A molecular epidemiological investigation of avian paramyxovirus type 1 viruses isolated from game birds of the order Galliformes

Understanding the disease and economic impact of avirulent avian paramyxovirus type 1 (APMV-1) infection in Great Britain

Newcastle disease (ND) is a notifiable disease affecting chickens and other avian species caused by virulent strains of Avian paramyxovirus type 1 (APMV-1). While outbreaks of ND can have devastating consequences, avirulent strains of APMV-1 generally cause subclinical infections or mild disease. However, viruses can cause different levels of disease in different species and virulence can evolve following cross-species transmission events. This report describes the detection of three cases of avirulent APMV-1 infection in Great Britain (GB). Case 1 emerged from the 'testing to exclude' scheme in chickens in Shropshire while cases 2 and 3 were made directly from notifiable avian disease investigations in chicken broilers in Herefordshire and on premises in Wiltshire containing ducks and mixed species, respectively). Class II/genotype I.1.1 APMV-1 from case 1 shared 99.94% identity to the Queensland V4 strain of APMV-1. Class II/genotype II APMV-1 was detected from case 2 while the class II/genotype I.2 virus from case 3 aligned closely with strains isolated from Anseriformes. Exclusion of ND through rapid detection of avirulent APMV-1 is important where clinical signs caused by avirulent or virulent APMV-1s could be ambiguous. Understanding the diversity of APMV-1s circulating in GB is critical to understanding disease threat from these adaptable viruses.

Game Birds Can Act as Intermediaries of Virulent Genotype VII Avian Orthoavulavirus-1 between Wild Birds and Domestic Poultry

Newcastle Disease (ND), caused by virulent forms of Avian orthoavulavirus serotype-1 (AOAV-1) is an economically important avian disease worldwide. The past two incursions of ND into the United Kingdom occurred in game bird populations during 2005 and 2006. The nature of the game bird semi-feral rearing system, which can bring these birds into close contact with both wild birds and commercial or backyard poultry, has been hypothesized to act as a bridge between these two environments. As such, the risk that AOAV-1-infected game birds may pose to the UK poultry industry was investigated. Pheasants, partridges and chickens were experimentally infected with the virulent strain APMV-1/Chicken/Bulgaria/112/13, a genotype VII.2 virus associated with ND outbreaks in Eastern Europe. The study demonstrated that both chickens and pheasants are susceptible to infection with APMV-1/Chicken/Bulgaria/112/13, which results in high mortality and onward transmission. Partridges by contrast are susceptible to infection, but mortality was reduced, as was onward transmission. However, the data indicated that both pheasants and partridges may serve as intermediate hosts of AOAV-1 and may bridge the wild bird-domestic poultry interface enabling transmission into an economically damaging environment where morbidity and mortality may be high.

Comparative pathogenesis of two genotype VI.2 avian paramyxovirus type-1 viruses (APMV-1) in pheasants, partridges and chickens

Newcastle disease (ND) is caused by virulent forms of avian paramyxovirus-1 (APMV-1) and is an economically important disease of poultry world-wide. Pigeon paramyxovirus 1 (PPMV-1), a sub-group of APMV-1 is endemic in Columbiformes and can cause infections of poultry. An outbreak of ND in partridges in Scotland, UK, in 2006 (APMV-1/partridge/UK(Scotland)/7575/06) was identified as a class II, genotype VI.2.1.1.2.1, more commonly associated with PPMV-1. It has been hypothesized that game birds may be a route of transmission into commercial poultry settings due to the semi-feral rearing system, which potentially brings them into contact with both wild-birds and poultry species. Therefore, the pathogenesis and transmission of APMV-1/partridge/UK(Scotland)/7575/06 in game birds and chickens was investigated, and compared to a contemporary PPMV-1 isolate, PPMV-1/pigeon/UK/015874/15. Viral shedding and seroconversion profiles demonstrated that pheasants were susceptible to infection with APMV-1/partridge/UK(Scotland)/7575/06 with limited clinical signs observed although they were able to excrete and transmit virus. In contrast, partridges and pheasants showed limited infection with PPMV-1/pigeon/UK/015874/15, causing mild clinical disease. Chickens, however, were productively infected and were able to transmit virus in the absence of clinical signs. From the data, it can be deduced that whilst game birds may play a role in the transmission and epidemiology of genotype VI.2 APMV-1 viruses, the asymptomatic nature of circulation within these species precludes evaluation of natural infection by clinical surveillance. It therefore remains a possibility that genotype VI.2 APMV-1 infection in game birds has the potential for asymptomatic circulation and remains a potential threat to avian production systems.RESEARCH HIGHLIGHTS Demonstration of infection of game birds with Pigeon paramyxovirus-1 (PPMV-1).There are differing dynamics of infection between different game bird species.Differing dynamics of infection between different PPMV-1 isolates and genotypes in game birds and chickens.

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.

Complete genome sequence of a subgenotype XXI.1.1 pigeon paramyxovirus type 1 virus (PPMV‑1) isolated from Iran in 2018 and phylogenetic analysis of a possible novel, but unassigned, PPMV-1 group isolated in 2014

Newcastle disease (ND) is one of the most serious infectious and contagious viral diseases in avian species. Recently, several ND outbreaks in pigeon caused by pigeon paramyxovirus serotype-1 (PPMV-1) have been reported from Iran, but unfortunately, phylogenetic studies have been mostly conducted on partial sequence of NDV fusion (F) gene. In addition, a complete genome data of Iranian PPMV-1 strains are not available. In the present study, a PPMV-1, named Avian avulavirus 1/pigeon/Iran/UT-EGV/2018, isolated from an infected pigeon, was subjected to whole-genome sequencing. The isolate showed an MDT of 74 h, thus categorizing it as mesogenic. The phylogenetic analysis based on the F gene sequence revealed the isolate belongs to XXI.1.1 subgenotype (min 0.9 % and max 3 %). To our knowledge, our study is the first study to publish the complete genome of a PPMV-1 from Iran. According to BLAST results, the whole genome of UT-EGV had high homology with some Russian, Egyptian and Ukrainian strains (the highest was 96.55 %). Additionally, we conducted a phylogenetic analysis on five PPMV-1 that we isolated in 2014 to find that they may belong to a completely unreported subgenotype (6 % distance when compared as a group). The information obtained from this study can be useful in preventive measures, including constructing an effective vaccine against PPMV-1 in Iran.

Comparative pathogenicity of two closely related Newcastle disease virus isolates from chicken and pigeon respectively

Newcastle disease (ND), caused by virulent Newcastle disease virus (NDV), is a highly contagious disease that has led to tremendous economic losses worldwide. Pigeon paramyxovirus type 1 (PPMV-1) is an antigenic and host variant of NDV. However, limited in-depth studies are available concerning side-by-side comparison of pathogenicity of PPMV-1 and its phylogenetically close NDV both in chickens and pigeons. To this end, two phylogenetically closely related NDV isolates, Kuwait 256 and JS/07/04/Pi from chicken and pigeon respectively were pathotypically and genotypically characterized in this study. The results indicated that Kuwait 256 was a velogenic strain, while JS/07/04/Pi was a mesogenic strain based on the mean death time of chick embryos (MDT) and intracerebral pathogenicity index in 1-day-old chicks (ICPI). Pathogenicity tests showed that Kuwait 256 caused severe clinical signs and 100 % mortality, while JS/07/04/Pi caused no apparent disease in chickens. Interestingly, both Kuwait 256 and JS/07/04/Pi caused morbidity and mortality in pigeons. Notably, pigeons infected with JS/07/04/Pi exhibited viral shedding for longer time compared to Kuwait 256-infected pigeons. Collectively, the findings of this study suggested that PPMV-1 decreased the pathogenicity in chickens but gained a survival advantage over NDV of chicken origin after its adaptive variation in pigeons based on the previous evidence that PPMV-1 originated from chicken-origin viruses. This study laid the foundation for the elucidation of the molecularmechanism underlying difference in pathogenicity of PPMV-1 and chicken-origin NDV in chickens.

Protective efficacy of the Newcastle disease virus genotype VII-matched vaccine in commercial layers

Newcastle disease virus (NDV) is a major threat to the poultry industry worldwide, with a diversity of genotypes associated with severe economic losses in all poultry sectors. Class II genotype VII NDV are predominant in the Middle East and Asia, despite intensive vaccination programs using conventional live and inactivated NDV vaccines. In Egypt, the disease is continuously spreading, causing severe economical losses in the poultry industry. In this study; the protective efficacy of a commercial, inactivated recombinant genotype VII NDV–matched vaccine (KBNP-C4152R2L strain) against challenge with the velogenic NDV strain (Chicken/USC/Egypt/2015) was evaluated in commercial layers. Two vaccination regimes were used; live NDV genotype II (LaSota) vaccine on days 10, 18, and 120, with either the inactivated NDV genotype II regime or inactivated NDV genotype VII–matched vaccine regime on days 14, 42, and 120. The 2 regimes were challenged at the peak of egg production on week 26. Protection by the 2 regimes was evaluated after experimental infection, based on mortality rate, clinical signs, gross lesions, virus shedding, seroconversion, and egg production schedule. The results show that these 2 vaccination regimes protected commercial layer chickens against mortality, but some birds showed mild clinical signs and reduced egg production temporarily. However, the combination of live NDV genotype II and recombinant inactivated genotype VII vaccines provided better protection against virus shedding (20% and 0% vs. 60% and 40%) as assessed in tracheal swabs and (20% and 0% vs. 20% and 20%) in cloacal swabs collected at 3 and 5 D post challenge (dpc), respectively. In addition, egg production levels in birds receiving the inactivated NDV genotype VII–matched vaccine regime and in those given inactivated genotype II vaccines were 76.6, 79, 82, and 87.4% and 77.7, 72.5, 69, and 82.5% at 7, 14, 21, and 28 dpc, respectively. The results of this study indicate that recombinant genotype-matched inactivated vaccine along with a live attenuated vaccine can reduce virus shedding and improve egg production in commercial layers challenged with a velogenic genotype VII virus under field conditions. This regime may ensure a proper control strategy in layers.

Molecular characterization of two novel sub-sublineages of pigeon paramyxovirus type 1 in China

Pigeon paramyxovirus type 1 (PPMV-1) infection is enzootic in pigeon flocks and poses a potential risk to the poultry industry in China. To gain insight into the biological characteristics and transmission routes of circulating PPMV-1 in pigeons, 13 PPMV-1 isolates from domestic pigeons isolated during 2011-2015 in Guangxi province, China, were characterized using a pathogenicity assessment and phylogenetic analysis. All PPMV-1 isolates were mesogenic or lentogenic strains and had a mean death time (MDT) in 9-day-old SPF chicken embryos and a intracerebral pathogenicity index (ICPI) values of 54-154 h and 0.00-0.90, respectively. Analysis of the F and HN gene sequences of the PPMV-1 isolates and the Newcastle Disease (ND) vaccine strain La Sota, revealed that the nucleotide sequence similarity of the F and HN genes were all < 85% between the PPMV-1 isolates and La Sota, significantly lower than those > 98% among the PPMV-1 isolates. The amino acids sequence of the F protein at the cleavage site of the 13 PPMV-1 isolates was ¹¹²RRQKR↓F¹¹⁷, characteristic of virulent Newcastle disease virus (NDV). All 13 isolates were classified as sublineage 4b by phylogenetic analysis and evolutionary distances, based on the F gene sequences. It was also found that the 13 isolates were divided into two novel sub-groups of sublineage 4b, sub-sublineages 4biig and 4biih. Since these two novel sub-sublineages had two different geographic sources, we speculated that they represent two different transmission routes of PPMV-1 in China. Phylogenetic analysis of these isolates will help to elucidate the sources of the transmission and evolution of PPMV-1 and may help to control PPMV-1 infection in the pigeon industry in China.

Genomic Characterizations of a Newcastle Disease Virus Isolated from Ducks in Live Bird Markets in China

One class I Newcastle disease virus (NDV), designated as duck/Guangxi/1261/2015 (GX1261), was isolated from asymptomatic ducks in live bird markets (LBM) from southern China during the national active surveillance for NDVs in 2015. The complete genome length of GX1261 isolate was 15,198 nucleotides with the gene order of 3'-NP-P-M-F-HN-L-5'. The motif at the cleavage site of F protein was 112ERQER/L117, which was typical of low virulence NDV. Several mutations were identified in the functional domains of F and HN proteins, including fusion peptide, heptad repeat region, transmembrane domains and neutralizing epitopes. Phylogenetic analysis based on the complete F gene revealed that the isolate was clustered into sub-genotype 1c in class I, and showed a high level of similarity with the strains isolated from waterfowl in the United States of America. This is the first report of this kind of virus in the mainland of China. These results demonstrated that GX1261-like viruses might exist in asymptomatic waterfowl, and remain undetected or unidentified. Thus, more investigation needs to be done in order to identify the source of the virus. This study revealed the genetic and phylogenetic characteristics of GX1261 isolate and could help us to better understand the epidemiological context of class I NDV in China.

Genomic Characterizations of Six Pigeon Paramyxovirus Type 1 Viruses Isolated from Live Bird Markets in China during 2011 to 2013

The genomes of six pigeon paramyxovirus type 1 (PPMV-1) isolated from symptomless pigeons in live poultry markets during the national active surveillance from 2011 to 2013 were sequenced and analyzed in this study. The complete genome lengths of all isolates were 15,192 nucleotides with the gene order of 3’-NP-P-M-F-HN-L-5’. All isolates had the same motif of ¹¹²RRQKRF¹¹⁷ at the cleavage site of the fusion protein, which was typical of velogenic Newcastle disease virus (NDV). Several mutations were identified in the functional domains of F and HN proteins, including fusion peptide, heptad repeat region, transmembrane domains and neutralizing epitopes. Phylogenetic analysis based on sequences of complete genomes and six genes revealed that all isolates belonged to genotype VI in class II, but at least 2 sub-genotypes were identified. Most isolates were placed into sub-genotype VIb with the exception of pi/GX/1015/13, which was classified in sub-genotype VIa. The obvious antigenic difference between PPMV-1 isolates and La Sota strain was found based on the R-value calculated by cross hemagglutination inhibition (HI) assay. These results provided the evidence that PPMV-1 could be detected from healthy pigeons, and our study may be useful in designing vaccines used in pigeon, and developing molecular diagnostic tools to monitor and prevent future PPMV-1 outbreaks.

Phylogenetic analysis and comparison of eight strains of pigeon paramyxovirus type 1 (PPMV-1) isolated in China between 2010 and 2012

Eight strains of pigeon paramyxovirus type 1 (PPMV-1) were isolated and identified in this study, from diseased pigeon flocks suspected to be infected with PPMV-1 in China between 2010 and 2012. These PPMV-1 isolates were purified using specific-pathogen-free (SPF) chicken embryo cells before full-length genomic sequencing. The complete genome of these isolates contained 15,192 nucleotides, similar to those of Newcastle disease virus (NDV) strains in genotypes V-XI, with the gene order 3'-NP-P-M-F-HN-L-5'. A six-nucleotide insertion was found to be located in the 5' non-coding region of the nucleoprotein gene in our eight PPMV-1 strains when compared with those of genotypes I, II, III, IV and V. The cleavage site of the fusion protein was (112)RRQKRF(117), a feature generally associated with virulent NDV strains. The structural proteins were in accordance with those of other PPMV-1 strains, with the exception of the W protein of pigeon/CHINA/LJL/100605. The length of the W protein was 227 amino acids, in common with PPMV-1 strains, whereas that of pigeon/CHINA/LJL/100605 was only 181 amino acids. Phylogenetic analysis, based on the genomic sequences and sequences of the fusion gene, revealed that our eight isolates should be classified as class II genotype VIb NDVs. To our knowledge, this is the first report to show that the strain pigeon/CHINA/LLN/110713 is similar to strains isolated abroad, but it was isolated in China, which implies that it may have been introduced to China from overseas. Differences between the Chinese and foreign strains were identified in three regions (nucleotide positions 1632-2229, 3023-3310 and 6103-6439). In addition, the values of ICPI and MDT demonstrated that PPMV-1 isolates were mesogenic or lentogenic, and virulence studies showed that these PPMV-1 strains were non-pathogenic in chickens, but they induced the generation of antibodies in vivo.

Use of reverse transcriptase polymerase chain reaction (RT-PCR) in molecular screening of Newcastle disease virus in poultry and free-living bird populations

The aim of this study was to evaluate a simple molecular method of reverse transcriptase polymerase chain reaction (RT-PCR) to differentiate Newcastle disease virus strains according to their pathogenicity, in order to use it in molecular screening of Newcastle disease virus in poultry and free-living bird populations. Specific primers were developed to differentiate LaSota--LS--(vaccine strain) and Sao Joao do Meriti--SJM--strain (highly pathogenic strain). Chickens and pigeons were experimentally vaccinated/infected for an in vivo study to determine virus shedding in feces. Validation of sensitivity and specificity of the primers (SJM and LS) by experimental models used in the present study and results obtained in the molecular analysis of the primers by BLAST made it possible to generalize results. The development of primers that differentiate the level of pathogenicity of NDV stains is very important, mainly in countries where real-time RT-PCR is still not used as a routine test. These primers were able to determine the presence of the agent and to differentiate it according to its pathogenicity.

The evolution of pigeon paramyxovirus type 1 (PPMV-1) in Great Britain: a molecular epidemiological study

Newcastle disease (ND), caused by virulent strains of avian paramyxovirus type 1 (APMV-1), is considered throughout the world as one of the most important animal diseases. For over three decades now, there has been a continuing panzootic caused by a variant virulent APMV-1 strain, so-called pigeon paramyxovirus type 1 (PPMV-1), primarily in racing pigeons, which has also spread to wild birds and poultry. PPMV-1 isolations have been made in Great Britain every year since 1983. In this study, we have completed a comparative phylogenetic analysis based on a 374 nucleotide section of the fusion protein gene of 63 isolates of PPMV-1 that were isolated over a 26-year period; 43 of these were sequenced for this study. Phylogenetic analysis of these sequences revealed that all were closely related and placed in the genetic sublineage 4b (VIb), subdivision 4biif.

Monitoring of wild birds for Newcastle disease virus in north Queensland, Australia

Wild aquatic birds (WABs) are considered as reservoir hosts for Newcastle disease viruses (NDVs) and may act as vectors for transferring these viruses to poultry, causing outbreaks of disease. A 3-year epidemiological study was conducted on WABs of north Queensland from April 2007 to March 2010. Swab and fresh moist faecal samples of WABs were screened to detect Newcastle disease viral (NDV) RNA by one-step real time reverse transcriptase polymerase chain reaction (rRT-PCR) in multiplex primers, targeting the matrix gene. The potential reactor samples in rRT-PCR were processed for sequencing of the different NDV genes using conventional PCR. The overall NDV RNA prevalence was 3.5% for live bird samples (N=1461) and 0.4% for faecal samples (N=1157). Plumed whistling ducks (PWDs) had a higher prevalence (4.2%) than Pacific black ducks (PBDs) (0.9%) (χ(2) test, p=0.001). Univariate and multivariate logistic regression analyses were used to estimate the association between the proportion of reactor and non-reactor NDV RNA samples of PWDs and potential risk factors. The odds of reactor samples were 2.7 (95% Confidence Interval 1.5-4.9) times more likely in younger than older ducks (p=0.001) (data set B, multivariate analysis). Both NDV RNA class-one and class-two types were identified in samples of WABs (12 and 59, respectively) (Supplementary Table 1). Phylogenetic analysis of the matrix gene identified two reactor sequences of class-one type NDV RNA (PWD-48 and 55) which were closely related to the sequences of Australian Ibis and duck isolates (Fig. 2). Another reactor sample sequence was determined as class-two type NDV RNA (PWD-46, avirulent) based on analysis of the matrix and fusion genes which was more similar to the sequences of Australian I-2 progenitor virus and vaccine strain virus (Figs. 3 and 4). Our findings of higher prevalence in PWDs along with confirmation of class-one and class-two type NDV RNAs will significantly contribute to the design of surveillance programs for NDVs in northern Australia.