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Title: Comparative full genome analysis of four infectious laryngotracheitis virus (gallid herpesvirus-1) virulent isolates from the United States

Author
item Spatz, Stephen
item KEELER, CALVIN - University Of Delaware
item KUTISH, GERALD - University Of Connecticut
item RIBLET, SILVA - University Of Georgia
item Volkening, Jeremy
item Zsak, Laszlo
item Afonso, Claudio
item MUNDT, EGBERT - University Of Georgia
item ROCK, DANIEL - University Of Illinois
item GARCIA, MARICARMEN - University Of Georgia

Submitted to: Virus Genes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/25/2011
Publication Date: 4/1/2012
Citation: Spatz, S.J., Keeler, C.L., Kutish, G.F., Riblet, S.M., Volkening, J.D., Zsak, L., Afonso, C.L., Mundt, E.S., Rock, D.L., Garcia, M. 2012. Comparative full genome analysis of four infectious laryngotracheitis virus (gallid herpesvirus-1) virulent isolates from the United States. Virus Genes. 44:273-85.

Interpretive Summary: The nucleotide sequences of four virulent strains of gallid herpesvirus type 1, the causative agent of infectious laryngotracheitis, were determined. Analysis of the sequencing data revealed numerous discrepancies with the published sequence of a composite genome. In a comparison excluding the composite sequencing data, the genomes and the open reading frames are fairly well conserved with differences only in 2, out of 80, genes. These encoding the protein kinase US2 and the immediate early protein ICP4. In fact 4 variants of ICP4 were discovered. In an analysis of synonymous and non-synonymous mutations, it was discovered that non-synonymous mutation in glycoproteins B, E, L and M were exclusively found in the vaccine strain Serva. Deletion in the genomes of certain strains localized to the 5’ genomic termini and the ICP4 loci.

Technical Abstract: Gallid herpesvirus type 1 (GaHV-1), commonly named infectious laryngotracheitis virus causes the respiratory disease in chickens known as infectious laryngotracheitis (ILT). Molecular determinants associated with differences in pathogenicity of GaHV-1 strains are not completely understood. Comparison of the genome sequences of phenotypically different strains could help to identify genes involved in virulence. Sanger dideoxy sequencing, 454 pyrosequencing and Illumina sequencing were used to determine the nucleotide sequences of four groups of virulent GaHV-1 strains (groups I, III, V and VI). 325 open reading frames (ORFs) were compared with those of the recently sequenced genome of the Serva vaccine strain. Only two ORFs, ICP4 and the US2 differed in amino acid (a.a.) lengths among the newly sequenced genomes. Genome sequence alignments were used to identify two regions (5’ terminus and the unique short/repeat junction) that contained various intragenic deletions. 78 synonymous and 118 non-synonymous amino acid substitutions were identified in a comparison that included ORFs encoded within the genomes of the Serva and group I, III, V and VI strains. Exclusive to the genomes of the Serva vaccine strains, 7 non-synonymous mutation were identified in the predicted translation products of the genes encoding glycoproteins gB, gE, gL and gM and three nonstructural proteins UL28 (DNA packaging protein), UL5 (helicase-primase) and the immediate early protein ICP4. Overall our comparative sequence analysis of virulent GaHV-1 strains has identified both intragenic and intergenic deletions as well as single nucleotide polymorphism mutations that differentiate the Serva vaccine genome from the genomes of 4 virulent strains.