Genomic Characterization of Some Infectious Laryngotracheitis Virus (ILTV) Field Isolates from Vaccinated Chicken Farms Reveals Evidence of Vaccine-Related Genetic Drift

Infectious laryngotracheitis virus (ILTV) is a highly contagious respiratory pathogen of poultry that causes significant economic losses to the poultry industry worldwide. Live attenuated vaccines have been used for decades to control ILTV outbreaks. Among the ILTV live attenuated vaccines, SA2 and A20 have been frequently used as commercial vaccines. Frequent changes occur in the ILTV genome due to its possibility of genome drift and recombination. The major goal of this study is to monitor genomic variations in recently circulating ILTV field isolates recovered from vaccinated chicken flocks. Tissue samples collected from an infected chickens flock suspected of ILTV were examined by real-time PCR. Samples with high viral load were selected for next-generation sequencing (NGS). Full length genome of three ILTV isolates (B1, B3, and B4) were obtained and submitted to GenBank with accession numbers PX492157, PX496590, and PX522223, respectively. The complete viral genome size of ILTV-B1, ILTV-B3, and ILTV-B4 was 152975, 152978, and 152978 nucleotides, respectively. These three ILTV isolates show 99.9% similarity with the Australian vaccinal strain SA2. The multiple sequence alignment showed that ILTV-B1, ILTV-B3, and ILTV-B4 belong to wild-type genotype VI-IX, which clustered together with Austrian isolates SA2 and A20, and American isolates S2.816 and 6.48.88 isolated in 2017. However, ILTV-B1, ILTV-B3, and ILTV-B4 also showed amino acid substitutions in the gB and gJ glycoproteins when compared with SA2, A20, and the USDA reference strain. Furthermore, most notable mutations were reported in the gB, gJ, ICP4, gG, gD, and gI when compared with American, Australian, and European vaccinal strains. Together, this study indicates the circulation of novel ILTV field isolates with the possible genomic divergence potentially associated with live vaccine-derived drift.