Embolic necrosuppurative pneumonia in domestic cats induced by a novel Neisseria species

Three cats, aged 2 to 11 years, presented to the University of Minnesota Veterinary Diagnostic Laboratory over a 3-year period following euthanasia or death due to respiratory distress. Thoracic radiographs revealed nodular, soft tissue opacities throughout the lung fields in all cases. On postmortem examination, approximately 60% to 80% of the lung parenchyma were expanded by multifocal to coalescing, well-demarcated, beige, semi-firm nodules. Histologically, large numbers of neutrophils, fewer macrophages, fibrin, and cellular and karyorrhectic debris effaced the pulmonary parenchyma. The inflammatory foci contained aggregates of gram-negative cocci. 16s rRNA Sanger sequencing and whole-genome sequencing identified the bacteria isolated from the lung of all cats under aerobic conditions as a novel Neisseria spp. Based on whole-genome sequence analysis, all 3 sequences shared 92.71% and 92.67% average nucleotide identity with closely related Neisseria animaloris NZ LR134440T and Neisseria animaloris GCA 002108605T, respectively. The in silico DNA-DNA hybridization identity compared to our isolates was 46.6% and 33.8% with strain DSM Neisseria zoodegmatis 21642 and strain DSM 21643, respectively. All 3 sequences have less than 95% average nucleotide identity and less than 70% DNA-DNA hybridization identity, suggesting that the 3 isolates are a novel species of the genus Neisseria. Infection with Neisseria spp. induces an embolic pneumonia in cats that radiographically and pathologically resembles a metastatic neoplastic process and should be considered among the etiologic differential diagnoses in cases of infectious pulmonary disease with a disseminated, nodular lung pattern.

Disease ecology and host range of Cyprinid herpesvirus 3 (CyHV-3) in CyHV-3 endemic lakes of North America

Cyprinid herpesvirus-3 (CyHV-3) is an important pathogen of common carp (Cyprinus carpio, carp) causing significant economic and ecological impacts worldwide. The recent emergence of CyHV-3 in the Upper Midwest region of the United States has raised questions related to the disease ecology and host specificity of CyHV-3 in wild carp populations. To determine the prevalence of CyHV-3 in wild populations of fishes in Minnesota, we surveyed five lakes in 2019 in which the virus was known to have caused mass mortality events in carp from 2017 to 2018. A total of 28 species (n = 756 total fish) of native fishes and 730 carp were screened for the presence of CyHV-3 DNA using specific qPCR. None of the native fish tissues tested positive for CyHV-3 although the prevalence of CyHV-3 in carp was 10%-50% in the five lakes. A single lake (Lake Elysian) with a 50% DNA detection rate and evidence of ongoing transmission and CyHV-3-associated mortality was surveyed again in 2020 from April to September. During this period, none of the tissues from 24 species (n = 607 total fish) tested positive for CyHV-3 though CyHV-3 DNA and mRNA (indicating viral replication) was detected in carp tissues during the sampling period. CyHV-3 DNA was detected most often in brain samples without evidence of replication, potentially indicating that brain tissue is a site for CyHV-3 latency. Paired qPCR and ELISA testing for Lake Elysian in 2019-2020 identified young carp (especially males) to be the primary group impacted by CyHV-3-associated mortality and acute infections, but with no positive detections in juvenile carp. Seroprevalence of carp from Lake Elysian was 57% in 2019, 92% in April of 2020 and 97% in September 2020. These results further corroborate the host specificity of CyHV-3 to carp in mixed wild populations of fishes in Minnesota and provide additional insights into the ecological niche of CyHV-3 in shallow lake populations of carp in North America.

Characterization and Whole Genome Sequencing of Chromobacterium violaceum OUAT_2017: A Zoonotic Pathogen Found Fatal to a Wild Asiatic Elephant

This study reports a rare fatal case of Chromobacterium violeceum OUAT_2017 strain infection in an Asiatic elephant calf in India. Necropsy revealed pus-filled nodules in liver, spleen, and lungs. Nutrient broth cultures of nodule content showed sediment of violet pigment whereas smooth, non-diffusible, violet-pigmented, homogeneous colonies appeared on nutrient agar. The organism was found to be non-haemolytic and resistant to 8 of the 24 antibiotics tested in vitro. Partial 16S rRNA gene sequence measuring 1410 bp revealed 97% homology with C. violeceum. The bacterial genome composed of 64.87% of G + C content with total size of 4,681,202 bp. The genome annotation has 42 genes responsible for multidrug antibiotic resistance with the presence of Aminoglycoside-modifying enzymes (AAC (6')) that targets streptomycin and spectinomycin. Our findings corroborated the lethal effect of C. violeceum in a new host (elephant) that enriched scientific information on epidemiological picture and whole genome sequencing as well.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-022-01047-4.

Infection and transmission dynamics of Turkey arthritis reovirus in different age Turkeys

Turkey arthritis reovirus (TARV) has been established as a cause of lameness in meat type turkeys in the past decade. However, no information is available on the age susceptibility of TARV or its transmission dynamics. We conducted this study to determine the age at which turkey poults are susceptible to TARV infection and whether infected birds can horizontally transmit the virus to their non-infected pen mates (sentinels). Five groups of turkeys were orally inoculated with TARV (∼10⁶ TCID₅₀/ml) at 2, 7, 14, 21 and 28 days of age (DOA). Two days after each challenge, four uninfected sentinel turkeys of equal age were added to the virus-inoculated groups. At one- and two-weeks post infection, turkeys from each group, including two sentinels, were euthanized followed by necropsy. Inoculated birds in all age groups had TARV replication in the intestine and gastrocnemius tendon with no statistically significant variation at p < 0.5. Furthermore, the inoculated birds at different age groups showed consistently high gastrocnemius tendon histologic lesion scores while birds in the 28-days-old age group had numerically lower lesion scores at 14 days post inoculation (dpi). The sentinels, in turn, also showed virus replication in their intestines and tendons and histologic lesions in gastrocnemius tendons. The findings indicate that turkeys at the age of 28 days or less are susceptible to infection with TARV following oral challenge. It was also found that TARV-infected birds could transmit the infection to naïve sentinel turkeys of the same age.

Genetic Characterization of a Novel Bovine Rotavirus A G37P[52] Closely Related to Human Strains

Bovine rotavirus A (boRVA) strains are common causative agents of diarrhea in calves, resulting in economic losses to the beef and dairy industry. Importantly, this virus has a zoonotic relevance due to its ability to reassort with human rotaviruses. In this study, fecal samples were collected from three calves with diarrhea during an outbreak on a dairy farm. The genetic material of boRVA was detected by real-time reverse transcription PCR (rtPCR) in two samples. Then the virus in one of these positive samples was identified as a novel boRVA genotype closely related with human rotavirus strains mainly from the USA based on whole-genome characterization. However, we consider the novel boRVA as the etiological agent of the outbreak due to the lesions associated with a rotavirus infection. Further studies are necessary to clarify the evolutionary advantages that novel rotavirus genotypes may have.

Adenoviral infection in 5 red-tailed hawks and a broad-winged hawk

Adenoviral infections among raptors are best described in falcons and are characterized most commonly by necrotizing hepatitis and splenitis; only one case has been reported in a hawk. Five red-tailed hawks (Buteo jamaicensis) and a broad-winged hawk (Buteo platypterus) had an adenoviral infection based on history, histopathology, negative-stain electron microscopy, and PCR. All birds had acute onset of illness resulting in death; 3 had evidence of a concurrent bacterial infection. Microscopically, all 6 birds had solitary, pale eosinophilic-to-amphophilic, intranuclear inclusion bodies within presumed hematopoietic cells in bone marrow and macrophages in spleen. Five of the 6 birds had similar inclusions within hepatocytes and Kupffer cells. All but one bird had severe bone marrow necrosis. There was moderate splenic necrosis (3 of 6) and mild-to-marked hepatic necrosis (4 of 6). Negative-stain electron microscopy demonstrated adenoviral particles in bone marrow (5 of 6), liver (1 of 5), and/or spleen (1 of 5). PCR was positive for adenovirus in bone marrow (3 of 5), liver (1 of 3), spleen (4 of 6), and/or intestinal contents (2 of 3). Viral DNA polymerase gene sequences clustered within the Siadenovirus genus. There was 99% nucleotide identity to one another and 90% nucleotide identity with the closest related adenovirus (Harris hawk, EU715130). Our case series expands on the limited knowledge of adenoviral infections in hawks. The splenic and hepatic necrosis, and particularly the hitherto unreported bone marrow necrosis, suggest that adenoviral infection is clinically relevant and potentially fatal in hawks.

Detection of Multiple Lineages of PRRSV in Breeding and Growing Swine Farms

The detection and co-circulation of multiple variants of porcine reproductive and respiratory syndrome virus (PRRSV) have been observed and reported in swine. However, the potential long-term impact of multiple prevailing PRRSV variants on pig-performance is not yet fully understood. The primary objective of this study was to describe the genetic variation of PRRSV in processing fluid (PF), oral fluid (OF), and tonsil scraping (TS) specimens from five swine farms with different production types and PRRS status over a period of time (~1 year). Furthermore, the association between PRRSV prevalence and production parameters was investigated. Results showed that PRRSV was detected by RT-qPCR in 21–25% of all types of specimens. In breeding farms, PRRSV detection in PF and/or TS samples was correlated with stillborn and mummified fetuses, and pre-weaning mortality throughout the study period. Although ORF5 sequences were obtained in &lt;16% of all sample types, simultaneous detection of PRRSV variants including field and vaccine strains within a single sampling event was identified in both breeding and growing pig farms. Phylogenetic analyses based on the ORF5 sequence classified the detected field PRRSV into L1A and L1H, two sub-lineages of lineage 1 (L1). Our study demonstrated the presence of multiple PRRSV lineages, sub-lineages, and variants in swine herds and its potential association with swine reproductive performance under field conditions.

Comparative Pathogenesis of Turkey Reoviruses

ABSTRACTTurkey reoviruses have been implicated in multiple disease syndromes resulting in significant economic losses to the turkey industry. Turkey enteric reovirus (TERV) has been known to be involved in poult enteritis complex for decades, but turkey arthritis reovirus (TARV), the causative agent of tenosynovitis in turkeys, emerged in 2011. Recently in 2019, we isolated reovirus from several cases of hepatitis in turkeys and tentatively named it as turkey hepatitis reovirus (THRV). The comparative pathogenesis of these viruses, and correlation with their genetic make-up (if any), is not known. In this study, we inoculated nine groups of 1-week-old turkey poults with 2 THRV, 5 TARV and 2 TERV via the oral route. A tenth group served as negative control. A subset of birds from each group was euthanized at 3-, 5-, 7-, 14-, 21-, and 28-days post inoculation (dpi). Tissues were collected for histology and real time RT-PCR. All nine viruses were found to be enterotropic; the virus gene copy number in the intestine reached a peak at 5 dpi followed by a sharp decline at 7 dpi. All viruses caused a significant decline in body weight gain of birds as compared to the negative control group. Both TARV and THRV strains replicated in tendons and produced histologic lesions consistent with tenosynovitis. Hepatic lesions were produced by THRV only and the virus was re-isolated from liver and spleen of inoculated birds fulfilling Koch's postulates. The results of this study should be helpful in facilitating diagnosis and designing future mitigation plans.

Prevalence of Newcastle Disease Virus in Wild and Migratory Birds in Haryana, India

Newcastle disease virus (NDV) can infect approximately 250 avian species and causes highly contagious Newcastle disease (ND) in domestic poultry, leading to huge economic losses. There are three different pathotypes of NDV, i.e., lentogenic, mesogenic, and velogenic. Wild resident (wild) and migratory birds are natural reservoirs of NDV and are believed to play a key role in transmitting the virus to domestic poultry. The present study was conducted to determine the prevalence of NDV in wild and migratory birds in the state of Haryana, India, during two migratory seasons (2018-19 and 2019-20). In total 1379 samples (1368 choanal swabs and 11 tissue samples) were collected from live (n = 1368) or dead birds (n = 4) belonging to 53 different avian species. These samples belonged to apparently healthy (n = 1338), sick (n = 30), and dead (n = 4) birds. All samples were tested for NDV by real-time reverse transcription-PCR using M gene specific primers and probe. Of the 1379 samples, 23 samples from wild birds [Columba livia domestica (n = 12, 52.17%), Pavo cristatus (n = 9, 39.13%), and Psittaciformes (n = 2, 8.69%)] were found positive for NDV. Only one of the 23 samples (from P. cristatus) was positive for F gene, indicating it to be a mesogenic/velogenic strain. These results indicate that both lentogenic and velogenic strains of NDV are circulating in wild birds in Haryana and that further studies are needed to characterize NDV strains from wild/migratory birds and domestic poultry to determine the extent of virus transmission among these populations. This study considers the disease transmission risk from domestic pigeons and parrots to commercial poultry and vice versa, and the results emphasize the need for strict biosecurity strategies to protect commercial poultry in the region.

Novel papillomavirus in a mallard duck with mesenchymal chondroid dermal tumors

Papillomaviruses, which are epitheliotropic and may induce epithelial tumors, have been identified in several avian species, including ducks. An adult female mallard duck (Anas platyrhynchos) was admitted to a wildlife rehabilitation center with 2 beige, well-demarcated, firm masses: one in the subcutis under a wing, and the other on a digit of the right foot. After euthanasia, the masses were fixed in formalin for histologic examination. Both tumors had a lobular organization with cartilage cores surrounded by densely cellular interlacing bundles of spindle cells. Neoplastic chondroblasts in both masses, particularly the digital mass, contained basophilic intranuclear inclusion bodies, which consisted of assembly complexes of icosahedral virions of 44-nm diameter. Next-generation sequencing allowed whole genome assembly of a novel papillomavirus (Anas platyrhynchos papillomavirus 2) related most closely to Fulmarus glacialis papillomavirus 1 (59.49% nucleotide identity). Our case supports the observation that certain papillomaviruses can productively infect mesenchymal cells and induce neoplasia.

Prevalence of Newcastle disease and associated risk factors in domestic chickens in the Indian state of Odisha

Newcastle disease (ND), caused by Newcastle disease virus (NDV), is a contagious disease that affects a variety of domestic and wild avian species. Though ND is vaccine-preventable, it is a persistent threat to poultry industry across the globe. The disease represents a leading cause of morbidity and mortality in chickens. To better understand the epidemiology of NDV among commercial and backyard chickens of Odisha, where chicken farming is being prioritized to assist with poverty alleviation, a cross-sectional study was conducted in two distinct seasons during 2018. Choanal swabs (n = 1361) from live birds (commercial layers, broilers, and backyard chicken) and tracheal tissues from dead birds (n = 10) were collected and tested by real-time reverse transcription polymerase chain reaction (RT-PCR) for the presence of matrix (M) and fusion (F) genes of NDV. Risk factors at the flock and individual bird levels (health status, ND vaccination status, geographical zone, management system, and housing) were assessed using multivariable logistic regression analyses. Of the 1371 samples tested, 160 were positive for M gene amplification indicating an overall apparent prevalence of 11.7% (95% CI 10.1–13.5%). Circulation of virulent NDV strains was also evident with apparent prevalence of 8.1% (13/160; 95% CI: 4.8–13.4%). In addition, commercial birds had significantly higher odds (75%) of being infected with NDV as compared to backyard poultry (p = 0.01). This study helps fill a knowledge gap in the prevalence and distribution of NDV in apparently healthy birds in eastern India, and provides a framework for future longitudinal research of NDV risk and mitigation in targeted geographies—a step forward for effective control of ND in Odisha.

Detection of Newcastle disease virus and assessment of associated relative risk in backyard and commercial poultry in Kerala, India

Background

Newcastle disease (ND) is an economically important viral disease affecting the poultry industry. In Kerala, a state in South India, incidences of ND in commercial and backyard poultry have been reported. But a systematic statewide study on the prevalence of the disease has not been carried out.

Objectives

A cross‐sectional survey was performed to detect the presence of Newcastle disease virus (NDV) in suspect cases and among apparently healthy commercial flocks and backyard poultry, in the state and to identify risk factors for NDV infection.

Methods

Real‐time reverse transcription‐PCR (RT‐PCR) was used to detect the M gene of NDV in choanal swabs and tissue samples collected from live and dead birds, respectively and the results were statistically analysed.

Results

The predominant clinical signs of the examined birds included mild respiratory signs, huddling together and greenish diarrhoea. Nervous signs in the form of torticollis were noticed in birds in some of the affected flocks. On necropsy, many birds had haemorrhages in the proventriculus and caecal tonsils which were suggestive of ND. Of the 2079 samples tested, 167 (8.0%) were positive for the NDV M‐gene by RT‐PCR. Among 893 samples collected from diseased flocks, 129 (14.5%), were positive for M gene with pairwise relative risk (RR) of 15.6 as compared to apparently healthy flocks where 6 out of 650 (0.9%) samples were positive. All positive samples were from poultry; none of the ducks, pigeons, turkey and wild birds were positive. Commercial broilers were at higher risk of infection than commercial layers (RR: 4.5) and backyard poultry (RR: 4.9). Similarly, birds reared under intensive housing conditions were at a higher risk of being infected as compared to those reared under semi‐intensive (RR: 6.7) or backyard housing (RR: 2.1). Multivariable analysis indicated that significantly higher risk of infection exists during migratory season and during ND outbreaks occurring nearby. Further, lower risk was observed with flock vaccination and backyard or semi‐intensive housing when compared to intensive housing. When the M gene positive samples were tested by RT‐PCR to determine whether the detected NDV were mesogenic/velogenic, 7 (4.2%) were positive.

Conclusions

In Kerala, NDV is endemic in poultry with birds reared commercially under intensive rearing systems being affected the most. The outcome of this study also provides a link between epidemiologic knowledge and the development of successful disease control measures. Statistical analysis suggests that wild bird migration season and presence of migratory birds influences the prevalence of the virus in the State. Further studies are needed to genotype and sub‐genotype the detected viruses and to generate baseline data on the prevalence of NDV strains, design better detection strategies, and determine patterns of NDV transmission across domestic poultry and wild bird populations in Kerala.

A study was carried out to detect Newcastle disease virus in commercial and backyard chicken in Kerala, India, by employing real time RT‐PCR. The overall percentage positivity obtained was 8%. Risk analysis revealed significantly higher risk for broiler birds and intensive type of housing. The risk was also higher for birds housed in facilities in areas with a history of occurrence of the disease, if migratory birds were present in the area, and during bird migration season. It was also observed that vaccination had a protective effect as indicated by lower relative risk values.

Investigation of Cyprinid Herpesvirus 3 (CyHV-3) Disease Periods and Factors Influencing CyHV-3 Transmission in A Low Stocking Density Infection Trial

Simple Summary

Pathogens are the primary limitation to aquaculture production of fish and a major issue in consideration of the interface between cultured and wild populations of fishes worldwide. While rapid spread of fish pathogens between populations (wild or farmed) is generally anthropogenic and the result of trade, the mechanisms of transmission once a pathogen has been introduced to a fish population are not well understood. The most widespread pathogen impacting both aquaculture and wild populations of common carp (Cyprinus carpio, carp) is Cyprinid herpesvirus 3 (CyHV-3). To understand how CyHV-3 is transmitted in a population we conducted a series of infection trials, designed to determine the kinetics CyHV-3 infections, identify the contributions of direct and indirect forms of CyHV-3 transmission, and to determine the contributions of contact rate, viral load, pathogenicity, and contact type. We found that direct contact between fish was the primary mechanism of CyHV-3 transmission rather than transmission through contaminated water. Additionally, CyHV-3 transmission occurred primarily during the incubation period of CyHV-3, prior to the appearance of disease signs and disease-associated reduction in contact rate.

Abstract

Cyprinid herpesvirus 3 (CyHV-3) is the etiological agent of koi herpesvirus disease (KHVD) and important pathogen of aquaculture and wild populations of common carp worldwide. Understanding the relative contributions of direct and indirect transmission of CyHV-3 as well as the factors that drive CyHV-3 transmission can clarify the importance of environmental disease vectors and is valuable for informing disease modeling efforts. To study the mechanisms and factors driving CyHV-3 transmission we conducted infection trials that determined the kinetics of KHVD and the contributions of direct and indirect forms of CyHV-3 transmission, as well as the contributions of contact rate, viral load, pathogenicity and contact type. The incubation period of KHVD was 5.88 + 1.75 days and the symptomatic period was 5.31 + 0.87 days. Direct transmission was determined to be the primary mechanism of CyHV-3 transmission (OR = 25.08, 95%CI = 10.73–99.99, p = 4.29 × 10⁻¹⁸) and transmission primarily occurred during the incubation period of KHVD. Direct transmission decreased in the symptomatic period of disease. Transmissibility of CyHV-3 and indirect transmission increased during the symptomatic period of disease, correlating with increased viral loads. Additionally, potential virulence-transmission tradeoffs and disease avoidance behaviors relevant to CyHV-3 transmission were identified.

Detection and molecular characterization of astro and bocaviruses in dogs in Minnesota

Canine astrovirus (CAstV) and canine bocavirus (CBoV) are involved in cases of mild, and sometimes severe, gastroenteritis in dogs. Fecal samples from two dead dogs with gastroenteritis were received at the University of Minnesota Veterinary Diagnostic Laboratory to determine the cause of death. Small round viruses of 20-35 nm diameter were observed by negative contrast electron microscopy. The samples were subjected to Illumina MiSeq sequencing. Both samples were strongly positive for CAstV; all viral reads were related to CAstV. In addition, sample number 1 had a few reads of CBoV. Two complete sequences of CAstV were identified (6625 and 6627 nt in length) with 95% nt identity. RT-PCR and PCR were used to confirm CAstV and CBoV infections in successive samples of canine gastroenteritis. Sanger sequencing was done on nucleic acids from positive samples. Of a total of ten samples, CAstV and CBoV infections were confirmed in six and eight animals, respectively. Four animals had mixed infection with both viruses. All sequences of ORF1b gene of CAstVs showed closest clusters in phylogenetic tree with 96-100% nucleotide and amino acids identity. On the other hand, identity between VP2 gene of different CBoV strains in this study ranged from 93%- 100%. All strains were located close to each other except the divergent MT078234 strain, which was arranged in a separate branch and was closer to reference strain JN648103/USA/2010. This study highlights the importance of electron microscopy and next generation sequencing for early detection and characterization of viruses associated with dog gastroenteritis.

Prevalence of Newcastle Disease Virus in Commercial and Backyard Poultry in Haryana, India

Newcastle disease virus (NDV) causes Newcastle disease (ND) in poultry. The ND is a highly contagious disease, which is endemic in several countries despite regular vaccination with live or killed vaccines. Studies on NDV in India are mostly targeted toward its detection and characterization from disease outbreaks. A surveillance study was undertaken to determine NDV prevalence throughout the state of Haryana from March 2018 to March 2020 using a stratified sampling scheme. The state was divided into three different zones and a total of 4,001 choanal swab samples were collected from backyard poultry, commercial broilers, and layers. These samples were tested for the M gene of NDV using real-time RT-PCR. Of the 4,001 samples tested, 392 were positive (9.8% apparent prevalence; 95% CI: 8.9–10.8%) for the M gene. Of these 392 M gene positive samples, 35 (8.9%; 95% CI: 6.4–12.3%) were found to be positive based on F gene real-time RT-PCR. Circulation of NDV in commercial and backyard poultry highlights the importance of surveillance studies even in apparently healthy flocks. The information generated in this study should contribute to better understanding of NDV epidemiology in India and may help formulate appropriate disease control strategies for commercial and backyard birds.

A longitudinal study on PRRSV detection in swine herds with different demographics and PRRSV management strategies

Porcine reproductive and respiratory syndrome virus (PRRSV) has been one of the major health-related concerns in the swine production industry. Through its rapid transmission and mutation, the simultaneous circulation of multiple PRRSV strains can be a challenge in PRRSV diagnostic, control and surveillance. The objective of this longitudinal study was to describe the temporal detection of PRRSV in swine farms with different production types and PRRS management strategies. Tonsil scraping (n = 344) samples were collected from three breeding and two growing herds for approximately one year. In addition, processing fluids (n = 216) were obtained from piglet processing batches within the three breeding farms while pen-based oral fluids (n = 125) were collected in the two growing pig farms. Viral RNA extraction and reverse-transcription quantitative PCR (RT-qPCR) were conducted for all samples. The sample positivity threshold was set at quantification cycle (Cq) of ≤ 37. Statistical analyses were performed using generalized linear modelling and post hoc pairwise comparisons with Bonferroni adjustments using R statistical software. The results suggested a higher probability of detection in processing fluids compared to tonsil scraping specimens [odds ratio (OR) = 3.86; p = .096] in breeding farms whereas oral fluids were outperformed by tonsil scrapings (OR = 0.26; p < .01) in growing pig farms. The results described herein may lead to an improvement in PRRSV diagnostic and surveillance by selecting proper specimens.

Genomic features of first bovine astrovirus detected in Egypt

Bovine astrovirus (BAstV) is a small single-stranded RNA virus, which belongs taxonomically to genus Mamastrovirus under the family Astroviridae. The BAstV is strongly linked to neonatal diarrhea of calves. A few studies are available on BAstV, mainly from Asia, and to a lesser extent from Europe, South America, and Africa. There is only one report from Egypt, in which BAstV was found in diarrheic calves, either in single- or co-infections, based on reverse transcription polymerase chain reaction (RT-PCR) and BAstV-polymerase enzyme targeting primers. One of the samples was further subjected to genomic characterization using Illumina platform for next generation sequencing (NGS). After being processed, the returned BAstV complete genome was subjected to sequence and phylogenetic analysis in comparison to reference strains. The BAstV open reading frames (ORF1a, ORF1b, and ORF2) followed a nearly similar genetic topology, as they belonged to the same unclassified lineage, which was earlier proposed as BAstV-lineage 1, and is known to be disseminated worldwide. This close phylogenetic relationship between the study strain and other members of this lineage was further confirmed by high nucleotide and amino acid (aa) identities. Additionally, a total of 24 unique aa residues were found through the entire BAstV genome. As being the first report in Egypt, indeed Africa, we believe that this record shall be useful in either taxonomic classification or epidemiological tracking of BAstV. The status of BAstV in Egypt should be carefully investigated with possible to-be-implemented precautions for the protection of animal-raising industries.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13337-021-00668-5.

Enteric Viruses Associated with Mid-growth Turkey Enteritis

Since August 2014, the University of Minnesota Veterinary Diagnostic Laboratory has received cases of turkey enteritis that are clinically different from previously described cases of poult enteritis syndrome and light turkey syndrome. The birds develop dark green and extremely foul-smelling diarrhea starting at 8-10 wk of age, which may last up to 15-16 wk of age. The affected turkey flocks show poor uniformity, and feed conversion and market weights are reduced. Multiple-age farms are affected more often than the single-age farms. Morbidity varies from flock to flock and in some cases reaches 100%. At necropsy, undigested feed with increased mucus is observed in the intestines along with prominent mucosal congestion and/or hemorrhage. Microscopically, lymphocytic infiltrates expand the villi in duodenum and jejunum to form lymphoid follicles, which are often accompanied by heterophils. Next generation sequencing (Illumina Miseq) on a pool of feces from affected birds identified genetic sequences of viruses belonging to Astroviridae, Reoviridae, Picornaviridae, Picobirnaviridae, and Adenoviridae. On testing pools of fecal samples from apparently healthy (16 pools) and affected birds (30 pools), there was a higher viral load in the feces of affected birds. Picobirnavirus was detected only in the affected birds; 20 of 30 pools (66.7%) were positive. These results indicate that a high viral load of turkey picobirnavirus alone, or in association with novel picornaviruses, may be a cause of this new type of turkey enteritis.

Influence of Environmental Stressors on the Microbiota of Zebra Mussels (Dreissena polymorpha)

Host-associated microbiota play a critical role in host fitness by providing nutrition, enhancing digestion capabilities, and by providing protection from pathogens. Here, we investigated the effects of two environmental stressors, temperature, and salinity, on the microbiota associated with zebra mussels (ZMs), a highly invasive bivalve in North America. To examine this in detail, lake-collected ZMs were acclimated to laboratory conditions, and subjected to temperature and salinity stress conditions. The impact of these stressors on the diversity, composition, and dynamics of ZM-associated microbiota were assessed by using amplicon- and shotgun-based sequencing, and qPCR-based approaches. Elevated temperature was found to be the primary driver of ZM mortality, although salinity alone also increased its likelihood. Stressor-induced ZM mortality, which ranged between 53 and 100%, was concomitant with significant increases in the relative abundance of several genera of putative opportunistic pathogens including Aeromonas. These genera were only present in low relative abundance in ZMs obtained from the control tank with 0% mortality. Shotgun sequencing and qPCR analyses indicated that the relative and absolute abundances of pathogenic Aeromonas species (particularly A. veronii) were significantly greater in temperature-induced dead ZMs. Taken together, our results show that environmental stress, especially elevated temperature (> 25 °C), is associated with the rapid mortality of ZMs as well as the proliferation of putative opportunistic bacterial pathogens.

Molecular characterization of a novel Camelus dromedarius papillomavirus

Papillomaviruses affect both human and non-human hosts. In camels, papillomatosis is caused by Camelus dromedarius papillomavirus type 1 and 2 (CdPV1 and CdPV2, respectively). In late 2018, an outbreak of camelpox occurred in a herd of fattening camels in Egypt. Several animals were found to be co-infected with camelpox and camel papillomaviruses. The morbidity with papillomatosis was 35 %. The infection was confirmed by PCR then Illumina sequencing revealed the presence of a complete genome of two CdPVs. One of these was CdPV1 (MT130101) and the other was a putative novel virus, tentatively named as CdPV3 (MT130100). Seven ORFs and a long upstream regulatory region were identified in the genomes of both viruses. Pairwise comparisons of L1 gene revealed 98.92 % nt identity between MT130101/CdPV1/Egypt/2018 and HQ912790/CdPV1/Sudan/2009 with 100 % coverage. However, MT130100/CdPV3/ Egypt/2018 showed only 68.99 % nt identity with the closest genome HQ912791/CdPV2/Sudan/2009. Phylogenetic analyses indicated that CdPV1 and CdPV3 belonged to the genus Deltapapillomavirus. These results should be useful for future CdPVs molecular surveillance and construction of evolutionary characteristics of this virus.

An Outbreak of Fowl Aviadenovirus A-Associated Gizzard Erosion and Ulceration in Captive Bobwhite Quail (Colinus virginianus)

A flock of captive bobwhite quail (Colinus virginianus) experienced loose droppings, depression, and increased mortality starting at 3 wk of age. Necropsy of the affected birds revealed intestines dilated with frothy and tan fluid. Irregular dark brown fissures within the koilin layer of the gizzard were found in 20%-30% of the birds. Histologically, gizzards showed multifocal koilin degeneration or fragmentation, degeneration and necrosis of the subjacent epithelial cells, and infiltration of macrophages, lymphocytes, and heterophils. Necrotic epithelial cells occasionally contained large, smudgy, basophilic intranuclear inclusion bodies with marginated nuclear chromatin. Adenoviral paracrystalline arrays composed of icosahedral virions (60-70 nm diameter) were seen on transmission electron microscopy in the nuclei of epithelial cells in the gizzard mucosa. Adenovirus was isolated from gizzard, liver, intestine, and trachea by inoculation of specific-pathogen-free embryonated chicken eggs. Homogenates of the gizzard, liver, and intestine were positive for the adenovirus hexon gene by PCR. Sequencing of PCR amplicons confirmed the virus as fowl aviadenovirus A. The study isolates showed more than 99% and 97% nucleotide identity with quail bronchitis virus and with aviadenoviruses from gizzard erosion and ulceration (GEU) in broilers, respectively. The viral isolates showed six substitutions (G1T, C174A, A229G, C513A, T579A, and G621C) of which two were nonsynonymous (G1T and A229G), resulting in a change in the translated amino acid as A1S and S77G, respectively. These results indicate that adenoviruses of the same type or species can cause different clinical presentations in quails, e.g., bronchitis or GEU.

Detection and molecular characterization of kobuvirus from diarrheic goats in Minnesota

Kobuvirus infections are common among humans, rodents, carnivores, pigs, and ruminants. We report herein the complete genome sequence of a novel caprine kobuvirus (MN604700) from diarrheic kids in Minnesota. Whole-genome sequencing revealed a kobuvirus genome of 8,139 nt with a single ORF region encoding a polyprotein of 2,480 amino acids. Further analysis revealed nt substitutions along the genome compared with that of the caprine kobuvirus reference strain, with 93% identity. Phylogenetic analysis indicated that the clade of the caprine kobuvirus was most closely related to porcine kobuviruses rather than bovine or ovine kobuviruses. Using primers designed from this genome, caprine kobuvirus was identified in the stools of other goats. Sanger sequencing of PCR products indicated 3D and VP1 gene nucleotides of this latter strain were 95% and 91% identical with those of MN604700, respectively. There were 35 and 101 nt substitutions in 3D and VP1 genes, respectively. Findings of kobuvirus over a 2-y period may indicate an endemic state, which needs further research. In addition, screening for kobuviruses over large geographic areas is needed to identify the evolutionary connections among different strains.

First report of porcine respirovirus 1 in South America

Porcine respirovirus 1 (PRV1) is an emerging virus in pigs that has been previously described in the USA and China. There are no reports of its presence in the rest of the world. The objective of this study was to determine the occurrence of PRV1 in Chile and to determine its phylogeny. Thus, we collected samples (oral fluids, nasal swabs, and lungs) from a swine influenza A virus (IAV) surveillance program, most of which belonged to pigs with respiratory disease. The samples were analyzed by RT-PCR, and the viral sequencing was obtained using RNA whole-genome sequencing approach. Maximum likelihood phylogeny was constructed with the available references. Thirty-one of 164 samples (18.9 %) were RT-PCR positive for PRV1: 62.5 % oral fluids, 19.0 % nasal swabs, and 8.6 % lungs. All 6 farms in this study had at least one positive sample, with 6-40 % of positive results per farm, which suggests that PRV1 is disseminated in Chilean swine farms. Twenty-one of 31 (677%) PRV1-positive samples were also positive for IAV, so the role of PRV1 as secondary pathogen in respiratory disease needs to be further evaluated. Near to complete genome of two PRV1s were obtained from two farms. The phylogenies, in general, showed low bootstrap support, except the concatenated genome and the L gene trees which showed clustering of the Chilean PRV1 with Asian sequences, suggesting a close genetic relationship. This is the first report of PRV1 in the Southern Hemisphere. Further studies are necessary to determine the genetic diversity of this virus in Chile.

Retrospective Analysis of Turkey Arthritis Reovirus Diagnostic Submissions in Minnesota

Turkey arthritis reovirus (TARV) causes tenosynovitis in turkeys, resulting in decreased profits for producers due to the increase in morbidity, mortality, and feed conversion ratio. There is limited information on TARV epidemiology, including the dynamics of diagnostic submissions to veterinary diagnostic laboratories. In this study, we retrospectively analyzed 719 cases of lameness in turkeys submitted to the Minnesota Veterinary Diagnostic Laboratory from March 2010 to May 2018. Almost all submissions were tendon pools, which were tested by virus isolation and/or real-time reverse transcription-polymerase chain reaction. Most of the submissions were from Minnesota. We found 52% of the submitted cases to be positive for TARV. The TARV-positive submissions increased considerably in the last few years. There was no statistical evidence that TARV diagnostic submissions were seasonal, although positive submissions were higher in January, April, July, and December. TARV-positive submissions also increased as flocks aged. In summary, we found that TARV submissions have increased in the last few years, have varied over time, and are correlated with age of the bird. This information is important guidance for conducting more studies to understand TARV infection dynamics.

Virulence factors and antibiograms of Escherichia coli isolated from diarrheic calves of Egyptian cattle and water buffaloes

Diarrhea caused by Escherichia coli in calves is an important problem in terms of survivability, productivity and treatment costs. In this study, 88 of 150 diarrheic animals tested positive for E. coli. Of these, 54 samples had mixed infection with other bacterial and/or parasitic agents. There are several diarrheagenic E. coli pathotypes including enteropathogenic E. coli (EPEC), Shiga-toxin producing E. coli (STEC), enterotoxigenic E. coli (ETEC) and necrotoxigenic E. coli (NTEC). Molecular detection of virulence factors Stx2, Cdt3, Eae, CNF2, F5, Hly, Stx1, and ST revealed their presence at 39.7, 27.2, 19.3, 15.9, 13.6, 9.0, 3.4, and 3.4 percent, respectively. As many as 13.6% of the isolates lacked virulence genes and none of the isolate had LT or CNF1 toxin gene. The odds of isolating ETEC from male calves was 3.6 times (95% CI: 1.1, 12.4; P value = 0.042) that of female calves, whereas the odds of isolating NTEC from male calves was 72.9% lower (95% CI: 91.3% lower, 15.7% lower; P value = 0.024) than that in females. The odds of isolating STEC in winter was 3.3 times (95% CI: 1.1, 10.3; P value = 0.037) that of spring. Antibiograms showed 48 (54.5%) of the isolates to be multi-drug resistant. The percent resistance to tetracycline, streptomycin, ampicillin, and trimethoprim-sulfamethoxazole was 79.5, 67.0, 54.5, and 43.0, respectively. Ceftazidime (14.8%), amoxicillin-clavulanic acid (13.6%) and aztreonam (11.3%) showed the lowest resistance, and none of the isolates was resistant to imipenem. The results of this study can help improve our understanding of the epidemiological aspects of E. coli infection and to devise strategies for protection against it. The prevalence of E. coli pathotypes can help potential buyers of calves to avoid infected premises. The antibiograms in this study emphasizes the risks associated with the random use of antibiotics.

Outbreaks of Duck Hepatitis A Virus in Egyptian Duckling Flocks

During 2015, duck farms (n = 27) in Sharkia Province, Egypt, experienced several disease outbreaks leading to mortality and nervous manifestations. Upon necropsy, the affected ducklings showed liver lesions, such as hemorrhage or necrosis, suggestive of duck virus hepatitis (DVH). Reverse transcription-PCR (RT-PCR), on the basis of the 3D gene, found duck livers from 21 farms to be positive for duck hepatitis A virus serotype 1 (DHAV-1). All duck breeds (Pekin, Mallard, and Muscovy) were infected. The virus was isolated in embryonated chicken eggs, which showed embryonic mortality (40%-80%) within 5-7 days, stunting or dwarfing (69.6%), and necrotic liver foci (60.9%). The VP1 gene of 11 DHAV-1 strains was characterized by RT-PCR and Sanger sequencing. All study strains were clustered in a monophyletic branch within subclade B2 of Group 4 and were separated from the Egyptian vaccine strain. Several amino acid (aa) residues, such as V129, S142 (only in four strains), L181, G184, and K217, were related to virus attenuation. However, two aa residues (N193 and E205), found in virulent DHAV-1 strains, were also observed in our strains. This study confirms the circulation of DHAV-1 (subclade B2) in Lower Egypt and elucidates the phylogenetic characters of the VP1 genes, which will be useful in following the local trends of DHAV-1 infections. Further studies are indicated to determine the correlation between these mutations and the virulence of the Egyptian DHAV-1 isolates.

Koi herpesvirus and carp oedema virus: Infections and coinfections during mortality events of wild common carp in the United States

Koi herpesvirus (KHV; cyprinid herpesvirus-3) and carp oedema virus (CEV) are important viruses of common and koi carp (Cyprinus carpio); however, the distribution of these viruses in wild common carp in North America is largely unknown. During the summers of 2017 and 2018, 27 mass mortalities of common carp were reported from four states in the USA (Minnesota, Iowa, Pennsylvania and Wisconsin), the majority of which were distributed across eight major watersheds in southern Minnesota. Samples from 22 of these mortality events and from five clinically healthy nearby carp populations were screened for KHV, CEV and SVCV using real-time polymerase chain reaction (qPCR). KHV was confirmed in 13 mortality events, CEV in two mortality events and coinfections of KHV/CEV in four mortality events. Nucleotide sequence analysis revealed that the KHV and CEV detected here are closely related to European lineages of these viruses. While molecular detection alone cannot conclusively link either virus with disease, the cases described here expand the known range of two important viruses. This is also the first reported detection of KHV and CEV coinfections in wild carp populations.

Cold argon-oxygen plasma species oxidize and disintegrate capsid protein of feline calicivirus

Possible mechanisms that lead to inactivation of feline calicivirus (FCV) by cold atmospheric-pressure plasma (CAP) generated in 99% argon-1% O₂ admixture were studied. We evaluated the impact of CAP exposure on the FCV viral capsid protein and RNA employing several cultural, molecular, proteomic and morphologic characteristics techniques. In the case of long exposure (2 min) to CAP, the reactive species of CAP strongly oxidized the major domains of the viral capsid protein (VP1) leading to disintegration of a majority of viral capsids. In the case of short exposure (15 s), some of the virus particles retained their capsid structure undamaged but failed to infect the host cells in vitro. In the latter virus particles, CAP exposure led to the oxidation of specific amino acids located in functional peptide residues in the P2 subdomain of the protrusion (P) domain, the dimeric interface region of VP1 dimers, and the movable hinge region linking the S and P domains. These regions of the capsid are known to play an essential role in the attachment and entry of the virus to the host cell. These observations suggest that the oxidative effect of CAP species inactivates the virus by hindering virus attachment and entry into the host cell. Furthermore, we found that the oxidative impact of plasma species led to oxidation and damage of viral RNA once it becomes unpacked due to capsid destruction. The latter effect most likely plays a secondary role in virus inactivation since the intact FCV genome is infectious even after damage to the capsid.

Outbreaks of foot and mouth disease in Egypt: Molecular epidemiology, evolution and cardiac biomarkers prognostic significance

Foot and mouth disease virus (FMDV) was isolated from sloughed tongue epithelium of Egyptian cattle presenting with mouth lesions and ropy salivation in two Egyptian governorates (El-Fayoum and Dakahlia). The virus was isolated in Madin-Darby bovine kidney (MDBK) cells and identified by reverse transcription-polymerase chain reaction (RT-PCR). The complete genome was obtained by next generation sequencing. The strains isolated from El-Fayoum and Dakahlia were serotype A and O, respectively and both isolates had identity with the previously reported Egyptian strains. This study reports successive outbreaks of FMDV that occurred in Egypt during 2015–2016 and describes the dynamics of two outbreaks in addition to the use of cardiac biomarkers in the diagnosis of FMD-related myocarditis in calves and its clinical relevance. Serum cardiac troponin1 (cTn I) and creatinine kinase myocardial band (CK-MB) were measured. Mean serum cardiac troponin1 (cTn I) showed significant increase (P < 0.001) in FMDV-infected calves. The increase in fatal and recovered cases was (2.794 ± 0.502 ng/mL) and (1.196 ± 0.443 ng/mL), respectively, compared to the healthy control cases (0.014 ± 0.002 ng/mL). Thus, the serum cTn-I successfully diagnosed FMD-associated myocarditis in calves but not prognostic for the fatal cases. The FMDV sequences described in this study should further help in studying FMDV endemicity in Egypt, tracking the source of infection, selection of control strategies and vaccine updates. The study also determines the clinical relevance of cardiac biomarkers in diagnosis of FMDV-related myocarditis in infected calves.

Detection and genetic characterization of bovine kobuvirus from calves in Egypt

Kobuviruses are small non-enveloped RNA viruses that probably cause diarrhea in cattle and swine. Since its discovery in 2003, few studies have addressed bovine kobuvirus (BKoV; a species of Aichivirus B) infections. BKoV has been reported in Europe, Asia, and South America, suggesting a worldwide distribution. To investigate the presence of BKoV in Egypt, 36 fecal specimens from diarrheic calves in two different Egyptian provinces (Cairo and Sharkia) were screened by RT-PCR and 24 (66.7%) were found positive for BKoV. RNA from one of the positive samples (BKoV/Egy-1/KY407744) was subjected to next-generation sequencing to determine the complete BKoV genome sequence. When compared to the only recorded BKoV genome sequence (BKoV/U-1/AB084788), the studied strain showed 94 amino acid (aa) substitutions through its entire polyprotein (2463 aa), one nucleotide (nt) insertion and one nt deletion in the 2B gene and 4-nt deletions in the UTRs (2 each). Additionally, five VP1 and seven 3D sequences were obtained from other samples by using RT-PCR and Sanger sequencing. A discrepancy in the phylogenetic topography of VP1 and 3D was observed, where the Egyptian VP1 sequences were classified as a distinct cluster within the proposed lineage 1 (genotype A), which also contained strains from the UK, Brazil, and Japan. While, the 3D sequences from Cairo were related to those of Chinese strains unlike Sharkia ones that were more closer to Korean  strains. To the best of our knowledge, this is the first detection and genomic characterization of BKoV in Egypt or indeed Africa.

Detection and molecular characterization of enteric viruses in enteritis-affected commercial broiler chickens in India

A study was conducted to detect and characterize the enteric viruses (chicken astrovirus, avian nephritis virus and avian orthoreovirus) present in flocks of commercial broiler chickens suffering from enteritis in Haryana, India. The intestinal contents were collected from 65 enteritis-affected flocks (cases) and tested by reverse transcription PCR (RT-PCR). Of these 65 cases, 35 (53.80%) were positive for a single virus and 26 (40.00%) for two viruses. The remaining four samples were negative for all three viruses tested. Of the 65 cases, 57 were positive for chicken astrovirus (CAstV) while 30 cases had avian nephritis virus (ANV). None of the cases were positive for orthoreovirus. Comparison of 12 CAstVs of this study with previously published CAstV sequences revealed nucleotide identities ranging from 73.20 to 98.00%. The nucleotide identities ranged between 83.10-95.50% when nine ANVs of this study were compared with previously reported ANV sequences. The amino acid sequences of CAstVs in comparison to previously published sequences revealed certain unique changes. Phylogeny based on polymerase gene revealed that CAstVs and ANVs of this study were under the same monophyletic clade. In conclusion, a large number of broiler chicken flocks experiencing enteritis were positive for CAstV and ANV by RT-PCR. The presence of more than one enteric virus in enteritis-affected flocks and changes at the genetic level in these viruses may affect the severity of disease.

Surveillance, isolation and complete genome sequence of bovine parainfluenza virus type 3 in Egyptian cattle

Parainfluenza virus type 3 (PIV-3) can infect a wide variety of mammals including humans, domestic animals, and wild animals. In the present study, bovine parainfluenza virus type 3 (BPIV-3) was isolated from nasal swabs of Egyptian cattle presenting with clinical signs of mild pneumonia. The virus was isolated in Madin-Darby bovine kidney (MDBK) cells and confirmed by reverse transcription-polymerase chain reaction (RT-PCR). The complete genome of Egyptian BPIV-3 strain was sequenced by using next generation (Illumina) sequencing. The new isolate classified with genotype A of BPIV-3 and was closely related to the Chinese NM09 strain (JQ063064). Subsequently in 2015–16, a molecular surveillance study was undertaken by collecting and testing samples from cattle and buffaloes with respiratory tract infections. The survey revealed a higher rate of BPIV-3 infection in cattle than in buffaloes. The infection was inversely proportional to the age of the animals and to warm weather. This report should form a basis for further molecular studies on animal viruses in Egypt.

Co-circulation of paramyxo- and influenza viruses in pigeons in Egypt

In recent years, avian influenza virus (AIV) and Newcastle disease virus (NDV) have caused large-scale outbreaks in many countries, including Egypt. The culling and vaccination strategies have failed to control both viruses in Egypt. In this study, we investigated the outbreaks of nervous manifestations and deaths in pigeons between 2013 and 2015. The H5N1 subtype of the highly pathogenic avian influenza virus and pigeon paramyxovirus-1, an antigenic variant of NDV, were found to be the cause; AIV and pigeon paramyxovirus-1 were isolated from 61.3% (19/31) and 67.8% (21/31) of tested pigeons, respectively. Co-infection with both viruses was detected in 51.6% of pigeons (16/31). The AIV sequences showed PQGEKRRKKR/GLF motif at the haemagglutinin gene cleavage site, which is typical of the highly pathogenic H5N1 subtype. The phylogenetic tree showed that the highly pathogenic avian influenza belonged to clade 2.2.1.2. The NDV sequences carried one of the three motifs, ¹¹²GKQGRL¹¹⁷, ¹¹²KRQKRF¹¹⁷ or ¹¹²RRQKRF¹¹⁷, at the fusion protein cleavage site and were classified as genotypes I, VI and II in NDV-class II, respectively. This indicated that different genotypes of NDV can circulate simultaneously among pigeons. Further analysis revealed the clustering of some sequences in sub-genotypes Ia and VIb.2. To the best of our knowledge, these sub-genotypes have not been previously reported from pigeons in Egypt. Our results should serve as a base for future studies on both viruses in Egypt.

Outbreak of highly pathogenic avian influenza in Minnesota in 2015

The incursion of highly pathogenic avian influenza (HPAI) into the United States during 2014 resulted in an unprecedented foreign animal disease (FAD) event; 232 outbreaks were reported from 21 states. The disease affected 49.6 million birds and resulted in economic losses of $950 million. Minnesota is the largest turkey-producing state, accounting for 18% of U.S. turkey production. Areas with concentrated numbers of turkeys in Minnesota were the epicenter of the outbreak. The first case was presumptively diagnosed in the last week of February 2015 at the Minnesota Veterinary Diagnostic Laboratory (MVDL) and confirmed as HPAI H5N2 at the National Veterinary Services Laboratories on March 4, 2015. A total of 110 farms were affected in Minnesota, and the MVDL tested >17,000 samples from March to July 2015. Normal service was maintained to other clients of the laboratory during this major FAD event, but challenges were encountered with communications, staff burnout and fatigue, training requirements of volunteer technical staff, test kit validation, and management of specific pathogen-free egg requirements.

Molecular detection of enteric viruses from diarrheic calves in Egypt

Neonatal calf diarrhea (NCD) is a major cause of morbidity, mortality and economic losses in the beef and dairy industries. This study was conducted to investigate the existence of enteric viruses in two Egyptian farms with a history of recurrent diarrhea. Fecal samples were collected from 25 diarrheic calves. RNA was extracted and tested by reverse transcription polymerase chain reaction (RT-PCR) for the presence of rotavirus, norovirus, astrovirus, torovirus, coronavirus and bovine viral diarrhea virus. Overall, 76 % (19/25) of samples tested positive for one or more viruses. Rota-, noro- and astroviruses were detected in 48 %, 24 % and 32 % of tested samples, respectively. About 37 % (7/19) of positive samples had two different viruses. One-month-old calves were the group most vulnerable to infections. Based on phylogenetic analysis, bovine rotaviruses were of genotypes G6 and G10, bovine noroviruses were in GIII.2, and bovine astroviruses were in the BAstV lineage 1. Astrovirus sequences showed a high level nucleotide sequence similarity with the Brazilian BAstV sequences available in GenBank. We believe this is the first report of bovine norovirus and bovine astrovirus circulating among calves in Egypt. Further epidemiological studies are recommended to investigate their presence on a wider scale, to predict their association with NCD, and to design appropriate diagnostic and control methods.

Prevalence of parvovirus in Minnesota turkeys

Poult enteritis syndrome (PES) is characterized by enteritis and decreased body weight gain in growing turkey poults between one d and 7 wk of age. Another syndrome called light turkey syndrome (LTS) causes a decrease in body weight of adult tom turkeys in Minnesota leading to huge economic losses. Reovirus, rotavirus, and astrovirus have been found in LTS and PES flocks in Minnesota. We tested 80 fecal pools collected from four LTS flocks and 35 fecal pools from non-LTS flocks for the presence of parvovirus. In addition, 116 fecal and meconium samples from turkeys submitted to the Minnesota Veterinary Diagnostic Laboratory (MVDL) also were tested. The samples were tested by PCR using primers for the non-structural 1 (NS1) gene of parvovirus. Of the 80 samples from LTS flocks, 41 were positive for parvovirus while 20 of 35 samples from non-LTS flocks were positive. The prevalence of parvovirus in fecal samples submitted to MVDL was relatively low; only five of the 116 pools were positive. The partial NS1 gene sequences from LTS and non-LTS samples showed 98 to 100% nt identity except for one divergent turkey parvovirus (TuPV) strain that revealed 90% identity and clustered with chicken-like parvoviruses. The presence of this divergent strain suggests circulation of a recombinant strain of TuPV in Minnesota turkeys. Our results indicate that TuPVs are circulating in both LTS and non-LTS flocks of turkeys in Minnesota, and further experimental studies are indicated to study the role of TuPV in LTS.

Detection and molecular characterization of astroviruses in turkeys

This study was conducted to determine the prevalence and molecular characteristics of turkey astrovirus 1 (TAstV-1) and avian nephritis virus (ANV) in turkeys with light turkey syndrome (LTS), which is characterized by lower body weight in market-age turkeys than their standard breed character. We collected pools of fecal samples from four LTS and two non-LTS turkey flocks in Minnesota at 2, 3, 5 and 8 weeks of age. Of the 80 LTS pools tested, 16 (20.0 %) and 11 (13.8 %) were positive for TAstV-1 and ANV, respectively. For non-LTS flocks, these numbers were 8 (20.0 %) and 5 (12.5 %), respectively. The maximum number of birds was positive at five weeks of age. We also tested 130 fecal samples of poult enteritis syndrome (PES) cases submitted to the Minnesota Veterinary Diagnostic Laboratory and found 19 and 11 positive for TAstV-1 and ANV, respectively. RdRp gene sequences were determined for a total of 29 TAstV-1 and 22 ANV samples. Phylogenetic analysis of the RdRp gene revealed 92-100 % and 88-100 % nucleotide sequence identity among TAstV-1 and ANV sequences, respectively. A large number of nucleotide and amino acid substitutions were observed in LTS and PES flocks than in non-LTS flocks. One of the PES sequences grouped with ANV-like sequences detected in chickens, indicating that regular screening of birds should be continued. Further, complete genome analysis should be conducted to determine whether this virus is a novel divergent strain or a recombinant of chicken and turkey ANV-like viruses. The detection of TAstV-1 and ANV in a considerable number of non-LTS cases emphasizes the need for further studies on the transmission pattern and pathogenesis of these viruses to determine their role as pathogens of turkeys.

A Newly Emergent Turkey Arthritis Reovirus Shows Dominant Enteric Tropism and Induces Significantly Elevated Innate Antiviral and T Helper-1 Cytokine Responses

Newly emergent turkey arthritis reoviruses (TARV) were isolated from tendons of lame 15-week-old tom turkeys that occasionally had ruptured leg tendons. Experimentally, these TARVs induced remarkable tenosynovitis in gastrocnemius tendons of turkey poults. The current study aimed to characterize the location and the extent of virus replication as well as the cytokine response induced by TARV during the first two weeks of infection. One-week-old male turkeys were inoculated orally with TARV (O'Neil strain). Copy numbers of viral genes were estimated in intestines, internal organs and tendons at ½, 1, 2, 3, 4, 7, 14 days Post inoculation (dpi). Cytokine profile was measured in intestines, spleen and leg tendons at 0, 4, 7 and 14 dpi. Viral copy number peaked in jejunum, cecum and bursa of Fabricius at 4 dpi. Copy numbers increased dramatically in leg tendons at 7 and 14 dpi while minimal copies were detected in internal organs and blood during the same period. Virus was detected in cloacal swabs at 1-2 dpi, and peaked at 14 dpi indicating enterotropism of the virus and its early shedding in feces. Elevation of IFN-α and IFN-β was observed in intestines at 7 dpi as well as a prominent T helper-1 response (IFN-γ) at 7 and 14 dpi. IFN-γ and IL-6 were elevated in gastrocnemius tendons at 14 dpi. Elevation of antiviral cytokines in intestines occurred at 7dpi when a significant decline of viral replication in intestines was observed. T helper-1 response in intestines and leg tendons was the dominant T-helper response. These results suggest the possible correlation between viral replication and cytokine response in early infection of TARV in turkeys. Our findings provide novel insights which help elucidate viral pathogenesis in turkey tendons infected with TARV.

Isolation and molecular characterization of bovine enteroviruses in Egypt

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Bovine enterovirus (BEV) was isolated from diarrheic calves in Egypt.

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Sequencing revealed of BEV/Egypt/2014//KM667941 to have 7417 nucleotides (nt).

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The organization of nt was typical of the BEV genome including 822 nt in 5′NTR, 6498 nt in ORF, and 97 nt in 3′NTR.

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Phylogenetic analysis revealed clustering of BEV/Egypt/2014/KM667941 with BEV-F.

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A specific RT-PCR for BEV was developed to detect this pathogen in cattle.

Enteroviruses belong to the Picornaviridae family and infect a wide range of mammals including cattle. Bovine enterovirus (BEV) has recently been reclassified into E and F serotypes. BEV was first isolated in Egypt in 1966 although it has been known in other countries since the 1950s. In this study, BEV-F2 was isolated from calves with severe diarrhea and the isolated viruses were subjected to molecular characterization. Illumina sequencing of one of the isolates revealed the presence of a complete BEV-F genome sequence. The phylogenetic analysis revealed nucleotide substitutions along the genome in comparison with other known strains of BEV-F (HQ663846, AY508697 and DQ092795). Two primer sets were designed from the 3D and 5′NTR regions and used for the examination of the remaining isolates, which were confirmed to be of the BEV-F2 serotype. The availability of the complete genome sequence of this virus adds to the sequence database of the members of Picornaviridae and should be useful in future molecular studies of BEV.

A multiplex RT-PCR assay for the detection of fish picornaviruses

With the emergence of high profile fish diseases in the Great Lakes region, surveillance and regulatory inspections of fish populations have increased. This has resulted in a better understanding of known pathogens and isolation of many new pathogens of fish. In this study, a multiplex RT-PCR assay was developed for the detection of three newly discovered fish picornaviruses: bluegill picornavirus-1 (BGPV-1), fathead minnow picornavirus (FHMPV), and eel picornavirus-1 (EPV-1). This assay was found to be very sensitive with a detection limit of 81.9pg/μl of extracted RNA from a pool of FHMPV and BGPV-1 and was able to detect 501 and 224 gene copies/μl of BGPV-1 and FHMPV, respectively. The assay was highly reproducible and did not cross react with other closely related pathogens. We believe that this new assay provides a rapid and cost effective tool for confirming cell culture isolates and conducting prevalence studies of these newly detected fish picornaviruses.

Efficacy of Five Commonly Used Disinfectants Against Turkey Arthritis Reovirus

Since late 2009, an unusual problem of reovirus-related lameness has been seen in market-age tom turkeys in the upper Midwest area of the United States. In this study, we determined the efficacy of five commonly used disinfectants (Virocid, Keno X5, Synergize, One Stroke, and Tek Trol) against turkey arthritis reoviruses (TARVs). For comparison, turkey enteric reovirus (TERV) and chicken arthritis reovirus (CARV) were also included. At their recommended concentrations, all five disinfectants were found to be effective virucidals, inactivating 99.99% of all viruses within 10 min. However, oxidizing agents and quaternary ammonium compounds + aldehyde types of disinfectants were more effective, killing the viruses in a shorter time (2-5 min) than the other types of disinfectants. These results indicate that these disinfectants can be an effective tool in the control of these viruses.

Description of the Microsporidian Parasite, Heterosporis sutherlandae n. sp., Infecting Fish in the Great Lakes Region, USA

Heterosporosis is an increasingly important microsporidian disease worldwide, impacting wild and farmed raised fishes in both marine and freshwater environments. A previously undescribed species (Heterosporis sp.), with widespread distribution in the Great Lakes region, was the subject of this study. Three angler-caught fish were submitted to the Minnesota Veterinary Diagnostic Laboratory from 2009–2010 with lesions caused by intracellular proliferation of parasitic spores, resulting in destruction and eventual widespread necrosis of the host skeletal muscles. Mature ovoid (5.8 x 3.5μm) spores of a microsporidian parasite, consistent with the genus Heterosporis, were observed by light and electron microscopy. Molecular identification was performed using primer walking to obtain a near-complete rRNA gene sequence (~3,600 bp). A unique species of Heterosporis was identified, demonstrating less than 96% sequence identity to other published Heterosporis sp. on the basis of partial rRNA gene sequence analysis. Heterosporis sutherlandae n. sp. (formerly Heterosporis sp.) was identified in yellow perch (Perca flavescens), northern pike (Esox lucius) and walleye (Sander vitreus) from inland lakes in Minnesota and Wisconsin. Previous research suggests this species may be even more widespread in the Great Lakes region and should be reexamined using molecular techniques to better understand the distribution of this novel species.

The occurrence of enteric viruses in Light Turkey Syndrome

Two studies were conducted to determine the role of enteric viruses in Light Turkey Syndrome (LTS), which is characterized by lower weight in market age turkeys than their standard breed character. In the surveillance study, we selected four LTS and two non-LTS turkey flocks in Minnesota and collected faecal samples at 2, 3, 5 and 8-weeks of age. Astrovirus, rotavirus, and reovirus were detected alone or in various combinations in both LTS and non-LTS flocks. No coronavirus was detected in LTS flocks and no corona- or reovirus was detected in non-LTS flocks. In the second study, 2-week-old turkey poults were divided into two groups; Group A (challenged) was inoculated orally with 10% pooled faecal suspension from LTS flocks and group B (control) was inoculated with phosphate buffered saline (PBS). Clinical signs of depression, huddling, and lack of uniform size were observed in the challenged group but not in the control group. diarrhoea was observed in both groups but was more severe in the challenged group than in the control group. Birds in the challenged group shed astrovirus, rotavirus and reovirus, while the control group shed only astrovirus. Virus shedding in both groups was observed for up to nine weeks of age. Significantly lower body weights were seen in the challenged group starting at seven weeks of age and lasting until 20 weeks of age. These findings suggest that viral enteritis at an early age may set up conditions for the development of LTS in adult turkeys.

The role of avian reoviruses in turkey tenosynovitis/arthritis

Turkey arthritis reovirus (TARV) has been isolated from the gastrocnemius tendons and tibiotarsal joint fluid of lame male turkeys >12 weeks old in the Midwest. Two experiments were conducted to compare the pathogenicity in turkeys of three TARVs (TARV-MN2, TARV-MN4 and TARV-O'Neil), one turkey enteric reovirus (TERV strain MN1) and one chicken arthritis reovirus (CARV strain MN1). Two hundred microlitres of virus were inoculated by the oral, intratracheal, or footpad route into 6-day-old poults placed in isolator units. Poults were necropsied at 1 and 4 weeks post infection in Experiment 1, and at 2 and 4 weeks post infection in Experiment 2. Reovirus was detected by reverse transcription-polymerase chain reaction and virus isolation in tendons of TARV-inoculated poults at 1, 2 and 4 weeks post infection. TARV-O'Neil and TARV-MN2 were detected in tendons of sentinal birds at 1 and 4 weeks and 1 week p.i., respectively. In general, TARVs produced lymphocytic tenosynovitis of the gastrocnemius and digital flexor tendon sheaths without inflammation of the tendons proper. In Experiment 1, poults inoculated with TARV-MN2 and TARV-O'Neil had significantly higher gastrocnemius tendon inflammation scores, as determined by histology, than those inoculated with TERV-MN1 or CARV-MN1. In Experiment 2, poults inoculated with TARV-MN2 and TARV-O'Neil had significantly higher gastrocnemius tendon inflammation scores than those inoculated with TARV-MN4 and virus-free medium (negative control group). Koch's postulates was fulfilled when TARV-MN2 and TARV-O'Neil were re-isolated from tendons of poults that had originally been challenged with either of these viruses. Results of these experiments indicate that TARVs have a unique ability to induce gastrocnemius tenosynovitis in turkeys and that administration of TARV-O'Neil through the oral or intratracheal route is a reproducible model to study pathogenesis of TARV infection.

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

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

One-step real-time reverse transcription-PCR for the detection of turkey reoviruses

During late 2010 and early 2011, an unusual problem of lameness and swollen hock joints in commercial turkeys was reported in the upper Midwest, which continues to this day. The disease caused substantial economic losses to turkey producers. Reovirus was isolated from tendons and joint fluids of lame turkeys submitted to the Minnesota Veterinary Diagnostic Laboratory. This study was undertaken to develop a TaqMan real-time reverse transcription-PCR (rRT-PCR) assay for the early detection of turkey reoviruses (both enteric and lameness strains). A primer probe set was designed from the conserved region of the S4 segment of the turkey reovirus genome. The newly developed rRT-PCR was specific for the detection of turkey reoviruses. The detection limit of this assay was 10 genome copies per reaction. For the TARV-MN4 strain of turkey arthritis reovirus, one 50% tissue culture infectious dose was equivalent to 11.6 +/- 0.2 genome copies. The highest coefficient of variation for intraexperimental and interexperimental variability was 0.08 and 0.06, respectively, indicating the reproducibility of the assay. This new test should be useful for the detection of turkey enteric and arthritis reoviruses.

Prevalence and complete genome characterization of turkey picobirnaviruses

The "light turkey syndrome" (LTS), in which birds weigh less than their standard breed character at the marketing time, is believed to be a consequence of viral enteritis at an early age (3-5 weeks) from which the birds never fully recover. In a previously published study, we collected fecal pools from 2, 3, 5 and 8 week old turkey poults (80 pools from LTS farms and 40 from non-LTS farms) and examined them for the presence of astro-, rota-, reo-, and coronaviruses. To determine the presence of additional enteric viruses, we analyzed a fecal pool by Illumina sequencing and found picobirnavirus (PBV). Segments 1 and 2 of this virus shared 45.8%aa and 60.9-64.5%aa identity with genogroup I of human PBV, respectively. Primers based on RNA-dependent RNA polymerase and capsid genes were designed for detection and molecular characterization of PBVs in the 120 fecal pools described above. From LTS farms, 39 of 80 (48.8%) pools were PBV positive while 23 of 40 (57.5%) were positive from non-LTS farms. The phylogenetic analysis of 15 randomly selected strains divided them into four subgroups within genogroup I (subgroups 1A-D). Nine strains were in subgroup IA showing 69.9-76.4%nt identity with human PBV GI strainVS111 from the Netherlands. Strains in subgroup IB (n=2) had 91.4-91.7%nt identity with chicken PBV GI strain AVE 42v1 from Brazil. Two strains in subgroup IC had 72.3-74.2%nt identity with chicken PBV strain AVE 71v3 from Brazil. In subgroup ID, two strains showed 72.4-81.8%nt identity with chicken PBV GI strain AVE 57v2 from Brazil. Subgroup IC and ID were the most divergent. Five of the 15 strains were typed using capsid gene primers. They showed 32.6-33.4%nt and 39.5-41.3%aa identity with VS10 human PBV strain. These results indicate co-circulation of divergent strains of PBVs among Minnesota turkeys.