Recombination of infectious laryngotracheitis virus (ILTV) and the role of vaccination

Abstract

Infectious laryngotracheitis virus (ILTV; Gallid alphaherpesvirus-1) is an alphaherpesvirus that causes respiratory disease in chickens, resulting in significant production losses in poultry industries worldwide. Recombination between different ILTV strains has recently been identified. Recombination in alphaherpesviruses was first described more than sixty years ago and since then, different techniques have been used to detect recombination in both natural (field) and experimental settings. In the past, natural recombination events between ILTV strains has resulted in the emergence of virulent recombinant viruses that have caused severe disease outbreaks in Australia.

In this work, a single nucleotide polymorphism (SNP) genotyping assay was developed to study ILTV recombination in vivo. This assay was used to study recombination in a large number of viruses retrieved from chickens co-inoculated with two Australian ILTV field strains. Further application of this SNP genotyping assay helped unveil other aspects of ILTV recombination such as viral diversity over time and dominant recombination patterns in the recombinant progeny. Whole genome sequencing (WGS) of dominant viruses was performed in order to analyse their recombination breakpoint locations. This latter analysis revealed the presence of recombination hot-spots. The location of these hotspots were consistent with those found after the analysis of publicly available whole genome sequences of ILTV from different geographical regions, such as Australia and the United States (US).

Additionally, the recombination output was determined in chickens after vaccination with three commercially available Australian ILTV vaccines (SA2, A20 and Serva), or two vaccines from the US (CEO-Tachivax and HVT-LT). For this later analysis a second SNP genotyping assay was develop to detect recombination between the USA field strains of ILTV used in that study. Results from these analyses indicated that vaccination can limit the number and diversity of recombinant progeny viruses and introduced new research questions about the role of the immune system in limiting recombination.

The studies reported in this thesis have provided new insights into recombination in alphaherpesviruses that will be useful for future studies regarding vaccine development and use in both Australia and elsewhere.