Genomic sequence analysis of the United States infectious laryngotracheitis vaccine strains chicken embryo origin (CEO) and tissue culture origin (TCO)

The genomic sequences of low and high passages of the United States infectious laryngotracheitis (ILT) vaccine strains CEO and TCO were determined using hybrid next generation sequencing in order to define genomic changes associated with attenuation and reversion to virulence. Phylogenetic analysis of available full genomes grouped strains into three major clades: TCO, CEO, and Australian. Comparative genomics revealed that TCO attenuation is likely the result of an ORF C truncation. Genes involved in attenuation are generally clade-specific, however four genes ORF C, UL27, UL28 and UL39 commonly contained various mutations across the CEO and TCO lineages. The Thr644 mutation in the UL27 gene encoding glycoprotein B was identified in all virulent US strains. The US10 gene was identified as a potential virulence factor for the TCO revertant 81658. The UL41 gene was responsible for the robust gain in virulence of CEO-Fowl Laryngotracheitis® after 20 passages in chickens.

► Virulent 63140 contains mutations in 12 genes relative to the genomes of all other CEO genomes.
► Five mutations were identified that differed among vaccine LT-Ivax® and virulent 81658.
► Vaccine strain LT-Ivax® contains a truncated ORF-C protein.
► ORF C, UL27, UL28 and UL39 are likely virulence factors of GaHV-1.