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

Newcastle disease virus (NDV) is a major threat to poultry production worldwide. In Peru, recurrent outbreaks and limited genomic data hinder the understanding of its molecular epidemiology. In this study, we characterized NDV from an outbreak in commercial poultry in southern Peru in 2025. A total of 105 pooled samples from affected birds were analyzed using real-time RT‒PCR (rRT–PCR) targeting the matrix (M) and fusion (F) genes. Thirteen samples with Ct values ≤ 25 were selected for virus isolation and sequenced using Oxford Nanopore Technologies, generating complete F gene sequences for all samples and whole-genome sequences for three representative isolates. NDV RNA was detected in 73/105 pools (69.5%), 95.9% of which were virulent strains. All the selected isolates were replicated in embryonated chicken eggs and exhibited high virulence, including embryo mortality, hemagglutinating activity, and high EID₅₀ titers. The sequenced isolates showed 99.6–100% nucleotide identity and harbored the canonical F protein cleavage site motif (¹¹²RRQKRF¹¹⁷) characteristic of virulent NDV strains. Phylogenetic analyses based on complete F gene and whole-genome sequences assigned all the isolates to class II, genotype VII, and subgenotype VII.1.1. These viruses formed a well-supported, genetically homogenous cluster distinct from that of previously reported Peruvian strains, which is consistent with recent trends of local diversification. Comparative analyses of the fusion and hemagglutinin–neuraminidase proteins also revealed amino acid differences relative to those of the genotype II reference strains. These findings identify the virulent NDV VII.1.1 lineage as the cause of the 2025 outbreak and underscore the need for routine genotyping and sustained genomic surveillance to strengthen outbreak detection and response in the region.