A Coronavirus Associated with Runting Stunting Syndrome in Broiler Chickens

Simultaneous detection and partial molecular characterization of five RNA viruses associated with enteric disease in chickens: chicken astrovirus, avian nephritis virus, infectious bronchitis virus, avian rotavirus a and avian orthoreovirus, via multiplex RT-qPCR

In the poultry industry, intestinal diseases can lead to significant economic losses due to diarrhea, weight loss and mortality, often linked to viral infections. Chicken astrovirus (CAstV), avian nephritis virus (ANV), infection bronchitis virus (IBV), avian rotavirus A (AvRVA) and avian orthoreovirus (ARV) are key pathogens on this disease including feed malabsorption and runting-stunting syndrome (RSS). This study proposes a multiplex RT-qPCR assay for the simultaneous detection of these five viruses in chickens with enteritis in Ecuador. Primers and hydrolysis probes were designed for the five viruses, along with a synthetic gBlock as a positive control. The method was evaluated for sensitivity, repeatability, and specificity, and 200 jejunal samples were tested. Genome regions of each virus were sequenced, and a phylogenetic analysis confirmed their presence in the samples. The optimized RT-qPCR assay showed efficiency between 98.8-105.9%, with a detection limit of 1 copy/μL. It specifically amplified the five target viruses without cross-reactivity. Among 200 chickens tested, 97% were positive for at least one virus, with ANV (89%) and CAstV (53%) being the most prevalent. Coinfections were common, especially between CAstV and ANV, with three samples positive for all viruses. Sequencing and phylogenetic analysis confirmed the circulation of multiple strains in chickens with enteric disease in Ecuador. This study describes a multiplex RT-qPCR assay for detecting key enteric viruses in Ecuadorian poultry highlighting the high prevalence of astroviruses, emphasizing the impact of coinfections, its possible role in the disease and the importance of improving disease control strategies.

First report of molecular detection of chicken astrovirus (CAstV) in chicks affected with enteric disease in Ecuador through a fast RT-qPCR assay based on SYBR® Green

BACKGROUND

Chicken meat production has expanded considerably on a global scale due to its ease of production compared to other species. As a result, the prevalence of avian viruses has grown. Chicken astrovirus (CAstV), an RNA virus with roughly 7 kb in length that is disseminated globally and exhibits both horizontal and vertical transmission, is one of the most important enteric pathogenic avian viruses. CAstV and some enteric viruses' infections causes significant economic losses because they are associated with high mortality in chickens. CAstV cause a variety of pathologic changes such as runting and stunning syndrome, nephritis, and white chick syndrome, making early detection critical. For this purpose, the objective of this study was to determine the presence of CAstV in chickens affected with enteric disease through a fast RT-qPCR assay based on SYBR® Green. For this, 120 samples of jejunum from seven-day-old chicks that succumbed to enteric disease characterized by pronounced lethargy, apathy, diarrhea and cloacal pasting were subjected to investigation.

RESULTS

At necropsy, the intestines of all chicks appear pale and filled with yellow or green liquid content, thin wall and presence of gas; at the jejunum it was evidenced the presence of remanent yolk sac. The liver, kidneys, spleen did not show any alteration. CAstV RNA was detected and quantified in 85 samples, revealing significant levels (9.6 × 10^6) of CAstV gene copies. This indicates the presence of the virus in Ecuadorian chicks from a few days of age, suggesting vertical transmission and potential sources for the virus's dissemination. The phylogenetic analysis clustered all Ecuadorian sequences in one group related to sequences from India and Brazil. The comparison identity of NT sequences in part of Orf 1b gene showed 83.27 - 93.5% with other sequences of CAstV from India and Brazil. Additionally, the LoD and LoQ were determined in 101 gene viral copies. The standard curve showed an efficiency of 97.3% and a melting curve showed a single peak without any alterations and a melting temperature of 77.5 °C. The assay was specific for amplification of the CAstV genome and no amplification was shown from other viral genomes (aMPV, NDV, IBV, AReV, ARoV, ANV) or from the negative controls.

CONCLUSIONS

Presents, for the first time, the detection of CAstV in chicks suffering from enteric disease in Ecuador. It also demonstrates that the assay developed herein is an effective tool for the early detection and quantification of CAstV in diseased chickens, while being a reliable, specific, cost-effective, and rapid diagnostic method.

Detection and molecular characterization of chicken parvovirus and chicken megrivirus in layer breeders affected by intestinal dilatation syndrome

RESEARCH HIGHLIGHTS

IDS presented pathognomonic dilatation of the jejunum up to Meckel's diverticulum.IDS caused weight loss, decreased egg production, and increased culling and mortality.Chicken parvovirus (ChPV) was consistently detected through PCR assays.Chicken megrivirus (ChMV) was consistently detected through viral metagenomics.

Intestinal microbiota diversity from broilers with runting and stunting syndrome performed by metagenomics

Runting and stunting syndrome (RSS) is an enteric viral disease in commercial poultry that directly affects gut health; however, its influence on gut microbiota remains unknown. This study aimed to investigate the compositional changes in the bacterial community of the ileum of 7-day-old broiler chicks naturally affected or not affected by RSS, using next-generation sequencing (NGS) technology. Twenty-one samples were obtained from the ileal contents and mucosa of 11 chicks with RSS and 10 healthy chicks, raised in a dark house system located on a farm in the state of Minas Gerais, Brazil. The results revealed overall changes in the gut microbiota of the chicks with RSS, including a decrease in microbial richness and diversity. In particular, there was a decrease in Lactobacillus and an increase in Candidatus Arthromitus and Clostridium sensu stricto 1. These results indicate a relationship between viral infection and the gut microbial composition, which can cause gut dysbiosis and may influence inflammation in this organ.RESEARCH HIGHLIGHTS RSS causes dysbiosis of the gut microbiota of the ilea of chicks.A difference was found in gut microbiota between chicks with or without RSS.Candidatus Arthromitus was predominant in chicks with RSS.Clostridium sensu stricto 1 was strictly associated with chicks with RSS.

Investigation of avian rotavirus infections in broiler chicks from commercial flocks with different performance efficiency indexes

The aim of this study was to investigate and compare the frequency of occurrence of avian rotavirus (AvRV) in poultry flocks according to its Performance Efficiency Index (PEI) scores. A total of 256 individual intestinal content samples of small sized-chicks (runts) with clinical signs of Runting Stunting Syndrome (RSS) and 24 clinically healthy chicks (control) were collected from twelve flocks in southern Brazil with different PEI scores: good (n = 4, PEI mean = 365); moderate (n = 4, PEI mean = 342) or poor (n = 4, PEI mean = 319). Silver-stained polyacrylamide gel electrophoresis (ss-PAGE) was used to detect and identify the AvRV species followed by RT-PCR and sequencing of the partial VP6 gene for species confirmation. AvRV was detected in 83% (10/12) of the flocks and 23.4% (60/256) of the chicks. The electrophoretic migration patterns of viral dsRNA segments were compatible with AvRV species A (AvRV- A), D (AvRV-D) and F (AvRV-F) in 9 (15%), 18 (30%), and 33 (55%) of the positive chicks fecal samples, respectively. The AvRV species identified by ss-PAGE were confirmed by RT-PCR and partial sequence analysis of the VP6 gene. The AvRV detection rate was statistically higher (p = 0.007) in chicks from flocks with poor PEI when compared to those with good PEI. The occurrence of AvRV-D and AvRV-F was statistically higher in 7 to 9 days old chicks, while AvRV-A was detected only in 13 to 14 days old animals.

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.

Characterization of an Infectious Bronchitis Virus Isolated from Commercial Layers Suffering from False Layer Syndrome

Infectious bronchitis virus (IBV) is a gammacoronavirus that primarily induces an upper respiratory disease in chickens, also affecting the urogenital tract and occasionally leading to a condition called false layer syndrome (FLS), where sexually mature hens ovulate normally but are unable to lay eggs. Here, we describe an outbreak of FLS in Arizona from which an IBV variant that is nearly 90% homologous to DMV/1639 using the Spike subunit 1 gene, named AZ/FLS/17, was isolated and used in challenge experiments. Three-day-old specific-pathogen-free chicks were challenged with AZ/FLS/17 or M41 in high and low doses, and the disease outcomes were compared. Overall, no differences in microscopic lesions or viral loads in the reproductive tract were detected between AZ/FLS/17- and M41-infected birds. To minimize the losses linked to FLS in the problematic flocks, an updated live-attenuated IBV vaccine protocol including the use of the Ma5 strain at the hatchery was implemented, resulting in a drastic reduction of false layers in the subsequent flocks. To monitor the circulation of wild-type and vaccine strains in this population, a molecular surveillance study was performed. Samples were collected at 1, 7, 14, and 21 days of age, and from laying hens at 30 and 36 wk. In older birds, the IBV strains detected were more diverse than at 1 and 7 days of age. Nevertheless, live vaccine combinations are still widely used to decrease the losses caused by FLS in commercial egg laying flocks worldwide.

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.

Runting and Stunting Syndrome in Broiler Chickens: Histopathology and Association With a Novel Picornavirus

Runting stunting syndrome (RSS) in commercial chickens has been reported worldwide, and although several studies have attempted to clarify the cause and describe the lesions, there are gaps in knowledge of the epidemiology, pathogenesis, and etiology. The study objective was to use commercial chicks naturally affected by RSS to describe the histologic changes of RSS in all segments of the small intestine in chicks of different ages and to identify viral gene sequences in affected chicks and their association with histologic lesions. Chicks lacking clinical signs but from the same houses and from unaffected houses were used as controls. The average weight of affected chicks was significantly lower than expected for their flocks. Macroscopically, the small intestines had paler serosa, with watery, mucoid, or foamy contents and poorly digested food. Histologic lesions were characterized by necrotic crypts, crypt dilation, and flattening of the crypt epithelium. Histomorphometry of the intestines revealed villous atrophy especially in the jejunum and ileum. Histologic changes in other organs were not observed. Random next-generation sequencing of total RNA extracted from formalin-fixed paraffin-embedded tissues detected avian nephritis virus, avian rotavirus, and picornavirus in jejunal segments from 7-day-old chicks. No viruses were detected in the jejunum of 1-day-old chicks. Detection of picornaviral reads was significantly associated (P < .05) with histologic lesions of RSS. Sequence analysis of the picornavirus revealed genetic similarity with the genus Gallivirus. Using in situ hybridization for galliviral nucleic acid sequences, the signal was associated with crypt lesion severity, although signal was detected both in chicks with and without RSS.

Intestinal Tropism of an Infectious Bronchitis Virus Isolate Not Explained by Spike Protein Binding Specificity

An infectious bronchitis virus (IBV) with an unusual enteric tropism (CalEnt) was isolated from a California broiler flock exhibiting runting-stunting syndrome. IBV was detected in the small intestine, but not in the respiratory tract or kidney. During virus isolation in embryos, it did not replicate in chorioallantoic membrane (CAM) but could be recovered from intestines. Its S1 protein showed 93% amino acid sequence identity to a California variant isolated in 1999 (Cal99). Intestinal lesions were reproduced following ocular/nasal inoculation of specific-pathogen-free chickens, but respiratory signs and lesions were also present. The virus was detected in both respiratory and intestinal tissues. To determine whether the novel tropism of IBV CalEnt was due to an increased ability of its S1 protein to bind to the intestinal epithelium, we compared the binding of soluble trimeric recombinant S1 proteins derived from CalEnt and Cal99 to chicken tissues. Contrary to expectations, the CalEnt S1 protein did not bind to small intestine and, unlike Cal99 S1, did not bind to the respiratory epithelium or CAM. Using only the CalEnt S1 N-terminal domain or including the S2 ectodomain (lacking membrane and cytoplasmic domains), which have been shown to improve ArkDPI S1 protein binding, did not lead to detectable binding at the standard protein concentration to any tissue tested. Our results indicate no/poor binding of the CalEnt spike protein to both respiratory and intestinal tissues and thus do not support better attachment to intestinal epithelial cells as a reason for CalEnt's extended tropism. These results might reflect shortcomings of the assay, including that it does not detect potential contributions of the S1 C-terminal domain to attachment. We used bioinformatic approaches to explore the possibility that the unique tropism of CalEnt might be a result of functions of the S protein in cell-entry steps subsequent to attachment. These analyses suggest that CalEnt's S2 coding region was acquired through a recombination event and encodes a unique amino acid sequence at the putative recognition site for the protease that activates the S protein for fusion. Thus, S2 activation by tissue-specific proteases might facilitate CalEnt entry into intestinal epithelial cells and compensate for poor binding by its S1 protein.

The ocular surface, coronaviruses and COVID-19

The ocular surface has been suggested as a site of infection with Coronavirus-2 (SARS-CoV-2) responsible for the coronavirus disease-19 (COVID-19). This review examines the evidence for this hypothesis, and its implications for clinical practice. Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), responsible for the COVID-19 pandemic, is transmitted by person-to-person contact, via airborne droplets, or through contact with contaminated surfaces. SARS-CoV-2 binds to angiotensin converting enzyme-2 (ACE2) to facilitate infection in humans. This review sets out to evaluate evidence for the ocular surface as a route of infection. A literature search in this area was conducted on 15 April 2020 using the Scopus database. In total, 287 results were returned and reviewed. There is preliminary evidence for ACE2 expression on corneal and conjunctival cells, but most of the other receptors to which coronaviruses bind appear to be found under epithelia of the ocular surface. Evidence from animal studies is limited, with a single study suggesting viral particles on the eye can travel to the lung, resulting in very mild infection. Coronavirus infection is rarely associated with conjunctivitis, with occasional cases reported in patients with confirmed COVID-19, along with isolated cases of conjunctivitis as a presenting sign. Coronaviruses have been rarely isolated from tears or conjunctival swabs. The evidence suggests coronaviruses are unlikely to bind to ocular surface cells to initiate infection. Additionally, hypotheses that the virus could travel from the nasopharynx or through the conjunctival capillaries to the ocular surface during infection are probably incorrect. Conjunctivitis and isolation of the virus from the ocular surface occur only rarely, and overwhelmingly in patients with confirmed COVID-19. Necessary precautions to prevent person-to-person transmission should be employed in clinical practice throughout the pandemic, and patients should be reminded to maintain good hygiene practices.

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.