Variability Assessment of California Infectious Bronchitis Virus Variants

Differential Impact of Massachusetts, Canadian 4/91, and California (Cal) 1737 Genotypes of Infectious Bronchitis Virus Infection on Lymphoid Organs of Chickens

Infectious bronchitis virus (IBV) induces severe economic losses in chicken farms due to the emergence of new variants leading to vaccine breaks. The studied IBV strains belong to Massachusetts (Mass), Canadian 4/91, and California (Cal) 1737 genotypes that are prevalent globally. This study was designed to compare the impact of these three IBV genotypes on primary and secondary lymphoid organs. For this purpose, one-week-old specific pathogen-free chickens were inoculated with Mass, Canadian 4/91, or Cal 1737 IBV variants, keeping a mock-infected control. We examined the IBV replication in primary and secondary lymphoid organs. The molecular, histopathological, and immunohistochemical examinations revealed significant differences in lesion scores and viral distribution in these immune organs. In addition, we observed B-cell depletion in the bursa of Fabricius and the spleen with a significant elevation of T cells in these organs. Further studies are required to determine the functional consequences of IBV replication in lymphoid organs.

Infectious Bronchitis Virus California Variant CA1737 Isolated from a Commercial Layer Flock with Cystic Oviducts and Poor External Egg Quality

False layer syndrome is a condition in which the reproductive tract of chicks is infected with infectious bronchitis virus (IBV) strains that cause permanent damage to the oviduct. These chickens subsequently develop cystic oviducts and do not lay eggs, and affected flocks fail to reach expected egg production peaks. The California Animal Health and Food Safety laboratory, Turlock Branch, received four separate case submissions from a 25-to-28-wk-old commercial ISA Brown layer flock. Birds were submitted for diagnostic evaluation due to suboptimal egg production and vent pecking. Submissions totaled 31 birds and consisted of live layers, recent mortality, and a flat of eggs. No clinical signs were observed in the submitted live birds. The most common gross findings included cystic left oviducts, signs of vent pecking, ovarian regression, and yolk coelomitis. The eggs were abnormally shaped with irregular, white, gritty deposits on the surface of the shell. Microscopically, there was atrophy of the oviducts, glandular hypoplasia, and lymphocytic salpingitis. In addition, lymphoplasmacytic tracheitis was observed, and renal tubules were dilated with multifocal areas of mineralization. IBV was identified by reverse transcription quantitative PCR from cecal tonsil tissue pools and tracheal swab pools. Sequencing of the S1 hypervariable region of IBV and whole-genome IBV sequencing were 97% homologous to the California variant CA1737/04. Definitive proof of the CA1737 strain's causing reproductive abnormalities will require challenge studies with fulfillment of Koch's postulates and evaluation of confounding and risk factors.

Infectious Bronchitis Virus Associated with Nephropathy Lesions in Diagnostic Cases from Commercial Broiler Chickens in California

In March 2019, the California Animal Health and Food Safety Laboratory (CAHFS), Turlock branch, received two submissions of broiler chickens from commercial flocks reporting increased mortality. Submissions consisted of either white or brown broilers. Submitted chickens appeared depressed with ruffled feathers. At necropsy, moderate to severely enlarged and pale kidneys were observed, with gross lesions indicative of dehydration. Microscopically, renal tubules were degenerated and distended with necrotic debris and tubular casts. The kidney parenchyma contained mononuclear inflammatory cell infiltrates and interstitial edema. Infectious bronchitis virus (IBV) was isolated and identified by reverse transcription quantitative PCR from kidney tissue pools and tracheal swab pools from both cases. Partial sequencing of the S1 hypervariable region was most similar to a local California variant, CA1737. The outbreak lasted roughly 1 wk in both flocks, with 2% total mortality in the brown broilers and 20% total mortality in the white broilers. Final proof of the IBV strains causing nephropathy will require fulfillment of Koch postulates. IBV associated with nephropathy has been sporadically reported in California chicken flocks and represents a significant pathogen due to its potential for inducing high flock mortality. The incidence of IBV associated with a nephropathy diagnosis in chicken necropsy submissions to the CAHFS system-wide from 1998 to 2019 is also reviewed.

Infectious Bronchitis Virus Prevalence, Characterization, and Strain Identification in California Backyard Chickens

Infectious bronchitis virus (IBV) causes significant losses in the poultry industry throughout the world. Here we characterize the lesions of infectious bronchitis (IB) and IBV prevalence and identify the circulating strains in small flocks in California. Backyard chickens (BYCs) submitted to the Davis (Northern California; NorCal) and San Bernardino (Southern California; SoCal) branches of the California Animal Health and Food Safety Laboratory System from January through March 2019 were included in the study. Trachea, kidney, and cecal tonsils were collected for real-time reverse transcriptase (qRT)-PCR, histology, immunohistochemistry (IHC), and sequence analysis. A total of 50 chickens out of 169 submissions tested positive for IBV by qRT-PCR. Of these, 16% (20/123) were from NorCal and 65% (30/46) from SoCal laboratory. The cecal tonsil was the most frequently positive tissue by qRT-PCR and IHC. Lymphoplasmacytic tracheitis was the most frequent histopathologic finding in 24 of 39 birds, while the kidney showed interstitial nephritis, tubular necrosis, tubular dilation, and/or gout in 14 of 43 chickens. Infectious bronchitis virus played a primary role or a synergistic effect in the mortality of chickens that succumbed to other infectious diseases. The sequences of IBV detected in 22 birds were analyzed, and 14 strains were most similar to CA1737. One strain each matched Conn46, Cal99, and ArkDPI, and the remaining five did not have a substantial match to any available reference strains. The findings in this study indicate that small flocks can be reservoirs of IBV and might facilitate evolution of new variants as well as reversion of attenuated strains to virulence.

Molecular Biology and Pathological Process of an Infectious Bronchitis Virus with Enteric Tropism in Commercial Broilers

Infectious bronchitis virus (IBV) induces respiratory and urogenital disease in chickens. Although IBV replicates in the gastrointestinal tract, enteric lesions are uncommon. We have reported a case of runting-stunting syndrome in commercial broilers from which an IBV variant was isolated from the intestines. The isolate, CalEnt, demonstrated an enteric tissue tropism in chicken embryos and SPF chickens experimentally. Here, we determined the full genome of CalEnt and compared it to other IBV strains, in addition to comparing the pathobiology of CalEnt and M41 in commercial broilers. Despite the high whole-genome identity to other IBV strains, CalEnt is rather unique in its nucleotide composition. The S gene phylogenetic analyses showed great similarity between CalEnt and Cal 99. Clinically, vent staining was slightly more frequent in CalEnt-infected birds than those challenged with M41. Furthermore, IBV IHC detection was more evident and the viral shedding in feces was overall higher with the CalEnt challenge compared with M41. Despite underlying intestinal lesions caused by coccidiosis and salmonellosis vaccination, microscopic lesions in CalEnt-infected chickens were more severe than in M41-infected chickens or controls, supporting the enteric tropism of CalEnt. Further studies in SPF chickens are needed to determine the pathogenesis of the virus, its molecular mechanisms for the enteric tropism, and its influence in intestinal health.

Effects of Chicken MHC Haplotype on Resistance to Distantly Related Infectious Bronchitis Viruses

The major histocompatibility complex (MHC) B locus of chickens has been associated with resistance to different viral diseases. We previously provided evidence that chicken lines expressing MHC haplotypes B2 and B19 exhibit different resistance to a challenge with infectious bronchitis virus (IBV) Massachusetts 41 (M41). In the current study, we attempted to determine if those differences were true for genetically diverse IB viruses, i.e., IBV M41 and Arkansas-Delmarva poultry industry (ArkDPI). Clinical, pathologic, molecular, and immunologic outcomes were compared. Our results showed subtle clinical and pathologic differences between the two MHC chicken lines tested. Clinical differences were observed in respiratory signs at 2 days postinfection (dpi) in M41-infected birds. Pathologic differences were detected in viral load at 2 dpi in M41-infected birds and in tracheal epithelial thickness at 6 dpi in ArkDPI-infected birds. Substantial differences were observed in antibody responses at 14 dpi. The transcriptome analysis showed that B19 chickens highly expressed genes related to inflammatory and innate immune responses. This increased immune gene expression detected in B19 birds at 6 dpi did not lead to enhanced antibody production at 14 dpi. On the other hand, B2-haplotype chickens highly expressed genes related to cell responses, suggesting that B2 is able to diligently control the infection. Although not identical, genes triggered by M41 and ArkDPI are part of communal pathways and suggest similar immune and cell responses to both IBV genotypes. This work provides modest evidence for differential resistance to IBV by chickens displaying different MHC haplotypes as well as insights into the expression of a variety of genes after IBV replication in the host.

Using Multinomial and Space-Time Permutation Models to Understand the Epidemiology of Infectious Bronchitis in California Between 2008 and 2012

Although infectious bronchitis virus (IBV) has been described as one of the most economically important viral respiratory diseases in poultry, there are few analyses of outbreaks that use spatial statistics. In order to better understand how the different genotypes of IBV behave spatially and temporally, we used geographic information system-based mapping coupled with spatial and spatial-temporal statistics to identify statistically significant clustering of multiple strains of infectious bronchitis (IB) between 2008 and 2012 in California. Specifically, space-time permutation and multinomial models were used to identify spatial and spatial-temporal clusters of various genotypes of IBV. Using time permutations (i.e., windows) spanning days to years, we identified three statistically significant ( P < 0.05) clusters. In contrast, multinomial models identified two statistically significant spatial-temporal clusters and one statistically significant spatial cluster. When comparing the space-time permutation and multinomial models against each other, we identified spatial and temporal overlap in two of the three statistically significant clusters. From a practical perspective, multinomial clustering approaches may be advantageous for studying IB because the model allows the different genotypes of IB to be independent nominal variables, thereby allowing for a more detailed spatial analysis. To that point, based on their risk ratios, the genotypes classified as vaccine-related were identified as the most significant contributor to two of the three mutinomial clusters. Additionally, statistically significant clusters were mapped and layered on a hot-spot analysis of commercial poultry farm density in order to qualitatively assess the relationship between farm density and clusters of IBV. Results showed that one of the three space-time permutations and one of the three multinomial clusters were spatially centered near the highest density farm areas, as determined by the hot-spot analysis.