identities and the putative capsid gene (ORF 2) of avian HEV shares 48-49% aa and 48-51% nt sequence identities with the corresponding regions of other known HEV strains. Phylogenetic analysis indicates that avian HEV is genetically related to, but distinct from, other known HEV strains. This discovery has important implications for HEV animal models, nomenclature and natural history.

Enhanced recovery of avian influenza virus isolates by a combination of chicken embryo inoculation methods.

Since 1993, 14 cases of avian influenza from four different states in the U.S.A. have been diagnosed by virus isolation from eight avian species. Only 11 of the 14 avian influenza virus (AIV) primary isolations would have been successful if only the standard protocol for AIV isolation, i.e., inoculation of specific-pathogen-free embryonating chicken eggs (ECEs) by the chorioallantoic sac (CAS) route, had been followed. Primary isolation attempts were negative for AIV in three cases in which ECEs were inoculated by the CAS route; AIV could not be detected by hemagglutinating activity, agar gel immunodiffusion test or negative stain electron microscopy. However, in these three cases, primary isolations of AIV were achieved by inoculation of ECEs into either the yolk sac or onto the chorioallantoic membrane.

Group I avian adenovirus and avian adeno-associated virus in turkey poults with inclusion body hepatitis.

Adenoviral inclusion body hepatitis (IBH) is rare in turkeys. Avian adenovirus group I and avian adeno-associated virus were isolated from the liver and pooled intestinal samples from 4-week-old turkey poults on two different ranches experiencing increased mortality. Grossly, a few birds from each ranch had a slightly enlarged liver with white foci of necrosis randomly scattered throughout. Microscopically, there was coagulative necrosis of hepatocytes with infiltration of a mixed population of inflammatory cells composed of lymphocytes, plasma cells, heterophils, and macrophages. In these livers, there were numerous basophilic intranuclear inclusion bodies in the hepatocytes. Transmission electron microscopy of the liver revealed 70 to 75 nm viral particles with icosahedral morphology consistent with adenovirus scattered throughout the nucleus of hepatocytes. All of the birds were serologically negative for haemorrhagic enteritis virus infection. Of some 5000 submissions over a 12-year period of turkey poults aged between 1 day and 10 weeks, only two single birds within two submissions had IBH.

Isolation of avian influenza virus (H10N7) from an emu (Dromaius novaehollandiae) with conjunctivitis and respiratory disease.

Avian influenza virus was isolated from the conjunctiva of a male emu chick. Clinical observations included ocular discharge, dyspnea, and mild respiratory signs. Lesions included conjunctivitis, tracheitis, bronchopneumonia, and airsacculitis. Escherichia coli was isolated from the conjunctiva and the sinus, and Staphylococcus sp. was isolated from the conjunctiva. Influenza A viral nucleoprotein was detected immunohistochemically in epithelial cells of the bronchi, lung parenchyma and tracheal mucosa, and mononuclear inflammatory cells within the exudate of the bronchial lumen; conjunctiva, air sacs, kidney, intestine, and liver were negative for the viral nucleoprotein. The isolated influenza virus was typed as H10N7 and was determined to be nonpathogenic for chickens.

Evidence of Muscovy duck parvovirus in Muscovy ducklings in California.

Muscovy duck parvovirus (MDPV) has been demonstrated in tissue samples from one- to four-week-old commercially reared Muscovy ducks that were weak, unable to walk and had a high mortality rate. On postmortem examination, the thigh and leg muscles, and the myocardium were found to be pale, and there was a fibrinous exudate on the capsule of the liver, and ascites. The parvovirus was isolated in embryonated Muscovy duck eggs and visualised by negative stain electron microscopy, detected by polymerase chain reaction (PCR) directly from the tissues, and antibodies to it were detected by immunoelectron microscopy, ELISA and immunofluorescence. In addition, the PCR products obtained that represented 1625 bp (74 per cent) of the capsid vP1 gene, including a hypervariable region between Derzsy's disease virus or goose parvovirus and MDPV, were sequenced and shown to be 100 per cent homologous with the MDPV 89384 reference strain, but only 82.3 per cent homologous with Derzsy's disease virus.

Exotic Newcastle disease in a game chicken flock.

A sudden increase in mortality, preceded by a short history of respiratory signs and diarrhea, occurred in a backyard flock of 48 game chickens in the Central Valley of California. Necropsy findings included severe generalized linear hemorrhages and/or ulcers in the digestive tract, larynx, and trachea. Histology revealed severe multifocal hemorrhages and necrosis in the mucosa of the respiratory and digestive tracts, vasculitis, and necrosis of lymphoid tissue. The birds were serologically negative to Newcastle disease virus; this was consistent with an acute infection. The avian paramyxovirus type 1 isolated was characterized as velogenic viscerotropic Newcastle disease virus. A thorough epidemiologic investigation was carried out, and no other premises were found to have birds with clinical signs or evidence of exposure. The entire outbreak was limited to the original backyard flock and resolved within 14 days of the onset of clinical signs.

Inclusion body tracheitis associated with avian adenovirus in turkeys.

Nine turkey flocks with basophilic intranuclear inclusion bodies, suggestive of adenovirus, within the epithelial cells of the tracheal mucosa were studied. Respiratory signs and increased mortality occurred in turkeys between 6 and 10 wk of age from nine commercial turkey meat flocks in central California. Necropsy findings included tracheitis and occasional mild sinusitis. Histopathology of the tracheas revealed epithelial deciliation, squamous metaplasia, large basophilic intranuclear inclusion bodies within epithelial cells, and lymphoplasmatic inflammation in the mucosa. Electron microscopy of the mucosa revealed hexagonal viral particles, approximately 73 nm in diameter, consistent with adenovirus within the nuclei of epithelial cells. All tracheal sections were negative for adenovirus group II by specific immunoperoxidase staining. Adenovirus group I was isolated from the trachea. In addition, Bordetella avium, Ornithobacterium rhinotracheale, and Klebsiella pneumoniae were isolated from the tracheas of three, three, and two flocks, respectively. Statistically greater total mortality and a smaller percentage of marketed turkeys were observed in the submitted flocks than in randomly selected flocks. No significant difference was observed between the two turkey groups in market weight, feed conversion, or percentage of grade "A" turkeys.