Newcastle disease virus evolution. II. Lack of gene recombination in generating virulent and avirulent strains

Whole genome sequencing and phylogenetic relative of a pure virulent Newcastle disease virus isolated from an outbreak in northeast Iran

Newcastle disease (ND) is a significant viral disease affecting poultry worldwide, with outbreaks persisting despite extensive vaccination efforts. This study characterizes a novel NDV strain, RT40, isolated from poultry farms in northeast Iran for the first time. RT40, classified as genotype VII, subgenotype VII.1.1, has a genome length of 15 192 nucleotides, with six genes, 12 UTRs, and five IGS, consistent with class II NDVs. Pathogenicity tests confirm its virulent velogenic nature, differentiating it from other known strains. Phylogenetic analysis points to a Western origin, suggesting possible cross-border transmission with Iraqi strains, highlighting the strain's relevance for NDV surveillance. Virus isolation, RNA sequencing, and cross-border transmission analysis were performed, revealing that RT40 shares a high nucleotide sequence identity with Iraqi strains, further supporting cross-border transmission concerns. The findings underscore the need for genotype-specific vaccines tailored to circulating strains. The genome, deposited in GenBank (accession ON184061), serves as an essential resource for future research and vaccine development. By emphasizing whole-genome sequencing, this study aims to improve NDV evolution tracking and enhance understanding of NDV diversity. This work calls for targeted vaccine strategies to effectively manage NDV spread, ensuring the sustainability of the poultry industry.

In Vitro Characterization of chIFITMs of Aseel and Kadaknath Chicken Breeds against Newcastle Disease Virus Infection

Newcastle disease (ND) is highly contagious and usually causes severe illness that affects Aves all over the world, including domestic poultry. Depending on the virus's virulence, it can impact the nervous, respiratory, and digestive systems and cause up to 100% mortality. The chIFITM genes are activated in response to viral infection. The current study was conducted to quantify the mRNA of chIFITM genes in vitro in response to ND viral infection. It also examined its ability to inhibit ND virus replication in chicken embryo fibroblast (CEF) cells of the Aseel and Kadaknath breeds. Results from the study showed that the expression of all chIFITM genes was significantly upregulated throughout the period in the infected CEF cells of both breeds compared to uninfected CEF cells. In CEF cells of the Kadaknath breed, elevated levels of expression of the chIFITM3 gene dramatically reduced ND viral growth, and the viral load was 60% lower than in CEF cells of the Aseel breed. The expression level of the chIFITMs in Kadaknath ranged from 2.39 to 11.68 log₂ folds higher than that of control CEFs and was consistently (p < 0.01) higher than Aseel CEFs. Similar to this, theIFN-γ gene expresses strongly quickly and peaks at 13.9 log₂ fold at 48 hpi. Based on these cellular experiments, the Kadaknath breed exhibits the potential for greater disease tolerance than Aseel. However, to gain a comprehensive understanding of disease resistance mechanisms in chickens, further research involving in vivo investigations is crucial.

The genetic and biological characterization of the first avian paramyxovirus serotype 14 isolated from chicken in China

In October 2020, an avian paramyxovirus serotype 14 (APMV-14)-designated chicken/Fujian/2160/2020 (FJ2160) was isolated from tracheal and cloacal swab sample of chicken collected from live bird market in Fujian province in China during the active surveillance program. The complete genome of FJ2160 comprised 15,444 nucleotides (nt) complying with the paramyxovirus "rule of six" and encoded six non-overlapping structural proteins in the order of 3'-NP-P-M-F-HN-L-'5. The complete genome sequence analysis showed that FJ2160 had the highest identity (90.0%) with the APMV-14 isolated from Japan, while the nucleotide sequence identities of FJ2160 and other APMVs ranged from 42.4 to 51.1%. The F protein cleavage site was TREGR↓L, which resembled a lentogenic strain of APMV-1. Phylogenetic analysis revealed that the FJ2160 closest relative was APMV-14. The intracerebral pathogenicity index (ICPI) tests indicated that the virus was lentogenic. This is the first report of APMV-14 in China. These results provide evidence that APMV-14 could infect chickens and reveal the genetic characteristics and biological properties of the virus, which can help to better understand this new emerging APMV-14.

A Novel Multi-Epitope Edible Vaccine Candidate for Newcastle Disease Virus: In Silico Approach

Background

Newcastle disease, is one of the most important illnesses in the aviculture industry which shows a constant threat. In this case, the vaccine could be considered an important solution to prevent and control this disease. So, the development of a new and more effective vaccine against Newcastle disease is an urgent need. Immune informatics is an important field that provides insight into the experimental procedure and could facilitate the analysis of large amounts of immunological data generated by experimental research and help to design a new vaccine candidate.

Objectives

This study is aimed at bioinformatics to investigate and select the most immunogenic and conserved epitopes derived from F and HN glycoproteins, which play a key role in pathogenesis and immunity. This strategy could cover a wide range of Newcastle disease viruses.

Materials and Method

For expression in both E. coli (as an injectable recombinant vaccine candidate) and maize plant (as an edible vaccine candidate) host, two constructs were designed and analyzed separately. Furthermore, the role of LTB as an effective bio-adjuvant for general eliciting of the immune system and simultaneous expressions with those two antigens was evaluated. Hence, here a multimeric recombinant protein with the abbreviation LHN2F from the highly immunogenic part of HN, F and LTB proteins were designed. The synthetic construct was analyzed based on different bioinformatics tools.

Results

The proper immunogenicity and stability of this multimeric fusion protein have been shown by immunoinformatic methods from various servers. To confirm the function of the designed protein, the final molecule was docked to chicken MHC class I using the Pyrex-python 0.8 program. the results of Immune Epitope analysis were confirmed by the docking results between protein and receptor.

Conclusions

‎The results of structural and immunological computational studies proposed that the protein deduced from this novel construct could act as a vaccine candidate for Newcastle disease virus‎ control and prophylactic.

Molecular characterisation and phylogenetic study of the fusion gene of Newcastle disease viruses isolated from broiler farms of Iran in 2018-2019

Avian orthoavulavirus, commonly known as Newcastle disease virus (NDV) has been a constant threat for the poultry industry of Iran for decades. Recently, a couple of preliminary studies on backyard and commercial chicken suggested that a major subgenotype circulating in Iran may be VII(L) subgenotype, which is now known as VII.1.1 according to the new classification system. The unique subgenotype was not reported from other parts of the world and was slightly (≥3%) different from the closest group that was VIId. The study was conducted between July 2018 and March 2019 to determine the exact NDV genotypes/subgenotypes circulating in Iranian broiler poultry farms; five-hundred and forty chickens were sampled from thirty-six broiler farms located in eighteen provinces of Iran. As other genotypes/subgenotypes such as XIII and VI.2 are circulating in neighbouring countries, border provinces were also sampled. The F gene of the NDV isolates was sequenced and phylogenetic analysis was conducted. All the isolates clustered under the VII.1.1 group. The evolutionary analysis also revealed that the distances were between 0.0 and 0.7% meaning that the Iranian NDV circulating in broiler farms were not only of VII.1.1 sub-genotype, but also genetically very identical, indicating that the routine control measures for ND in Iran were not able to prevent the circulating NDVs. Although stricter biosecurity measures have been really effective in developed countries, surveillance of NDV to determine the circulating genotypes might also help us to implement better vaccination strategies in the future.

Epitope Peptide-Based Predication and Other Functional Regions of Antigenic F and HN Proteins of Waterfowl and Poultry Avian Avulavirus Serotype-1 Isolates From Uganda

Uganda is a Newcastle disease (ND) endemic country where the disease is controlled by vaccination using live LaSota (genotype II) and I₂ (genotype I) vaccine strains. Resurgent outbreak episodes call for an urgent need to understand the antigenic diversity of circulating wild Avian Avulavirus serotype-1 (AAvV-1) strains. High mutation rates and the continuous emergence of genetic and antigenic variants that evade immunity make non-segmented RNA viruses difficult to control. Antigenic and functional analysis of the key viral surface proteins is a crucial step in understanding the antigen diversity between vaccine lineages and the endemic wild ND viruses in Uganda and designing ND peptide vaccines. In this study, we used computational analysis, phylogenetic characterization, and structural modeling to detect evolutionary forces affecting the predicted immune-dominant fusion (F) and hemagglutinin-neuraminidase (HN) proteins of AAvV-1 isolates from waterfowl and poultry in Uganda compared with that in LaSota vaccine strain. Our findings indicate that mutational amino acid variations at the F protein in LaSota strain, 25 poultry wild-type and 30 waterfowl wild-type isolates were distributed at regions including the functional domains of B-cell epitopes or N-glycosylation sites, cleavage site, fusion site that account for strain variations. Similarly, conserved regions of HN protein in 25 Ugandan domestic fowl isolates and the representative vaccine strain varied at the flanking regions and potential linear B-cell epitope. The fusion sites, signal peptides, cleavage sites, transmembrane domains, potential B-cell epitopes, and other specific regions of the two protein types in vaccine and wild viruses varied considerably at structure by effective online epitope prediction programs. Cleavage site of the waterfowl isolates had a typical avirulent motif of ¹¹¹GGRQGR'L¹¹⁷ with the exception of one isolate which showed a virulent motif of ¹¹¹GGRQKR'F¹¹⁷. All the poultry isolates showed the ¹¹¹GRRQKR'F¹¹⁷ motif corresponding to virulent strains. Amino acid sequence variations in both HN and F proteins of AAvV-1 isolates from poultry, waterfowl, and vaccine strain were distributed over the length of the proteins with no detectable pattern, but using the experimentally derived 3D structure data revealed key-mapped mutations on the surfaces of the predicted conformational epitopes encompassing the experimental major neutralizing epitopes. The phylogenic tree constructed using the full F gene and partial F gene sequences of the isolates from poultry and waterfowl respectively, showed that Ugandan ND aquatic bird and poultry isolates share some functional amino acids in F sequences yet do remain unique at structure and the B-cell epitopes. Recombination analyses showed that the C-terminus and the rest of the F gene in poultry isolates originated from prevalent velogenic strains. Altogether, these could provide rationale for antigenic diversity in wild ND isolates of Uganda compared with the current ND vaccine strains.

Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus

Several Avian paramyxoviruses 1 (synonymous with Newcastle disease virus or NDV, used hereafter) classification systems have been proposed for strain identification and differentiation. These systems pioneered classification efforts; however, they were based on different approaches and lacked objective criteria for the differentiation of isolates. These differences have created discrepancies among systems, rendering discussions and comparisons across studies difficult. Although a system that used objective classification criteria was proposed by Diel and co-workers in 2012, the ample worldwide circulation and constant evolution of NDV, and utilization of only some of the criteria, led to identical naming and/or incorrect assigning of new sub/genotypes. To address these issues, an international consortium of experts was convened to undertake in-depth analyses of NDV genetic diversity. This consortium generated curated, up-to-date, complete fusion gene class I and class II datasets of all known NDV for public use, performed comprehensive phylogenetic neighbor-Joining, maximum-likelihood, Bayesian and nucleotide distance analyses, and compared these inference methods. An updated NDV classification and nomenclature system that incorporates phylogenetic topology, genetic distances, branch support, and epidemiological independence was developed. This new consensus system maintains two NDV classes and existing genotypes, identifies three new class II genotypes, and reduces the number of sub-genotypes. In order to track the ancestry of viruses, a dichotomous naming system for designating sub-genotypes was introduced. In addition, a pilot dataset and sub-trees rooting guidelines for rapid preliminary genotype identification of new isolates are provided. Guidelines for sequence dataset curation and phylogenetic inference, and a detailed comparison between the updated and previous systems are included. To increase the speed of phylogenetic inference and ensure consistency between laboratories, detailed guidelines for the use of a supercomputer are also provided. The proposed unified classification system will facilitate future studies of NDV evolution and epidemiology, and comparison of results obtained across the world.

Co-infection of Newcastle disease virus genotype XIII with low pathogenic avian influenza exacerbates clinical outcome of Newcastle disease in vaccinated layer poultry flocks

Newcastle disease (ND) and avian influenza (AI) are economically important infectious diseases of poultry. Sometime, concomitant secondary viral/or bacterial infections significantly alters the pathobiology of ND and AI in poultry. As of now, the disease patterns and dynamics of co-infections caused by ND virus (NDV, genotype XIII) and Low Pathogenic AI viruses (LPAI, H9N2) are explicitly elusive. Thus, we examined the clinicopathological disease conditions due to these two economically important viruses to understand the complex disease outcomes by virus-virus interactions in vaccinated flocks. The findings of clinicopathological and molecular investigations carried on 37 commercial ND vaccinated poultry flocks revealed simultaneous circulation of NDV and AIV in same flock/bird. Further, molecular characterization of hemagglutinin (HA) and neuraminidase (NA) genes confirmed that all the identified AIVs were of low pathogenicity H9N2 subtype and fusion (F) gene analysis of detected NDVs belong to NDV class II, genotype XIII, a virulent type. The NDV and H9N2 alone or co-infected flocks (NDV + LPAI) exhibit clinical signs and lesions similar to that of virulent NDV except the degree of severity, which was higher in H9N2-NDV co-infected flocks. Additionally, avian pathogenic E. coli and mycoplasma infections were detected in majority of the ailing/dead birds from the co-infected flocks during progression of the clinical disease. Overall, the findings highlight the multi-factorial disease complexity in commercial poultry and suggest the importance of NDV genotype XIII in intensifying the clinical disease in vaccinated birds.

Genotypic characterisation of Avian paramyxovirus type-1 viruses isolated from aquatic birds in Uganda

Avian paramyxovirus type-1 (APMV-1) viruses of the lentogenic pathotypes are often isolated from wild aquatic birds and may mutate to high pathogenicity when they cross into poultry and cause debilitating Newcastle disease. This study characterised AMPV-1 isolated from fresh faecal droppings from wild aquatic birds roosting sites in Uganda. Fresh faecal samples from wild aquatic birds at several waterbodies in Uganda were collected and inoculated into 9–10-day-old embryonated chicken eggs. After isolation, the viruses were confirmed as APMV-1 by APMV-1-specific polymerase chain reaction (PCR). The cleavage site of the fusion protein gene for 24 representative isolates was sequenced and phylogenetically analysed and compared with representative isolates of the different APMV-1 genotypes in the GenBank database. In total, 711 samples were collected from different regions in the country from which 72 isolates were recovered, giving a prevalence of 10.1%. Sequence analysis of 24 isolates revealed that the isolates were all lentogenic, with the typical ¹¹¹GGRQGR’L¹¹⁷ avirulent motif. Twenty-two isolates had similar amino acid sequences at the cleavage site, which were different from the LaSota vaccine strain by a silent nucleotide substitution T357C. Two isolates, NDV/waterfowl/Uganda/MU150/2011 and NDV/waterfowl/Uganda/MU186/2011, were different from the rest of the isolates in a single amino acid, with aspartate and alanine at positions 124 and 129, respectively. The results of this study revealed that Ugandan aquatic birds indeed harbour APMV-1 that clustered with class II genotype II strains and had limited genetic diversity.

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 sensitive haemadsorption technique based RT-PCR for concentration and detection of Newcastle disease virus from clinical samples and allantoic fluid

The present study describes the exploitation of haemadsorption (HAd) property of the Newcastle disease virus (NDV) for the development of a novel sensitive HAd technique based RT-PCR for detection of NDV from clinical samples of virus infected experimental birds. The NDV propagated allantoic fluid from the infected embryonated chicken eggs or supernatant of the processed clinical samples (tissue triturate, cloaca and tracheal swabs) from the experimentally infected birds were added with chicken red blood cells (RBC) to adsorb the virus on RBC's surface. The virus adsorbed RBCs were subjected to trizol method of RNA extraction and reverse transcription-polymerase chain reaction (RT-PCR) for detection of NDV. The HAd based RNA extraction showed better yield of 700-900 ng RNA and when subjected to RT-PCR detection revealed a 100 times higher sensitivity than the conventional RNA extraction and RT-PCR detection system. This could be an alternate technique which can be exploited in low NDV load situations in clinical samples.

Molecular Survey of Respiratory and Immunosuppressive Pathogens Associated with Low Pathogenic Avian Influenza H9N2 Subtype and Virulent Newcastle Disease Viruses in Commercial Chicken Flocks

The study was carried out in 48 poultry flocks to elucidate the roles of various complicating pathogens involved along with Newcastle disease (ND)/ low pathogenic avian influenza (LPAI) outbreaks. Necropsy was conducted and samples were collected for the isolation of Newcastle disease virus (NDV), Influenza A virus, infectious bronchitis virus (IBV), pathogenic bacteria; molecular detection of infectious laryngotracheitis virus (ILTV), fowl adeno virus (FAV), chicken anaemia virus (CAV), Mycoplasma synoviae (MS) and Mycoplasma gallisepticum (MG). The isolation results confirmed that 18/48 flocks (37%) were positive for the presence of hemagglutinating agents. Out of 18 hemagglutination (HA) positive flocks, 11 flocks (61%) were positive for both avian influenza virus (AIV) and NDV; 4 flocks (22%) were positive for NDV; and 3 flocks (17%) were positive for AIV. Sequence analysis of hemagglutinin and neuraminidase genes of AIV revealed that all were belonging to LPAI-H9N2 subtype. Sequence analysis of F gene of NDV revealed that they belong to virulent type. The PCR results confirmed the presence of three to seven etiological agents (CAV, FAV, ILTV, MG, MS and avian pathogenic E. coli along with LPAI/NDV from all the 18 HA-positive flocks. The detection rate of triple, quadruple, quintuple, sextuple and sevenfold infections was 17% (3 flocks), 28% (5 flocks), 11%, (2 flocks) 28% (5 flocks) and 17% (3 flocks), respectively. In conclusion, the disease complex involved more than one pathogen, primarily resulting from the interplay between LPAI-H9N2 and NDV; subsequently this could be exacerbated by co-infection with other agents which may cause exacerbated outbreaks that may otherwise go undetected in field.

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.

Phylogenetic analysis of Newcastle disease virus isolates occurring in India during 1989-2013

The study details characterization of Newcastle disease virus (NDV) isolates recovered from commercial poultry flocks (chicken) and wild birds (crane) of India during the time period from 1989 to 2013. Phylogenetic analysis revealed that most of the NDV isolates belongs to class II, genotype XIIIa and a chicken isolate (108/BAREILLY/AD-IVRI/91) was of genotype VI, where it showed diversity of 3 % from the other viruses belonging to same genotype. Another chicken isolate (75/RAMPUR/AD-IVRI/89) grouped in genotype III and showed 4 % diversity with viruses of genotype III. The crane origin NDV identified as of genotype II corresponding to the vaccine virus. This appears to be the first report about existence of genotype XIIIa and its ancestral viruses are circulating in India for the last two decades in different species of birds. Furthermore, genetically distinct viruses belonging to genotypes II, III and VI are also circulating in India.

Isolation and characterization of genotype XIII Newcastle disease virus from Emu in India

Newcastle disease virus (NDV) infects at least 241 species of pet and free-living birds in addition to domesticated avian species. Wild, feral and domesticated birds are recognized reservoirs of NDV, and contribute to the epidemiology of NDV in the domesticated poultry. The biological and molecular characterization of velogenic NDV (vNDV) from emus is limited. In this study, 54 tissues were collected from eight Emu flocks between May 2010 and January 2012 from highly poultry-dense areas of India including Namakkal, Hyderabad and Bareilly regions. The presence of vNDV was confirmed by virus isolation, fusion (F)-gene based RT-PCR, sequencing of the cleavage site and the virulence scored. One out of eight flocks received from Hyderabad region was found positive for NDV and the in vivo pathotyping revealed the isolate to be vNDV type. The sequence analysis revealed that the isolate had cleavage site of 112-R-R-R-K-R-F-117, which is typical for vNDV. Sequence and phylogenetic analysis of the partial 'F' gene coding regions suggested that the NDV strain belongs to genotype XIII. The Emu isolate had 98-100 % nucleotide identity with the vNDVs previously reported in poultry flocks of India. The findings of present study based on the biological and molecular characterization of Emu-origin vNDV, highlights the circulation of genotype XIII in Emus for the first time in the country. There is need to understand the possible spill over of these genetically diverse NDV strains into the commercial poultry and their possible implications in disease control strategies.

Temporal, geographic, and host distribution of avian paramyxovirus 1 (Newcastle disease virus)

Newcastle disease is caused by virulent forms of avian paramyxovirus of serotype 1 (APMV-1) and has global economic importance. The disease reached panzootic proportions within two decades after first being identified in 1926 in the United Kingdom and Indonesia and still remains endemic in many countries across the world. Here we review information on the host, temporal, and geographic distribution of APMV-1 genetic diversity based on the evolutionary systematics of the complete coding region of the fusion gene. Strains of APMV-1 are phylogenetically separated into two classes (class I and class II) and further classified into genotypes based on genetic differences. Class I viruses are genetically less diverse, generally present in wild waterfowl, and are of low virulence. Class II viruses are genetically and phenotypically more diverse, frequently isolated from poultry with occasional spillovers into wild birds, and exhibit a wider range of virulence. Waterfowl, cormorants, and pigeons are natural reservoirs of all APMV-1 pathotypes, except viscerotropic velogenic viruses for which natural reservoirs have not been identified. Genotypes I and II within class II include isolates of high and low virulence, the latter often being used as vaccines. Viruses of genotypes III and IX that emerged decades ago are now isolated rarely, but may be found in domestic and wild birds in China. Containing only virulent viruses and responsible for the majority of recent outbreaks in poultry and wild birds, viruses from genotypes V, VI, and VII, are highly mobile and have been isolated on different continents. Conversely, virulent viruses of genotypes XI (Madagascar), XIII (mainly Southwest Asia), XVI (North America) and XIV, XVII and XVIII (Africa) appear to have a more limited geographic distribution and have been isolated predominantly from poultry.

Characterization of cytopathogenicity of classical swine fever virus isolate induced by Newcastle disease virus

Classical swine fever virus (CSFV), the causative agent of classical swine fever, belongs to the family Flaviviridae and genus Pestivirus. Some pestiviruses exhibit cytopathic effect in cell culture but exact phenomenon is unknown. Over expression of NS2-3 gene, presence of defective interfering particle and exaltation of Newcastle disease virus (END) phenomenon could be the reasons of cytopathogenicity. In the present study, a CSFV isolate exhibiting cytopathic effect (CPE) in Madin-Darby Canine Kidney (MDCK) cell line was characterized. To characterize cytopathogenicity of such isolate, END test was carried out. Interference of Newcastle disease virus (NDV) in MDCK adapted CSFV was confirmed by RT-PCR and virus neutralization test. Absence of CPE and NDV specific nucleic acid after neutralization confirmed the induction of CPE by NDV. Further, identity of the CSFV isolate in MDCK cell line by immunoperoxidase test, immunoblotting and RT-PCR post NDV neutralization established the virus replication without CPE (non-cytopathic isolate). Findings suggest that, there could be a chance of mixed infection of both CSFV and NDV in the piglet from which the sample was collected for virus isolation.

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.

Development of slide ELISA (SELISA) for detection of four poultry viral pathogens by direct heat fixation of viruses on glass slides

The development of an easy and simpler method of slide enzyme-linked immunosorbent assay (SELISA) for the diagnosis of four economically important poultry viruses viz., Newcastle disease virus (NDV), infectious bronchitis virus (IBV), infectious bursal disease virus (IBDV) and egg drop syndrome 76 virus (EDS 76) and the use of SELISA for semi quantitation of NDV are described. The positive signals for viral aggregates were detected under light microscope. This is the first report regarding the development of SELISA based on heat fixation for the diagnosis of viral pathogens.

Detection of Newcastle disease virus in organs and faeces of experimentally infected chickens using RT-PCR

Newcastle disease (ND) is a highly contagious avian disease. Rapid diagnosis of ND plays an important role in controlling outbreaks. Until now, time-consuming isolation of ND virus (NDV) in embryonated chicken eggs was used for NDV detection. For rapid diagnosis, reverse transcription-polymerase chain reaction (RT-PCR) with RNA extracted from tissue samples and faeces originating from experimentally and contact-infected chickens was established. Conjunctiva, lung, caecal tonsil and kidney proved to be the most suitable organs. In infected animals, NDV was detected most frequently between day 4 and 6 post-infection. Contact-infected animals gave most positive results between day 6 and 13 after exposure. RT-PCR was also able to reproducibly detect NDV in faecal samples. The RT-PCR did not show any cross-reactivity with other avian paramyxovirus serotypes, and additionally offers the possibility of subsequent sequencing of the amplified DNA allowing pathotyping of the isolate.

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.

Analysis of Newcastle disease virus quasispecies and factors affecting the emergence of virulent virus

Genome sequence analysis of a number of avirulent field isolates of Newcastle disease virus revealed the presence of viruses (within their quasispecies) that contained virulent F0 sequences. Detection of these virulent sequences below the ~1% level, using standard cloning and sequence analysis, proved difficult, and thus a more sensitive reverse-transcription real-time PCR procedure was developed to detect both virulent and avirulent NDV F0 sequences. Reverse-transcription real-time PCR analysis of the quasispecies of a number of Newcastle disease virus field isolates, revealed variable ratios (approximately 1:4–1:4,000) of virulent to avirulent viral F0 sequences. Since the ratios of these sequences generally remained constant in the quasispecies population during replication, factors that could affect the balance of virulent to avirulent sequences during viral infection of birds were investigated. It was shown both in vitro and in vivo that virulent virus present in the quasispecies did not emerge from the “avirulent background” unless a direct selection pressure was placed on the quasispecies, either by growth conditions or by transient immunosuppression. The effect of a prior infection of the host by infectious bronchitis virus or infectious bursal disease virus on the subsequent emergence of virulent Newcastle disease virus was examined.

Lentogenic field isolates of Newcastle disease virus isolated in Canada and Hungary are identical with the vaccine type used in the region

Lentogenic field isolates of Newcastle disease virus were examined by restriction enzyme analysis of RT-PCR products generated from the matrix protein gene that discriminates between strains LaSota and B-1, the two most widely used lentogenic vaccine viruses. Isolates were derived from regions where, exclusively or predominantly, only one type of vaccine was employed. Viruses collected in Hungary for two decades were exclusively of LaSota-type while the Canadian collection predominantly included B-1, which corresponded to the vaccine types used in the regions. Isolation of vaccine type lentogenic viruses from unvaccinated flocks supports the occurrence of area spread of these lentogenic viruses.

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.

Isolation and analysis of two naturally-occurring multi-recombination Newcastle disease viruses in China

Two Newcastle disease viruses (NDV), designated QG/Hebei/07 and XD/Shandong/08, were isolated from infected chicken flocks in China in 2007 and 2008, respectively. The results of phylogenetic and recombination analyses on complete NDV genome sequences (excluding terminal segments) show that the QG/Hebei/07 isolate had evidence of recombination in the M and F genes, and recombination in the XD/Shandong/08 isolate in the F, L genes and the non-coding region between the HN and L genes. These two naturally-occurring recombinants we found to be descended from at least three putative parents from vaccine and circulating virus lineages. Moreover, we found that evidence that homologous recombination also occurred between NDV viruses of chicken and swine lineages, while the major putative parent is likely to have been derived from the chicken avirulent vaccine lineage. This study suggests that homologous recombination can occur in all coding and non-coding regions of the NDV genome and a live vaccine strain is capable of recombination with circulating viruses resulting in significant genetic change. The potential role of swine-origin viruses in the evolution of virulent NDV warrants further investigation.

Phylogenetic and pathogenic analysis of Newcastle disease virus isolated from house sparrow (Passer domesticus) living around poultry farm in southern China

House sparrow (Passer domesticus) is one of the most widely distributed wild birds in China. Five Newcastle disease virus (NDV) strains were isolated from house sparrows living around the poultry farms in southern China. These isolates were characterized by pathogenic assays and phylogenetic analysis. The results showed that all NDV isolates except one were velogenic and virulent for chickens. These four virulent strains for chickens possess the amino acid sequence (112)R/K-R-Q-K/R-R-F(117) in the F(0) cleavage site which is typical of velogenic NDV. Phylogenetic analysis indicated that these isolates belong to genotype VII and were closely related to the strains which were isolated from NDV outbreaks in chickens since 2000. One isolate of NDV from house sparrow belong to genotype II and was proved to be vaccine strain (Chicken/U.S./LaSota/46). The result of this study proved that house sparrow can carry the virulent NDV strains and the same genotype of viruses that are circulating in poultry are existing in house sparrows living around poultry farm in southern China.

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.

Sequence and phylogenetic analysis of Newcastle disease virus genotypes isolated in Malaysia between 2004 and 2005

Sequence analysis of the fusion (F) gene of eight Malaysian NDV isolates showed that all the isolates were categorized as velogenic viruses, with the F cleavage site motif (112)R-R-Q-K-R(116) or (112)R-R-R-K-R(116) at the C-terminus of the F(2) protein and phenylalanine (F) at residue 117 at the N-terminus of the F(1) protein. Phylogenetic analysis revealed that all of the isolates were grouped in two distinct clusters under sub-genotype VIId. The isolates were about 4.8-11.7% genetically distant from sub-genotypes VIIa, VIIb, VIIc and VIIe. When the nucleotide sequences of the eight Malaysian isolates were compared phylogenetically to those of the old published local isolates, it was found that genotype VIII, VII, II and I viruses exist in Malaysia and caused sporadic infections. It is suggested that genotype VII viruses were responsible for most of the outbreaks in recent years.

The interferon antagonistic activities of the V proteins from two strains of Newcastle disease virus correlate with their known virulence properties

Newcastle disease virus (NDV) is an avian paramyxovirus that exists as hundreds of strains with widely different virulence properties. The NDV V protein exhibits interferon (IFN) antagonistic activity, which contributes to the virulence of the virus. The IFN-antagonistic activities of the V proteins from the avirulent strain La Sota and the moderately virulent strain Beaudette C (BC) were compared in an assay for the rescue of a recombinant NDV expressing the green fluorescent protein (NDV-GFP). Consistent with the virulence properties of the two viruses, the BC V protein exhibits a 4-fold greater ability to rescue replication of NDV-GFP than the La Sota V protein. Four amino acid differences in the C-terminal region of V, as well as the N-terminal region, contribute to the difference in IFN-antagonistic activity between the two V proteins.

Characterization of Newcastle disease viruses isolated from chicken, gamefowl, pigeon and quail in Mexico

Velogenic Newcastle disease has threatened the Mexican poultry industry since 1946. Seven strains of velogenic Newcastle disease virus were isolated from poultry and other avian species in central and northern Mexico from 1998 to 2006 and subjected to phylogenetic analysis and biological characterization using standard pathogenicity tests and challenge studies. Phylogenetic analysis showed that all velogenic strains belonged to genetic group V and are clearly divided in two lineages, since phylogenetic similarities between groups are of only 93-94%. Isolates from 1998 to 2001 are closely related to the strain responsible for the 2000 year outbreak raised in La Laguna region (Torreon strain), and are phylogenetically distinct from viruses isolated between 2004 and 2006 that are genetically related to the Chimalhuacan strain isolated in 1973. All the viruses of both, the Chimalhuacan and the Torreon groups, contained a virulent fusion protein cleavage site represented by the motif "GGRRQKRF", revealing that evolutionary changes occurred at a different site. Chicken embryo mean death time value was shorter for the Chimalhuacan-like viruses (43.9 hours), when compared with the 1998-2001 average (54.3 hours). ICPI average value was higher (1.92) for viruses isolated during 2004-2006 than that for viruses isolated before 2001 (1.74). Microscopic evaluation of bursa of Fabricius and thymus of 5w-o broiler chickens challenged with 10⁶ LD₅₀/0.2 ml showed that Chimalhuacan-like isolate caused more severe lesions at 48 hpi in bursa and 72 and 96 hpi in thymus than Torreon-like isolate. Along with the MDT, ICPI and microscopic results, our findings suggest that some distinct selective pressure on the very virulent Chimalhuacan strain isolated in early 1970's may have led to the appearance of the still velogenic but less virulent new group (Torreon-like) in the middle of 1990's.

Detection and differentiation of velogenic and lentogenic Newcastle disease viruses using SYBR Green I real-time PCR with nucleocapsid gene-specific primers

SYBR Green I real-time PCR was developed for detection and differentiation of Newcastle disease virus (NDV). Primers based on the nucleocapsid (NP) gene were designed to detect specific sequence of velogenic strains and lentogenic/vaccine strains, respectively. The assay was developed and tested with NDV strains which were characterized previously. The velogenic strains were detected only by using velogenic-specific primers with a threshold cycle (C(t)) 18.19+/-3.63 and a melting temperature (T(m)) 86.0+/-0.28 degrees C. All the lentogenic/vaccine strains, in contrast, were detected only when lentogenic-specific primers were used, with the C(t) value 14.70+/-2.32 and T(m) 87.4+/-0.21 degrees C. The assay had a dynamic detection range which spans over a 5log(10) concentration range, 10(9)-10(5) copies of DNA plasmid/reaction. The velogenic and lentogenic amplifications showed high PCR efficiency of 100% and 104%, respectively. The velogenic and lentogenic amplifications were highly reproducible with assay variability 0.45+/-0.31% and 1.30+/-0.65%, respectively. The SYBR Green I real-time PCR assay detected successfully the virus from tissue samples and oral swabs collected from the velogenic and lentogenic NDV experimental infection, respectively. In addition, the assay detected and differentiated accurately NDV pathotypes from suspected field samples where the results were in good agreement with both virus isolation and analysis of the fusion (F) cleavage site sequence. The assay offers an attractive alternative method for the diagnosis of NDV.

Degenerate primers based RT-PCR for rapid detection and differentiation of airborne chicken Newcastle disease virus in chicken houses

Airborne Newcastle disease (ND) viruses in the air of five chicken houses were detected and differentiated by reverse transcriptase polymerase chain reaction (RT-PCR) using degenerate primers. Fifteen air samples were collected with All Glass Impinger-30 (AGI-30) air samplers in each house. Airborne ND viruses were also isolated and virulence identified by in vivo tests. Avirulent viruses were detected both in air samples and swab samples in four houses by degenerate primers based RT-PCR. Virulent viruses were detected only in the air samples by degenerate primers based RT-PCR in two houses. Seven strains viruses were isolated from the RT-PCR positive air samples. Of the seven strains, three strains were virulent viruses and four strains were avirulent viruses identified by in vivo tests. The results showed that it was feasible to detect and differentiate NDV in the air samples using degenerate primers based RT-PCR. This technique could decrease the time it required identify NDV infected flocks while distinguishing between virulent and avirulent viruses. It will help effectively to control Newcastle disease.

Biological and phylogenetic characterization of virulent Newcastle disease virus circulating in Mexico

In 2002-2003, velogenic Newcastle Disease Virus outbreaks, closely related to the Mexican isolates, were confirmed in the United States (U.S.) in southern California, Arizona, Nevada, and Texas. In this report, virulent NDVs isolated in Mexico between 1998 and 2006 were subjected to biologic characterization, using standard pathogenicity tests, and to phylogenetic analysis. Chicken embryo mean death time (MDT) test results ranged from 39.7 to 61.5 hours, and intracerebral pathogenicity index (ICPI) values were between 1.59 and 1.94, compared to a possible maximum value of 2.0. These isolates showed a dibasic amino acid motif at the fusion protein cleavage site sequence required for host systemic replication. Phylogenetic analysis indicated that the Mexican virulent NDVs belong to the class II, genotype V viruses and can be clearly divided in two groups as follows: isolates from 1998 to 2001 with close epidemiologic relationship with the latest U.S. NDV outbreaks, and phylogenetically distinct viruses, isolated from 2004 to 2006, which showed higher virulence. The assessment of the evolution of viruses from Mexico and other neighboring countries will aid in the U.S surveillance efforts for early detection of highly virulent NDV.

Newcastle disease virus: propagation, quantification, and storage

Newcastle disease virus (NDV) is a prototype paramyxovirus used to define basic steps in the life cycle of this family of viruses. NDV is also an ideal virus system for elucidating determinants of viral pathogenicity. Some strains of this virus are important agricultural pathogens that cause disease in poultry with a high mortality while other strains are avirulent and used for vaccines. Methods for preparation and titration of virus stocks are essential for all of these purposes. Procedures for growth and purification of NDV stocks in embryonated chicken eggs as well as in tissue culture cells are described. Use of embryonated chicken eggs to grow the virus is the superior method since infectious stocks of all strains of NDV result. Stocks of avirulent NDV prepared in tissue culture are noninfectious. Virus stocks are routinely titered using plaque assays or hemagglutination assays, both of which are described.

Pathotypical characterization and molecular epidemiology of Newcastle disease virus isolates from different hosts in China from 1996 to 2005

Thirty Newcastle disease virus (NDV) strains isolated from outbreaks in China during 1996 to 2005 were characterized pathotypically and genotypically. All strains except one were velogenic. An analysis of the variable region (nucleotides 47 to 420) of the F gene indicated that 6 isolates belonged to genotype II, 3 to genotype III, 1 (isolated from a pigeon) to genotype VI, and 20 to genotype VII. Isolates belonging to genotype VII were further divided into five subtypes, VIIa, VIIb, VIIc, VIId, and VIIe, and subtype VIId was made up of VIId1 to VIId5. These results showed that genotype VII isolates might have been the most prevalent in China during the past two decades. Genotype VII isolates shared high homology, but the homology was less than that between genotype VII viruses and the vaccine virus LaSota. Among these NDV isolates, 25 isolates had the velogenic motif (112)R/K-R-Q-K/R-R-F(117) that is consistent with results of the biological tests. However, four of five LaSota-type isolates that contained the lentogenic motif (112)G-R-Q-G-R-L(117) were velogenic, except SY/03, in the view of the biological test. The majority of genotype VII isolates had lost one or two N-glycosylation sites. Finally, a cross-protection experiment in which specific-pathogen-free chickens vaccinated with LaSota were challenged by six NDV isolates showed that more than three isolates were antigenic variants that could be responsible for recent outbreaks of Newcastle disease.

Molecular characterization of three new virulent Newcastle disease virus variants isolated in China

Three cases of Newcastle disease virus (NDV) found in nature had the lentogenic motif (112)G-R-Q-G-R-L(117) in their fusion protein cleavage sites. However, both intracerebral pathogenicity and intravenous pathogenicity indexes showed that these NDV isolates were virulent. In comparison with the LaSota live virus vaccine, these viruses had significant genetic variations in the hemagglutinin-neuraminidase gene.

Effect of host selective pressure on Newcastle disease virus virulence

Newcastle disease virus (NDV) causes an economically important disease that can vary from clinically inapparent to highly virulent forms. Generally, NDV strains isolated from wild birds are non-pathogenic for chicken. However, there are evidences supporting the fact that avirulent viruses maintained in feral birds could have caused outbreaks of virulent NDV in poultry. The strain-specific difference in virulence is determined by structural variations on the fusion glycoprotein (F). More basic amino acids are present in the F cleavage site of virulent strains. Nevertheless, other regions have been involved in virulence determination. When we subjected an avirulent NDV isolated from a wild bird to a host change we found that the virus arose was virulent for chicken. Nucleotide changes in the F protein cleavage site amino acid sequence and in the hemagglutinin-neuraminidase protein sequence are reported.

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.