Genomic characterization of some infectious laryngotracheitis virus (ILTV) field isolates from vaccinated chicken farms reveals evidence of vaccine-related genetic drift.

Abstract

ILTV remains a highly contagious respiratory pathogen causing substantial economic losses on the global poultry industry. Despite the long-term implementation of routine vaccination programs, recurrent outbreaks in vaccinated flocks suggest that the virus's genomic flexibility, driven by both genetic drift and inter-strain recombination, may be undermining traditional control measures. This study aimed to characterize the genomic sequences of some circulating ILTV field isolates to outline the molecular drivers of these vaccinal strains. Tracheal tissues from symptomatic chickens were screened using real-time PCR, and three isolates with high viral titers (low Ct values) were used for whole-genome next-generation sequencing (NGS). The full-length genomes of isolates B1 (152,975 bp), B3 (152,978 bp), and B4 (152,978 bp) were successfully assembled and deposited in GenBank under accession numbers PX492157, PX496590, and PX522223. Comparative genomic analysis revealed that these isolates share high nucleotide identity with the Australian vaccinal strain SA2. Phylogenetic analysis placed these isolates within the wild-type genotype VI-IX cluster, grouping them with contemporary Australian and American strains. Despite high overall homology, significant non-synonymous substitutions were identified in the gB and gJ glycoproteins relative to the USA reference and vaccinal strains. Furthermore, notable mutations were localized in the (ICP4, gG, gD, and gI) genes when compared to global vaccinal lineages. These findings demonstrate the circulation of novel ILTV field isolates and suggest that genomic divergence, potentially resulting from vaccine-derived drift, is facilitating viral persistence. Such data underscores the critical need for continuous genomic surveillance to monitor viral evolution and optimize future immunization strategies.