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

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Abstract

Gallid herpesvirus-1 (GaHV-1), commonly named infectious laryngotracheitis (ILT) virus, causes the respiratory disease in chickens known as ILT. The molecular determinants associated with differences in pathogenicity of GaHV-1 strains are not completely understood, and a comparison of genomic sequences of isolates that belong to different genotypes could help identify genes involved in virulence. Dideoxy sequencing, 454 pyrosequencing and Illumina sequencing-by-synthesis were used to determine the nucleotide sequences of four genotypes of virulent strains from GaHV-1 groups I–VI. Three hundred and twenty-five open reading frames (ORFs) were compared with those of the recently sequenced genome of the Serva vaccine strain. Only four ORFs, ORF C, UL37, ICP4 and US2 differed in amino acid (aa) lengths among the newly sequenced genomes. Genome sequence alignments were used to identify two regions (5′ terminus and the unique short/repeat short junction) that contained deletions. Seventy-eight synonymous and 118 non-synonymous amino acid substitutions were identified with the examined ORFs. Exclusive to the genome of the Serva vaccine strain, seven non-synonymous mutations were identified in the predicted translation products of the genes encoding glycoproteins gB, gE, gL and gM and three non-structural proteins UL28 (DNA packaging protein), UL5 (helicase-primase) and the immediate early protein ICP4. Furthermore, our comparative sequence analysis of published and newly sequenced GaHV-1 isolates has provided evidence placing the cleavage/packaging site (a-like sequence) within the inverted repeats instead of its placement at the 3′ end of the UL region as annotated in the GenBank’s entries NC006623 and HQ630064.

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Acknowledgments

We thank Robert Mullis for his contributions in the bioinformatic analysis of the sequencing data. This research was funded by the United States Department of Agriculture CRIS program (project number 6612-32000-052) and the US Poultry and Egg Association (Project F032).

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Authors and Affiliations

  1. United States Department of Agriculture, Southeast Poultry Research Laboratory, Agricultural Research Service, Athens, GA, 30605, USA

    S. J. Spatz, L. Zsak & C. L. Afonso

  2. BASE2BIO, Madison, WI, 53714, USA

    J. D. Volkening

  3. Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716-2150, USA

    C. L. Keeler, C. M. Boettger & K. F. Clark

  4. Department of Pathobiology and Veterinary Science and Center of Excellence for Vaccine Research, University of Connecticut, Storrs, CT, 06269, USA

    G. F. Kutish

  5. Poultry Diagnostic and Research Center, College of Veterinary Medicine, University of Georgia, 953 College Station Road, Athens, GA, USA

    S. M. Riblet, E. S. Mundt & M. Garcia

  6. Department of Pathobiology, College of Veterinary Medicine, University of Illinois, Urbana, IL, 61802, USA

    D. L. Rock

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  1. S. J. Spatz
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  2. J. D. Volkening
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Correspondence to S. J. Spatz.

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11262_2011_696_MOESM1_ESM.pptx

Sup. 1 Single nucleotide polymorphisms resulting in synonymous amino acid substitutions in ORFs within the genome of five GaHV-1 strains. All Serva ORFs encoding amino acid of lengths >60 were examined for synonymous amino acids substitutions in comparison with homologous ORFs found within the genomes of the USDA (group I), 81658 (group III), 63140 (group V) and 1874C5 (group VI) strains. The list includes 80 ORFs as defined by Lee et al. within the Serva genome as well as three additional short ORFs (ilt240, ilt247 and ilt249, located between the ICP4 and US10 genes) that contained synonymous substitutions. Codons in bold are not found in the Serva ORF. (PPTX 101 kb)

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Spatz, S.J., Volkening, J.D., Keeler, C.L. et al. Comparative full genome analysis of four infectious laryngotracheitis virus (Gallid herpesvirus-1) virulent isolates from the United States. Virus Genes 44, 273–285 (2012). https://doi.org/10.1007/s11262-011-0696-3

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