title: Low genetic diversity among historical and contemporary clinical isolates of felid herpesvirus 1.
abstract: Felid herpesvirus 1 (FHV-1) causes upper respiratory tract diseases in cats worldwide, including nasal and ocular discharge, conjunctivitis and oral ulceration. The nature and severity of disease can vary between clinical cases. Genetic determinants of virulence are likely to contribute to differences in the in vivo phenotype of FHV-1 isolates, but to date there have been limited studies investigating FHV-1 genetic diversity. This study used next generation sequencing to compare the genomes of contemporary Australian clinical isolates of FHV-1, vaccine isolates and historical clinical isolates, including isolates that predated the introduction of live attenuated vaccines into Australia. Analysis of the genome sequences aimed to assess the level of genetic diversity, identify potential genetic markers that could influence the in vivo phenotype of the isolates and examine the sequences for evidence of recombination.
  
  
  
  The full genome sequences of 26 isolates of FHV-1 were determined, including two vaccine isolates and 24 clinical isolates that were collected over a period of approximately 40 years. Analysis of the genome sequences revealed a remarkably low level of diversity (0.0-0.01 %) between the isolates. No potential genetic determinants of virulence were identified, but unique single nucleotide polymorphisms (SNPs) in the UL28 and UL44 genes were detected in the vaccine isolates that were not present in the clinical isolates. No evidence of FHV-1 recombination was detected using multiple methods of recombination detection, even though many of the isolates originated from cats housed in a shelter environment where high infective pressures were likely to exist. Evidence of displacement of dominant FHV-1 isolates with other (genetically distinct) FHV-1 isolates over time was observed amongst the isolates obtained from the shelter-housed animals.
  
  
  
  The results show that FHV-1 genomes are highly conserved. The lack of recombination detected in the FHV-1 genomes suggests that the risk of attenuated vaccines recombining to generate virulent field viruses is lower than has been suggested for some other herpesviruses. The SNPs detected only in the vaccine isolates offer the potential to develop PCR-based methods of differentiating vaccine and clinical isolates of FHV-1 in order to facilitate future epidemiological studies.
authors: Asia Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
authors: Paola K
authors: PK
authors: Vaz
authors: Asia Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
authors: Natalie
authors: N
authors: Job
authors: Asia Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.|Present address: Australian Animal Health Laboratory, CSIRO, 5 Portarlington Rd, East Geelong, VIC, 3220, Australia.
authors: Jacquelyn
authors: J
authors: Horsington
authors: Centre for Equine Infectious Diseases, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
authors: Nino
authors: N
authors: Ficorilli
authors: Centre for Equine Infectious Diseases, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
authors: Michael J
authors: MJ
authors: Studdert
authors: Asia Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
authors: Carol A
authors: CA
authors: Hartley
authors: Centre for Equine Infectious Diseases, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
authors: James R
authors: JR
authors: Gilkerson
authors: Asia Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
authors: Glenn F
authors: GF
authors: Browning
authors: Asia Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia. devlinj@unimelb.edu.au.
authors: Joanne M
authors: JM
authors: Devlin
mesh_terms: D000818:Animals; D002371:Cat Diseases / Q000821:virology*; D002415:Cats; D005260:Female; D014644:Genetic Variation; D016679:Genome, Viral; D023281:Genomics / Q000379:methods; D006564:Herpesviridae / Q000145:classification / Q000235:genetics*; D006566:Herpesviridae Infections / Q000662:veterinary*; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D011110:Polymorphism, Genetic; D011995:Recombination, Genetic
keywords: Diversity; Felid herpesvirus; Feline; Genome; Recombination