Phylogenetic and recombination analysis of the herpesvirus genus varicellovirus
Abstract Background The varicelloviruses comprise a genus within the alphaherpesvirus subfamily, and infect both humans and other mammals. Recently, next-generation sequencing has been used to generate genomic sequences of several members of the Varicellovirus genus. Here, currently available varice...
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| Format: | Article |
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BMC
2017-11-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-017-4283-4 |
| _version_ | 1819157843906920448 |
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| author | Aaron W. Kolb Andrew C. Lewin Ralph Moeller Trane Gillian J. McLellan Curtis R. Brandt |
| author_facet | Aaron W. Kolb Andrew C. Lewin Ralph Moeller Trane Gillian J. McLellan Curtis R. Brandt |
| author_sort | Aaron W. Kolb |
| collection | DOAJ |
| description | Abstract Background The varicelloviruses comprise a genus within the alphaherpesvirus subfamily, and infect both humans and other mammals. Recently, next-generation sequencing has been used to generate genomic sequences of several members of the Varicellovirus genus. Here, currently available varicellovirus genomic sequences were used for phylogenetic, recombination, and genetic distance analysis. Results A phylogenetic network including genomic sequences of individual species, was generated and suggested a potential restriction between the ungulate and non-ungulate viruses. Intraspecies genetic distances were higher in the ungulate viruses (pseudorabies virus (SuHV-1) 1.65%, bovine herpes virus type 1 (BHV-1) 0.81%, equine herpes virus type 1 (EHV-1) 0.79%, equine herpes virus type 4 (EHV-4) 0.16%) than non-ungulate viruses (feline herpes virus type 1 (FHV-1) 0.0089%, canine herpes virus type 1 (CHV-1) 0.005%, varicella-zoster virus (VZV) 0.136%). The G + C content of the ungulate viruses was also higher (SuHV-1 73.6%, BHV-1 72.6%, EHV-1 56.6%, EHV-4 50.5%) compared to the non-ungulate viruses (FHV-1 45.8%, CHV-1 31.6%, VZV 45.8%), which suggests a possible link between G + C content and intraspecies genetic diversity. Varicellovirus clade nomenclature is variable across different species, and we propose a standardization based on genomic genetic distance. A recent study reported no recombination between sequenced FHV-1 strains, however in the present study, both splitstree, bootscan, and PHI analysis indicated recombination. We also found that the recently sequenced Brazilian CHV-1 strain BTU-1 may contain a genetic signal in the UL50 gene from an unknown varicellovirus. Conclusion Together, the data contribute to a greater understanding of varicellovirus genomics, and we also suggest a new clade nomenclature scheme based on genetic distances. |
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| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-22T16:15:13Z |
| publishDate | 2017-11-01 |
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| spelling | doaj.art-105970e13bd74b2a88a9ff967bf670fe2022-12-21T18:20:23ZengBMCBMC Genomics1471-21642017-11-0118111710.1186/s12864-017-4283-4Phylogenetic and recombination analysis of the herpesvirus genus varicellovirusAaron W. Kolb0Andrew C. Lewin1Ralph Moeller Trane2Gillian J. McLellan3Curtis R. Brandt4Department of Ophthalmology and Visual Sciences, School of Medicine and Public Health, University of Wisconsin-MadisonDepartment of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-MadisonDepartment of Ophthalmology and Visual Sciences, School of Medicine and Public Health, University of Wisconsin-MadisonDepartment of Ophthalmology and Visual Sciences, School of Medicine and Public Health, University of Wisconsin-MadisonDepartment of Ophthalmology and Visual Sciences, School of Medicine and Public Health, University of Wisconsin-MadisonAbstract Background The varicelloviruses comprise a genus within the alphaherpesvirus subfamily, and infect both humans and other mammals. Recently, next-generation sequencing has been used to generate genomic sequences of several members of the Varicellovirus genus. Here, currently available varicellovirus genomic sequences were used for phylogenetic, recombination, and genetic distance analysis. Results A phylogenetic network including genomic sequences of individual species, was generated and suggested a potential restriction between the ungulate and non-ungulate viruses. Intraspecies genetic distances were higher in the ungulate viruses (pseudorabies virus (SuHV-1) 1.65%, bovine herpes virus type 1 (BHV-1) 0.81%, equine herpes virus type 1 (EHV-1) 0.79%, equine herpes virus type 4 (EHV-4) 0.16%) than non-ungulate viruses (feline herpes virus type 1 (FHV-1) 0.0089%, canine herpes virus type 1 (CHV-1) 0.005%, varicella-zoster virus (VZV) 0.136%). The G + C content of the ungulate viruses was also higher (SuHV-1 73.6%, BHV-1 72.6%, EHV-1 56.6%, EHV-4 50.5%) compared to the non-ungulate viruses (FHV-1 45.8%, CHV-1 31.6%, VZV 45.8%), which suggests a possible link between G + C content and intraspecies genetic diversity. Varicellovirus clade nomenclature is variable across different species, and we propose a standardization based on genomic genetic distance. A recent study reported no recombination between sequenced FHV-1 strains, however in the present study, both splitstree, bootscan, and PHI analysis indicated recombination. We also found that the recently sequenced Brazilian CHV-1 strain BTU-1 may contain a genetic signal in the UL50 gene from an unknown varicellovirus. Conclusion Together, the data contribute to a greater understanding of varicellovirus genomics, and we also suggest a new clade nomenclature scheme based on genetic distances.http://link.springer.com/article/10.1186/s12864-017-4283-4VaricellovirusGenomeHerpesVeterinaryPhylogenyVirus |
| spellingShingle | Aaron W. Kolb Andrew C. Lewin Ralph Moeller Trane Gillian J. McLellan Curtis R. Brandt Phylogenetic and recombination analysis of the herpesvirus genus varicellovirus BMC Genomics Varicellovirus Genome Herpes Veterinary Phylogeny Virus |
| title | Phylogenetic and recombination analysis of the herpesvirus genus varicellovirus |
| title_full | Phylogenetic and recombination analysis of the herpesvirus genus varicellovirus |
| title_fullStr | Phylogenetic and recombination analysis of the herpesvirus genus varicellovirus |
| title_full_unstemmed | Phylogenetic and recombination analysis of the herpesvirus genus varicellovirus |
| title_short | Phylogenetic and recombination analysis of the herpesvirus genus varicellovirus |
| title_sort | phylogenetic and recombination analysis of the herpesvirus genus varicellovirus |
| topic | Varicellovirus Genome Herpes Veterinary Phylogeny Virus |
| url | http://link.springer.com/article/10.1186/s12864-017-4283-4 |
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