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ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Endemic Poultry Viral Diseases Research » Research » Publications at this Location » Publication #338987

Research Project: Genetic and Biological Determinants of Avian Herpesviruses Pathogenicity, Transmission, and Evolution to Inform the Development of Effective Control Strategies

Location: Endemic Poultry Viral Diseases Research

Title: Infectious laryngotracheitis genomics: What’s circulating in the backyard flocks from the United States?

item Spatz, Stephen
item RIBLET, SYLVA - University Of Georgia
item Ross, Teresa
item GARCIA, MARICARMEN - University Of Georgia

Submitted to: Western Poultry Disease Conference
Publication Type: Proceedings
Publication Acceptance Date: 1/19/2017
Publication Date: 3/20/2017
Citation: Spatz, S.J., Riblet, S., Ross, T.A., Garcia, M. 2017. Infectious laryngotracheitis genomics: What’s circulating in the backyard flocks from the United States?. In Proceedings of the 66th Western Poultry Disease Conference, March 20-22, 2017 Sacramento, California. 2017 p. 177-182.

Interpretive Summary: Most of the strains of infectious laryngotracheitis are genetically related to vaccine strains. To identify true wild type (not vicinal revertant) strains the nucleotide sequences of strains isolated from backyard flocks in the US were determined. Surprisingly, some US strains were related to strains circulating in Australia. The geographic distribution of ILTV strains suggests that virulent strains of infectious laryngotracheitis virus (ILTV) were introduced into Australia.

Technical Abstract: Phylogenetic and comparative genomic studies of infectious laryngotracheitis virus (ILTV) has mainly focused on the differences among live attenuated vaccines, vicinal revertants and natural recombinant strains from Australia, the United States, and China. This analysis suggests that most strains from the US have a close relationship with the vaccine viruses and are largely considered vicinal revertants. In a search to identify wild type parental strains, the genomes of 5 ILTV isolates from backyard and commercial flocks in the US were sequenced using the MiSeq technology. Two isolates, S2.816 and 6.48.88 showed evolutionary relatedness to the vaccine strains SA2 and A20 licensed for use in Australia. Virulent strain 3.26.90 isolated from a backyard flock shared 99.9 percent sequence identity with the genome of the commercial ILTV vaccine strain chicken embryo origin (CEO) TRVX as did 14.939, a commercial flock isolate from the mid-Atlantic region. Only one newly sequenced genome J2 partitioned outside the vaccine clades sharing 96.2 percent sequence identity with the genome of virulent isolate 1874C5. A diagnostic assay was developed to differentiate ILTV strains based on single nucleotide polymorphisms in the loci encoding open reading frames A (ORFA) and open reading frames B (ORFB) from 27 complete ILTV genomic sequences within the GenBank sequence database. This assay will be useful to quickly identify non-vicinal revertants in order to develop new vaccines against circulating field viruses. Even though modified-live ILTV vaccines tissue culture origin (TCO) and CEO have been used for decades in the US, an extensive recombination study failed to detect any ILTV recombinants that were the progeny of these two licensed vaccines.