Virulent Newcastle Disease Virus Subgenotype VII.1.1 Behind 2025 Poultry Outbreak in Southern Peru, Whole-Genome Study Finds

A virulent strain of Newcastle disease virus belonging to subgenotype VII.1.1 was responsible for a 2025 outbreak in commercial poultry in southern Peru, according to a whole-genome characterization and phylogenetic analysis published in Virology Journal. The study, led by Doris Villanueva-Pérez and colleagues at FARVET SAC, provides the most detailed genomic picture to date of the virus circulating in that region and highlights how limited surveillance capacity has long obscured the molecular epidemiology of one of the world’s most economically damaging poultry pathogens. Newcastle disease virus, or NDV, is an enveloped, negative-sense, single-stranded RNA virus of the genus Orthoavulavirus in the family Paramyxoviridae, and virulent strains can devastate unvaccinated flocks with mortality rates that approach one hundred percent. For a country such as Peru, where recurrent outbreaks have been reported but genomic data remain scarce, the identification of the exact lineage driving a field outbreak is a critical step toward designing targeted control strategies and understanding how the virus is moving through commercial production networks.

The investigation began when affected birds from a commercial poultry operation in southern Peru were submitted for laboratory diagnosis during a confirmed Newcastle disease outbreak in 2025. The researchers assembled a panel of 105 pooled samples taken from the affected birds and screened them using real-time reverse transcription polymerase chain reaction assays targeting two regions of the viral genome: the matrix gene, or M gene, which encodes an internal structural protein involved in virion assembly, and the fusion gene, or F gene, which encodes the surface glycoprotein responsible for merging the viral envelope with host cell membranes. This dual-target approach is standard practice in NDV diagnostics because it increases sensitivity and provides an early indication of whether a detected virus is likely to be virulent. NDV RNA was detected in 73 of the 105 pools, a positivity rate of 69.5 percent, and 95.9 percent of the detected strains were classified as virulent based on the molecular markers recovered during screening.

From the positive pools, the team selected thirteen samples with cycle threshold values of 25 or lower, a cutoff indicating high viral loads suitable for downstream work. Each of these samples was used to attempt virus isolation in embryonated chicken eggs, the classical method for propagating avian viruses in the laboratory, in which inoculated eggs are incubated and the allantoic fluid is later harvested for testing. All thirteen isolates replicated successfully, exhibiting the hallmarks of highly pathogenic NDV: embryo mortality following inoculation, strong hemagglutinating activity reflecting the activity of the hemagglutinin-neuraminidase protein in binding red blood cells, and high titers expressed as the 50 percent egg infectious dose, or EID50. These phenotypic observations were fully consistent with the genetic evidence of virulence recovered later during sequencing and provided independent confirmation that a highly pathogenic virus was circulating in the affected flocks.

Sequencing was performed using Oxford Nanopore Technologies, a platform that reads long DNA molecules and can generate complete viral genomes rapidly and at relatively low cost, an advantage for laboratories working in regions where turnaround time can determine how quickly an outbreak response is mounted. The sequencing effort yielded complete F gene sequences for all thirteen selected samples and whole-genome sequences for three representative isolates. The whole-genome approach is particularly valuable for NDV because the virus genome, roughly 15,000 nucleotides in length, encodes six structural proteins and a small set of accessory proteins, and recombination or divergent ancestry in any genomic region can be missed when only the F gene is examined. By generating complete genomes from representative isolates and near-complete F gene coverage across the panel, the researchers maximized both breadth and depth of the dataset available for phylogenetic inference.

The sequence analysis revealed that the thirteen isolates were extremely closely related to one another, sharing 99.6 to 100 percent nucleotide identity across the regions sequenced. This homogeneity suggests a single introduction event into the affected operation, followed by clonal spread, rather than multiple independent introductions of distinct viruses. Every isolate harbored the canonical fusion protein cleavage site motif 112RRQKRF117, a polybasic amino acid sequence at positions 112 through 117 that is characteristic of virulent NDV strains. The cleavage site is the primary molecular determinant of pathogenicity in NDV: in virulent strains, the polybasic motif allows intracellular proteases such as furin to cleave the F0 precursor protein into its active F1 and F2 subunits in a wide range of host tissues, enabling systemic infection. Lentogenic, or low-virulence, strains lack this motif and can be cleaved only by proteases restricted to the respiratory and intestinal tracts, which limits their pathology. The presence of 112RRQKRF117 in all isolates therefore confirmed that the outbreak strain was velogenic, or highly virulent, at the molecular level.

Phylogenetic analyses based on both complete F gene sequences and whole-genome sequences placed all of the Peruvian isolates in class II of the NDV classification scheme, within genotype VII, and more precisely within subgenotype VII.1.1. Class II NDV encompasses the vast majority of characterized strains, including both vaccine strains and the virulent viruses responsible for most global epizootics, while class I contains predominantly avirulent aquatic bird viruses. Genotype VII has been the dominant virulent genotype circulating across Asia, Africa, the Middle East, and parts of Latin America since the late twentieth century, and subgenotype VII.1.1 has emerged in recent years as an important lineage in several countries. The placement of the 2025 southern Peruvian isolates within this subgenotype links the outbreak to a broader regional and international epidemiological context and underscores that the viruses driving disease in Peru belong to the same phylogenetic group that continues to circulate elsewhere.

A particularly significant finding of the study is that the 2025 viruses formed a well-supported, genetically homogeneous cluster that is distinct from previously reported Peruvian NDV strains. This separation is consistent with recent trends of local diversification, in which the virus lineage present in the country has accumulated unique mutations as it has circulated within Peruvian poultry populations over time. Such differentiation matters for practical reasons as well as evolutionary ones. Genotype VII viruses have a documented ability to escape immunity induced by some vaccines derived from genotype II strains, and the comparative protein analyses in this study reinforced that concern. When the researchers compared the fusion and hemagglutinin-neuraminidase proteins of the Peruvian isolates against genotype II reference strains, which include the classical vaccine lineages, they identified amino acid differences in both proteins. Because the hemagglutinin-neuraminidase protein facilitates receptor binding and neuraminidase activity and assists the fusion protein in mediating cell entry, substitutions in these surface glycoproteins can influence both antigenicity and viral fitness.

The implications of these amino acid differences extend to vaccination strategy and diagnostics. Hemagglutination inhibition testing, one of the most widely used serological tools in poultry medicine, depends on the interaction between the hemagglutinin-neuraminidase protein and antibodies raised against vaccine strains, so antigenic divergence between circulating field viruses and vaccine viruses can reduce the reliability of serological surveillance. Similarly, molecular assays designed around conserved regions must be periodically revalidated as locally circulating lineages diverge. The authors argue that their findings identify the virulent NDV VII.1.1 lineage as the direct cause of the 2025 outbreak and that routine genotyping should be incorporated into standard outbreak investigation protocols in the region. Without genotyping, an outbreak is simply diagnosed as Newcastle disease, with no information about which lineage is involved, whether it matches vaccine strains, or how it relates to viruses in neighboring production areas and countries.

Sustained genomic surveillance emerges from the study as the central recommendation for Peru and, by extension, for other countries where NDV data are sparse. The researchers note that recurrent outbreaks combined with limited genomic data have hindered understanding of the virus’s molecular epidemiology in Peru, and their work demonstrates how modern sequencing technology can close that gap. Nanopore sequencing of outbreak isolates delivered complete F gene sequences for a dozen isolates and whole genomes for three within a single investigation, at a cost and speed compatible with routine diagnostic workflows. The study was conducted on diagnostic samples collected exclusively from naturally dead or clinically affected birds submitted for laboratory testing, with no experimental infections performed, and all work with infectious material followed Peruvian biosafety regulations and World Organisation for Animal Health guidelines. The research was fully funded by FARVET SAC, and the authors declared no competing interests.

As NDV continues to evolve and as genotype VII lineages expand their geographic range, studies of this kind provide the foundational data on which national control programs depend. Knowing that a genetically homogeneous VII.1.1 virus caused the southern Peruvian outbreak allows veterinarians and regulators to assess whether existing vaccination programs are matching the field challenge, to trace potential transmission routes through the commercial poultry sector, and to establish a genomic baseline against which future isolates can be compared. The 99.6 to 100 percent identity among the 2025 isolates offers a snapshot of a single, tightly contained viral population, while the clear distinction from earlier Peruvian strains documents the ongoing evolutionary turnover of the virus in the country. Continued sampling, whole-genome sequencing, and phylogenetic monitoring will be required to determine whether this lineage persists, is replaced, or spreads beyond the region, and to ensure that the molecular epidemiology of Newcastle disease in South America is understood with the resolution needed to protect a poultry industry that feeds millions.

Subject of Research: Molecular characterization and phylogenetic analysis of virulent Newcastle disease virus subgenotype VII.1.1 from a 2025 poultry outbreak in southern Peru

Article Title: Whole-genome characterization and phylogenetic analysis of virulent Newcastle disease virus subgenotype VII.1.1 from a poultry outbreak in southern Peru

Article References: Villanueva-Pérez, D., Tataje-Lavanda, L., Montalván-Avalos, A., Montoya-Ortiz, S., Rios-Matos, D., Paredes-Inofuente, D., Ticona, J., Monasi, L., Cadillo-Kuroda, J., Jayo-Cucho, J., Goggín-Ortiz, J., Fernández-Sánchez, M., & Fernández-Díaz, M. (2026). Whole-genome characterization and phylogenetic analysis of virulent Newcastle disease virus subgenotype VII.1.1 from a poultry outbreak in southern Peru. Virology Journal. https://doi.org/10.1186/s12985-026-03319-7

Image Credits: AI Generated

DOI: 10.1186/s12985-026-03319-7

Keywords: Newcastle disease virus, subgenotype VII.1.1, whole-genome sequencing, fusion gene, phylogenetic analysis, poultry outbreak, Oxford Nanopore, Peru, virulence, genomic surveillance, virology, molecular epidemiology