Complete Genome Sequence Determination And Analysis Of Three Infectious Laryngotracheitis Virus Strains

ILT is an acute respiratory disease which is caused by infectious laryngotracheitis virus. Economiclosses result from mortality and decreased egg production in poultry worldwide. The disease wasdiscovered in China in1950s and now is one of the epidemic which endanger the poultry industry andprevalent in many provinces.Recent epidemiological studies indicated that vaccine strains may cause the outbreak of ILT. However,most of the reseraches above were based on the special genes, such as ICP4/TK and glycoprotein genes.As the development of the high-throughput sequening technology,18complete genome sequences havebeen published since2011. But no genome information for Chinese ILTV strains was available.In2009, a virulent ILTV field strain, named LJS09, was isolated from Jiangsu Province. In order tofurther evaluate the molecular characteristics and the differences between the field strain and vaccinestrain，the complete genome sequences of virulent strain WG, field strain LJS09and vaccine strainK317were determined and analyzed.91pairs of primers were used to amplify the ULand USregion in this research. The repeat regionswere determined using the single primer amplification in combination with the conventional PCRmethod. The GenBank accession number of LJS09, K317, WG was JX458822, JX458823andJX458824respectively. ORF prediction, Phylogenetic analysis, SNP analysis and the noncoding regionanalysis were performed using the bioinformatics software including DNAMAN, DNAStar, Geneious,ORF Finder, MEGA and MAFFT.The full-length genomic of LJS09, WG, K317was153201bp,153505bp,153639bp longrespectively. The genome structure was similar to the class D alphaherpesviruses. A total of79ORFswere predicted and no novel ORF was found. The amino acid mutations on glycoprotein gB, gC, gDand gH/gL may associated with the cell tropism of the ILTV strains LJS09, WG, and K317. There was alarge fragment deletion within the noncoding region of unique long region (UL) of ILTV LJS09, WG,and K317compared with SA2and A20strains. Though the origin binding protein of ILTV LJS09andWG existed, there was no AT-rich region in strain LJS09and WG. Phylogenetic tree based on thecomplete genome sequence indicates that LJS09and K317have the closest relationship and a smallerphylogenetic distance with the vaccine strain Serva. However, the WG strain has the closestevolutionary relationship with the Australian vaccine strain SA2and A20. The homologies of the ORFamino acid sequences of LJS09, K317and WG to the published strains were over98%. LJS09, K317and WG shared high nucleotide similarities (identity>96%) with the reference strains. And there was nolarge variation.In this research the genome sequences of Chinese prevalent strain, virulent strain and vaccine strainwere determined and analyzed for the first time. And the differences between the virulent strains andvaccine strains at home and abroad were founded on the gene level. This is the first genome sequence of Chinese strains which will facilitate the future research of the molecular biology and gene function ofILTV and provide a reference for the prevention and control of ILT.