Molecular evolution of the Newcastle disease virus matrix protein gene and phylogenetic relationships among the paramyxoviridae

Genetic Diversity of Newcastle Disease Virus Involved in the 2021 Outbreaks in Backyard Poultry Farms in Tanzania

Newcastle disease virus is a significant avian pathogen with the potential to decimate poultry populations all over the world and cause enormous economic losses. Distinct NDV genotypes are currently causing outbreaks worldwide. Due to the high genetic diversity of NDV, virulent strains that may result in a lack of vaccine protection are more likely to emerge and ultimately cause larger epidemics with massive economic losses. Thus, a more comprehensive understanding of the circulating NDV genotypes is critical to reduce Newcastle disease (ND) burden. In this study, NDV strains were isolated and characterized from backyard poultry farms from Tanzania, East Africa in 2021. Reverse-transcription polymerase chain reaction (RT-PCR) based on fusion (F) gene amplification was conducted on 79 cloacal or tracheal swabs collected from chickens during a suspected ND outbreak. Our results revealed that 50 samples out 79 (50/79; 63.3%) were NDV-positive. Sequencing and phylogenetic analyses of the selected NDV isolates showed that 39 isolates belonged to subgenotype VII.2 and only one isolate belonged to subgenotype XIII.1.1. Nucleotide sequences of the NDV F genes from Tanzania were closely related to recent NDV isolates circulating in southern Africa, suggesting that subgenotype VII.2 is the predominant subgenotype throughout Tanzania and southern Africa. Our data confirm the circulation of two NDV subgenotypes in Tanzania, providing important information to design genotype-matched vaccines and to aid ND surveillance. Furthermore, these results highlight the possibility of the spread and emergence of new NDV subgenotypes with the potential of causing future ND epizootics.

First detection and characterisation of sub-genotype XIII.2.1 Newcastle disease virus isolated from backyard chickens in Iran

BACKGROUND

Newcastle disease (ND) is an economically significant poultry disease worldwide. During field surveillance for ND in 2010 in Iran, a backyard chicken flock showed clinical signs of ND with 100% mortality.

OBJECTIVES

We aimed to characterise genetically, biologically and epidemiologically an exotic virulent ND virus (NDV) detected in Iran.

METHODS

After observing high mortality, dead birds were sampled and then disposed of by burial, and the chicken house was disinfected. Tissue samples were molecularly tested for NDV. The genetic homogeneity of the isolate RT30/2010 was tested by plaque assay, and then a large virus plaque was used for the second step of plaque purification. Fusion and matrix complete genes were sequenced and used for genotyping and epidemiological tracing. We tested biological pathotypes using mean death time (MDT) and intracerebral pathogenicity index (ICPI) assays.

RESULTS

The isolate formed heterogeneous plaques in chicken embryo fibroblast cells. The second step of plaque purification produced homogeneous and large plaques. Phylogenetic analysis using both genes classified the virus into sub-genotype XIII.2.1. Nucleic acid and amino acid identities of RT30/2010 fusion gene with the closest available isolate SPVC/Karachi/NDV/43 are 97.95% and 98.73%, respectively. Isolate has ¹¹² RRRKRF¹¹⁷ motif at the fusion cleavage site, and pathogenicity tests showed MDT of 56.4 h and ICPI of 1.85.

CONCLUSIONS

This study presents the first detection and characterisation of a velogenic NDV of sub-genotype XIII.2.1 from Iran. Our follow-up surveillance for ND shows that timely virus detection and carcass management have led to the cessation of virus transmission in Iran.

Development of Molecular Mechanisms and Their Application on Oncolytic Newcastle Disease Virus in Cancer Therapy

Cancer is caused by the destruction or mutation of cellular genetic materials induced by environmental or genetic factors. It is defined by uncontrolled cell proliferation and abnormality of the apoptotic pathways. The majority of human malignancies are characterized by distant metastasis and dissemination. Currently, the most common means of cancer treatment include surgery, radiotherapy, and chemotherapy, which usually damage healthy cells and cause toxicity in patients. Targeted therapy is an effective tumor treatment method with few side effects. At present, some targeted therapeutic drugs have achieved encouraging results in clinical studies, but finding an effective solution to improve the targeting and delivery efficiency of these drugs remains a challenge. In recent years, oncolytic viruses (OVs) have been used to direct the tumor-targeted therapy or immunotherapy. Newcastle disease virus (NDV) is a solid oncolytic agent capable of directly killing tumor cells and increasing tumor antigen exposure. Simultaneously, NDV can trigger the proliferation of tumor-specific immune cells and thus improve the therapeutic efficacy of NDV in cancer. Based on NDV’s inherent oncolytic activity and the stimulation of antitumor immune responses, the combination of NDV and other tumor therapy approaches can improve the antitumor efficacy while reducing drug toxicity, indicating a broad application potential. We discussed the biological properties of NDV, the antitumor molecular mechanisms of oncolytic NDV, and its application in the field of tumor therapy in this review. Furthermore, we presented new insights into the challenges that NDV will confront and suggestions for increasing NDV’s therapeutic efficacy in cancer.

Development, Biological Characterization, and Immunological Evaluation of Virosome Vaccine against Newcastle Disease in Pakistan

Newcastle disease (ND) is a highly fatal, infectious, viral disease, and despite immunization with live and inactivated vaccines, the disease is still endemic, causing heavy morbidity and mortality leading to huge economic losses to the poultry industry in Pakistan. Therefore, the present study was aimed for the first time in the country at using novel virosomal technology to develop the ND vaccine using an indigenous highly virulent strain of the virus. ND virosome was prepared using Triton X-100, and SM2 Bio-Beads were used to remove the detergent and reconstitute the viral membrane into virosome. Confirmation was done by transmission electron microscopy and protein analysis by SDS-PAGE. In vitro cell adhesion property was observed by incorporating green fluorescent protein (GFP), producing plasmid into virosome and in vitro cell culture assay. Sterility, safety, and stability of the vaccine were tested before in vivo evaluation of immunogenicity and challenge protection study in commercial broiler. The virosome vaccine was administered (30 μg/bird) at days 7 and 14 through the intranasal route in comparison with commercially available live and inactivated ND vaccines. Results revealed significantly high (p < 0.05) and clinically protective hemagglutination inhibition (HI) antibody titers at 7, 14, 21, and 28 days postimmunization with the virosome vaccine in comparison to the negative control. The GMTs were comparable to live and inactivated vaccines with nonsignificant (p > 0.05) differences throughout the experiment. Antibody levels increased in all vaccinated groups gradually from the 7^th day and were maximum at 28^th-day postvaccination. In the virosome-administered group, GMT was 83.18 and 77.62 at 21^st and 28^th-days postvaccination, respectively. Challenge revealed 100%, 90%, and 80% protection in virosome, live, and inactivated vaccinated groups, respectively. Under given experimental conditions, we can conclude that ND virosome vaccine prepared from the indigenous virus was found to be safe and immunogenic.

Genomic Diversity and Evolution of Quasispecies in Newcastle Disease Virus Infections

Newcastle disease virus (NDV) infections are well known to harbour quasispecies, due to the error-prone nature of the RNA polymerase. Quasispecies variants in the fusion cleavage site of the virus are known to significantly change its virulence. However, little is known about the genomic patterns of diversity and selection in NDV viral swarms. We analyse deep sequencing data from in vitro and in vivo NDV infections to uncover the genomic patterns of diversity and the signatures of selection within NDV swarms. Variants in viruses from in vitro samples are mostly localised in non-coding regions and 3′ and 5′ untranslated regions (3′UTRs or 5′UTRs), while in vivo samples contain an order of magnitude more variants. We find different patterns of genomic divergence and diversity among NDV genotypes, as well as differences in the genomic distribution of intra-host variants among in vitro and in vivo infections of the same strain. The frequency spectrum shows clear signatures of intra-host purifying selection in vivo on the matrix protein (M) coding gene and positive or diversifying selection on nucleocapsid (NP) and haemagglutinin-neuraminidase (HN). The comparison between within-host polymorphisms and phylogenetic divergence reveals complex patterns of selective pressure on the NDV genome at between- and within-host level. The M sequence is strongly constrained both between and within hosts, fusion protein (F) coding gene is under intra-host positive selection, and NP and HN show contrasting patterns: HN RNA sequence is positively selected between hosts while its protein sequence is positively selected within hosts, and NP is under intra-host positive selection at the RNA level and negative selection at the protein level.

Sequence analysis and pathogenicity of Avian Orthoavulavirus 1 strains isolated from poultry flocks during 2015-2019

Background

Newcastle disease (ND) causes severe economic losses in poultry industry worldwide. Egyptian poultry industry suffered from severe economic losses since the isolation of Velogenic Newcastle disease virus (vNDV) genotype VIId in 2011 and up till now despite the use of different vaccination programs. So, this study aimed to isolate and characterize the vNDV from a total of 120 poultry flocks from ten provinces in the Egyptian Delta region with a history of respiratory manifestation, high mortalities or a decrease in egg production between 2015 and 2019. Seventy-three samples’ allantoic fluid (73/120, 60.8%) were positive for hemagglutination with chicken RBCs. These samples were submitted to molecular examination using qRT-PCR specific primers for AOAV-1, highly pathogenic avian influenza (HPAI-H5), low pathogenic avian influenza (LPAI-H9) and infectious bronchitis virus (IBV).

Results

Fifty samples (50/120: 41.6%) were confirmed positive for AOAV-1, based on genetic analysis of matrix and fusion protein. The co-infection rate of other respiratory viral diseases examined was 1.6, 14.1, and 4.1%, for HPAI-H5, LPAI-H9, and IBV, respectively. Biologically, the intracerebral pathogenicity index of ten selected AOAV-1 isolates ranged from 1.70 to 1.98, which indicated the velogenic nature of these isolates. All the sixteen sequenced isolates were AOAV-1 genotype VII.1.1. The full F gene sequence of six examined AOAV-1 VII.1.1 isolates contained the seven neutralizing epitopes, and the glycosylation motif of six-potential sites for N linked glycosylation at residues 85, 191, 366, 447, 471, and 541.

Conclusion

It could be concluded that the high prevalence of AOAV-1 genotype VII.1.1 in the Egyptian chicken flocks despite the intensive vaccination with live and killed ND vaccines, as all the 16 isolates tested were belonged to this genotype. Homologous vaccination is badly needed to control and reduce the spread of AOAV-1 genotype VII.1.1infection in Egyptian poultry flocks.

Identification of Two Distinct Linear B Cell Epitopes of the Matrix Protein of the Newcastle Disease Virus Vaccine Strain LaSota

Matrix (M) protein of Newcastle disease virus (NDV) is an abundant protein that can induce a robust humoral immune response. However, its antigenic epitopes remain unknown. In this study, we used a pepscan approach to map linear B cell immunodominant epitopes (IDEs) of M protein with NDV-specific chicken antisera. The six epitopes with the highest reactivity by peptide scanning were obtained as IDE candidates. Among them, aa71-85 and aa349-363 were identified by immunological assays with NDV-specific or IDE-specific antisera. The minimal antigenic epitopes of the two IDEs were further characterized as ⁷⁷MIDDKP⁸² and ³⁵⁴HTLAKYNPFK³⁶³. Moreover, an amino acid sequence alignment and immunoblot analysis revealed the conservation of the two IDEs in the M protein of strains of different genotypes. These two IDEs of M protein could be genetically eliminated as negative markers in recombinant NDV for serologically differential diagnosis in the development of marker vaccines.

Comparative efficacy of commercial inactivated Newcastle disease virus vaccines against Newcastle disease virus genotype VII in broiler chickens

Newcastle disease is still causing huge economic losses and devastating outbreaks in poultry flocks despite implementation of extensive vaccination programs. Five commercial broiler chicken groups were established as G1 (non-vaccinated, non-challenged group) and G2 (non-vaccinated, challenged group), and 3 vaccinated challenged groups as G3 (vaccinated with heterologous inactivated Newcastle disease virus (NDV) genotype II (NDV II) vaccine), G4 (vaccinated with homologous inactivated NDV genotype VII (NDV VII) vaccine), and G5 (vaccinated with bivalent (heterologous inactivated NDV II plus H5) vaccine) were used. Challenge test was done using a velogenic NDV genotype VII (vNDV VII) at 28-d olds. Respiratory signs, greenish diarrhea, and obvious post-mortem lesions of vNDV VII appeared in all the challenged birds whether vaccinated or not. In addition, the mortality rate decreased from 93.3% in G2 to 46.7%, 53.3%, and 66.7% in G4, G5, and G3, respectively. Overall, 2 wk postchallenge; body weight loss (%) had increased mainly in G2, with some improvement in chickens in G4 followed by G5 and chickens of G3 showed the least improvement. At 28 d (day of challenge), the highest hemagglutination inhibition values were 4.3 and 5.4 log2 in chickens in G4 and G5, respectively, which increased in all groups after the challenge. Cytokine (IL-6 and IFN-γ) levels were significantly higher (P < 0.05) in the vaccinated groups than that in the non-vaccinated group, especially in G5. Viral shedding in the trachea was higher than that in the cloacal swabs in all vaccinated and non-vaccinated challenged groups with peak shedding on the 6th day post challenge for both swabs, and the lowest viral shedding titers were observed in chickens in G5. Therefore, the use of homologous genotype NDV with inactivated vaccine conferred a higher clinical protection in terms of body weight loss and mortality against vNDV VII challenge in broiler chickens; however, the heterologous vaccine used in G5 induced the highest cell-mediated immune response and hemagglutination inhibition titers with the lowest viral shedding titer.

Solution Structure, Self-Assembly, and Membrane Interactions of the Matrix Protein from Newcastle Disease Virus at Neutral and Acidic pH

Newcastle disease virus (NDV) is an enveloped paramyxovirus. The matrix protein of the virus (M-NDV) has an innate propensity to produce virus-like particles budding from the plasma membrane of the expressing cell without recruiting other viral proteins. The virus predominantly infects the host cell via fusion with the host plasma membrane or, alternatively, can use receptor-mediated endocytic pathways. The question arises as to what are the mechanisms supporting such diversity, especially concerning the assembling and membrane binding properties of the virus protein scaffold under both neutral and acidic pH conditions. Here, we suggest a novel method of M-NDV isolation in physiological ionic strength and employ a combination of small-angle X-ray scattering, atomic force microscopy with complementary structural techniques, and membrane interaction measurements to characterize the solution behavior/structure of the protein as well as its binding to lipid membranes at pH 4.0 and pH 7.0. We demonstrate that the minimal structural unit of the protein in solution is a dimer that spontaneously assembles in a neutral milieu into hollow helical oligomers by repeating the protein tetramers. Acidic pH conditions decrease the protein oligomerization state to the individual dimers, tetramers, and octamers without changing the density of the protein layer and lipid membrane affinity, thus indicating that the endocytic pathway is a possible facilitator of NDV entry into a host cell through enhanced scaffold disintegration.IMPORTANCE The matrix protein of the Newcastle disease virus (NDV) is one of the most abundant viral proteins that regulates the formation of progeny virions. NDV is an avian pathogen that impacts the economics of bird husbandry due to its resulting morbidity and high mortality rates. Moreover, it belongs to the Avulavirus subfamily of the Paramyxoviridae family of Mononegavirales that include dangerous representatives such as respiratory syncytial virus, human parainfluenza virus, and measles virus. Here, we investigate the solution structure and membrane binding properties of this protein at both acidic and neutral pH to distinguish between possible virus entry pathways and propose a mechanism of assembly of the viral matrix scaffold. This work is fundamental for understanding the mechanisms of viral entry as well as to inform subsequent proposals for the possible use of the virus as an adequate template for future drug or vaccine delivery.

Evaluating the efficacy of LaSota vaccination induced protection in chickens upon challenge with a genotype IV strain of Newcastle disease virus

Newcastle disease (ND) is a major risk to the poultry industry which results in severe economic loss throughout the world even with vaccination. The vaccine viruses that are used in many countries include the LaSota and other live viruses that were isolated in the early and late 1950s. Reports from several laboratories including ours indicate a greater variance of the circulating strains and recent classification indicates the existence of XVIII different genotypes of NDV strains. The efficiency of the LaSota vaccination in inducing protective immunity to different heterologous strains has been a question and its efficacy upon exposure to a virulent genotype IV strain has not been reported after 1989 world-wide except for India. Serum antibody negative (SAN) chicks of either sex obtained by hatching specific-pathogen-free (SPF) eggs were vaccinated with increasing doses of the vaccine virus from 10¹ to 10⁷ EID₅₀ per bird delivered through occulo-nasal route and challenged 20 days later with NDV-2K3 (genotype IV) strain of virus isolated in the year 2000 from pigeon in India. The birds were monitored for serum antibody titers and following challenge for morbidity, mortality, viral load in the cloacal swab and different tissues. We could clearly show that a minimum vaccine titre of 10⁴ EID₅₀ could establish protective antibody levels and also prevent viral replication post challenge upon exposure to the virulent genotype IV strain. We conclude based on our results and previous observation that there do exist differences in the levels of the antibody that could limit viral replication and shedding upon exposure to different heterologous genotype of NDV. Developing a strain matched vaccine might less potential to result in better protection by limiting the viral shedding.

Analysis of molecular evolution of nucleocapsid protein in Newcastle disease virus

The present study investigated the molecular evolution of nucleocapsid protein (NP) in different Newcastle disease virus (NDV) genotypes. The evolutionary timescale and rate were estimated using the Bayesian Markov chain Monte Carlo (MCMC) method. The p-distance, Bayesian skyline plot (BSP), and positively selected sites were also analyzed. The MCMC tree indicated that NDV diverged about 250 years ago with a rapid evolution rate (1.059 × 10^-2 substitutions/site/year) and that different NDV genotypes formed three lineages. The p-distance results reflected the great genetic diversity of NDV. BSP analysis suggested that the effective population size of NDV has been increasing since 2000 and that the basic reproductive number (R₀) of NDV ranged from 1.003 to 1.006. The abundance of negatively selected sites in the NP and the mean dN/dS value of 0.07 indicated that the NP of NDV may have undergone purifying selection. However, the predicted positively selected site at position 370 was located in the known effective epitopic region of the NP. In conclusion, although NDV evolved at a high rate and showed great genetic diversity, the structure and function of the NP had been well conserved. However, R₀>1 suggests that NDV might have been causing an epidemic since the time of radiation.

A single R36Q mutation in the matrix protein of pigeon paramyxovirus type 1 reduces virus replication and shedding in pigeons

Pigeon paramyxovirus type 1 (PPMV-1) is considered an antigenic and variant of avian paramyxovirus type 1 (APMV-1) that has adapted to pigeons as hosts. However, how this host-specific adaption of PPMV-1 is related to its biological characteristics is unknown. In this study, seven unique amino acids in PPMV-1 that are not present in other APMV-1 strains (n = 39 versus n = 106) were identified. R36 of the M protein was found to be not only a unique amino acid but also a positive-selection site. To investigate the role of R36 in host adaptation, a recombinant PPMV-1 with R36Q mutation was constructed. Our results indicated that the an R36Q mutation significantly attenuates pathogenicity in chickens, viral growth in both chicken embryo fibroblasts (CEFs) and pigeon embryo fibroblasts (PEFs), and virus replication and shedding in pigeons in comparison with the wild-type virus, suggesting that R36 is a key residue that evolved during the adaptation of PPMV-1 in pigeons.

The long view: a selective review of 40 years of Newcastle disease research

This review is written for the series celebrating the 40th year since the first issue of Avian Pathology. The aim of the authors was to cover the developments in Newcastle disease (ND) research over the last 40 years that they considered significant. During those 40 years there have been several panzootics of this serious disease in poultry and for the last 30 years there has been a continuing panzootic in domestic pigeons, which has spread to wild birds and poultry. The 40-year period began with worldwide outbreaks of severe ND, which served as an important impetus for ND research work. Although early work was concerned with controlling the disease, specifically by improving and developing new vaccines and vaccine regimens, even prior to the 1970s ND virus was seen as a useful laboratory virus for replication and virulence studies. This review covers the historical developments in the following areas: understanding the molecular basis of virulence; epidemiology and relatedness of different ND strains, both antigenically and genetically; the emergence of virulent strains and their relationship with viruses of low virulence; sequencing and understanding the viral genome and genes; the development of rapid molecular-based diagnostic tests; and the phylogeny and molecular taxonomy of ND virus. The authors suggest areas in which future research could or should be undertaken.

Newcastle disease virus: current status and our understanding

Newcastle disease (ND) is one of the highly pathogenic viral diseases of avian species. ND is economically significant because of the huge mortality and morbidity associated with it. The disease is endemic in many third world countries where agriculture serves as the primary source of national income. Newcastle disease virus (NDV) belongs to the family Paramyxoviridae and is well characterized member among the avian paramyxovirus serotypes. In recent years, NDV has lured the virologists not only because of its pathogenic potential, but also for its oncolytic activity and its use as a vaccine vector for both humans and animals. The NDV based recombinant vaccine offers a pertinent choice for the construction of live attenuated vaccine due to its modular nature of transcription, minimum recombination frequency, and lack of DNA phase during replication. Our current understanding about the NDV biology is expanding rapidly because of the availability of modern molecular biology tools and high-throughput complete genome sequencing.

Application of green fluorescent protein-labeled assay for the study of subcellular localization of Newcastle disease virus matrix protein

Green fluorescent protein (GFP) used as a powerful marker of gene expression in vivo has so far been applied widely in studying the localizations and functions of protein in living cells. In this study, GFP-labeled assay was used to investigate the subcellular localization of matrix (M) protein of different virulence and genotype Newcastle disease virus (NDV) strains. The M protein of ten NDV strains fused with GFP (GFP-M) all showed nuclear-and-nucleolar localization throughout transfection, whereas that of the other two strains were observed in the nucleus and nucleolus early in transfection but in the cytoplasm late in transfection. In addition, mutations to the previously defined nuclear localization signal in the GFP-M fusion protein were studied as well. Single changes at positions 262 and 263 did not affect nuclear localization of M, while changing both of these arginine residues to asparagine caused re-localization of M mainly to the cytoplasm. The GFP-M was validated as a suitable system for studying the subcellular localization of M protein and could be used to assist us in further identifying the signal sequences responsible for the nucleolar localization and cytoplasmic localization of M protein.

Transcriptional response of chicken embryo cells to Newcastle disease virus (D58 strain) infection

Newcastle disease virus (NDV), the causative agent of Newcastle disease (ND) in chicken causes significant economic loss for the poultry industry worldwide. The mechanism involved in host response to NDV infection is not well understood. For better understanding of the virus-host interaction; transcriptional profile of some genes of chicken embryo (CE) cells infected with NDV vaccine strain D58 was established using quantitative RT-PCR SYBR Green method. The relative standard curve method was used to measure the level of transcripts of the cellular genes against an endogenous control (β actin) gene. Among the genes studied, IFN α, IFN γ, MHC I and DDX 1 were up-regulated while IL 6 was down regulated. The expression of viral genes (M and F) in the infected CE cells was also confirmed by relative quantification. The host cellular genes involved in pro-inflammatory response, interferon-regulated proteins and the cellular immune response were affected by NDV infection, indicating involvement of complex signaling pathways of host cell responses to the infection. Thus, this study contributes to the understanding of the pathogenesis of ND and provides an insight into the virus-host interaction.

Heterologous expression, characterization and evaluation of the matrix protein from Newcastle disease virus as a target for antiviral therapies

Newcastle disease virus (NDV) is an infectious agent of a large variety of birds, including chicken, which poses a real threat to the agriculture industry. Matrix (M) proteins of NDV and many other viruses perform critical functions during viral assembly and budding from the host cell. M-proteins are well conserved and therefore are potential targets for antiviral therapies. To validate this, we expressed the NDV M-protein in its native form in Saccharomyces cerevisiae and in inclusion bodies in Escherichia coli. Proper refolding of the recombinant protein produced in E. coli was verified using circular dichroism and infrared spectroscopies and electron microscopy. Immunization of chickens with the NDV M-protein elicited significant serum antibody titers. However, the antibodies conferred little protection against the ND following lethal viral challenges. We conclude that the M-protein is not exposed on the surface of the host cell or the virus at any stage during its life cycle. We discuss how the conserved M-protein can further be exploited as an antiviral drug target.

Genetic diversity of Newcastle disease virus in Pakistan: a countrywide perspective

Background

Newcastle disease (ND) is one of the most deadly diseases of poultry around the globe. The disease is endemic in Pakistan and recurrent outbreaks are being reported regularly in wild captive, rural and commercial poultry flocks. Though, efforts have been made to characterize the causative agent in some of parts of the country, the genetic nature of strains circulating throughout Pakistan is currently lacking.

Material and methods

To ascertain the genetics of NDV, 452 blood samples were collected from 113 flocks, originating from all the provinces of Pakistan, showing high mortality (30–80%). The samples represented domesticated poultry (broiler, layer and rural) as well as wild captive birds (pigeons, turkeys, pheasants and peacock). Samples were screened with real-time PCR for both matrix and fusion genes (1792 bp), positive samples were subjected to amplification of full fusion gene and subsequent sequencing and phylogenetic analysis.

Results

The deduced amino acid sequence of the fusion protein cleavage site indicated the presence of motif (¹¹²RK/RQRR↓F¹¹⁷) typical for velogenic strains of NDV. Phylogenetic analysis of hypervariable region of the fusion gene indicated that all the isolates belong to lineage 5 of NDV except isolates collected from Khyber Pakhtunkhwa (KPK) province. A higher resolution of the phylogenetic analysis of lineage 5 showed the distribution of Pakistani NDV strains to 5b. However, the isolates from KPK belonged to lineage 4c; the first report of such lineage from this province.

Conclusions

Taken together, data indicated the prevalence of multiple lineages of NDV in different poultry population including wild captive birds. Such understanding is crucial to underpin the nature of circulating strains of NDV, their potential for interspecies transmission and disease diagnosis and control strategies.

Newcastle disease virus: macromolecules and opportunities

Over the past two decades, enormous advances have occurred in the structural and biological characterization of Newcastle disease virus (NDV). As a result, not only the complete sequence of the viral genome has been fully determined, but also a clearer understanding of the viral proteins and their respective roles in the life cycle has been achieved. This article reviews the progress in the molecular biology of NDV with emphasis on the new technologies. It also identifies the fundamental problems that need to be addressed and attempts to predict some research opportunities in NDV that can be realized in the near future for the diagnosis, prevention and treatment of disease(s).

Newcastle disease virus in pakistan: genetic characterization and implication in molecular diagnosis

Newcastle disease (ND) is a fatal and contagious disease that poses a constant threat to the poultry industry around the globe. Due to the complex clinico-pathological picture and high genetic variability, the efficient diagnosis of NDV strains is a challenge. In an emerging wave of ND in the north of Pakistan, samples from six outbreaks in commercial poultry and two from healthy backyard poultry flocks were screened for NDV. A real-time PCR based on the fusion and polymerase genes of NDV detected all six isolates whereas a validated real-time PCR based on the matrix gene failed to detect any of these isolates, most likely due to substantial mismatches in the probe-binding site. All isolates have shown ICPI and MDT values similar to the velogenic form of NDV strains. The cleavage site in the F protein was found to be (112)RRQKR↓F(117), typical of virulent NDV. Phylogenetic reconstruction, based on fusion and matrix genes, provided enough evidences to consider these isolates as a new subgenotype within genotype VII. This study raised concerns about the genetic variability of NDV circulating in Pakistan, and sensitivity of the assays for the detection of the NDV isolates in clinical samples.

Newcastle disease: a review of field recognition and current methods of laboratory detection

Newcastle disease (ND) remains a constant threat to the poultry industry and is a limiting disease for poultry producers worldwide. The variety of clinical presentations and the emergence and spread of new genetic variants make recognition and diagnosis challenging. The current review details the pertinent features of the clinicopathologic disease in the main susceptible species, including chicken, turkey, duck, goose, pigeon, and other birds such as cormorants, psittacines, and canaries. Furthermore, the available and emerging laboratory diagnostic methodologies for the detection and typing of the virus are reviewed, including traditional techniques such as virus isolation and immunohistochemistry as well as rapid procedures based on molecular tools, such as real-time polymerase chain reaction, gene sequencing, and microarrays. The relevant genetic variability of ND viruses probably represents the major limitation in the validation and application of the current, advanced diagnostic molecular techniques. This underscores the importance of a multidisciplinary and comprehensive diagnostic approach, which should include, next to the new generation assays of the genomic era, the more traditional techniques such as histopathology, immunohistochemistry, and virus isolation.

Entire genome sequence analysis of genotype IX Newcastle disease viruses reveals their early-genotype phylogenetic position and recent-genotype genome size

BACKGROUND

Six nucleotide (nt) insertion in the 5'-noncoding region (NCR) of the nucleoprotein (NP) gene of Newcaslte disease virus (NDV) is considered to be a genetic marker for recent genotypes of NDV, which emerged after 1960. However, F48-like NDVs from China, identified a 6-nt insert in the NP gene, have been previously classified into genotype III or genotype IX.

RESULTS

In order to clarify their phylogenetic position and explore the origin of NDVs with the 6-nt insert and its significance in NDV evolution, we determined the entire genome sequences of five F48-like viruses isolated in China between 1946 and 2002 by RT-PCR amplification of overlapping fragments of full-length genome and rapid amplification of cDNA ends. All the five NDV isolates shared the same genome size of 15,192-nt with the recent genotype V-VIII viruses whereas they had the highest homology with early genotype III and IV isolates.

CONCLUSIONS

The unique characteristic of the genome size and phylogenetic position of F48-like viruses warrants placing them in a separate geno-group, genotype IX. Results in this study also suggest that genotype IX viruses most likely originate from a genotype III virus by insertion of a 6-nt motif in the 5'-NCR of the NP gene which had occurred as early as in 1940 s, and might be the common origin of genotype V-VIII viruses.

Molecular characterization of partial fusion gene and C-terminus extension length of haemagglutinin-neuraminidase gene of recently isolated Newcastle disease virus isolates in Malaysia

Background

Newcastle disease (ND), caused by Newcastle disease virus (NDV), is a highly contagious disease of birds and has been one of the major causes of economic losses in the poultry industry. Despite routine vaccination programs, sporadic cases have occasionally occurred in the country and remain a constant threat to commercial poultry. Hence, the present study was aimed to characterize NDV isolates obtained from clinical cases in various locations of Malaysia between 2004 and 2007 based on sequence and phylogenetic analysis of partial F gene and C-terminus extension length of HN gene.

Results

The coding region of eleven NDV isolates fusion (F) gene and carboxyl terminal region of haemagglutinin-neuraminidase (HN) gene including extensions were amplified by reverse transcriptase PCR and directly sequenced. All the isolates have shown to have non-synonymous to synonymous base substitution rate ranging between 0.081 - 0.264 demonstrating presence of negative selection. Analysis based on F gene showed the characterized isolates possess three different types of protease cleavage site motifs; namely ¹¹²RRQKRF¹¹⁷, ¹¹²RRRKRF¹¹⁷ and ¹¹²GRQGRL¹¹⁷ and appear to show maximum identities with isolates in the region such as cockatoo/14698/90 (Indonesia), Ch/2000 (China), local isolate AF2240 indicating the high similarity of isolates circulating in the South East Asian countries. Meanwhile, one of the isolates resembles commonly used lentogenic vaccine strains. On further characterization of the HN gene, Malaysian isolates had C-terminus extensions of 0, 6 and 11 amino acids. Analysis of the phylogenetic tree revealed that the existence of three genetic groups; namely, genotype II, VII and VIII.

Conclusions

The study concluded that the occurrence of three types of NDV genotypes and presence of varied carboxyl terminus extension lengths among Malaysian isolates incriminated for sporadic cases.

The effect of vaccination on the evolution and population dynamics of avian paramyxovirus-1

Newcastle Disease Virus (NDV) is a pathogenic strain of avian paramyxovirus (aPMV-1) that is among the most serious of disease threats to the poultry industry worldwide. Viral diversity is high in aPMV-1; eight genotypes are recognized based on phylogenetic reconstruction of gene sequences. Modified live vaccines have been developed to decrease the economic losses caused by this virus. Vaccines derived from avirulent genotype II strains were developed in the 1950s and are in use globally, whereas Australian strains belonging to genotype I were developed as vaccines in the 1970s and are used mainly in Asia. In this study, we evaluated the consequences of attenuated live virus vaccination on the evolution of aPMV-1 genotypes. There was phylogenetic incongruence among trees based on individual genes and complete coding region of 54 full length aPMV-1 genomes, suggesting that recombinant sequences were present in the data set. Subsequently, five recombinant genomes were identified, four of which contained sequences from either genotype I or II. The population history of vaccine-related genotype II strains was distinct from other aPMV-1 genotypes; genotype II emerged in the late 19^th century and is evolving more slowly than other genotypes, which emerged in the 1960s. Despite vaccination efforts, genotype II viruses have experienced constant population growth to the present. In contrast, other contemporary genotypes showed population declines in the late 1990s. Additionally, genotype I and II viruses, which are circulating in the presence of homotypic vaccine pressure, have unique selection profiles compared to nonvaccine-related strains. Collectively, these data show that vaccination with live attenuated viruses has changed the evolution of aPMV-1 by maintaining a large effective population size of a vaccine-related genotype, allowing for coinfection and recombination of vaccine and wild type strains, and by applying unique selective pressures on viral glycoproteins.

Modified live virus (MLV) vaccines have been effective in reducing disease burden and economic loss caused by Newcastle Disease (ND) in domestic poultry. Because the vaccine is a live virus, it is transmissible among birds. Thus, vaccination strategies have the potential to impact the evolutionary genetics of wild type strains of aPMV-1 including those that cause ND. In this report, we provided evidence that viruses isolated from wild and domestic birds have recombined with vaccine strains, because vaccinated birds are protected from disease but not infection with other strains of aPMV-1. Despite the use of vaccines since the 1950s, the population size of the strain from which the most widely used vaccine was derived has steadily increased. In contrast, other contemporary genotypes, which emerged in the 1960s, experienced a decline in population size in 1998, which may reflect a change in poultry farming practices or disease. Vaccination imposed a unique selection profile on the genotypes derived from the vaccine-related strains when compared with nonvaccine-related strains. Although modified live viruses are important for controlling Newcastle Disease, the potential of vaccination strategies to change viral diversity and population dynamics should be considered.

Selection characterization on overlapping reading frame of multiple-protein-encoding P gene in Newcastle disease virus

The aim of this study was to characterize the molecular evolution of P and V protein genes of the Newcastle disease virus (NDV). The P gene sequences of 55 NDV isolates, representing different chronological and geographic origins, were obtained from GenBank. In this paper, the evolution of the specific regions of the NDV P gene, encoding the P and V proteins, was analyzed. The nucleotides from the shared P/V region encoded the co-amino terminus of the two proteins, while the P-V/V-P region was respectively encoded by the nucleotides within the P ORF or the V ORF in the common sequence (after the mRNA editing site). As well, the P-cut region exclusively encoded the P protein. Finally, the P-V and V-P regions were further broken down into P1 and P2 fragments with the corresponding V1 and V2 fragments. In the P gene, the P-cut portion corresponding to the C-terminal of the P protein was the most highly conserved, while the P-V region was the most variable. This was interpreted as a lower constraint for function in the common sequence than in the unique P sequence that is known to contain an important function. Interestingly, in the common P-V/V-P function, variability of V1 was compensated by a higher conservation of the corresponding P1, and conversely for the P2/V2, which suggested that the flexibility of one ORF with less function served the purpose of allowing positive selection in the other overlapping ORF that exhibited more function.

Increase in the neuraminidase activity of a nonpathogenic Newcastle disease virus isolate during passaging in chickens

A pathogenic mutant of the Newcastle disease virus (NDV) was previously generated by passaging a non-pathogenic isolate from wild waterfowl. Velogenic mutant 9a5b (IVPI=2.67) contains three amino acid substitutions (128H, 495K and 573stop) in the hemagglutinin-neuraminidase (HN) protein, as compared with nonpathogenic waterfowl isolate 415/91 strain, and two of these (128H and 495K) were introduced after mesogenic 9a3b (IVPI=1.88). To investigate the role of the HN protein in NDV virulence, the function of HN protein such as neuraminidase (NA), Hemadsorption (HAd) and fusion promotion activities was examined by introducing the point mutations observed in passaged mutants into the HN gene cDNAs. In vitro functional assay using mutant protein expression demonstrated that the 128H substitution markedly increases NA activity and 573stop substitution increase NA and HAd activities. On the other hand, 495K substitution had little effect on any activities. These results indicate that a single amino acid substitution (128P to H) in the NDV HN protein affects the neuraminidase activity and is possibly correlated with the virulence.

Reassessing conflicting evolutionary histories of the Paramyxoviridae and the origins of respiroviruses with Bayesian multigene phylogenies

The evolution of paramyxoviruses is still poorly understood since past phylogenetic studies have revealed conflicting evolutionary signals among genes, and used varying methods and datasets. Using Bayesian phylogenetic analysis of full length single and concatenated sequences for the 6 genes shared among paramyxovirus genera, we reassess the ambiguous evolutionary relationships within the family, and examine causes of varying phylogenetic signals among different genes. Relative to a pneumovirus outgroup, the concatenated gene phylogeny, splits the Paramyxovirinae into two lineages, one comprising the avulaviruses and rubulaviruses, and a second containing the respiroviruses basal to the henipaviruses, and morbilliviruses. Phylogenies for the matrix (M), RNA dependent RNA polymerase (L) and the fusion (F) glycoprotein genes, are concordant with the topology from the concatenated dataset. In phylogenies derived from the nucleocapsid (N) and phosphoprotein (P) genes, the respiroviruses form the most basal genus of the Paramyxovirinae subfamily, with the avulaviruses and rubulaviruses in one lineage, and the henipaviruses, and morbilliviruses in a second. The phylogeny of the hemagglutinin (H) gene places the respiroviruses basal to the avula-rubulavirus group, but the relationship of this lineage with henipa and morbillviruses is not resolved. Different genes may be under varying evolutionary pressures giving rise to these conflicting signals. Given the level of conservation in the M and L genes, we suggest that together with F gene, these or concatenated datasets for all six genes are likely to reveal the most reliable phylogenies at a family level, and should be used for future phylogenetic studies in this group. Split decomposition analysis suggests that recombination within genera, may have a contributed to the emergence of dolphin morbillivirus, and several species within respiroviruses. A partial L gene alignment, resolves the relationship of 25 unclassified paramxyoviruses into 4 clades (Chiopteran-, Salmon-, Rodentian- and Ophidian paramyxoviruses) which group with rubula-, respiro-, morbilliviruses, and within the paramxyovirinae respectively.

Antigenic differences among Newcastle disease virus strains of different genotypes used in vaccine formulation affect viral shedding after a virulent challenge

Strains of Newcastle disease virus (NDV) can be separated into genotypes based on genome differences even though they are antigenically considered to be of a single serotype. It is widely recognized that an efficacious Newcastle disease (ND) vaccine made with any NDV does induce protection against morbidity and mortality from a virulent NDV challenge. However, those ND vaccines do not protect vaccinates from infection and viral shed from such a challenge. Vaccines prepared from ND viruses corresponding to five different genotypes were compared to determine if the phylogenetic distance between vaccine and challenge strain influences the protection induced and the amount of challenge virus shed. Six groups of 4-week-old specific pathogen-free Leghorn chickens were given oil-adjuvanted vaccines prepared from one of five different inactivated ND viruses including strains B1, Ulster, CA02, Pigeon84, Alaska 196, or an allantoic fluid control. Three weeks post-vaccination, serum was analyzed for antibody content using a hemagglutination inhibition assay against each of the vaccine antigens and a commercial NDV ELISA. After challenge with virulent CA02, the birds were examined daily for morbidity and mortality and were monitored at selected intervals for virus shedding. All vaccines except for the control induced greater than 90% protection to clinical disease and mortality. The vaccine homologous with the challenge virus reduced oral shedding significantly more than the heterologous vaccines. NDV vaccines formulated to be phylogenetically closer to potential outbreak viruses may provide better ND control by reducing virus transmission from infected birds.

Genotyping of Newcastle Disease Viruses Isolated from 2002 to 2004 in China

The main function region of the fusion (F) protein gene of 124 strains of Newcastle disease virus isolated from 2002 to 2004 in China was amplified and sequenced for further phylogenetic and residue substitutive analysis. Most of the isolates were classified into genotype VIIc, VIId, VIf, and VIb, while others into genotype IX, III, or II. The genotype IX, a unique genotype which includes strain F48, the first Chinese virulent NDV strain isolated in 1948, were still found inducing sporadic infections in certain areas. Subgenotype VIIc, VIId, and VIIe viruses, which were distributed in clusters in the phylogenetic tree distinct from members of subgenotypes VIIa and VIIb, were responsible for most outbreaks in China and circulated predominantly in China in recent years. Strain NDV03-026, an isolate of the genotype II which was normally lentogenic, was found carrying (112)RRQKRF(117) motif at the cleavage site of F protein as the virulent strain.

Third genome size category of avian paramyxovirus serotype 1 (Newcastle disease virus) and evolutionary implications

The goal of the study was to establish if there was a relationship between molecular patterns and virus evolution. Therefore the complete genome sequence of two distinct apathogenic Newcastle disease virus (NDV) strains was determined and a third genome size category, containing 15,198 nucleotides, was recognized. Phylogenetic analysis revealed that two major separations resulting in three genome size categories occurred during the history of NDV. An ancient division in the primordial reservoir (wild waterbird species) led to two basal sister clades, class I and II, with genome sizes 15,198 (due to a 12 nucleotide insert in the phosphoprotein gene) and 15,186 nucleotides, respectively. Ancestors of only class II viruses colonized chicken populations and subsequently converted to virulent forms. These took place more than once and resulted in an early lineage [including genotypes I-IV and H33(W)] with genome size of 15,186 nucleotides. A second division occurred in the 20th century in the secondary (chicken) host. This gave rise to the branching-off of a clade (including recent genotypes V-VIII consisting of only pathogenic viruses) with the concomitant insertion of six nucleotides into the 5' non-coding region of the nucleoprotein gene thereby increasing the genome size to 15,192 nucleotides.

Complete genome sequence and biological characterizations of a novel goose paramyxovirus-SF02 isolated in China

A paramyxovirus designated as APMV-1 (NDV) isolate SF02 (abbre. as SF02) was recently isolated from goose in China. SF02 was identified as a member of Newcastle disease virus (NDV) genotype VII. NDV strains are generally pathogenic only for fowls, including chicken and pigeon, and not for waterfowls such as goose and duck, whereas SF02 is highly pathogenic for both fowls and waterfowls. In the present study the complete genome consisting of 15, 192 nucleotides of SF02 was sequenced. Genomes of SF02 and all known APMV-1, Strains contain 6 ORFs in the order of NP-P-M-F-HN-L, and that of SF02 had an extra 6 nts between NP and P genes. Moreover, an anti-sense ORF consisting of 549 nt at the 1960 to 1412 and deduced 182 amino acids was found in SF02. The SF02 genome shared 83% identity and its 6 ORFs 81.9-86.1% identities with the reference APMV-1 strains. The possible mechanism determining different host range and pathogenicity is discussed based on genetic analyses.

Nucleotide sequence of the matrix protein gene of avian paramyxovirus, serotype 3b: evidence on another member of the suggested new genus of the subfamily Paramyxovirinae

The complete nucleotide sequence of the gene encoding the matrix protein (M) of the avian paramyxovirus, serotype 3b (APMV-3b), has been determined by means of the direct sequencing of viral RNA using reverse transcriptase reaction. The adjacent portions of the neighboring phosphoprotein (P) and fusion (F) protein genes were also sequenced that permitted to determine the consensus sequence of the viral genome, the poly(A) tract, downstream and upstream non-coding portions of the P and F genes, respectively, as well as the corresponding intergenic regions. The gene is 1478 nucleotides long with a protein-coding sequence of 1194 nucleotides. The deduced protein consists of 398 amino acids with a calculated MW 44,465. According to the multalignment and phylogenetic analyses, the APMV-3b M protein has shown the closest relatedness towards Newcastle disease virus (NDV) which has recently been suggested to be excluded from the Rubulavirus genus and assigned (together with APMV-6) to a new Avulavirus genus within the subfamily Paramyxovirinae of the Paramyxoviridae family. On the basis of the M protein genetic multalignment, phylogenetic relationships, bipartite nuclear localization signal identification in combination with the cysteine residues distribution, and by the degree of intrageneric heterogeneity, the APMV-3b is proposed to be another member (together with NDV and APMV-6) of the new genus.

Molecular epidemiology of Newcastle disease viruses isolated in South Korea using sequencing of the fusion protein cleavage site region and phylogenetic relationships

The study, using sequence analysis and the phylogenetic relationship of the fusion protein gene, divided the Korean epizootic isolates of Newcastle disease virus (NDV) into several lineages to determine the molecular epidemiology of the virus. A 695 base pair fragment was amplified by polymerase chain reaction between matrix protein gene and fusion protein gene of 30 Korean NDV isolates, which were isolated from field outbreaks of Newcastle disease between 1949 and 2002. All isolates showed the amino acid sequence 112R-R-Q/R-K-R116 at the C-terminus of the F2 protein and phenylalanine (F) at the N-terminus of the F1 protein, residue 117. These amino acid sequences were identical to a known virulent motif. The region of the F gene between nucleotides 47 and 435 was compared by phylogenetic analysis. Based on nucleotide sequence, the Korean NDV isolates belonged to genotype III, V, VI and VII corresponding to isolates in 1949, 1982 to 1984, 1988 to 1997, and 1995 to 2002, respectively. These data showed that genotypes of five Korean Newcastle disease epizootics had replaced each other serially (III, V, VI and VII) in chronological order. Further, the five Korean Newcastle disease epizootics were closely related with the Newcastle disease panzootics or Newcastle disease epizootics in other countries. Present study showed that the Korean genotype V isolated before 1984 was related with European Newcastle disease epizootics in the 1970s, whereas the Korean genotypes VI and VII isolated after 1988 were more closely related with Far East Newcastle disease epizootics, especially Newcastle disease epizootics in Japan, Taiwan and China. Since 1988, the genotypes VI and VII of Far East origin were dominant in South Korea. That might be due to the increased trade of agricultural products including poultry among Far East Asian countries.

Antigenic and genotypical characterization of Newcastle disease viruses isolated in Taiwan between 1969 and 1996

Three major epidemics of Newcastle disease (ND) occurred in Taiwan over the past three decades (in 1969, 1984, and 1995). In order to gain a better understanding of the relationships between past ND epizootics in Taiwan, 36 ND viruses (NDVs) isolated between 1969 and 1996 were characterized antigenically and genotypically. The antigenicity of these viruses was analysed by their ability to cause binding of mouse monoclonal antibodies (mAbs) to cell cultures infected with the isolate. Using a panel of 22 mAbs to divide NDVs into subgroups, a total of 18 binding patterns were revealed. The sequences covering the cleavage site of the fusion protein gene of these isolates were also determined. The results of the phylogenetic analysis placed 36 NDVs into I, II, VIb, VIIa, VIII and two novel genotypes (provisionally termed X and VIh). The 1969 velogenic isolates were of genotypes X and VIh; the 1984-1985 velogenic isolates were genotyped VIb, VIh, VIIa, and X; while the 1995-1996 velogenic isolates were genotyped VIIa or VIII. Some 1969 and 1984 velogenic isolates were of the same mAbs binding pattern and genotype, and the mAbs binding patterns of the 1995-1996 isolates have not been seen before. It is concluded that velogenic NDVs of different genotype and antigenic type have co-circulated in Taiwan at least since 1969. Also there were epizootiological links between strains isolated in 1969 and 1984, whereas the 1995-1996 epidemic was caused by new antigenic variants.

RNA-dependent RNA polymerase gene analysis of worldwide Newcastle disease virus isolates representing different virulence types and their phylogenetic relationship with other members of the paramyxoviridae

Nucleotide sequence was determined for the RNA-dependent RNA polymerase (L) gene of 16 Newcastle disease virus (NDV) isolates from diverse geographic and chronological origins. The observed consensus amino acid sequence conformed to the six domains previously identified among paramyxovirus L proteins, and the putative 749QGDNQ753 active site was strictly conserved among all isolates. Analysis of predicted amino acid sequences allowed us to identify a sequencing error in the previously reported L genes for NDV. The correct sequences reported herein provided a more accurate alignment with predicted l-amino acid sequences of other paramyxoviruses. Comparison of L gene coding sequences among isolates revealed that synonymous substitutions dominated non-synonymous substitutions, as observed previously with other NDV genes. However, the overall substitution rate was lower than other genes examined making the L gene the most conserved of the NDV genome. Phylogenetic analysis of L genes among NDV isolates was consistent with previous results that suggested the existence of two major lineages. One group contained strains isolated in North America prior to 1970 and included virulent and vaccine strains, while the second group included virulent viruses isolated worldwide. A comparison of the NDV L coding sequences to other Paramyxoviridae illustrated the unique clustering of the avian-specific paramyxoviruses, further justifying the newly created Avulavirus genus.

Development of a real-time reverse-transcription PCR for detection of newcastle disease virus RNA in clinical samples

A real-time reverse-transcription PCR (RRT-PCR) was developed to detect avian paramyxovirus 1 (APMV-1) RNA, also referred to as Newcastle disease virus (NDV), in clinical samples from birds. The assay uses a single-tube protocol with fluorogenic hydrolysis probes. Oligonucleotide primers and probes were designed to detect sequences from a conserved region of the matrix protein (M) gene that recognized a diverse set (n = 44) of APMV-1 isolates. A second primer-probe set was targeted to sequences in the fusion protein (F) gene that code for the cleavage site and detect potentially virulent NDV isolates. A third set, also directed against the M gene, was specific for the North American (N.A.) pre-1960 genotype that includes the common vaccine strains used in commercial poultry in the United States. The APMV-1 M gene, N.A. pre-1960 M gene, and F gene probe sets were capable of detecting approximately 10(3), 10(2), and 10(4) genome copies, respectively, with in vitro-transcribed RNA. Both M gene assays could detect approximately 10(1) 50% egg infective doses (EID(50)), and the F gene assay could detect approximately 10(3) EID(50). The RRT-PCR test was used to examine clinical samples from chickens experimentally infected with the NDV strain responsible for a recent epizootic in the southwestern United States. Overall, a positive correlation was obtained between the RRT-PCR results and virus isolation for NDV from clinical samples.

Complete genome sequence of Fer-de-Lance virus reveals a novel gene in reptilian paramyxoviruses

The complete RNA genome sequence of the archetype reptilian paramyxovirus, Fer-de-Lance virus (FDLV), has been determined. The genome is 15,378 nucleotides in length and consists of seven nonoverlapping genes in the order 3' N-U-P-M-F-HN-L 5', coding for the nucleocapsid, unknown, phospho-, matrix, fusion, hemagglutinin-neuraminidase, and large polymerase proteins, respectively. The gene junctions contain highly conserved transcription start and stop signal sequences and tri-nucleotide intergenic regions similar to those of other Paramyxoviridae. The FDLV P gene expression strategy is like that of rubulaviruses, which express the accessory V protein from the primary transcript and edit a portion of the mRNA to encode P and I proteins. There is also an overlapping open reading frame potentially encoding a small basic protein in the P gene. The gene designated U (unknown), encodes a deduced protein of 19.4 kDa that has no counterpart in other paramyxoviruses and has no similarity with sequences in the National Center for Biotechnology Information database. Active transcription of the U gene in infected cells was demonstrated by Northern blot analysis, and bicistronic N-U mRNA was also evident. The genomes of two other snake paramyxovirus genotypes were also found to have U genes, with 11 to 16% nucleotide divergence from the FDLV U gene. Pairwise comparisons of amino acid identities and phylogenetic analyses of all deduced FDLV protein sequences with homologous sequences from other Paramyxoviridae indicate that FDLV represents a new genus within the subfamily Paramyxoviridae. We suggest the name Ferlavirus for the new genus, with FDLV as the type species.

Molecular characterisation of three avian paramyxovirus type 1 isolated from pigeons in France

Three avian Paramyxovirus type 1 (aPMV-1) isolated from pigeons duringpigeon paramyxovirosis outbreaks were molecularly characterised by sequencing parts of the six genes (NP, P, M, F, HN and L) of each strain. Virulent 99143 isolate was found to be very closely related to non-pathogenic vaccine strains of aPMV-1, even for its F protein cleavage site motif. Strains 99299 and 99106, typical pigeon paramyxovirus type 1 (pPMV-1) variants, exhibited between 10% and 20% difference with aPMV-1 at the nucleotide level. The aPMV-1 specific pattern of eight amino acids in the intracellular domain of HN protein was found different by one residue for these two isolates, and might represent a specific pattern for pPMV-1. The unique sequence of the polycistronic P gene editing site of 99299 and 99106 was characterised by four instead of three cytosine residues, and might so have an influence on the expression level of the three proteins encoded by P. This work is also the first to provide molecular data on NP, P and L genes of typical pPMV-1.

Newcastle disease virus fusion and haemagglutinin-neuraminidase gene motifs as markers for viral lineage

Reverse transcriptase polymerase chain reaction was used to generate sequence data for 91 Australian Newcastle disease viruses (NDV) isolated from 1932 to 2000 covering the cleavage site of the fusion (F) protein and the C-terminus of the haemagglutinin-neuraminidase (HN) protein. Comparison of sequences at these two sites indicates distinct evolutionary relationships between these viruses. Typically, HN gene relationships revealed by phylogenetic analyses were also maintained in comparisons between F gene cleavage sites; however, the former analyses appeared to give a clearer indication of the lineage of a virus isolate. This data supports and extends earlier observations in that there is no evidence for gene exchange by recombination but that different strains appear to have evolved through synonymous mutations. Inter-relationships, especially between Australian NDV isolates, appear to be associated with lineages having the same C-terminal HN extensions rather than associated with virulence of the virus. A proposed mechanism for this observation is discussed.

Pathogenesis of chicken-passaged Newcastle disease viruses isolated from chickens and wild and exotic birds

The pathogenesis of six Newcastle disease virus (NDV) isolates recovered from chickens (Ckn-LBM and Ckn-Australia) and wild (Anhinga) and exotic (YN parrot, pheasant, and dove) birds was examined after the isolates had been passaged four times in domestic chickens. Groups of 10 4-wk-old specific-pathogen-free white leghorn chickens were inoculated intraconjunctivally with each one of the isolates. The infected birds were observed for clinical disease and were euthanatized and sampled at selected times from 12 hr to 14 days postinoculation or at death. Tissues were examined by histopathology, by immunohistochemistry (IHC) to detect viral nucleoprotein (IHC/NP), and by in situ hybridization to detect viral mRNA and were double labeled for apoptosis (terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling ([TUNEL] or IHC/caspase-3) and viral nucleoprorein (IHC/NP). Birds infected with the three low virulence viruses (Ckn-LBM, YN parrot, and Ckn-Australia) did not develop clinical disease. Microscopic lesions were observed only at the inoculation site and in organs of the respiratory system. The detection of viral nucleoprotein (N) was restricted to the inoculation site. The pheasant and dove isolates were highly virulent for chickens with marked tropism for lymphoid tissues, confirmed by the presence of large numbers of cells positive for viral N protein and viral mRNA. Viral N protein was detected early in the cytoplasm of cells in the center of the splenic ellipsoids. The apoptosis assays (TUNEL and IHC/caspase-3) showed increased apoptosis in the splenic ellipsoids as well. Apparently, apoptosis is an important mechanism in lymphoid depletion during NDV infection.

Effect of fusion protein cleavage site mutations on virulence of Newcastle disease virus: non-virulent cleavage site mutants revert to virulence after one passage in chicken brain

Virulence of Newcastle disease virus (NDV) is mainly determined by the amino acid sequence of the fusion (F0) protein cleavage site. Full-length NDV cDNA clone pNDFL was used to generate infectious NDV with defined mutations in the F0 cleavage site (RRQRR downward arrow L, GRQGR downward arrow F, RRQGR downward arrow F, RGQRR downward arrow F and RKQKR downward arrow F). All the mutants were viable and the mutations were maintained after virus propagation in embryonated eggs. The mutants showed single-cell infections on chicken embryo fibroblasts, which suggested that they were non-virulent. However, virulence tests in 1-day-old chickens resulted in an intracerebral pathogenicity index (ICPI) between 0 and 1.3. Moreover, virulent virus was isolated from chickens that had died in the virulence tests. Subsequent sequence analysis showed that the mutants RRQRR downward arrow L, RRQGR downward arrow F, RGQRR downward arrow F and RKQKR downward arrow F gave rise to the appearance of revertants containing the virulent cleavage site RRQ(K/R)R downward arrow F and an ICPI of 1.4 or higher. This indicated that reversion to virulence was caused by alteration of the amino acid sequence of the F0 cleavage site from a non-virulent to a virulent type. Furthermore, the ICPI of the revertants was higher than that of cDNA-derived strain NDFLtag, which has the same cleavage site, RRQRR downward arrow F (ICPI=1.3). NDFLtag(Pass), which was isolated from dead chickens after intracerebral inoculation of NDFLtag, also showed an increase in the ICPI from 1.3 to 1.5. This study proves that reversion to virulence occurs within non-virulent NDV populations and that the virulence may increase after one passage in chicken brain.

Phylogenetic analysis of Newcastle disease virus genotypes isolated in Japan

We genetically analyzed field isolates of the Newcastle disease (ND) virus isolated in Japan from 1930 to 2001. The coding region of the fusion protein was amplified by reverse transcriptase PCR and directly sequenced. Phylogenetic analysis revealed the presence of viruses belonging to six of the eight known genotypes. It can be concluded from this study that ND outbreaks in Japan have been of multiple etiologies. [All sequences used in this study were sent to DDBJ and assigned accession numbers AB 070382 to AB 074042.]

Pathogenesis of six pigeon-origin isolates of Newcastle disease virus for domestic chickens

The pathogenesis of six pigeon-origin isolates of Newcastle disease virus (NDV) was investigated in chickens. Four isolates were previously defined as the variant pigeon paramyxovirus 1 (PPMV-1), and two isolates were classified as avian paramyxovirus 1 (APMV-1). Birds inoculated with PPMV-1 isolates were euthanatized, and tissue samples were collected at 2, 5, and 10 days postinoculation (DPI). Birds inoculated with APMV-1 isolates died or were euthanatized, and tissue samples were collected at 2, 4, and 5 DPI. Tissues were examined by histopathology, immunohistochemistry (IHC) for the presence of NDV nucleoprotein, and in situ hybridization (ISH) for the presence of viral mRNA for the matrix gene. Spleen sections were stained by the terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling (TUNEL) assay and by IHC using an anti-active caspase-3 antibody (IHC-Casp) to detect apoptotic cells. Brain sections of PPMV-1-infected birds were examined by IHC to detect T and B lymphocytes and glial fibrillary acidic protein (GFAP). Histologically, birds inoculated with PPMV-1 isolates had marked lesions in the heart and brain. Presence of viral nucleoprotein and viral mRNA in the affected tissues was confirmed by IHC and ISH, respectively. Numerous reactive astrocytes were observed in brain sections stained for GFAP Among all the isolates, the IHC-Casp demonstrated that apoptosis was very prominent in the ellipsoid-associated cells of the spleen at 2 DPI. Results of the TUNEL assay indicated that apoptotic cells were prominent at 5 DPI and were more randomly distributed. The clinical signs and gross and histopathologic changes observed in the APMV-1-infected birds were characteristic of an extensive infection with highly virulent NDV evident by IHC.

Nucleotide sequence analysis of the Newcastle disease virus nucleocapsid protein gene and phylogenetic relationships among the Paramyxoviridae

The nucleocapsid (N) protein genes from 24 Newcastle disease virus (NDV) isolates representing various pathotypes with different geographical and chronological origins were cloned and sequenced. The N-terminal region of the N protein to residue 401 was highly conserved among isolates with several conservative substitutions occurring that correlated with phylogenetic relationships. Variability of the N protein was detected in the C-terminal portion similar to what has been reported for other members of the Paramyxovirinae. Amino acids previously identified as invariant or highly conserved in N proteins of other paramyxoviruses were also present in the NDV protein. Phylogenetic analysis of N gene coding sequences among NDV isolates again demonstrated the existence of two major groups. One clade contained viruses that included vaccine and virulent strains isolated in the USA prior to 1970 while a second clade included vaccine and virulent viruses isolated worldwide. Comparison of N protein amino acid sequences among members of the Paramyxoviridae resulted in NDV and avian paramyxovirus 6 separating as a cluster distinct from the Rubulavirus genus. This provides further support for avian paramyxoviruses being considered for their own genus among the Paramyxovirinae.

Molecular evolution of viral fusion and matrix protein genes and phylogenetic relationships among the Paramyxoviridae

Phylogenetic relationships among the Paramyxoviridae, a broad family of viruses whose members cause devastating diseases of wildlife, livestock, and humans, were examined with both fusion (F) and matrix (M) protein-coding sequences. Neighbor-joining trees of F and M protein sequences showed that the Paramyxoviridae was divided into the two traditionally recognized subfamilies, the Paramyxovirinae and the Pneumovirinae. Within the Paramyxovirinae, the results also showed groups corresponding to three currently recognized genera: Respirovirus, Morbillivirus, and Rubulavirus. The relationships among the three genera of the Paramyxovirinae were resolved with M protein sequences and there was significant bootstrap support (100%) showing that members of the genus Respirovirus and the genus Morbillivirus were more closely related to each other than to members of the genus Rubulavirus. Both F and M phylogenies showed that Newcastle disease virus (NDV) was more closely related to the genus Rubulavirus than to the other two genera but were consistent with the proposal (B. S. Seal et al., 2000, Virus Res. 66, 1-11) that NDV be classified as a separate genus within the Paramyxovirinae. Both F and M phylogenies were also consistent with the proposal (L. Wang et al., 2000, J. Virol 74, 9972-9979) that Hendra virus be classified as a new genus closely related and basal to the genus Morbillivirus. Rinderpest was most closely related to measles and a more derived virus than to canine distemper virus, phocine distemper virus, or dolphin morbillivirus.