{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,3]],"date-time":"2026-11-03T05:19:02Z","timestamp":1793683142707,"version":"4.5.1"},"reference-count":86,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2017,11,21]],"date-time":"2017-11-21T00:00:00Z","timestamp":1511222400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2017,11,21]],"date-time":"2017-11-21T00:00:00Z","timestamp":1511222400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000053","name":"National Eye Institute","doi-asserted-by":"publisher","award":["EYP30016665"],"award-info":[{"award-number":["EYP30016665"]}],"id":[{"id":"10.13039\/100000053","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Retinal Research Foundation","award":["unrestricted grant"],"award-info":[{"award-number":["unrestricted grant"]}]},{"DOI":"10.13039\/100006108","name":"National Center for Advancing Translational Sciences","doi-asserted-by":"crossref","award":["National Center for Advancing Translational Sciences"],"award-info":[{"award-number":["National Center for Advancing Translational Sciences"]}],"id":[{"id":"10.13039\/100006108","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"published-print":{"date-parts":[[2017,12]]},"DOI":"10.1186\/s12864-017-4283-4","type":"journal-article","created":{"date-parts":[[2017,11,21]],"date-time":"2017-11-21T01:12:37Z","timestamp":1511226757000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":42,"title":["Phylogenetic and recombination analysis of the herpesvirus genus varicellovirus"],"prefix":"10.1186","volume":"18","author":[{"given":"Aaron W.","family":"Kolb","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew C.","family":"Lewin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ralph","family":"Moeller Trane","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gillian J.","family":"McLellan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Curtis R.","family":"Brandt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2017,11,21]]},"reference":[{"issue":"11","key":"4283_CR1","doi-asserted-by":"publisher","first-page":"2683","DOI":"10.1007\/s00705-015-2537-5","volume":"160","author":"TC Cardoso","year":"2015","unstructured":"Cardoso TC, Ferreira HL, Okamura LH, Oliveira BR, Rosa AC, Gameiro R, Flores EF. Comparative analysis of the replication of bovine herpesvirus 1 (BHV1) and BHV5 in bovine-derived neuron-like cells. Arch Virol. 2015;160(11):2683\u201391.","journal-title":"Arch Virol"},{"issue":"1","key":"4283_CR2","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1177\/030098587601300107","volume":"13","author":"KM Charlton","year":"1976","unstructured":"Charlton KM, Mitchell D, Girard A, Corner AH. Meningoencephalomyelitis in horses associated with equine herpesvirus 1 infection. Vet Pathol. 1976;13(1):59\u201368.","journal-title":"Vet Pathol"},{"issue":"16","key":"4283_CR3","first-page":"456","volume":"143","author":"K Verheyen","year":"1998","unstructured":"Verheyen K, Newton JR, Wood JL, Birch-Machin I, Hannant D, Humberstone RW. Possible case of EHV-4 ataxia in warmblood mare. Vet Rec. 1998;143(16):456.","journal-title":"Vet Rec"},{"issue":"6","key":"4283_CR4","doi-asserted-by":"crossref","first-page":"1974","DOI":"10.1523\/JNEUROSCI.10-06-01974.1990","volume":"10","author":"JP Card","year":"1990","unstructured":"Card JP, Rinaman L, Schwaber JS, Miselis RR, Whealy ME, Robbins AK, Enquist LW. Neurotropic properties of pseudorabies virus: uptake and transneuronal passage in the rat central nervous system. J Neurosci. 1990;10(6):1974\u201394.","journal-title":"J Neurosci"},{"issue":"11","key":"4283_CR5","doi-asserted-by":"publisher","first-page":"1015","DOI":"10.1016\/S1474-4422(07)70267-3","volume":"6","author":"I Steiner","year":"2007","unstructured":"Steiner I, Kennedy PG, Pachner AR. The neurotropic herpes viruses: herpes simplex and varicella-zoster. Lancet Neurol. 2007;6(11):1015\u201328.","journal-title":"Lancet Neurol"},{"issue":"1","key":"4283_CR6","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1006\/viro.1996.8296","volume":"227","author":"H Fukushi","year":"1997","unstructured":"Fukushi H, Tomita T, Taniguchi A, Ochiai Y, Kirisawa R, Matsumura T, Yanai T, Masegi T, Yamaguchi T, Hirai K. Gazelle herpesvirus 1: a new neurotropic herpesvirus immunologically related to equine herpesvirus 1. Virology. 1997;227(1):34\u201344.","journal-title":"Virology"},{"issue":"4","key":"4283_CR7","doi-asserted-by":"publisher","first-page":"282","DOI":"10.1111\/j.1463-5224.2012.01064.x","volume":"16","author":"EC Ledbetter","year":"2013","unstructured":"Ledbetter EC, Marfurt CF, Dubielzig RR. Metaherpetic corneal disease in a dog associated with partial limbal stem cell deficiency and neurotrophic keratitis. Vet Ophthalmol. 2013;16(4):282\u20138.","journal-title":"Vet Ophthalmol"},{"issue":"2","key":"4283_CR8","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1128\/JCM.02462-12","volume":"51","author":"AS Hora","year":"2013","unstructured":"Hora AS, Tonietti PO, Guerra JM, Leme MC, Pena HF, Maiorka PC, Brandao PE. Felid herpesvirus 1 as a causative agent of severe nonsuppurative meningoencephalitis in a domestic cat. J Clin Microbiol. 2013;51(2):676\u20139.","journal-title":"J Clin Microbiol"},{"issue":"1","key":"4283_CR9","first-page":"22","volume":"58","author":"WL Gray","year":"2008","unstructured":"Gray WL. Simian varicella in old world monkeys. Comp Med. 2008;58(1):22\u201330.","journal-title":"Comp Med"},{"key":"4283_CR10","first-page":"428","volume":"1","author":"W Heberden","year":"1767","unstructured":"Heberden W. On the chicken-pox. Med Trans Coll Phys. 1767;1:428.","journal-title":"Med Trans Coll Phys"},{"key":"4283_CR11","volume-title":"U.S. National List of Reportable Animal Diseases (NLRAD)- National Animal Health Reporting System (NAHRS) reportable disease list","author":"USDA","year":"2017","unstructured":"USDA: U.S. National List of Reportable Animal Diseases (NLRAD)- National Animal Health Reporting System (NAHRS) reportable disease list. 2017."},{"issue":"7892","key":"4283_CR12","doi-asserted-by":"publisher","first-page":"1288","DOI":"10.1016\/S0140-6736(74)90144-5","volume":"2","author":"M Takahashi","year":"1974","unstructured":"Takahashi M, Otsuka T, Okuno Y, Asano Y, Yazaki T. Live vaccine used to prevent the spread of varicella in children in hospital. Lancet. 1974;2(7892):1288\u201390.","journal-title":"Lancet"},{"issue":"2","key":"4283_CR13","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1006\/viro.1996.0652","volume":"226","author":"N Osterrieder","year":"1996","unstructured":"Osterrieder N, Neubauer A, Brandmuller C, Kaaden OR, O'Callaghan DJ. The equine herpesvirus 1 IR6 protein influences virus growth at elevated temperature and is a major determinant of virulence. Virology. 1996;226(2):243\u201351.","journal-title":"Virology"},{"issue":"6","key":"4283_CR14","doi-asserted-by":"crossref","first-page":"1359","DOI":"10.2460\/ajvr.1985.46.06.1359","volume":"46","author":"S Kit","year":"1985","unstructured":"Kit S, Kit M, Pirtle EC. Attenuated properties of thymidine kinase-negative deletion mutant of pseudorabies virus. Am J Vet Res. 1985;46(6):1359\u201367.","journal-title":"Am J Vet Res"},{"issue":"5","key":"4283_CR15","doi-asserted-by":"crossref","first-page":"780","DOI":"10.2460\/ajvr.1987.48.05.780","volume":"48","author":"S Kit","year":"1987","unstructured":"Kit S, Sheppard M, Ichimura H, Kit M. Second-generation pseudorabies virus vaccine with deletions in thymidine kinase and glycoprotein genes. Am J Vet Res. 1987;48(5):780\u201393.","journal-title":"Am J Vet Res"},{"issue":"Pt 7","key":"4283_CR16","doi-asserted-by":"publisher","first-page":"1591","DOI":"10.1099\/0022-1317-71-7-1591","volume":"71","author":"RJ Moormann","year":"1990","unstructured":"Moormann RJ, de Rover T, Briaire J, Peeters BP, Gielkens AL, van Oirschot JT. Inactivation of the thymidine kinase gene of a gI deletion mutant of pseudorabies virus generates a safe but still highly immunogenic vaccine strain. J Gen Virol. 1990;71(Pt 7):1591\u20135.","journal-title":"J Gen Virol"},{"issue":"5","key":"4283_CR17","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1016\/0264-410X(94)90122-8","volume":"12","author":"MJ Kaashoek","year":"1994","unstructured":"Kaashoek MJ, Moerman A, Madic J, Rijsewijk FA, Quak J, Gielkens AL, van Oirschot JT. A conventionally attenuated glycoprotein E-negative strain of bovine herpesvirus type 1 is an efficacious and safe vaccine. Vaccine. 1994;12(5):439\u201344.","journal-title":"Vaccine"},{"issue":"2","key":"4283_CR18","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1016\/S0264-410X(96)00165-X","volume":"15","author":"JA Galeota","year":"1997","unstructured":"Galeota JA, Flores EF, Kit S, Kit M, Osorio FA. A quantitative study of the efficacy of a deletion mutant bovine herpesvirus-1 differential vaccine in reducing the establishment of latency by wildtype virus. Vaccine. 1997;15(2):123\u20138.","journal-title":"Vaccine"},{"issue":"30","key":"4283_CR19","doi-asserted-by":"publisher","first-page":"4307","DOI":"10.1016\/S0264-410X(01)00131-1","volume":"19","author":"JG Heldens","year":"2001","unstructured":"Heldens JG, Hannant D, Cullinane AA, Prendergast MJ, Mumford JA, Nelly M, Kydd JH, Weststrate MW, van den Hoven R. Clinical and virological evaluation of the efficacy of an inactivated EHV1 and EHV4 whole virus vaccine (Duvaxyn EHV1,4). Vaccination\/challenge experiments in foals and pregnant mares. Vaccine. 2001;19(30):4307\u201317.","journal-title":"Vaccine"},{"issue":"1","key":"4283_CR20","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1016\/j.tvjl.2008.05.025","volume":"182","author":"D Jas","year":"2009","unstructured":"Jas D, Aeberle C, Lacombe V, Guiot AL, Poulet H. Onset of immunity in kittens after vaccination with a non-adjuvanted vaccine against feline panleucopenia, feline calicivirus and feline herpesvirus. Vet J. 2009;182(1):86\u201393.","journal-title":"Vet J"},{"issue":"3","key":"4283_CR21","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1016\/j.jfms.2005.12.001","volume":"8","author":"MR Lappin","year":"2006","unstructured":"Lappin MR, Sebring RW, Porter M, Radecki SJ, Veir J. Effects of a single dose of an intranasal feline herpesvirus 1, calicivirus, and panleukopenia vaccine on clinical signs and virus shedding after challenge with virulent feline herpesvirus 1. J Feline Med Surg. 2006;8(3):158\u201363.","journal-title":"J Feline Med Surg"},{"issue":"22","key":"4283_CR22","doi-asserted-by":"publisher","first-page":"691","DOI":"10.1136\/vr.148.22.691","volume":"148","author":"H Poulet","year":"2001","unstructured":"Poulet H, Guigal PM, Soulier M, Leroy V, Fayet G, Minke J, Chappuis Merial G. Protection of puppies against canine herpesvirus by vaccination of the dams. Vet Rec. 2001;148(22):691\u20135.","journal-title":"Vet Rec"},{"issue":"3","key":"4283_CR23","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1016\/j.tvjl.2014.05.040","volume":"201","author":"K Raaperi","year":"2014","unstructured":"Raaperi K, Orro T, Viltrop A. Epidemiology and control of bovine herpesvirus 1 infection in Europe. Vet J. 2014;201(3):249\u201356.","journal-title":"Vet J"},{"issue":"Pt 9","key":"4283_CR24","doi-asserted-by":"publisher","first-page":"1759","DOI":"10.1099\/0022-1317-67-9-1759","volume":"67","author":"AJ Davison","year":"1986","unstructured":"Davison AJ, Scott JE. The complete DNA sequence of varicella-zoster virus. J Gen Virol. 1986;67(Pt 9):1759\u2013816.","journal-title":"J Gen Virol"},{"issue":"1","key":"4283_CR25","doi-asserted-by":"publisher","first-page":"304","DOI":"10.1016\/0042-6822(92)90706-U","volume":"189","author":"EA Telford","year":"1992","unstructured":"Telford EA, Watson MS, McBride K, Davison AJ. The DNA sequence of equine herpesvirus-1. Virology. 1992;189(1):304\u201316.","journal-title":"Virology"},{"issue":"Pt 5","key":"4283_CR26","doi-asserted-by":"publisher","first-page":"1197","DOI":"10.1099\/0022-1317-79-5-1197","volume":"79","author":"EA Telford","year":"1998","unstructured":"Telford EA, Watson MS, Perry J, Cullinane AA, Davison AJ. The DNA sequence of equine herpesvirus-4. J Gen Virol. 1998;79(Pt 5):1197\u2013203.","journal-title":"J Gen Virol"},{"issue":"19","key":"4283_CR27","doi-asserted-by":"publisher","first-page":"10339","DOI":"10.1128\/JVI.77.19.10339-10347.2003","volume":"77","author":"G Delhon","year":"2003","unstructured":"Delhon G, Moraes MP, Lu Z, Afonso CL, Flores EF, Weiblen R, Kutish GF, Rock DL. Genome of bovine herpesvirus 5. J Virol. 2003;77(19):10339\u201347.","journal-title":"J Virol"},{"issue":"22","key":"4283_CR28","doi-asserted-by":"publisher","first-page":"10401","DOI":"10.1128\/JVI.74.22.10401-10406.2000","volume":"74","author":"DJ McGeoch","year":"2000","unstructured":"McGeoch DJ, Dolan A, Ralph AC. Toward a comprehensive phylogeny for mammalian and avian herpesviruses. J Virol. 2000;74(22):10401\u20136.","journal-title":"J Virol"},{"issue":"14","key":"4283_CR29","doi-asserted-by":"publisher","first-page":"7133","DOI":"10.1128\/JVI.00437-15","volume":"89","author":"P Norberg","year":"2015","unstructured":"Norberg P, Depledge DP, Kundu S, Atkinson C, Brown J, Haque T, Hussaini Y, MacMahon E, Molyneaux P, Papaevangelou V, et al. Recombination of globally circulating varicella-zoster virus. J Virol. 2015;89(14):7133\u201346.","journal-title":"J Virol"},{"key":"4283_CR30","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1016\/j.virol.2016.01.016","volume":"491","author":"C Ye","year":"2016","unstructured":"Ye C, Guo JC, Gao JC, Wang TY, Zhao K, Chang XB, Wang Q, Peng JM, Tian ZJ, Cai XH, et al. Genomic analyses reveal that partial sequence of an earlier pseudorabies virus in China is originated from a Bartha-vaccine-like strain. Virology. 2016;491:56\u201363.","journal-title":"Virology"},{"issue":"3","key":"4283_CR31","doi-asserted-by":"publisher","first-page":"747","DOI":"10.1099\/jgv.0.000378","volume":"97","author":"PK Vaz","year":"2016","unstructured":"Vaz PK, Horsington J, Hartley CA, Browning GF, Ficorilli NP, Studdert MJ, Gilkerson JR, Devlin JM. Evidence of widespread natural recombination among field isolates of equine herpesvirus 4 but not among field isolates of equine herpesvirus 1. J Gen Virol. 2016;97(3):747\u201355.","journal-title":"J Gen Virol"},{"issue":"1","key":"4283_CR32","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1292\/jvms.16-0506","volume":"79","author":"S Izume","year":"2017","unstructured":"Izume S, Kirisawa R, Ohya K, Ohnuma A, Kimura T, Omatsu T, Katayama Y, Mizutani T, Fukushi H. The full genome sequences of 8 equine herpesvirus type 4 isolates from horses in Japan. J Vet Med Sci. 2017;79(1):206\u201312.","journal-title":"J Vet Med Sci"},{"issue":"15","key":"4283_CR33","doi-asserted-by":"publisher","first-page":"6181","DOI":"10.1093\/nar\/17.15.6181","volume":"17","author":"A Marin","year":"1989","unstructured":"Marin A, Bertranpetit J, Oliver JL, Medina JR. Variation in G + C-content and codon choice: differences among synonymous codon groups in vertebrate genes. Nucleic Acids Res. 1989;17(15):6181\u20139.","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"4283_CR34","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1016\/j.virusres.2005.05.001","volume":"113","author":"K Sau","year":"2005","unstructured":"Sau K, Gupta SK, Sau S, Ghosh TC. Synonymous codon usage bias in 16 Staphylococcus aureus phages: implication in phage therapy. Virus Res. 2005;113(2):123\u201331.","journal-title":"Virus Res"},{"issue":"1","key":"4283_CR35","doi-asserted-by":"publisher","first-page":"534","DOI":"10.1186\/s12864-017-3935-8","volume":"18","author":"G Li","year":"2017","unstructured":"Li G, Ji S, Zhai X, Zhang Y, Liu J, Zhu M, Zhou J, Su S. Evolutionary and genetic analysis of the VP2 gene of canine parvovirus. BMC Genomics. 2017;18(1):534.","journal-title":"BMC Genomics"},{"issue":"10","key":"4283_CR36","doi-asserted-by":"publisher","DOI":"10.1038\/emi.2016.106","volume":"5","author":"AM Butt","year":"2016","unstructured":"Butt AM, Nasrullah I, Qamar R, Tong Y. Evolution of codon usage in Zika virus genomes is host and vector specific. Emerg Microbes Infect. 2016;5(10):e107.","journal-title":"Emerg Microbes Infect"},{"key":"4283_CR37","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1016\/j.virusres.2016.05.008","volume":"221","author":"NK Singh","year":"2016","unstructured":"Singh NK, Tyagi A, Kaur R, Verma R, Gupta PK. Characterization of codon usage pattern and influencing factors in Japanese encephalitis virus. Virus Res. 2016;221:58\u201365.","journal-title":"Virus Res"},{"issue":"1\u20132","key":"4283_CR38","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1016\/j.virusres.2009.11.018","volume":"148","author":"S Roychoudhury","year":"2010","unstructured":"Roychoudhury S, Mukherjee D. A detailed comparative analysis on the overall codon usage pattern in herpesviruses. Virus Res. 2010;148(1\u20132):31\u201343.","journal-title":"Virus Res"},{"issue":"5","key":"4283_CR39","doi-asserted-by":"publisher","first-page":"551","DOI":"10.1007\/s00239-005-0221-1","volume":"62","author":"LA Shackelton","year":"2006","unstructured":"Shackelton LA, Parrish CR, Holmes EC. Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses. J Mol Evol. 2006;62(5):551\u201363.","journal-title":"J Mol Evol"},{"key":"4283_CR40","doi-asserted-by":"publisher","first-page":"458","DOI":"10.1016\/j.meegid.2017.08.012","volume":"54","author":"W He","year":"2017","unstructured":"He W, Zhang H, Zhang Y, Wang R, Lu S, Ji Y, Liu C, Yuan P, Su S. Codon usage bias in the N gene of rabies virus. Infect Genet Evol. 2017;54:458\u201365.","journal-title":"Infect Genet Evol"},{"issue":"14","key":"4283_CR41","doi-asserted-by":"publisher","first-page":"3059","DOI":"10.1093\/nar\/gkf436","volume":"30","author":"K Katoh","year":"2002","unstructured":"Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30(14):3059\u201366.","journal-title":"Nucleic Acids Res"},{"issue":"15","key":"4283_CR42","doi-asserted-by":"publisher","first-page":"1899","DOI":"10.1093\/bioinformatics\/btq224","volume":"26","author":"K Katoh","year":"2010","unstructured":"Katoh K, Toh H. Parallelization of the MAFFT multiple sequence alignment program. Bioinformatics. 2010;26(15):1899\u2013900.","journal-title":"Bioinformatics"},{"issue":"12","key":"4283_CR43","doi-asserted-by":"publisher","first-page":"2725","DOI":"10.1093\/molbev\/mst197","volume":"30","author":"K Tamura","year":"2013","unstructured":"Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30(12):2725\u20139.","journal-title":"Mol Biol Evol"},{"issue":"3","key":"4283_CR44","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1093\/sysbio\/syr010","volume":"60","author":"SA Berger","year":"2011","unstructured":"Berger SA, Krompass D, Stamatakis A. Performance, accuracy, and web server for evolutionary placement of short sequence reads under maximum likelihood. Syst Biol. 2011;60(3):291\u2013302.","journal-title":"Syst Biol"},{"issue":"2","key":"4283_CR45","doi-asserted-by":"publisher","first-page":"254","DOI":"10.1093\/molbev\/msj030","volume":"23","author":"DH Huson","year":"2006","unstructured":"Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 2006;23(2):254\u201367.","journal-title":"Mol Biol Evol"},{"issue":"4","key":"4283_CR46","doi-asserted-by":"publisher","first-page":"2665","DOI":"10.1534\/genetics.105.048975","volume":"172","author":"TC Bruen","year":"2006","unstructured":"Bruen TC, Philippe H, Bryant D. A simple and robust statistical test for detecting the presence of recombination. Genetics. 2006;172(4):2665\u201381.","journal-title":"Genetics"},{"key":"4283_CR47","doi-asserted-by":"crossref","unstructured":"Darriba D, Taboada GL, Doallo R, Posada D. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods. 9(8):772.","DOI":"10.1038\/nmeth.2109"},{"issue":"19","key":"4283_CR48","doi-asserted-by":"publisher","first-page":"2462","DOI":"10.1093\/bioinformatics\/btq467","volume":"26","author":"DP Martin","year":"2010","unstructured":"Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P. RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics. 2010;26(19):2462\u20133.","journal-title":"Bioinformatics"},{"issue":"1\u20132","key":"4283_CR49","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1016\/j.vetmic.2007.09.007","volume":"128","author":"L Grau-Roma","year":"2008","unstructured":"Grau-Roma L, Crisci E, Sibila M, Lopez-Soria S, Nofrarias M, Cortey M, Fraile L, Olvera A, Segales J. A proposal on porcine circovirus type 2 (PCV2) genotype definition and their relation with postweaning multisystemic wasting syndrome (PMWS) occurrence. Vet Microbiol. 2008;128(1\u20132):23\u201335.","journal-title":"Vet Microbiol"},{"issue":"1","key":"4283_CR50","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1016\/0378-1119(90)90491-9","volume":"87","author":"F Wright","year":"1990","unstructured":"Wright F. The 'effective number of codons' used in a gene. Gene. 1990;87(1):23\u20139.","journal-title":"Gene"},{"key":"4283_CR51","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1007\/978-1-59745-251-9_17","volume":"537","author":"J Rozas","year":"2009","unstructured":"Rozas J. DNA sequence polymorphism analysis using DnaSP. Methods Mol Biol. 2009;537:337\u201350.","journal-title":"Methods Mol Biol"},{"issue":"1","key":"4283_CR52","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1016\/0168-1702(86)90057-2","volume":"6","author":"M Engels","year":"1986","unstructured":"Engels M, Giuliani C, Wild P, Beck TM, Loepfe E, Wyler R. The genome of bovine herpesvirus 1 (BHV-1) strains exhibiting a neuropathogenic potential compared to known BHV-1 strains by restriction site mapping and cross-hybridization. Virus Res. 1986;6(1):57\u201373.","journal-title":"Virus Res"},{"key":"4283_CR53","unstructured":"ICTV Taxonomy [ https:\/\/talk.ictvonline.org\/taxonomy\/w\/ictv-taxonomy ]."},{"key":"4283_CR54","unstructured":"WHO. Updated unified nomenclature system for the highly pathogenic H5N1 avian influenza viruses. In: Global influenza surveillance and response system (GISRS): World Health Organization; 2011. http:\/\/www.who.int\/influenza\/gisrs_laboratory\/h5n1_nomenclature\/en\/ ."},{"issue":"Pt 7","key":"4283_CR55","doi-asserted-by":"publisher","first-page":"1830","DOI":"10.1099\/vir.0.000100","volume":"96","author":"CT Xiao","year":"2015","unstructured":"Xiao CT, Halbur PG, Opriessnig T. Global molecular genetic analysis of porcine circovirus type 2 (PCV2) sequences confirms the presence of four main PCV2 genotypes and reveals a rapid increase of PCV2d. J Gen Virol. 2015;96(Pt 7):1830\u201341.","journal-title":"J Gen Virol"},{"issue":"26","key":"4283_CR56","doi-asserted-by":"publisher","first-page":"867","DOI":"10.1136\/vr.162.26.867","volume":"162","author":"J Segales","year":"2008","unstructured":"Segales J, Olvera A, Grau-Roma L, Charreyre C, Nauwynck H, Larsen L, Dupont K, McCullough K, Ellis J, Krakowka S, et al. PCV-2 genotype definition and nomenclature. Vet Rec. 2008;162(26):867\u20138.","journal-title":"Vet Rec"},{"issue":"18","key":"4283_CR57","doi-asserted-by":"publisher","first-page":"9558","DOI":"10.1128\/JVI.00357-12","volume":"86","author":"C Grose","year":"2012","unstructured":"Grose C. Pangaea and the out-of-africa model of varicella-zoster virus evolution and phylogeography. J Virol. 2012;86(18):9558\u201365.","journal-title":"J Virol"},{"key":"4283_CR58","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1186\/1471-2148-7-66","volume":"7","author":"LJ DeRose-Wilson","year":"2007","unstructured":"DeRose-Wilson LJ, Gaut BS. Transcription-related mutations and GC content drive variation in nucleotide substitution rates across the genomes of Arabidopsis thaliana and Arabidopsis lyrata. BMC Evol Biol. 2007;7:66.","journal-title":"BMC Evol Biol"},{"issue":"3","key":"4283_CR59","doi-asserted-by":"crossref","first-page":"458","DOI":"10.2460\/ajvr.1991.52.03.458","volume":"52","author":"JM Miller","year":"1991","unstructured":"Miller JM, Whetstone CA, Van der Maaten MJ. Abortifacient property of bovine herpesvirus type 1 isolates that represent three subtypes determined by restriction endonuclease analysis of viral DNA. Am J Vet Res. 1991;52(3):458\u201361.","journal-title":"Am J Vet Res"},{"issue":"4","key":"4283_CR60","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1016\/S0378-1135(02)00126-8","volume":"88","author":"RC D'Arce","year":"2002","unstructured":"D'Arce RC, Almeida RS, Silva TC, Franco AC, Spilki F, Roehe PM, Arns CW. Restriction endonuclease and monoclonal antibody analysis of Brazilian isolates of bovine herpesviruses types 1 and 5. Vet Microbiol. 2002;88(4):315\u201324.","journal-title":"Vet Microbiol"},{"issue":"2","key":"4283_CR61","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1051\/vetres:2006059","volume":"38","author":"B Muylkens","year":"2007","unstructured":"Muylkens B, Thiry J, Kirten P, Schynts F, Thiry E. Bovine herpesvirus 1 infection and infectious bovine rhinotracheitis. Vet Res. 2007;38(2):181\u2013209.","journal-title":"Vet Res"},{"issue":"Pt 6","key":"4283_CR62","doi-asserted-by":"publisher","first-page":"1477","DOI":"10.1099\/0022-1317-80-6-1477","volume":"80","author":"FA Rijsewijk","year":"1999","unstructured":"Rijsewijk FA, Kaashoek MJ, Langeveld JP, Meloen R, Judek J, Bienkowska-Szewczyk K, Maris-Veldhuis MA, van Oirschot JT. Epitopes on glycoprotein C of bovine herpesvirus-1 (BHV-1) that allow differentiation between BHV-1.1 and BHV-1.2 strains. J Gen Virol. 1999;80(Pt 6):1477\u201383.","journal-title":"J Gen Virol"},{"key":"4283_CR63","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1016\/j.virol.2017.03.013","volume":"506","author":"X Wang","year":"2017","unstructured":"Wang X, CX W, Song XR, Chen HC, Liu ZF. Comparison of pseudorabies virus China reference strain with emerging variants reveals independent virus evolution within specific geographic regions. Virology. 2017;506:92\u20138.","journal-title":"Virology"},{"key":"4283_CR64","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1016\/j.jas.2010.07.024","volume":"38","author":"HT-BA Cucchi","year":"2011","unstructured":"Cucchi HT-BA, Yuan J, Dobney K, et al. J Archeol Sci. 2011;38:11\u201322.","journal-title":"J Archeol Sci"},{"key":"4283_CR65","doi-asserted-by":"publisher","first-page":"47","DOI":"10.3406\/paleo.2001.4731","volume":"27","author":"A Ervynck","year":"2001","unstructured":"Ervynck A, Dobney K, Hongo H, Meadow R. Born free? New evidence for the status of Sus Scrofa at Neolithic \u00c7ay\u00f6n\u00fc Tepesi (southeastern Anatolia, Turkey). Pal\u00e9orient. 2001;27:47\u201373.","journal-title":"Pal\u00e9orient"},{"issue":"1\u20132","key":"4283_CR66","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1016\/j.vetmic.2013.12.011","volume":"169","author":"A Abdelgawad","year":"2014","unstructured":"Abdelgawad A, Azab W, Damiani AM, Baumgartner K, Will H, Osterrieder N, Greenwood AD. Zebra-borne equine herpesvirus type 1 (EHV-1) infection in non-African captive mammals. Vet Microbiol. 2014;169(1\u20132):102\u20136.","journal-title":"Vet Microbiol"},{"issue":"18","key":"4283_CR67","doi-asserted-by":"publisher","first-page":"1727","DOI":"10.1016\/j.cub.2012.07.035","volume":"22","author":"AD Greenwood","year":"2012","unstructured":"Greenwood AD, Tsangaras K, Ho SY, Szentiks CA, Nikolin VM, Ma G, Damiani A, East ML, Lawrenz A, Hofer H, et al. A potentially fatal mix of herpes in zoos. Curr Biol. 2012;22(18):1727\u201331.","journal-title":"Curr Biol"},{"key":"4283_CR68","first-page":"533","volume":"27","author":"MARE Kennedy","year":"1996","unstructured":"Kennedy MARE, Diderrich V, Richman L, Allen GP, Potgieter LND. Encephalitis associated with a variant of equine herpesvirus 1 in a Thomson\u2019s gazelle (Gazella Thomsoni). J Zoo Wildl Med. 1996;27:533\u20138.","journal-title":"J Zoo Wildl Med"},{"issue":"11","key":"4283_CR69","doi-asserted-by":"crossref","first-page":"1248","DOI":"10.2460\/javma.1985.187.11.1248","volume":"187","author":"RJ Montali","year":"1985","unstructured":"Montali RJ, Allen GP, Bryans JT, Phillips LG, Bush M. Equine herpesvirus type 1 abortion in an onager and suspected herpesvirus myelitis in a zebra. J Am Vet Med Assoc. 1985;187(11):1248\u20139.","journal-title":"J Am Vet Med Assoc"},{"issue":"4","key":"4283_CR70","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1016\/S0021-9975(98)80043-1","volume":"119","author":"AS Blunden","year":"1998","unstructured":"Blunden AS, Smith KC, Whitwell KE, Dunn KA. Systemic infection by equid herpesvirus-1 in a Grevy's zebra stallion (Equus Grevyi) with particular reference to genital pathology. J Comp Pathol. 1998;119(4):485\u201393.","journal-title":"J Comp Pathol"},{"key":"4283_CR71","doi-asserted-by":"crossref","unstructured":"Goehring LS, van Winden SC, van Maanen C, Sloet van Oldruitenborgh-Ossterbaan MM: Equine herpesvirus type 1-associated myeloencephalopathy in The Netherlands: a four-year retrospective study (1999\u20132003). J Vet Intern Med 2006, 20(3):601-607.","DOI":"10.1111\/j.1939-1676.2006.tb02903.x"},{"issue":"2","key":"4283_CR72","doi-asserted-by":"publisher","first-page":"105","DOI":"10.2746\/042516408X253127","volume":"40","author":"GP Allen","year":"2008","unstructured":"Allen GP, Bolin DC, Bryant U, Carter CN, Giles RC, Harrison LR, Hong CB, Jackson CB, Poonacha K, Wharton R, et al. Prevalence of latent, neuropathogenic equine herpesvirus-1 in the thoroughbred broodmare population of central Kentucky. Equine Vet J. 2008;40(2):105\u201310.","journal-title":"Equine Vet J"},{"issue":"11","key":"4283_CR73","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.0030160","volume":"3","author":"LB Goodman","year":"2007","unstructured":"Goodman LB, Loregian A, Perkins GA, Nugent J, Buckles EL, Mercorelli B, Kydd JH, Palu G, Smith KC, Osterrieder N, et al. A point mutation in a herpesvirus polymerase determines neuropathogenicity. PLoS Pathog. 2007;3(11):e160.","journal-title":"PLoS Pathog"},{"issue":"9","key":"4283_CR74","doi-asserted-by":"publisher","first-page":"1309","DOI":"10.1292\/jvms.14-0183","volume":"76","author":"X Guo","year":"2014","unstructured":"Guo X, Izume S, Okada A, Ohya K, Kimura T, Fukushi H. Full genome sequences of zebra-borne equine herpesvirus type 1 isolated from zebra, onager and Thomson's gazelle. J Vet Med Sci. 2014;76(9):1309\u201312.","journal-title":"J Vet Med Sci"},{"issue":"8","key":"4283_CR75","doi-asserted-by":"publisher","first-page":"4047","DOI":"10.1128\/JVI.80.8.4047-4060.2006","volume":"80","author":"J Nugent","year":"2006","unstructured":"Nugent J, Birch-Machin I, Smith KC, Mumford JA, Swann Z, Newton JR, Bowden RJ, Allen GP, Davis-Poynter N. Analysis of equid herpesvirus 1 strain variation reveals a point mutation of the DNA polymerase strongly associated with neuropathogenic versus nonneuropathogenic disease outbreaks. J Virol. 2006;80(8):4047\u201360.","journal-title":"J Virol"},{"key":"4283_CR76","doi-asserted-by":"publisher","first-page":"746","DOI":"10.1126\/science.3022376","volume":"234","author":"RT Javier","year":"1986","unstructured":"Javier RT, Sedarati F, Stevens JG. Two avirulent herpes simplex viruses generate lethal recombinants in vivo. Science. 1986;234:746\u20138.","journal-title":"Science"},{"issue":"2","key":"4283_CR77","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1007\/BF01309859","volume":"140","author":"RL Kintner","year":"1995","unstructured":"Kintner RL, Allan RW, Brandt CR. Recombinants are isolated at high frequency following in vivo mixed ocular infection with two avirulent herpes simplex virus type 1 strains. Arch Virol. 1995;140(2):231\u201344.","journal-title":"Arch Virol"},{"issue":"3","key":"4283_CR78","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1005499","volume":"12","author":"AW Kolb","year":"2016","unstructured":"Kolb AW, Lee K, Larsen I, Craven M, Brandt CR. Quantitative trait locus based virulence determinant mapping of the HSV-1 genome in murine ocular infection: genes involved in viral regulatory and innate immune networks contribute to virulence. PLoS Pathog. 2016;12(3):e1005499.","journal-title":"PLoS Pathog"},{"key":"4283_CR79","doi-asserted-by":"publisher","first-page":"8115","DOI":"10.1128\/JVI.00821-16","volume":"90","author":"K Lee","year":"2016","unstructured":"Lee K, Kolb AW, Larsen I, Craven M, Brandt CR. Mapping murine corneal neovascularization and weight loss virulence determinants in the HSV-1 genome and the detection of an epistatic interaction between the UL and IRS\/US regions. J Virol. 2016;90:8115\u201331.","journal-title":"J Virol"},{"issue":"2","key":"4283_CR80","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1292\/jvms.54.207","volume":"54","author":"T Matsumura","year":"1992","unstructured":"Matsumura T, Sugiura T, Imagawa H, Fukunaga Y, Kamada M. Epizootiological aspects of type 1 and type 4 equine herpesvirus infections among horse populations. J Vet Med Sci. 1992;54(2):207\u201311.","journal-title":"J Vet Med Sci"},{"issue":"1","key":"4283_CR81","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1016\/j.jfms.2009.12.004","volume":"12","author":"C Hartley","year":"2010","unstructured":"Hartley C. Aetiology of corneal ulcers assume FHV-1 unless proven otherwise. J Feline Med Surg. 2010;12(1):24\u201335.","journal-title":"J Feline Med Surg"},{"issue":"2","key":"4283_CR82","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1051\/vetres:2006063","volume":"38","author":"R Gaskell","year":"2007","unstructured":"Gaskell R, Dawson S, Radford A, Thiry E. Feline herpesvirus. Vet Res. 2007;38(2):337\u201354.","journal-title":"Vet Res"},{"key":"4283_CR83","doi-asserted-by":"publisher","first-page":"704","DOI":"10.1186\/s12864-016-3050-2","volume":"17","author":"PK Vaz","year":"2016","unstructured":"Vaz PK, Job N, Horsington J, Ficorilli N, Studdert MJ, Hartley CA, Gilkerson JR, Browning GF, Devlin JM. Low genetic diversity among historical and contemporary clinical isolates of felid herpesvirus 1. BMC Genomics. 2016;17:704.","journal-title":"BMC Genomics"},{"key":"4283_CR84","doi-asserted-by":"publisher","first-page":"7214","DOI":"10.1128\/JVI.00880-15","volume":"89","author":"K Lee","year":"2015","unstructured":"Lee K, Kolb AW, Sverchkov Y, Cuellar JA, Craven M, Brandt CR. Recombination analysis of herpes simplex virus type 1 reveals a bias towards GC content and the inverted repeat regions. J Virol. 2015;89:7214\u201323.","journal-title":"J Virol"},{"issue":"23","key":"4283_CR85","doi-asserted-by":"publisher","first-page":"12535","DOI":"10.1128\/JVI.77.23.12535-12542.2003","volume":"77","author":"F Schynts","year":"2003","unstructured":"Schynts F, Meurens F, Detry B, Vanderplasschen A, Thiry E. Rise and survival of bovine herpesvirus 1 recombinants after primary infection and reactivation from latency. J Virol. 2003;77(23):12535\u201342.","journal-title":"J Virol"},{"issue":"5","key":"4283_CR86","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0156015","volume":"11","author":"KV Papageorgiou","year":"2016","unstructured":"Papageorgiou KV, Suarez NM, Wilkie GS, McDonald M, Graham EM, Davison AJ. Genome sequence of canine herpesvirus. PLoS One. 2016;11(5):e0156015.","journal-title":"PLoS One"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-017-4283-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12864-017-4283-4\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-017-4283-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,27]],"date-time":"2025-06-27T05:24:32Z","timestamp":1751001872000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/s12864-017-4283-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,11,21]]},"references-count":86,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["4283"],"URL":"https:\/\/doi.org\/10.1186\/s12864-017-4283-4","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,11,21]]},"assertion":[{"value":"11 July 2017","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 November 2017","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 November 2017","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The experiments in this study did not directly involve humans, animals, or plants.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"887"}}