Single-Nucleotide Polymorphism Analysis to Select Conserved Regions for an Improved Real-Time Reverse Transcription-PCR Test Specific for Newcastle Disease Virus.

A bioinformatics approach using single-nucleotide polymorphism (SNP) analysis was performed to improve the current real-time reverse transcription-PCR (RRT-PCR) tests for the rapid detection of Newcastle disease virus (NDV). In total, 422 NDV complete genomes were analyzed using the Virus Pathogen Resource to compare the conservation of the primer and probe sequences and to select regions to develop new RRT-PCR tests. The sensitivity and specificity of the three new RRT-PCR tests targeting the nucleoprotein (NP) and polymerase (L) genes were optimized and were compared with established tests for NDV detection. The SNP analysis was also used to identify the number of mismatches between selected primers/probes and the NDV complete genome sequences. The SNP analysis, averaged over the entire primer or probe, showed the primer/probe sequences of three new tests were more conserved than the primer/probe sequences of the commonly used test targeting the matrix (M) gene. The M RRT-PCR test was compared with the new tests on a panel of 46 viruses, comprising 31 NDV isolates. Limit of detection (LOD) varied from 1.3 to 3.7 log 50% egg-infective doses using five isolates from different genotypes by all tests. The two RRT-PCR tests targeting the L and M genes detected three out of five isolates with the lowest LOD. The NP and M RRT-PCR tests had the lowest and highest rates of genetic variants, respectively, among all probes. Because currently used tests are likely to miss some isolates, the availability of validated alternative tests provides alternatives for detection of viral variants that can be rapidly deployed to diagnostic laboratories.

Análisis del polimorfismo de un nucleótido simple para seleccionar regiones conservadas para establecer prueba mejoradas de transcripción reversa y PCR en tiempo real específicas para el virus de la enfermedad de Newcastle. Se llevó a cabo un enfoque bioinformático utilizando el análisis del polimorfismo de un nucleótido simple (SNP) para mejorar las pruebas actuales de transcripción reversa y PCR en tiempo real (RRT-PCR) para la detección rápida del virus de la enfermedad de Newcastle (NDV). Se analizaron un total de 422 genomas completos del virus de Newcastle utilizando la base de datos llamada Recursos en Patógenos Virales (Virus Pathogen Resource) para comparar la conservación de las secuencias de iniciadores y de sondas y para seleccionar regiones adecuadas para desarrollar nuevas pruebas de transcripción reversa y PCR en tiempo real. La sensibilidad y especificidad de las tres nuevas pruebas dirigidas a los genes de la nucleoproteína (NP) y de la polimerasa (L) se optimizaron y se compararon con las pruebas establecidas para la detección del virus de Newcastle. El análisis del polimorfismo de un nucleótido simple también se usó para identificar el número de discrepancias entre los iniciadores y sondas seleccionados con las secuencias completas del genoma del virus de Newcastle. El análisis del polimorfismo de un nucleótido simple, promediado sobre el iniciador o sonda completos, mostró que las secuencias de iniciadores y sondas de las tres pruebas nuevas estaban más conservadas que las secuencias de iniciadores y sondas de la prueba comúnmente utilizada dirigida al gene de la matriz (M). La prueba dirigida para la matriz se comparó con las pruebas nuevas mediante un panel de 46 virus, que comprendió 31 virus de Newcastle. El límite de detección (LOD) mostró un rango de 1.3 a 3.7 logaritmos de dosis infecciosas de embrión de pollo 50% usando cinco aislamientos de diferentes genotipos en todas las pruebas. Las dos pruebas dirigidas a los genes L y M detectaron tres de cinco aislamientos con los límites de detección más bajos. Las pruebas dirigidas a los genes NP y M mostraron las tasas más bajas y las más altas de variantes genéticas, respectivamente, de entre todas las sondas. Debido a que es probable que las pruebas utilizadas actualmente pueden omitir algunos aislamientos, la disponibilidad de pruebas alternativas validadas proporciona alternativas para la detección de variantes virales que se pueden establecer rápidamente en los laboratorios de diagnóstico.

Presence of Newcastle disease viruses of sub-genotypes Vc and VIn in backyard chickens and in apparently healthy wild birds from Mexico in 2017.

Virulent Newcastle disease viruses (NDV) have been present in Mexico since 1946, and recently, multiple outbreaks have been reported in the country. Here, we characterized eleven NDV isolated from apparently healthy wild birds and backyard chickens in three different locations of Jalisco, Mexico in 2017. Total RNA from NDV was reverse-transcribed, and 1285 nucleotides, which includes 3/4 of the fusion gene, was amplified and sequenced using a long-read MinION sequencing method. The sequences were 99.99-100% identical to the corresponding region obtained using the Illumina MiSeq. Phylogenetic analysis using MinION sequences demonstrated that nine virulent NDV from wild birds belonged to sub-genotypes Vc and VIn, and two backyard chicken isolates were of sub-genotype Vc. The sub-genotype Vc viruses had nucleotide sequence identity that ranged from 97.7 to 98% to a virus of the same sub-genotype isolated from a chicken in Mexico in 2010. Three viruses from pigeons had 96.3-98.7% nucleotide identity to sub-genotype VIn pigeon viruses, commonly referred to as pigeon paramyxovirus, isolated in the USA during 2000-2016. This study demonstrates that viruses of sub-genotype Vc are still present in Mexico, and the detection of this sub-genotype in both chickens and wild birds suggests that transmission among these species may represent a biosecurity risk. This is the first detection and complete genome sequencing of genotype VI NDV from Mexico. In addition, the utilization of an optimized long-read sequencing method for rapid virulence and genotype identification using the Oxford nanopore MinION system is demonstrated.

Vaccine effectiveness and use of collar impregnated with insecticide for reducing incidence of Leishmania infection in dogs in an endemic region for visceral leishmaniasis, in Brazil.

Although a national programme for control of visceral leishmaniosis (VL) is being run in Brazil, the disease continues to spread. This programme is essentially based on culling infected dogs from endemic regions. Thus, there is an urgent need to develop other control measures against VL to deter its advance. Here, a subunit vaccine, a recombinant vaccine, an insecticide-impregnated collar and the associations between these measures were evaluated for reducing the incidence of Leishmania infection in dogs. This was through a cohort study conducted in an endemic region of Brazil, considering the incidence and time of total exposure over a period of 1 year. The incidence of VL was estimated by means of serological and molecular diagnostic tests, 180 and 360 days after the application of the control measures. The estimates of the effectiveness (EF) were not significant in any cohort. The EF of the subunit vaccine, the recombinant vaccine and the collar were 26.4%, 32.8% and 57.7% and the upper limit of the 95% confidence interval for EF were 63.7%, 67.9% and 82.5%, respectively. In conclusion, under the conditions of this study, none of the immunogens for VL control was sufficiently effective to protect dogs against infection. On the other hand, use of collars impregnated with insecticide seems to constitute a method with better prognosis, corroborating other studies in this field.

Serological and molecular diagnostic tests for canine visceral leishmaniasis in Brazilian endemic area: one out of five seronegative dogs are infected.

Euthanasia of infected dogs is one of the measures adopted in Brazil to control visceral leishmaniasis (VL) in endemic areas. To detect infected dogs, animals are screened with the rapid test DPP® Visceral Canine Leishmaniasis for detection of antibodies against K26/K39 fusion antigens of amastigotes (DPP). DPP-positives are confirmed with an immunoenzymatic assay probing soluble antigens of promastigotes (ELISA), while DPP-negatives are considered free of infection. Here, 975 dogs from an endemic region were surveyed by using DPP, ELISA and real-time PCR (qPCR) for the diagnosis of VL. When DPP-negative dogs were tested by qPCR applied in blood and lymph node aspirates, 174/887 (19·6%) were positive in at least one sample. In a second sampling using 115 cases, the DPP-negative dogs were tested by qPCR in blood, lymph node and conjunctival swab samples, and 36/79 (45·6%) were positive in at least one sample. Low-to-moderate pairwise agreement was observed between all possible pair of tests. In conclusion, the official diagnosis of VL in dogs in Brazilian endemic areas failed to accuse an expressive number of infected animals and the impact of the low accuracy of serological tests in the success of euthanasia-based measure for VL control need to be assessed.

Brucella canis infection in dogs from commercial breeding kennels in Brazil.

Canine brucellosis caused by Brucella canis is a neglected zoonosis worldwide and is a leading cause of reproductive failure in dogs, often causing substantial economic losses in breeding kennels. This study aimed to investigate the occurrence of B. canis infection in dogs of commercial breeding kennels located in São Paulo State, Brazil. A total of 753 dogs (183 males and 570 females) from 38 commercial kennels were clinically examined, and blood samples were collected for brucellosis diagnosis through blood culture. The association between clinical manifestations suggestive of brucellosis and positive results through blood culture was determined. Of the 753 dogs tested, 166 (22.0%) had at least one clinical sign suggestive of brucellosis and 158 (20.9%) had positive blood cultures. Seventy-two dogs had positive blood culture and had at least one clinical sign suggestive of brucellosis, while 91 dogs showed at least one clinical manifestation suggestive of brucellosis although blood culture was negative. Of the 38 kennels, 16 (42.1%) had at least one positive dog. The prevalence of infection in each kennel varied from 3.8% to 62.6%. Abortion/stillbirth, failure to conceive and enlargement of lymph nodes were significantly associated with brucellosis in female. No association of clinical signs and positive results in blood culture was observed in males. None of the kennels has been carrying out programmes to control brucellosis, and the sale of infected dogs was considered a common practice yielding risks to the public health, in view of the zoonotic potential of the infection.

Tumour necrosis factor-alpha-induced protein 8 (TNFAIP8) expression associated with cell survival and death in cancer cell lines infected with canine distemper virus.

Oncolytic virotherapy is a novel strategy for treatment of cancer in humans and companion animals as well. Canine distemper virus (CDV), a paramyxovirus, has proven to be oncolytic through induction of apoptosis in canine-derived tumour cells, yet the mechanism behind this inhibitory action is poorly understood. In this study, three human mammary tumour cell lines and one canine-derived adenofibrosarcoma cell line were tested regarding to their susceptibility to CDV infection, cell proliferation, apoptosis, mitochondrial membrane potential and expression of tumour necrosis factor-alpha-induced protein 8 (TNFAIP8). CDV replication-induced cytopathic effect, decrease of cell proliferation rates, and >45% of infected cells were considered death and/or under late apoptosis/necrosis. TNFAIP8 and CDVM gene expression were positively correlated in all cell lines. In addition, mitochondrial membrane depolarization was associated with increase in virus titres (p < 0.005). Thus, these results strongly suggest that both human and canine mammary tumour cells are potential candidates for studies concerning CDV-induced cancer therapy.

A three-dimensional cell culture system as an in vitro canine mammary carcinoma model for the expression of connective tissue modulators.

In this study, derived complex carcinoma (CC) and simple carcinoma (SC) cell lines were established and cultured under two-dimensional (2D) and three-dimensional (3D) conditions. The 3D was performed in six-well AlgiMatrix™ (LifeTechnologies®, Carlsbad, CA, USA) scaffolds, resulting in spheroids sized 50-125 µm for CC and 175-200 µm for SC. Cell viability was demonstrated up to 14 days for both models. Epidermal growth factor receptor (EGFR) was expressed in CC and SC in both systems. However, higher mRNA and protein levels were observed in SC 2D and 3D systems when compared with CC (P < 0.005). The connective tissue modulators, metalloproteinases-1, -2, -9 and -13 (MMPs), relaxin receptors 1 and 2 (RXR1 and RXR2) and E-cadherin (CDH1) were quantitated. All were upregulated similarly when canine mammary tumour (CMT)-derived cell lines were cultured under 3D AlgiMatrix, except CDH1 that was downregulated (P < 0.005). These results are promising towards the used of 3D system to increase a high throughput in vitro canine tumour model.

Cellular response markers and cytokine gene expression in the central nervous system of cattle naturally infected with bovine herpesvirus 5.

The present study reports an investigation on the phenotype of inflammatory and immune cells, cytokine and viral gene expression in the brains of cattle naturally infected with bovine herpesvirus 5 (BHV5). Brain sections of 38 affected animals were analysed for the nature and extent of perivascular cuffs in the Virchow-Robin space and parenchyma. Histopathological changes were severe in the olfactory bulbs (Obs), hippocampus, piriform, frontal, temporal and parietal cortices/lobes and were characterized by inflammatory infiltrates in Virchow-Robin spaces. The histopathological changes correlated positively with the distribution of BHV5 antigens (r = 0.947; P < 0.005). Cells of CD3+ phenotype were predominant in areas with severe perivascular cuffs. Viral antigens and genomic viral DNA were detected in the Obs and piriform lobe, simultaneously (r = 0.987; P < 0.005). Similarly, pro-inflammatory cytokine genes INFG, IL2, TNF and LTBR were expressed in the same brain areas (P < 0.005). These results provide important information on the inflammatory and immunological events accompanying BHV5 neurological infections. Our findings provide the first evidence for increased immune activation followed by inflammatory cytokine expression, positively correlated with viral replication in the cranial areas of the brain. Taken together, these results suggest that the host immune response and inflammation play a crucial role in the pathogenesis of acute encephalitis by BHV5 in cattle.

Evaluation of an Immunochromatographic Test to the Diagnosis of Canine Brucellosis Caused by Brucella canis.

This study evaluated the performance of an immunochromatographic test (ICT) for the diagnosis of canine brucellosis caused by Brucella canis, comparing its results with that of the rapid slide agglutination test with and without the use of 2-mercaptoethanol and the agar gel immunodiffusion test (AGID). The microbiological culture, PCR and clinical examination were used as reference. According to the results obtained in clinical examination, blood culture, culture of semen and vaginal swab and PCR in blood, semen and vaginal swab, a total of 102 dogs were divided into three groups: B. canis-infected dogs (Group 1), B. canis-non-infected dogs (Group 2) and dogs with suspected brucellosis (Group 3). The diagnostic sensitivity of RSAT, 2ME-RSAT, AGID and ICT in Group 1 was, respectively, 75%, 37.5%, 27.8% and 89.58%. The diagnostic specificity of RSAT, 2ME-RSAT, AGID and ICT in Group 2 was, respectively, 91%, 100%, 100%, and 100%. In dogs with suspected brucellosis, 9.67% were RSAT positive, none was positive by 2ME-RSAT, 3.22% were AGID positive and 6.45% were ICT positive. The main drawback concerning canine brucellosis diagnosis is the lack of a highly sensitive serological assay to be used as a screening test to the rapid identification of infected animals. The ICT showed a high diagnostic specificity and a diagnostic sensitivity value greater than that observed in the RSAT, 2ME-RSAT and AGID. However, 10.41% of infected dogs had negative results by ICT. These dogs were positive by microbiological culture and/or PCR, indicating active infection and consequently a higher potential of spreading Brucella. Although rapid and simple to perform, the ICT lacked sensitivity to be used as a screening test.

Prevalence of newcastle disease virus in broiler chickens (gallus gallus) in Brazil

This study was carried out during 2002/2003, aiming to determine the prevalence of virulent Newcastle disease virus strains (NDV) in Brazilian commercial poultry farms. Clinical samples were obtained from the Southeastern, Southern and Central-Western regions, which comprise the main area of the Brazilian poultry production. Serum samples and tracheal and cloacal swabs of 23,745 broiler chickens from 1,583 flocks, including both vaccinated chickens and those with no vaccination information, were tested for NDV using a diagnostic ELISA kit. The seropositivity was 39.1 percent, and the isolation percentage by flock varied from 1.0 to 7.6 percent, and by region from 6.5 to 58.4 percent. Higher isolation rates (74.3-83.3 percent) were obtained after three passages in embryonated chicken eggs. All isolates preliminarily identified as NDV were characterized as nonpathogenic strains, as their Intracerebral Pathogenicity Index (ICPI) was below 0.7. Based on results of this study, Brazil can claim a virulent NDV-free status for commercial flocks.

A survey for maintenance of virulent newcastle disease virus-free area in poultry production in Brazil

In 2003, Brazil was recognized as a pathogenic Newcastle Disease Virus (NDV) strain-free country for commercial poultry. This research was conducted in Brazil between December 2003 and March 2005 to verify the maintenance of this virulent NDV-free status. Serum samples from 5,455 flocks for commercial poultry farms were collected, comprising 81,825 broiler chickens. The farms were located in nine states of the country, grouped in three geographic regions. Serological evidence of NDV infection was detected in 28.8 percent of the surveyed farms. However, all fifteen viruses isolated and identified as Newcastle Disease Virus (NDV) were characterized as nonpathogenic strains, based on the Intracerebral Pathogenicity Index. These results showed that Brazil preserves the virulent NDV-free status for commercial flocks.

Prevalence of newcastle disease virus in broiler chickens (Gallus gallus) in Brazil.

This study was carried out during 2002/2003, aiming to determine the prevalence of virulent Newcastle disease virus strains (NDV) in Brazilian commercial poultry farms. Clinical samples were obtained from the Southeastern, Southern and Central-Western regions, which comprise the main area of the Brazilian poultry production. Serum samples and tracheal and cloacal swabs of 23,745 broiler chickens from 1,583 flocks, including both vaccinated chickens and those with no vaccination information, were tested for NDV using a diagnostic ELISA kit. The seropositivity was 39.1%, and the isolation percentage by flock varied from 1.0 to 7.6%, and by region from 6.5 to 58.4%. Higher isolation rates (74.3-83.3%) were obtained after three passages in embryonated chicken eggs. All isolates preliminarily identified as NDV were characterized as nonpathogenic strains, as their Intracerebral Pathogenicity Index (ICPI) was below 0.7. Based on results of this study, Brazil can claim a virulent NDV-free status for commercial flocks.

A survey for maintenance of virulent newcastle disease virus-free area in poultry production in Brazil.

In 2003, Brazil was recognized as a pathogenic Newcastle Disease Virus (NDV) strain-free country for commercial poultry. This research was conducted in Brazil between December 2003 and March 2005 to verify the maintenance of this virulent NDV-free status. Serum samples from 5,455 flocks for commercial poultry farms were collected, comprising 81,825 broiler chickens. The farms were located in nine states of the country, grouped in three geographic regions. Serological evidence of NDV infection was detected in 28.8% of the surveyed farms. However, all fifteen viruses isolated and identified as Newcastle Disease Virus (NDV) were characterized as nonpathogenic strains, based on the Intracerebral Pathogenicity Index. These results showed that Brazil preserves the virulent NDV-free status for commercial flocks.

A universal avian endogenous real-time reverse transcriptase-polymerase chain reaction control and its application to avian influenza diagnosis and quantification.

Real-time reverse transcriptase-polymerase chain reaction (RRT-PCR) is becoming an established first-line diagnostic assay as well as a precise quantification tool for avian influenza virus detection. However, there remain some limitations. First, we show that the sensitivity of RRT-PCR influenza detection can be 10- to 100-fold inhibited in oropharyngeal and cloacal swabs. Adding 0.5 U of heat-activated Taq DNA polymerase successfully reverses PCR inhibition. Second, an excellent strategy for detecting false negative samples is the coamplification of an internal control from each sample. We developed a universal avian endogenous internal control (bird beta-actin) and apply it to influenza A diagnosis. Moreover, this internal control proves useful as a normalizer control for virus quantification, because beta-actin gene expression does not change in infected vs. uninfected ducks. A combined panel of wild bird cloacal swabs, wild bird tissue samples, experimental duck swabs, and experimental duck and chicken tissue samples was used to validate the endogenous control. The application of an endogenous internal control proves an excellent strategy both for avoiding false negative diagnostic results and for standardizing virus quantification studies.