| dc.description.abstract | Low pathogenic Newcastle disease viruses (LoNDVs) circulate widely among wild aquatic birds and occasionally spill over into domestic poultry. To investigate how these viruses adapt to chickens, LoNDV isolates from wild waterfowls were serially passaged ten times in specific pathogen-free (SPF) and commercial chicken embryos. Whole genome sequencing of passage 1 (P1) and 10 (P10) viruses was performed using the Illumina iSeq platform. Variants were identified with iVar bioinformatics tool with a 3% allele frequency threshold compared to reference strain LaSota. In SPF embryos, all isolates remained lentogenic after 10 passages as determined by mean death time (MDT) assays, exhibiting limited genetic diversification and high genomic stability. Compared to LaSota, most nucleotide and amino acid changes were shared between passages. Recurrent and frequency-shifting variants were concentrated in the hemagglutinin-neuraminidase (HN) gene, particularly at codons 169, 235, 495, and the C-terminal stop codon. These changes were localized within the globular head domain, which mediates receptor binding and neuraminidase activity, suggesting selective adaptation in this region. In contrast, replication complex genes nucleoprotein (NP), phosphoprotein (P) and large polymerase (L) genes remained conserved. In commercial embryos with maternally derived antibodies (MDA), immune pressure shaped distinct evolutionary patterns. Genomic variation between P1 and P10 remained low, with shared variants concentrated in untranslated and intergenic regions. Variants unique to P1 were more frequent than those in P10, with several high-frequency non-synonymous substitutions in the replication genes matrix (M), phosphoprotein (P), and nucleoprotein (NP). Codon-level analysis identified recurrent substitutions at HN position 495, where valine was replaced by glutamate, lysine, or alanine. Compared to SPF embryos, MDA presence in commercial embryos limited HN gene variation but allowed more mutations in replication-associated genes, indicating that transient antibody pressure constrained HN diversification while promoting optimization of replication and assembly functions. Chicken embryo responses to LoNDV infection were investigated by transcriptomic analysis at 48 h post-inoculation. Lung and jejunum tissues infected with P1 and P10 viruses were compared with controls infected with LaSota and PBS. Differential expression analysis (edgeR, FDR < 0.05), Gene Ontology (GO) enrichment, and protein–protein interaction (PPI) network analyses revealed strong tissue-dependent responses. The lung showed pronounced antiviral responses, while the jejunum exhibited minimal changes, consistent with NDV’s respiratory tropism. Serial passaging did not markedly alter host transcriptional profiles, indicating stability of host response across passages. Core antiviral pathways, including defense response to virus, negative regulation of viral replication, and interferon signaling, were activated across isolates. Hub genes (IRF7, MX1, RSAD2, OASL, IFI6, ZNFX1, IFIT5, CMPK2) formed a tightly connected interferon-driven antiviral cluster, reflecting conserved host defense mechanisms. Overall, these findings demonstrate that LoNDVs maintained genomic stability during passaging, while host transcriptional responses remained conserved. Genetic changes were concentrated in the HN gene in SPF embryos and in replication genes in MDA embryos, while host antiviral responses remained conserved. This work provides a molecular and transcriptomic framework for understanding LoNDV adaptation and helps with the assessment of the risk of LoNDVs from waterfowl causing disease in poultry populations. | en_US |
