Phylogenetic and molecular epidemiological studies reveal evidence of multiple past recombination events between infectious laryngotracheitis viruses

• Published in: PloS one Vol. 8; no. 2; p. e55121
• Main Authors: Lee, Sang-Won, Devlin, Joanne M, Markham, John F, Noormohammadi, Amir H, Browning, Glenn F, Ficorilli, Nino P, Hartley, Carol A, Markham, Philip F
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.02.2013; Public Library of Science (PLoS)
• Subjects: Amino Acid Sequence; Analysis; Animals; Australia; Base Sequence; Bioinformatics; Biology; Chickens - virology; Deoxyribonucleic acid; DNA; DNA viruses; Epidemiology; Evolution; Evolution, Molecular; Gene sequencing; Genetic aspects; Genome, Viral - genetics; Genomes; Genotype; Herpesvirus 1, Gallid - genetics; Herpesviruses; High-Throughput Nucleotide Sequencing; Infectious diseases; Laboratories; Laryngotracheitis; Likelihood Functions; Mammals; Mitochondrial DNA; Models, Genetic; Molecular Sequence Data; Phylogenetics; Phylogeny; Recombinants; Recombination; Recombination, Genetic - genetics; Ribonucleic acid; RNA; RNA viruses; Science; Sequence Alignment; Sequence Homology; Species Specificity; Strains (organisms); Studies; Vaccines; Veterinary Science; Viruses; Australia; Asia; Victoria Australia
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0055121

In contrast to the RNA viruses, the genome of large DNA viruses such as herpesviruses have been considered to be relatively stable. Intra-specific recombination has been proposed as an important, but underestimated, driving force in herpesvirus evolution. Recently, two distinct field strains of infectious laryngotracheitis virus (ILTV) have been shown to have arisen from independent recombination events between different commercial ILTV vaccines. In this study we sequenced the genomes of additional ILTV strains and also utilized other recently updated complete genome sequences of ILTV to confirm the existence of a number of ILTV recombinants in nature. Multiple recombination events were detected in the unique long and repeat regions of the genome, but not in the unique short region. Most recombinants contained a pair of crossover points between two distinct lineages of ILTV, corresponding to the European origin and the Australian origin vaccine strains of ILTV. These results suggest that there are two distinct genotypic lineages of ILTV and that these commonly recombine in the field.