Phylogenetic Evidence of a Close Relationship Between the Peruvian Strain VFAR-043 and Two U.S. Origin ILTV Field Strains

Infectious laryngotracheitis virus (ILTV) is the causative agent of an acute respiratory avian disease known as infectious laryngotracheitis (ILT) which has been associated with economic losses in poultry. The presence of ILTV has been widely reported in South-American countries; however, only one full genomic sequence (VFAR-043 strain) has been recently published from an outbreak in Peru. The aim of this study was to determine the genetic relationship of the Peruvian strain with other ILTV strains from different geographic regions. The phylogenetic analyses revealed a close relationship between VFAR-043 and two United Sates origin strains (1874C5 and J2) using only the whole genome, Unique Long (UL) and Unique Short (US) genomic regions. Then, these three genomic sequences were compared to evaluate their genetic variations using the USDAref as a reference strain. Genetic variations such as synonymous and non-synonymous single nucleotide polymorphisms (SNPs), insertions, deletions and nucleotide-codon var...