Sequence and Phylogenetic Analysis of the Tk Gene of Infectious laryngo Tracheitis Virus (ILTV) from a field outbreak in Namakkal Region, Tamilnadu

A recent explosive outbreak of Infectious laryngotracheitis (ILT) in commercial layer farms during May 2012 in this Namakkal region (Tamilnadu) where nearly 3.5 million layers are reared attempted this study to know the virulent gene involved in this disease. One of the important genes associated with virulence of Infectious laryngo tracheitis virus (ILTV) is the thymidine kinase (Tk gene) gene. There is very little information about this gene at the genetic and functional levels of the Infectious laryngotracheitis virus in India and the genetic and phylogeny analyses of the Tk gene of ILTV virus from a field outbreak is reported. The field isolate was sequenced and the obtained nucleotide sequences and the deduced amino acid sequences of 649 bp Tk gene of ILTV isolates were edited and compared with five international reference ILTVs derived from Gen Bank for the homology analysis. Among these, one vaccine strain (Gallivac vaccine) was added for comparison. The nucleotide mutations/deletions were observed when compared with reference strains-Beijing (AH 008045.1 and AF 161068.1) and UK strain (D00565.1).The nucleotide mutations in the Tk gene of ILTV were displayed at six positions viz.,108,109,110 and 164, 350 and 440 in the field isolates in the present study. The mutations at positions 290 (G to C), 414 (T to A), 440 (G to T) and 448 (C to T) were unique and there was a single nucleotide mutation at these positions. There was two single nucleotide mutation at position 110 and 111, 130 and 131 and 157 and 158 in all the isolates. There was a tri-nucleotide deletion mutation at positions 345 to 347 in all the isolates. This deletion may have a role in virulence of the viruses in different host species. The homology analysis of Tk gene showed that the homology of the nucleotide sequences within the twenty isolates and vaccine strain was in the range between 96.5 – 100.0 per cent and the divergence was in the between 0.1 to 1.4. Phylogenetic analysis on the Tk gene sequence of the twenty isolates and three reference strains based on nucleotide sequences of Tk gene displayed that the twenty isolates subjected to analysis were indistinguishable between the field isolates and vaccine strain. Furthermore, there is a need for functional studies to elaborate the specific role played by this gene.