Jan 2026· Veterinary Medicine International· Vol 2026· 0 citations· 59 references
Medicine
TL;DR
This research presents a comprehensive analysis of the genetic landscape of prevalent NDV strains in Bangladesh between 2010 and 2024 using full‐length coding sequences of the fusion (F) gene and unraveled considerable genetic divergence.
Abstract
Newcastle disease, caused by avian orthoavulavirus serotype 1, is a highly contagious and economically devastating viral infection affecting both wild and domestic birds. The disease is characterized by severe respiratory, gastrointestinal, and neurological symptoms, often leading to high mortality and substantial production losses, particularly in commercial poultry. In Bangladesh, multiple virulent and avirulent Newcastle disease virus (NDV) genotypes and subgenotypes continue to circulate despite ongoing vaccination programs. This research presents a comprehensive analysis of the genetic landscape of prevalent NDV strains in Bangladesh between 2010 and 2024 using full‐length coding sequences of the fusion (F) gene. Specifically, we focused on genotypes, subgenotypes, host species, and annual distribution patterns in the country. We further investigated phylogenetic relationships, evolutionary divergence, and amino acid substitutions in the full‐length F protein. Comparative analyses of amino acid variability and sequence similarity between currently used vaccine strains and prevalent Bangladeshi field isolates were also scrutinized. We have unraveled considerable genetic divergence, and highlighted mismatches in genotypic coverage. These findings underscore the urgent need to reevaluate existing NDV vaccines strain to ensure improved protection against circulating NDVs in Bangladesh.
Newcastle disease virus (NDV) remains an important threat to poultry health, while complete genome data from Kazakhstan remain limited. In this study, two NDV-positive samples obtained from domestic chicken carcasses in the Almaty region were propagated in embryonated chicken eggs and characterized by diagnostic PCR/RT-PCR, infectivity assessment, whole-genome sequencing, phylogenetic analysis, and comparative molecular analysis. Both isolates replicated efficiently in embryonated eggs, reaching 9.6–9.7 log10 EID50/mL, with HA titers of 1:128–1:256 and no virus-attributable embryo mortality or marked embryo lesions. The complete consensus genomes of NDV_KZ_I and NDV_KZ_II were 15,186 bp and contained six major coding sequences arranged in the canonical 3′-N-P-M-F-HN-L-5′ order. Both isolates were closely related to the lentogenic vaccine-like strain AVIVAK-NDV-LaSota, and the F protein cleavage site motif was 112GRQGRL117, consistent with a lentogenic molecular profile. The F and HN proteins were identical between the isolates, with conserved predicted N-linked glycosylation motifs and predicted linear B-cell epitope profiles. The complete genome sequences were submitted to GenBank under submission number SUB16299204. Because the vaccination history of the source birds was unavailable and ICPI/MDT assays were not performed, the isolates should be interpreted as vaccine-like NDV detected during diagnostic investigation rather than confirmed causative agents of mortality. These data expand available NDV genomic information from Kazakhstan and support future molecular surveillance.
A. Nurpeisova, Makay Zheney, P. Akshalova et al.· Frontiers in Veterinary Scie...· 0 citations
Newcastle disease virus (NDV) remains one of the most economically important avian pathogens worldwide, causing recurrent outbreaks in poultry despite decades of vaccination and disease control efforts. Since the first reported outbreak of NDV a hundred years ago, numerous molecular epidemiological studies have been conducted globally across diverse geographic and production settings. Following a century of NDV circulation and evolution, the present study aimed to compile all publicly available NDV sequence data and perform a comprehensive global analysis of the genetic diversity, phylogenetic relationship, and global spatiotemporal distribution of NDV over a 100-year timescale. All publicly available NDV complete genome and full-length fusion (F) gene sequences were retrieved from GenBank up to February 2026. Following rigorous quality control, phylogenetic analyses were performed based on complete genomes and F gene datasets. Phylogenetic analysis identified two genotypes within Class I and 20 genotypes within Class II NDVs, with extensive diversification at the sub-genotype level. Genotype XIII exhibited the greatest sub-genotypic diversity, while genotype VII represented the most globally disseminated genotype, reported across 36 countries. Chronological assessment based on the earliest available reports indicated an increasing number of recognized genotypes from the 1930s to recently described sub-genotypes such as XIII.2.3 and XXII.2.2. Regional diversity analysis revealed the highest genotype diversity in Western Africa, Eastern Asia, and Southern Asia. Comparative residue analysis demonstrated substantial genotype-specific variation within critical functional domains of the fusion protein, including cleavage sites, neutralizing epitopes, and heptad repeat regions. Overall, this study provides the first comprehensive 100-year global overview of NDV evolution and phylogeography. The findings highlight continuous viral diversification, broad geographic dissemination of multiple genotypes, and ongoing molecular variation, emphasizing the need for sustained genomic surveillance and periodic evaluation of vaccine compatibility with emerging NDV genotypes.
Aziz ul-Rahman, M. Shabbir, M. Munir· Virus Research· 0 citations
The H9N2 subtype of avian influenza A virus has been endemic in poultry populations across Asia and the Middle East, posing ongoing economic and public health concerns. Since their initial detection in Pakistan in the 1990s, H9N2 viruses have caused repeated outbreaks in commercial poultry, leading to substantial economic losses and raising concerns about zoonotic transmission. To characterize the recent genetic evolution and zoonotic potential of circulating strains, five H9N2 isolates were obtained from poultry in Pakistan between January and March 2023. Phylogenetic analysis of the haemagglutinin gene revealed that all five isolates belong to the G5.3.2, formerly known as B2, sub-lineage of the G1 Eurasian lineage, in accordance with the revised global classification system for H9 viruses. Comparative genomic analysis confirmed that all eight gene segments were closely related to previously reported Pakistani strains, with no evidence of recent reassortment, suggesting localized persistence and ongoing genetic drift. Notably, several mammalian-adaptive mutations were identified in internal gene segments of the isolates, suggesting a potential risk of cross-species transmission. In addition, all five isolates exhibited dual receptor-binding characteristics, recognizing both α2,3-linked (avian-type) and α2,6-linked (human-type) sialic acid glycans, with a stronger affinity for α2,6-linked glycans. These findings underscore the need for continuous surveillance and risk assessment of H9N2 viruses circulating in Pakistan.
Kai-Yun Tan, Nousheen Arshad, Salman L. Butt et al.· Avian Pathology· 0 citations
Spanning almost six decades (1966–2024), 23 whole-genome sequences of Chandipura virus (CHPV), a neurotropic rhabdovirus associated with acute encephalitis primarily in India, have been analyzed. The virus is believed to be transmitted mainly by Sergentomyia and Phlebotomus sandflies. An epidemiological geographical map was developed showing global CHPV detection in sandflies, district-level human encephalitis reports in India, and sandfly species distribution across the country. This integrated landscape links viral occurrence with vector ecology and outbreak potential. To investigate evolutionary dynamics, we analyzed 23 complete genomes, comprising 5 human-derived isolates from India, 17 sandfly-derived isolates from Senegal and Kenya, and one hedgehog-derived isolate from Nigeria. Phylogenetic reconstruction revealed clear lineage segregation between Indian and African strains, indicating region-specific evolution. Despite this divergence, overall genomic variability remained low. Among all genes, the phosphoprotein exhibited relatively higher variability, while human-derived Indian sequences showed lower genetic diversity than the predominantly sandfly-derived African sequences; however, this comparison is confounded by differences in geography, sampling period, and host origin. Selection pressure analyses indicated predominantly purifying selection across coding regions. Episodic diversification analysis detected adaptive events in structural proteins. In the glycoprotein, all diversification sites (P272H, L424W, K503R) overlapped with predicted B-cell epitopes. In the matrix protein, both sites (K20R, D97N) mapped to predicted B-cell epitope regions. In contrast, among the two diversification sites in the nucleoprotein (N35E, A187V), only A187V overlapped with an epitope, whereas N35E was outside predicted antigenic domains. Collectively, these findings provide a comprehensive evolutionary and epidemiological perspective on CHPV and highlight the urgent need for systematic genomic surveillance to inform future diagnostic, vaccine and public health intervention strategies.
P. Kuri, Amit Sharma· PLoS Neglected Tropical Dise...· 0 citations
Newcastle disease remains a major constraint on poultry production worldwide, with recurrent outbreaks reported even in vaccinated flocks. In Pakistan, the persistence of Newcastle disease raises concerns about the ongoing evolution of Newcastle disease virus and the effectiveness of existing vaccines. This study aimed to investigate the molecular epidemiology and genetic characteristics of Newcastle disease virus circulating in commercial poultry farms in Punjab Province, Pakistan. A cross-sectional molecular surveillance study was conducted from May to November 2025 across five major poultry-producing districts. Clinical samples consisting of pooled oropharyngeal swabs and tissue homogenates were collected from affected flocks and organized into 100 pooled samples obtained from 25 commercial farms experiencing severe disease characterized by respiratory and neurological signs with high mortality (>40%), despite routine vaccination, and clinically suspected of Newcastle disease. Reverse transcription–polymerase chain reaction targeting the fusion (F) gene detected Newcastle disease virus in 91.1% of the prioritized tissue homogenates and oropharyngeal swabs from the sampled flocks. Based on RNA quality, successful amplification of the target region, geographic distribution, and epidemiological relevance, four representative reverse transcription–polymerase chain reaction-positive clinical samples were selected for complete F-gene sequencing. All sequenced samples possessed the polybasic cleavage site motif 112RRQKR↓F117, indicating a molecular signature consistent with a velogenic pathotype. Phylogenetic analysis consistently clustered the Newcastle disease virus sequences within Class II, further divided into sub-genotypes VII.2 and VII.1.1, indicating the co-circulation of at least two endemic lineages. Comparative sequence analysis revealed substantial genetic divergence between field samples and commonly used vaccine strains, with an average nucleotide difference of 10.7% relative to the LaSota vaccine strain. Additionally, several amino acid substitutions were identified in known neutralizing epitopes, along with evidence of positive selection at antigenically significant sites. These findings demonstrate the endemic circulation of genetically diverse genotype VII Newcastle disease virus strains in Punjab and provide molecular insights into potential antigenic divergence between vaccine and field strains, highlighting the need for further functional efficacy studies. Continuous molecular surveillance and the reassessment of vaccination strategies are essential for achieving effective and sustainable control of Newcastle disease in Pakistan.
Cite this article as: Naveed, M. T., Gulzar, M. W., Ahmad, M. M., Azeem, M. W., Ali, M. A., Anwar, M. N., Riaz, S., Shah, M. S., & Habib, M. (2026). Molecular and phylogenetic evidence of endemic genotype VII Newcastle disease virus circulation and vaccine mismatch in Punjab, Pakistan. Acta Veterinaria Eurasia, 52, 0072, doi: 10.5152/actavet.2026.26072.
Influenza D virus (IDV) is an emerging
Orthomyxovirus
primarily associated with cattle and increasingly recognized as a pathogen of veterinary and zoonotic relevance. Despite growing evidence of its circulation across Asia, Europe, and North America, no data have previously been available from Kazakhstan or Central Asia. This study investigated the presence of IDV in domestic livestock samples collected during active surveillance between 2023 and 2026. A total of 867 biological samples were obtained from cattle (
n
= 611), camels (
n
= 175), Maral Deer (
n
= 51), and pigs (
n
= 30) across multiple regions of Kazakhstan. Viral RNA was screened by reverse transcription polymerase chain reaction (RT-PCR) targeting the
HEF
,
PB1
,
PB2
, and
P3
genes using a newly designed primer panel. Positive amplicons were subjected to Sanger sequencing and phylogenetic analysis. IDV RNA was detected in 11 animals, corresponding to an overall prevalence of 1.27%. Positive samples were identified in several geographically distinct regions, indicating wider circulation than previously recognized. Complete
HEF
gene sequences were successfully obtained from two representative cattle strains, designated D/bovine/Zhetysu/KAZ/678/2025 and D/bovine/Zhetysu/KAZ/680/2025. Phylogenetic analysis demonstrated that both strains clustered within the D/Yama2019 lineage and shared >98.83% nucleotide identity with contemporary Asian strains. To our knowledge, this is the first report of IDV detection in Kazakhstan. These findings expand the known geographic range of IDV and suggest possible transboundary transmission routes across Central Asia. Continued molecular surveillance is warranted to clarify epidemiology, host range, and potential economic impact.
Yermukhammet Kassymbekov, T. Sabyrzhan, S.Sh. Nuralibekov et al.· Frontiers in Veterinary Scie...· 0 citations