Molecular phylogenetics of Newcastle disease viruses isolated from vaccinated flocks during outbreaks in Southern India reveals circulation of a novel sub‐genotype

Genetic evolution of Newcastle Disease Virus sub-genotype VII.2 isolates, diagnosed from vaccinated poultry farms of Gujarat, India

Newcastle disease was suspected in 37 commercial poultry farms, including 12 layer and 25 broiler farms in four districts of Gujarat, India. Vaccination had been done in 32 (20 broilers and 12 layers) farms. Tissue samples from each farm were pooled as one sample. In egg embryo inoculation, HA-HI and PCR, respectively, 32/37, 29/37, and 24/37 samples were found positive. Pathotyping by mean death time calculation and primer combination PCR revealed velogenic NDV, which was later confirmed with the presence of the 112-RRQKR*F-117 sequence at the F protein cleavage site. Phylogenetic analysis of full F gene sequences (N=10) confirmed the presence of sub-genotype VII.2 in 9/10 sequences, and genotype II in one sample. These 9 sequences were only 0.7 to 2.6 % divergent with two VII.2 (=VIIi) sequences (HQ697254.1 chicken/Banjarmas/Indonesia and KU862293.1 Parakeet/Karachi/Pakistan) but had 2.2 to 3.6 % diversion from two VII.2 sequences (OR185447 and MZ546197) from India. Then branching was found from sequences of VIIh, VIIk (VII.2), and VIIa (VII.1.2), and then from sub-genotypes VII.1.1 and VII.1.2. Due to less than 5 % diversion, these sequences could not be qualified as new sub-genotype in evolutionary distance analysis. At the amino acid level, our sequences had aa N-T-I-A-L-T at 24-79-125-385-445-482. Whereas at the same positions, in most of the retrieved VII.2 sequences and vaccines, the sequence was S-A-V-T-Q/I- E/A. Two sequences revealed additional six and four amino acid differences,respectively.This indicates rapid continuous genetic evolution of sub-genotype VII.2 and partially explains vaccinal immunity escape.

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.

Emergence of a novel genotype of class II New Castle Disease virus in North Eastern States of India

Outbreaks of New Castle Disease from three north eastern states of India were confirmed by clinico-pathological examination followed by reverse transcription-PCR detection of F gene of ND Virus (NDV). Irrespective of vaccination, the outbreaks resulted 90-100% mortality in the affected flocks. The analysis of fusion protein sequences from ten field isolates revealed them as the velogenic or highly virulent strain. Phylogenetic analyses based on the complete F gene nucleotide sequences of the isolates have characterized only one of the isolate (OK149201) in the genotype XIII.2.2. The rest of the nine isolates are depicted in a distinct monophyletic group with average nucleotide distances from the other 20 genotypes ranged from 10.90 - 20.70. The nine isolates were further divided into two sub branches with the bootstrap support value of 100% at the nodes that define the two subgroups with an average evolutionary nucleotide distance of 6.00between the isolates in the two subgroups. As per the recommendation put forth in recently updated unified phylogenetic classification system for NDV, our findings clearly indicates emergence of a novel genotype of class II NDV in the biodiversity hot spot region of NER, India. The isolates in the newly identified genotype is designated with next available Roman numerals XXII. Further, the two subgroups within the genotype are designated as XXII.1 and XXII.2.

Immunogenicity and protective efficacy of an inactivated Newcastle disease virus vaccine encapsulated in poly-(lactic-co-glycolic acid) nanoparticles

An immunization experiment was conducted in specific pathogen-free chickens with the inactivated Newcastle disease virus (NDV) vaccine encapsulated in the poly-(lactic-co-glycolic) acid (PLGA) nanoparticles (NP) to evaluate its immunogenicity and protective efficacy. The NDV vaccine was prepared by inactivating one virulent Indian strain of NDV belonging to Genotype VII by using beta-propiolactone. PLGA nanoparticles encapsulating inactivated NDV were prepared by the solvent evaporation method. Scanning electron microscopy and zeta sizer analysis revealed that the (PLGA+NDV) NP were spherical, with an average size of 300 nm, having a zeta potential of -6 mV. The encapsulation efficiency and loading efficiency were 72% and 2.4%, respectively. On immunization trial in chicken, the (PLGA+NDV) NP induced significantly (P < 0.0001) higher levels of HI and IgY antibodies with the peak HI titer of 2⁸ and higher expression of IL-4 mRNA. The consistency of higher antibody levels suggests slow and pulsatile release of the antigens from the (PLGA+NDV) NP. The nano-NDV vaccine also induced cell mediated immunity with higher expression of IFN-γ indicating strong Th1 mediated immune responses in contrast to the commercial oil adjuvanted inactivated NDV vaccine. Further, the (PLGA+NDV) NP afforded 100% protection against the virulent NDV challenge. Our results suggested that PLGA NP have adjuvant potential on induction of humoral as well as Th1 biased cell mediated immune responses and also enhanced protective efficacy of the inactivated NDV vaccine. This study provides an insight for development of PLGA NP based inactivated NDV vaccine using the same genotype circulating in the field as well as for other avian diseases at exigencies.

A study of risk factors associated with Newcastle disease and molecular characterization of genotype XIII Newcastle disease virus in backyard and commercial poultry in Assam, India

The continuous emergence of Newcastle disease virus (NDV) poses a persistent threat to the poultry industry. Recent increasing outbreaks of NDV in the North East region of India have highlighted the need to closely monitor and analyze the potential risk factors for Newcastle disease (ND) outbreaks. In the present study, an attempt was made to genotype the circulating Newcastle disease virus (NDV) in the backyard and commercial poultry flocks in Assam, India. Sera samples from unvaccinated backyard poultry flocks and tissue samples of ND suspected cases were collected and tested for the presence of NDV antibodies using the Haemagglutination inhibition (HI) test. A total of seven NDV isolates were analyzed from different districts of Assam, India, both genotypically and pathotypically. All isolates were characterized as virulent, carrying 112RRKQRF117 amino acid residues at the cleavage site. As determined by phylogenetic analysis, the isolates clustered with members of genotype XIII of class II NDV. Further analysis of risk factors of ND occurrence was conducted through a questionnaire survey. All the results indicated an occurrence of genotype XIII of NDV in the farms with inadequate biosecurity and farming practices.

Risky business in Georgia's wild birds: contact rates between wild birds and backyard chickens is influenced by supplemental feed

Backyard chickens are increasingly popular, and their husbandry varies widely. How backyard chickens are housed may influence the accessibility of chicken feed and water to wild birds, and thus, the contact rates between both groups. Increased contacts have implications for pathogen transmission; for instance, Newcastle disease virus or avian influenza virus may be transmitted to and from backyard chickens from contaminated water or feed. Given this potentially increased pathogen risk to wild birds and backyard chickens, we examined which wild bird species are likely to encounter backyard chickens and their resources. We performed a supplemental feeding experiment followed by observations at three sites associated with backyard chickens in North Georgia, USA. At each site, we identified the species of wild birds that: (a) shared habitat with the chickens, (b) had a higher frequency of detection relative to other species and (c) encountered the coops. We identified 14 wild bird species that entered the coops to consume supplemental feed and were considered high-risk for pathogen transmission. Our results provide evidence that contact between wild birds and backyard chickens is frequent and more common than previously believed, which has crucial epidemiological implications for wildlife managers and backyard chicken owners.

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

Background

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

Objectives

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

Methods

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

Results

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

Conclusions

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

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

Comparison of Chicken Immune Responses to Immunization with Vaccine La Sota or ZG1999HDS Strain of Newcastle Disease Virus

Newcastle disease (ND) is a highly contagious avian disease. Global control of ND is mainly based on vaccination of poultry; however, reported outbreaks of ND in vaccinated flocks indicate a constant need to re-evaluate the existing vaccines and a development of the new ones. In this study, 4-week-old male chickens of the layer commercial hybrid were immunized oculonasally with a commercial NDV live La Sota vaccine (LS group), a suspension of lyophilized NDV strain ZG1999HDS (ZG group), or saline (Control (K) group). Antibody response was determined by haemagglutination inhibition (HI) assay. Cell-mediated immunity (CMI) was characterized by immunophenotyping of leukocyte's and T-lymphocyte's subpopulations (flow cytometry). Applied NDV strains did not cause any adverse reaction in treated chickens. Both strains induced the significantly higher HI antibody response in comparison to the control group, and overall antibody titer was higher in ZG group than in LS group. CMI, manifested as a higher proliferation of B- and T-helper cells, yielded better results in the ZG groups than in the LS group. Based on the obtained results, we conclude that the strain ZG1999HDS is immunogenic and is a suitable candidate for further research and development of poultry vaccines.

Genetic and biological characterization of Newcastle disease viruses circulating in Bangladesh during 2010-2017: further genetic diversification of class II genotype XIII in Southcentral Asia

Newcastle disease virus (NDV) is endemic in Bangladesh and is a major threat to commercial poultry operations. While complete fusion (F) genes are recommended for molecular characterization and classification of NDV isolates, heretofore, only partial F gene data have been available for Bangladeshi NDVs. To this end, we obtained the full-length F gene coding sequences of 11 representative NDVs isolated in Bangladesh between 2010 and 2017. In addition, one of the viruses (MK934289/chicken/Bangladesh/C161/2010) was used in an experimental infection of chickens to establish the viral pathotype and study gross and microscopic lesions. Phylogenetic analysis provided evidence that all studied Bangladeshi isolates belong to genotype XIII.2 of class II NDVs. Six of the viruses were isolated between 2010 and 2017 and grouped together with isolates from neighbouring India during 2013-2016. Another four Bangladeshi isolates (2010-2016) formed a separate monophyletic branch within XIII.2 and showed high nucleotide distance from the isolates from India and the other six Bangladeshi viruses within the sub-genotype; however, none of these groups fulfils all classification criteria to be named as a separate sub-genotype. The eleventh Bangladeshi virus studied here (C162) was genetically more distant from the remaining isolates. It out-grouped the viruses from sub-genotypes XIII.2.1 and XIII.2.2 and showed more than 9.5 % nucleotide distance from all genotype XIII sub-genotypes. This isolate may represent an NDV variant that is evolving independently from the other viruses in the region. The experimental infection in chickens revealed that the tested isolate (C161) is a velogenic viscerotropic virus. Massive haemorrhages, congestion and necrosis in different visceral organs, and lymphoid depletion in lymphoid tissues, typical for infection with velogenic NDV, were observed. Our findings demonstrate the endemic circulation of sub-genotype XIII.2 in Southcentral Asia and further genetic diversification of these viruses in Bangladesh and neighbouring India. This constant evolution of the viruses may lead to the establishment of new genetic groups in the region. Additional historical and prospective virus and surveillance data from the region and neighbouring countries will allow a more detailed epidemiological inference.

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.