Evidence of widespread natural recombination among field isolates of equine herpesvirus 4 but not among field isolates of equine herpesvirus 1

Vaz, Paola K.; Horsington, Jacquelyn; Hartley, Carol A.; Browning, Glenn F.; Ficorilli, Nino; Studdert, M. J.; Gilkerson, James R.; Devlin, Joanne M.

doi:10.1099/jgv.0.000378

Cited by 34 publications

(67 citation statements)

References 37 publications

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“…Two virus isolates with the same genotype pattern (code 9) were included to enable comparisons within a genotype pattern. Each virus was first amplified in LMH cells, and then viral DNA was extracted from purified nucleocapsids as previously described (20) and sequenced using the Illumina MiSeq platform at the Medical Genomic Facility in the Monash Health Translation Precinct (MHTP), Hudson Institute of Medical Research. The genome was assembled by mapping to CSW-1 (GenBank accession number JX646899) as a reference sequence using the Geneious mapper method.…”

Section: Methodsmentioning

confidence: 99%

“…Separate recombination analyses were performed for the viruses originated from different geographical regions and for the recombinant viruses generated during this study. To enable analysis for recombination events the sequences were first aligned and curated as previously described (20,47). Recombination analyses were then performed using reticulate network analysis and the phi test within SplitsTree4 V 4.14.4 (48), as well as seven methods for detection of recombination breakpoints (RDP, GENECONV, 3Seq, SiScan, Chimarea, MaxChi, and Bootscan) within RDP4 V 4.83 (49).…”

Section: Methodsmentioning

confidence: 99%

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Genetic Diversity of Infectious Laryngotracheitis Virus duringIn VivoCoinfection Parallels Viral Replication and Arises from Recombination Hot Spots within the Genome

Loncoman

Hartley

Coppo

et al. 2017

Appl Environ Microbiol

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Recombination is a feature of many alphaherpesviruses that infect people and animals. Infectious laryngotracheitis virus (ILTV; Gallid alphaherpesvirus 1) causes respiratory disease in chickens, resulting in significant production losses in poultry industries worldwide. Natural (field) ILTV recombination is widespread, particularly recombination between attenuated ILTV vaccine strains to create virulent viruses. These virulent recombinants have had a major impact on animal health. Recently, the development of a single nucleotide polymorphism (SNP) genotyping assay for ILTV has helped to understand ILTV recombination in laboratory settings. In this study, we applied this SNP genotyping assay to further examine ILTV recombination in the natural host. Following coinoculation of specific-pathogen-free chickens, we examined the resultant progeny for evidence of viral recombination and characterized the diversity of the recombinants over time. The results showed that ILTV replication and recombination are closely related and that the recombinant viral progeny are most diverse 4 days after coinoculation, which is the peak of viral replication. Further, the locations of recombination breakpoints in a selection of the recombinant progeny, and in field isolates of ILTV from different geographical regions, were examined following full-genome sequencing and used to identify recombination hot spots in the ILTV genome.IMPORTANCE Alphaherpesviruses are common causes of disease in people and animals. Recombination enables genome diversification in many different species of alphaherpesviruses, which can lead to the evolution of higher levels of viral virulence. Using the alphaherpesvirus infectious laryngotracheitis virus (ILTV), we performed coinfections in the natural host (chickens) to demonstrate high levels of virus recombination. Higher levels of diversity in the recombinant progeny coincided with the highest levels of virus replication. In the recombinant progeny, and in field isolates, recombination occurred at greater frequency in recombination hot spot regions of the virus genome. Our results suggest that control measures that aim to limit viral replication could offer the potential to limit virus recombination and thus the evolution of virulence. The development and use of vaccines that are focused on limiting virus replication, rather than vaccines that are focused more on limiting clinical disease, may be indicated in order to better control disease.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Genetic Diversity of Infectious Laryngotracheitis Virus duringIn VivoCoinfection Parallels Viral Replication and Arises from Recombination Hot Spots within the Genome

Loncoman

Hartley

Coppo

et al. 2017

Appl Environ Microbiol

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show abstract

“…A recombination pairwise homoplasy index (PHI) test was performed within SplitsTree4 and found to be significant (P < 0.01). Additional analyses in RDP4 [47] were performed as described previously [48] and confirmed the SpiltsTree4 results, with 20 predicted recombination events detected by three or more of the methods used (RDP, GENECONV, Chimaera, SiScan, MaxChi and Bootscan …”

Section: Current Opinion In Virologymentioning

confidence: 99%

Impacts of poultry vaccination on viruses of wild bird

Devlin

Vaz

Coppo

et al. 2016

Current Opinion in Virology

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Spillover of viruses from farmed poultry into wild birds is a relatively new area of study at the livestock-wildlife interface. These transmission events can threaten the health of wild birds. There is growing evidence of transmission of vaccine viruses from poultry to wild birds, including attenuated vaccine strains of Newcastle disease virus and infectious bronchitis virus, and also spread of virulent viruses that may have evolved under the pressure of vaccine use, such as Marek's disease virus. Viral contaminants of poultry vaccines, including reticuloendotheliosis virus, may also be transmitted to wild birds and result in disease. New, vectored vaccines are less likely to directly spread to wild birds but this risk may rise as a result of recombination.

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“…The majority of strains analysed were low passage clinical isolates from outbreaks in the UK. Together with 26 EHV‐1 genome sequences sequenced in the USA and Australia (Vaz et al., 2016) and deposited in GenBank during the course of this project, these data provide an invaluable database of genetic information for this important pathogen.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks

Bryant

Wilkie

Russell

et al. 2018

Transbound Emerg Dis

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SummaryEquine herpesvirus 1 (EHV‐1) causes respiratory disease, abortion, neonatal death and neurological disease in equines and is endemic in most countries. The viral factors that influence EHV‐1 disease severity are poorly understood, and this has hampered vaccine development. However, the N752D substitution in the viral DNA polymerase catalytic subunit has been shown statistically to be associated with neurological disease. This has given rise to the term “neuropathic strain,” even though strains lacking the polymorphism have been recovered from cases of neurological disease. To broaden understanding of EHV‐1 diversity in the field, 78 EHV‐1 strains isolated over a period of 35 years were sequenced. The great majority of isolates originated from the United Kingdom and included in the collection were low passage isolates from respiratory, abortigenic and neurological outbreaks. Phylogenetic analysis of regions spanning 80% of the genome showed that up to 13 viral clades have been circulating in the United Kingdom and that most of these are continuing to circulate. Abortion isolates grouped into nine clades, and neurological isolates grouped into five. Most neurological isolates had the N752D substitution, whereas most abortion isolates did not, although three of the neurological isolates from linked outbreaks had a different polymorphism. Finally, bioinformatic analysis suggested that recombination has occurred between EHV‐1 clades, between EHV‐1 and equine herpesvirus 4, and between EHV‐1 and equine herpesvirus 8.

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Evidence of widespread natural recombination among field isolates of equine herpesvirus 4 but not among field isolates of equine herpesvirus 1

Cited by 34 publications

References 37 publications

Genetic Diversity of Infectious Laryngotracheitis Virus duringIn VivoCoinfection Parallels Viral Replication and Arises from Recombination Hot Spots within the Genome

Genetic Diversity of Infectious Laryngotracheitis Virus duringIn VivoCoinfection Parallels Viral Replication and Arises from Recombination Hot Spots within the Genome

Impacts of poultry vaccination on viruses of wild bird

Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks

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