High-throughput sequencing of avian Infectious Laryngotracheitis virus (ILTV).

BACKGROUND-AIM Infectious laryngotracheitis (ILT) is an acute and highly contagious respiratory disease of chickens, caused by an alphaherpesvirus, named Infectious Laryngotracheitis virus (ILTV). Recently, full genome sequences of wild-type and vaccine strains have been analysed, but none was from Europe. The aim of this study was to determine and analyse the complete genome sequences of five Italian ILTV strains. Sequences were also compared to reveal the similarity of strains across time and to discriminate between wild-type and vaccine strains. METHODS Genomes of 3 ILTV field isolates from outbreaks occurred in Italy in 1980, 2007 and 2011, and 2 commercial chicken embryo origin (CEO) vaccines were sequenced using the 454 Life Sciences technology. Sequences were mapped on the reference sequence (Serva strain, GenBank accession no. HQ630064) using Roche gsMapper. RESULTS The length of the five ILTV genomes ranged from 153,650 bp to 153,662 bp. The comparison with the Serva genome showed that 35 open reading frames (ORFs) differed across the five ILTV genomes. Overall, 54 single nucleotide polymorphisms (SNPs) and 27 amino acid differences in 19 ORFs and 2 insertions of 9 and 3 nucleotides in two different ILTV genes were identified. Similarity among the wild-type and between the wild-type and the vaccine strains ranged from 99.95% to 99.98%. Phylogenetic analysis of the five strains and all the ILTV complete genomes available within the NCBI GenBank database showed a close relatedness of the three wild-type isolates, whereas the two vaccine strains grouped into separate clusters. CONCLUSION This study generated data on genomic variation among Italian ILTV strains revealing that the genome is well conserved across time and between wild-type and vaccine strains. Results of this study may contribute to the understanding of the molecular bases of ILTV pathogenicity and the genetic differences between wild-type and vaccine ILTV strains.