title: Development and application of a TaqMan single nucleotide polymorphism genotyping assay to study infectious laryngotracheitis virus recombination in the natural host.
abstract: To date, recombination between different strains of the avian alphaherpesvirus infectious laryngotracheitis virus (ILTV) has only been detected in field samples using full genome sequencing and sequence analysis. These previous studies have revealed that natural recombination is widespread in ILTV and have demonstrated that recombination between two attenuated ILTV vaccine strains generated highly virulent viruses that produced widespread disease within poultry flocks in Australia. In order to better understand ILTV recombination, this study developed a TaqMan single nucleotide polymorphism (SNP) genotyping assay to detect recombination between two field strains of ILTV (CSW-1 and V1-99 ILTV) under experimental conditions. Following in vivo co-inoculation of these two ILTV strains in specific pathogen free (SPF) chickens, recovered viruses were plaque purified and subjected to the SNP genotyping assay. This assay revealed ILTV recombinants in all co-inoculated chickens. In total 64/87 (74%) of the recovered viruses were recombinants and 23 different recombination patterns were detected, with some of them occurring more frequently than others. The results from this study demonstrate that the TaqMan SNP genotyping assay is a useful tool to study recombination in ILTV and also show that recombination occurs frequently during experimental co-infection with ILTV in SPF chickens. This tool, when used to assess ILTV recombination in the natural host, has the potential to greatly contribute to our understanding of alphaherpesvirus recombination.
authors.affiliation: Asia Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia.
authors.forename: Carlos A
authors.identifier: http://orcid.org/0000-0002-4321-8873
authors.initials: CA
authors.lastname: Loncoman
authors.affiliation: Asia Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia.
authors.forename: Carol A
authors.initials: CA
authors.lastname: Hartley
authors.affiliation: Asia Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia.
authors.forename: Mauricio J C
authors.initials: MJ
authors.lastname: Coppo
authors.affiliation: Asia Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia.
authors.forename: Paola K
authors.initials: PK
authors.lastname: Vaz
authors.affiliation: Asia Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia.
authors.forename: Andrés
authors.initials: A
authors.lastname: Diaz-Méndez
authors.affiliation: Asia Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia.
authors.forename: Glenn F
authors.initials: GF
authors.lastname: Browning
authors.affiliation: Asia Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia.
authors.forename: Sang-Won
authors.initials: SW
authors.lastname: Lee
authors.affiliation: Asia Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia.
authors.forename: Joanne M
authors.initials: JM
authors.lastname: Devlin
mesh_terms: D000818:Animals; D001315:Australia; D001483:Base Sequence; D045744:Cell Line, Tumor; D002645:Chickens; D016679:Genome, Viral / Q000235:genetics; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D006566:Herpesviridae Infections / Q000821:virology*; D001352:Herpesvirus 1, Gallid / Q000145:classification / Q000235:genetics* / Q000254:growth & development; D008297:Male; D020641:Polymorphism, Single Nucleotide; D011201:Poultry Diseases / Q000821:virology*; D011995:Recombination, Genetic; D013045:Species Specificity; D013047:Specific Pathogen-Free Organisms; D014764:Viral Proteins / Q000235:genetics
chemical_list: D014764:Viral Proteins