1. Shaw AE, Hughes J, Gu Q, Behdenna A, Singer JB, Dennis T, Orton RJ, Varela M, Gifford RJ, Wilson SJ, Palmarini M. 2017 Dec. Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses. PLoS biology 15:e2004086
  2. Volokhov DV, Becker DJ, Bergner LM, Camus MS, Orton RJ, Chizhikov VE, Altizer SM, Streicker DG. 2017 Nov. Novel hemotropic mycoplasmas are widespread and genetically diverse in vampire bats. Epidemiology and infection 145:3154-3167
  3. Lefkowitz EJ, Dempsey DM, Hendrickson RC, Orton RJ, Siddell SG, Smith DB. 2017 Oct 13. Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV). Nucleic acids research :
  4. Simmonds P, Adams MJ, Benkő M, Breitbart M, Brister JR, Carstens EB, Davison AJ, Delwart E, Gorbalenya AE, Harrach B, Hull R, King AM, Koonin EV, Krupovic M, Kuhn JH, Lefkowitz EJ, Nibert ML, Orton R, Roossinck MJ, Sabanadzovic S, Sullivan MB, Suttle CA, Tesh RB, van der Vlugt RA, Varsani A, Zerbini FM. 2017 Mar. Consensus statement: Virus taxonomy in the age of metagenomics. Nature reviews. Microbiology 15:161-168
  5. Adams MJ, Lefkowitz EJ, King AM, Harrach B, Harrison RL, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Mushegian AR, Nibert ML, Sabanadzovic S, Sanfaçon H, Siddell SG, Simmonds P, Varsani A, Zerbini FM, Orton RJ, Smith DB, Gorbalenya AE, Davison AJ. 2017 May. 50 years of the International Committee on Taxonomy of Viruses: progress and prospects. Archives of virology 162:1441-1446
  6. Conley M, Emmott E, Orton R, Taylor D, Carneiro DG, Murata K, Goodfellow IG, Hansman GS, Bhella D. 2017 Jan. Vesivirus 2117 capsids more closely resemble sapovirus and lagovirus particles than other known vesivirus structures. The Journal of general virology 98:68-76
  7. Orton RJ, Gu Q, Hughes J, Maabar M, Modha S, Vattipally SB, Wilkie GS, Davison AJ. 2016 Apr. Bioinformatics tools for analysing viral genomic data. Revue scientifique et technique (International Office of Epizootics) 35:271-85
  8. King DJ, Freimanis GL, Orton RJ, Waters RA, Haydon DT, King DP. 2016 Oct. Investigating intra-host and intra-herd sequence diversity of foot-and-mouth disease virus. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 44:286-92
  9. Jacobs M, Rodger A, Bell DJ, Bhagani S, Cropley I, Filipe A, Gifford RJ, Hopkins S, Hughes J, Jabeen F, Johannessen I, Karageorgopoulos D, Lackenby A, Lester R, Liu RS, MacConnachie A, Mahungu T, Martin D, Marshall N, Mepham S, Orton R, Palmarini M, Patel M, Perry C, Peters SE, Porter D, Ritchie D, Ritchie ND, Seaton RA, Sreenu VB, Templeton K, Warren S, Wilkie GS, Zambon M, Gopal R, Thomson EC. 2016 Jul 30. Late Ebola virus relapse causing meningoencephalitis: a case report. Lancet (London, England) 388:498-503
  10. Orton RJ, Wright CF, Morelli MJ, King DJ, Paton DJ, King DP, Haydon DT. 2015 Mar 24. Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data. BMC genomics 16:229
  11. Fahnøe U, Pedersen AG, Dräger C, Orton RJ, Blome S, Höper D, Beer M, Rasmussen TB. 2015. Creation of Functional Viruses from Non-Functional cDNA Clones Obtained from an RNA Virus Population by the Use of Ancestral Reconstruction. PloS one 10:e0140912
  12. Gandar F, Wilkie GS, Gatherer D, Kerr K, Marlier D, Diez M, Marschang RE, Mast J, Dewals BG, Davison AJ, Vanderplasschen AF. 2015 Nov. The Genome of a Tortoise Herpesvirus (Testudinid Herpesvirus 3) Has a Novel Structure and Contains a Large Region That Is Not Required for Replication In Vitro or Virulence In Vivo. Journal of virology 89:11438-56
  13. Dridi M, Rosseel T, Orton R, Johnson P, Lecollinet S, Muylkens B, Lambrecht B, Van Borm S. 2015 Oct. Next-generation sequencing shows West Nile virus quasispecies diversification after a single passage in a carrion crow (Corvus corone) in vivo infection model. The Journal of general virology 96:2999-3009
  14. Stewart M, Hardy A, Barry G, Pinto RM, Caporale M, Melzi E, Hughes J, Taggart A, Janowicz A, Varela M, Ratinier M, Palmarini M. 2015 Nov. Characterization of a second open reading frame in genome segment 10 of bluetongue virus. The Journal of general virology 96:3280-93
  15. Nomikou K, Hughes J, Wash R, Kellam P, Breard E, Zientara S, Palmarini M, Biek R, Mertens P. 2015 Aug. Widespread Reassortment Shapes the Evolution and Epidemiology of Bluetongue Virus following European Invasion. PLoS pathogens 11:e1005056
  16. Thorburn F, Bennett S, Modha S, Murdoch D, Gunson R, Murcia PR. 2015 Aug. The use of next generation sequencing in the diagnosis and typing of respiratory infections. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 69:96-100
  17. Boutier M, Ronsmans M, Rakus K, Jazowiecka-Rakus J, Vancsok C, Morvan L, Peñaranda MM, Stone DM, Way K, van Beurden SJ, Davison AJ, Vanderplasschen A. 2015. Cyprinid Herpesvirus 3: An Archetype of Fish Alloherpesviruses. Advances in virus research 93:161-256
  18. Chang CH, Kist NC, Stuart Chester TL, Sreenu VB, Herman M, Luo M, Lunn D, Bell J, Plummer FA, Ball TB, Katzourakis A, Iversen AK. 2015 Jun 17. HIV-infected sex workers with beneficial HLA-variants are potential hubs for selection of HIV-1 recombinants that may affect disease progression. Scientific reports 5:11253
  19. Fusaro A, Tassoni L, Hughes J, Milani A, Salviato A, Schivo A, Murcia PR, Bonfanti L, Cattoli G, Monne I. 2015 Aug. Evolutionary trajectories of two distinct avian influenza epidemics: Parallelisms and divergences. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 34:457-66
  20. Blomström AL, Gu Q, Barry G, Wilkie G, Skelton JK, Baird M, McFarlane M, Schnettler E, Elliott RM, Palmarini M, Kohl A. 2015 Apr 19. Transcriptome analysis reveals the host response to Schmallenberg virus in bovine cells and antagonistic effects of the NSs protein. BMC genomics 16:324
  21. Wilkinson GW, Davison AJ, Tomasec P, Fielding CA, Aicheler R, Murrell I, Seirafian S, Wang EC, Weekes M, Lehner PJ, Wilkie GS, Stanton RJ. 2015 Jun. Human cytomegalovirus: taking the strain. Medical microbiology and immunology 204:273-84
  22. Verweij MC, Horst D, Griffin BD, Luteijn RD, Davison AJ, Ressing ME, Wiertz EJ. 2015 Apr. Viral inhibition of the transporter associated with antigen processing (TAP): a striking example of functional convergent evolution. PLoS pathogens 11:e1004743
  23. Hsu JL, van den Boomen DJ, Tomasec P, Weekes MP, Antrobus R, Stanton RJ, Ruckova E, Sugrue D, Wilkie GS, Davison AJ, Wilkinson GW, Lehner PJ. 2015 Apr. Plasma membrane profiling defines an expanded class of cell surface proteins selectively targeted for degradation by HCMV US2 in cooperation with UL141. PLoS pathogens 11:e1004811
  24. Robinson MW, Aranday-Cortes E, Gatherer D, Swann R, Liefhebber JM, Filipe Ada S, Sigruener A, Barclay ST, Mills PR, Patel AH, McLauchlan J. 2015 Oct. Viral genotype correlates with distinct liver gene transcription signatures in chronic hepatitis C virus infection. Liver international : official journal of the International Association for the Study of the Liver 35:2256-64
  25. Wilkie GS, Kerr K, Stewart JP, Studdert MJ, Davison AJ. 2015 Mar 12. Genome sequences of equid herpesviruses 2 and 5. Genome announcements 3:
  26. Tilston-Lunel NL, Hughes J, Acrani GO, da Silva DE, Azevedo RS, Rodrigues SG, Vasconcelos PF, Nunes MR, Elliott RM. 2015 Jul. Genetic analysis of members of the species Oropouche virus and identification of a novel M segment sequence. The Journal of general virology 96:1636-50
  27. Zhu H, Hughes J, Murcia PR. 2015 May. Origins and Evolutionary Dynamics of H3N2 Canine Influenza Virus. Journal of virology 89:5406-18
  28. Boutier M, Ronsmans M, Ouyang P, Fournier G, Reschner A, Rakus K, Wilkie GS, Farnir F, Bayrou C, Lieffrig F, Li H, Desmecht D, Davison AJ, Vanderplasschen A. 2015 Feb. Rational development of an attenuated recombinant cyprinid herpesvirus 3 vaccine using prokaryotic mutagenesis and in vivo bioluminescent imaging. PLoS pathogens 11:e1004690
  29. Gaunt E, Harvala H, Österback R, Sreenu VB, Thomson E, Waris M, Simmonds P. 2015 May. Genetic characterization of human coxsackievirus A6 variants associated with atypical hand, foot and mouth disease: a potential role of recombination in emergence and pathogenicity. The Journal of general virology 96:1067-79
  30. McGonigle R, Yap WB, Ong ST, Gatherer D, Bakker SE, Tan WS, Bhella D. 2015 Feb. An N-terminal extension to the hepatitis B virus core protein forms a poorly ordered trimeric spike in assembled virus-like particles. Journal of structural biology 189:73-80
  31. Rihn SJ, Hughes J, Wilson SJ, Bieniasz PD. 2015 Jan. Uneven genetic robustness of HIV-1 integrase. Journal of virology 89:552-67
  32. Abdelrahman T, Hughes J, Main J, McLauchlan J, Thursz M, Thomson E. 2015 Jan. Next-generation sequencing sheds light on the natural history of hepatitis C infection in patients who fail treatment. Hepatology (Baltimore, Md.) 61:88-97
  33. Bęczkowski PM, Hughes J, Biek R, Litster A, Willett BJ, Hosie MJ. 2014 Sep 17. Feline immunodeficiency virus (FIV) env recombinants are common in natural infections. Retrovirology 11:80
  34. van Beurden SJ, Hughes J, Saucedo B, Rijks J, Kik M, Haenen OL, Engelsma MY, Gröne A, Verheije MH, Wilkie G. 2014 Dec 24. Complete genome sequence of a common midwife toad virus-like ranavirus associated with mass mortalities in wild amphibians in the Netherlands. Genome announcements 2:
  35. Bęczkowski PM, Hughes J, Biek R, Litster A, Willett BJ, Hosie MJ. 2015 Apr. Rapid evolution of the env gene leader sequence in cats naturally infected with feline immunodeficiency virus. The Journal of general virology 96:893-903
  36. Wilkie GS, Davison AJ, Kerr K, Stidworthy MF, Redrobe S, Steinbach F, Dastjerdi A, Denk D. 2014 Sep 9. First fatality associated with elephant endotheliotropic herpesvirus 5 in an Asian elephant: pathological findings and complete viral genome sequence. Scientific reports 4:6299
  37. Stanton RJ, Prod'homme V, Purbhoo MA, Moore M, Aicheler RJ, Heinzmann M, Bailer SM, Haas J, Antrobus R, Weekes MP, Lehner PJ, Vojtesek B, Miners KL, Man S, Wilkie GS, Davison AJ, Wang ECY, Tomasec P, Wilkinson GWG. 2014 Aug 13. HCMV pUL135 remodels the actin cytoskeleton to impair immune recognition of infected cells. Cell host & microbe 16:201-214
  38. Keck ZY, Angus AG, Wang W, Lau P, Wang Y, Gatherer D, Patel AH, Foung SK. 2014 Aug. Non-random escape pathways from a broadly neutralizing human monoclonal antibody map to a highly conserved region on the hepatitis C virus E2 glycoprotein encompassing amino acids 412-423. PLoS pathogens 10:e1004297
  39. Arriagada G, Gifford RJ. 2014 Oct. Parvovirus-derived endogenous viral elements in two South American rodent genomes. Journal of virology 88:12158-62
  40. Hussain M, Gatherer D, Wilson JB. 2014 Dec. Modelling the structure of full-length Epstein-Barr virus nuclear antigen 1. Virus genes 49:358-72
  41. Caporale M, Di Gialleonorado L, Janowicz A, Wilkie G, Shaw A, Savini G, Van Rijn PA, Mertens P, Di Ventura M, Palmarini M. 2014 Sep. Virus and host factors affecting the clinical outcome of bluetongue virus infection. Journal of virology 88:10399-411
  42. Busnadiego I, Kane M, Rihn SJ, Preugschas HF, Hughes J, Blanco-Melo D, Strouvelle VP, Zang TM, Willett BJ, Boutell C, Bieniasz PD, Wilson SJ. 2014 Jul. Host and viral determinants of Mx2 antiretroviral activity. Journal of virology 88:7738-52
  43. Abdelrahman T, Hughes J, Main J, McLauchlan J, Thursz M, Thomson E. 2015 Jan. Next-generation sequencing sheds light on the natural history of hepatitis C infection in patients who fail treatment. Hepatology (Baltimore, Md.) 61:88-97
  44. Cotmore SF, Agbandje-McKenna M, Chiorini JA, Mukha DV, Pintel DJ, Qiu J, Soderlund-Venermo M, Tattersall P, Tijssen P, Gatherer D, Davison AJ. 2014 May. The family Parvoviridae. Archives of virology 159:1239-47
  45. Fielding CA, Aicheler R, Stanton RJ, Wang EC, Han S, Seirafian S, Davies J, McSharry BP, Weekes MP, Antrobus PR, Prod'homme V, Blanchet FP, Sugrue D, Cuff S, Roberts D, Davison AJ, Lehner PJ, Wilkinson GW, Tomasec P. 2014 May. Two novel human cytomegalovirus NK cell evasion functions target MICA for lysosomal degradation. PLoS pathogens 10:e1004058
  46. Tenzer S, Crawford H, Pymm P, Gifford R, Sreenu VB, Weimershaus M, de Oliveira T, Burgevin A, Gerstoft J, Akkad N, Lunn D, Fugger L, Bell J, Schild H, van Endert P, Iversen AK. 2014 Apr 24. HIV-1 adaptation to antigen processing results in population-level immune evasion and affects subtype diversification. Cell reports 7:448-63
  47. Monne I, Fusaro A, Nelson MI, Bonfanti L, Mulatti P, Hughes J, Murcia PR, Schivo A, Valastro V, Moreno A, Holmes EC, Cattoli G. 2014 Apr. Emergence of a highly pathogenic avian influenza virus from a low-pathogenic progenitor. Journal of virology 88:4375-88
  48. Rima BK, Gatherer D, Young DF, Norsted H, Randall RE, Davison AJ. 2014 Apr. Stability of the parainfluenza virus 5 genome revealed by deep sequencing of strains isolated from different hosts and following passage in cell culture. Journal of virology 88:3826-36
  49. Henzy JE, Gifford RJ, Johnson WE, Coffin JM. 2014 Mar. A novel recombinant retrovirus in the genomes of modern birds combines features of avian and mammalian retroviruses. Journal of virology 88:2398-405
  50. Ouyang P, Rakus K, van Beurden SJ, Westphal AH, Davison AJ, Gatherer D, Vanderplasschen AF. 2014 Feb. IL-10 encoded by viruses: a remarkable example of independent acquisition of a cellular gene by viruses and its subsequent evolution in the viral genome. The Journal of general virology 95:245-62
  51. Szpara ML, Gatherer D, Ochoa A, Greenbaum B, Dolan A, Bowden RJ, Enquist LW, Legendre M, Davison AJ. 2014 Jan. Evolution and diversity in human herpes simplex virus genomes. Journal of virology 88:1209-27
  52. Gatherer D, Galpin V. 2013 Nov 17. Rosen's (M,R) system in process algebra. BMC systems biology 7:128
  53. Murrell I, Tomasec P, Wilkie GS, Dargan DJ, Davison AJ, Stanton RJ. 2013 Oct. Impact of sequence variation in the UL128 locus on production of human cytomegalovirus in fibroblast and epithelial cells. Journal of virology 87:10489-500
  54. Leggewie M, Sreenu VB, Abdelrahman T, Leitch EC, Wilkie GS, Klymenko T, Muir D, Thursz M, Main J, Thomson EC. 2013 Sep 24. Natural NS3 resistance polymorphisms occur frequently prior to treatment in HIV-positive patients with acute hepatitis C. AIDS (London, England) 27:2485-8
  55. Wilkie GS, Davison AJ, Watson M, Kerr K, Sanderson S, Bouts T, Steinbach F, Dastjerdi A. 2013 Jun. Complete genome sequences of elephant endotheliotropic herpesviruses 1A and 1B determined directly from fatal cases. Journal of virology 87:6700-12
  56. Killip MJ, Young DF, Gatherer D, Ross CS, Short JA, Davison AJ, Goodbourn S, Randall RE. 2013 May. Deep sequencing analysis of defective genomes of parainfluenza virus 5 and their role in interferon induction. Journal of virology 87:4798-807
  57. Davison AJ, Kurobe T, Gatherer D, Cunningham C, Korf I, Fukuda H, Hedrick RP, Waltzek TB. 2013 Mar. Comparative genomics of carp herpesviruses. Journal of virology 87:2908-22
  58. van Beurden SJ, Peeters BP, Rottier PJ, Davison AJ, Engelsma MY. 2013 Feb 6. Genome-wide gene expression analysis of anguillid herpesvirus 1. BMC genomics 14:83
  59. Jarrett RF, Gallagher A, Gatherer D. 2013. Molecular methods of virus detection in lymphoma. Methods in molecular biology (Clifton, N.J.) 971:277-93
  60. Varela M, Verschoor E, Lai RP, Hughes J, Mooj P, McKinley TJ, Fitzmaurice TJ, Landskron L, Willett BJ, Frost SD, Bogers WM, Heeney JL. 2013. Genetic imprint of vaccination on simian/human immunodeficiency virus type 1 transmitted viral genomes in rhesus macaques. PloS one 8:e70814
  61. Hughes J, Allen RC, Baguelin M, Hampson K, Baillie GJ, Elton D, Newton JR, Kellam P, Wood JL, Holmes EC, Murcia PR. 2012 Dec. Transmission of equine influenza virus during an outbreak is characterized by frequent mixed infections and loose transmission bottlenecks. PLoS pathogens 8:e1003081
  62. Kaján GL, Davison AJ, Palya V, Harrach B, Benko M. 2012 Nov. Genome sequence of a waterfowl aviadenovirus, goose adenovirus 4. The Journal of general virology 93:2457-65
  63. van Beurden SJ, Gatherer D, Kerr K, Galbraith J, Herzyk P, Peeters BP, Rottier PJ, Engelsma MY, Davison AJ. 2012 Sep. Anguillid herpesvirus 1 transcriptome. Journal of virology 86:10150-61
  64. Vanni E, Gatherer D, Tong L, Everett RD, Boutell C. 2012 Jun. Functional characterization of residues required for the herpes simplex virus 1 E3 ubiquitin ligase ICP0 to interact with the cellular E2 ubiquitin-conjugating enzyme UBE2D1 (UbcH5a). Journal of virology 86:6323-33
  65. Towler JC, Ebrahimi B, Lane B, Davison AJ, Dargan DJ. 2012 May. Human cytomegalovirus transcriptome activity differs during replication in human fibroblast, epithelial and astrocyte cell lines. The Journal of general virology 93:1046-58
  66. Prod'homme V, Tomasec P, Cunningham C, Lemberg MK, Stanton RJ, McSharry BP, Wang EC, Cuff S, Martoglio B, Davison AJ, Braud VM, Wilkinson GW. 2012 Mar 15. Human cytomegalovirus UL40 signal peptide regulates cell surface expression of the NK cell ligands HLA-E and gpUL18. Journal of immunology (Baltimore, Md. : 1950) 188:2794-804
  67. Cui X, Adler SP, Davison AJ, Smith L, Habib el-SE, McVoy MA. 2012. Bacterial artificial chromosome clones of viruses comprising the towne cytomegalovirus vaccine. Journal of biomedicine & biotechnology 2012:428498
  68. Angus AG, Loquet A, Stack SJ, Dalrymple D, Gatherer D, Penin F, Patel AH. 2012 Jan. Conserved glycine 33 residue in flexible domain I of hepatitis C virus core protein is critical for virus infectivity. Journal of virology 86:679-90
  69. Horst D, Burrows SR, Gatherer D, van Wilgenburg B, Bell MJ, Boer IG, Ressing ME, Wiertz EJ. 2012 Jan. Epstein-Barr virus isolates retain their capacity to evade T cell immunity through BNLF2a despite extensive sequence variation. Journal of virology 86:572-7
  70. Murcia PR, Hughes J, Battista P, Lloyd L, Baillie GJ, Ramirez-Gonzalez RH, Ormond D, Oliver K, Elton D, Mumford JA, Caccamo M, Kellam P, Grenfell BT, Holmes EC, Wood JL. 2012. Evolution of an Eurasian avian-like influenza virus in naïve and vaccinated pigs. PLoS pathogens 8:e1002730
  71. Gatherer D, Seirafian S, Cunningham C, Holton M, Dargan DJ, Baluchova K, Hector RD, Galbraith J, Herzyk P, Wilkinson GW, Davison AJ. 2011 Dec 6. High-resolution human cytomegalovirus transcriptome. Proceedings of the National Academy of Sciences of the United States of America 108:19755-60
  72. Davison AJ. 2011 Aug. Evolution of sexually transmitted and sexually transmissible human herpesviruses. Annals of the New York Academy of Sciences 1230:E37-49
  73. Reed DL, Currier RW, Walton SF, Conrad M, Sullivan SA, Carlton JM, Read TD, Severini A, Tyler S, Eberle R, Johnson WE, Silvestri G, Clarke IN, Lagergård T, Lukehart SA, Unemo M, Shafer WM, Beasley RP, Bergström T, Norberg P, Davison AJ, Sharp PM, Hahn BH, Blomberg J. 2011 Aug. The evolution of infectious agents in relation to sex in animals and humans: brief discussions of some individual organisms. Annals of the New York Academy of Sciences 1230:74-107
  74. Aoki K, Benkö M, Davison AJ, Echavarria M, Erdman DD, Harrach B, Kajon AE, Schnurr D, Wadell G. 2011 Jun. Toward an integrated human adenovirus designation system that utilizes molecular and serological data and serves both clinical and fundamental virology. Journal of virology 85:5703-4
  75. Horst D, Verweij MC, Davison AJ, Ressing ME, Wiertz EJ. 2011 Feb. Viral evasion of T cell immunity: ancient mechanisms offering new applications. Current opinion in immunology 23:96-103
  76. Gatherer D. 2010 Nov 30. Tempo and mode in the molecular evolution of influenza C. PLoS currents 2:RRN1199
  77. Gatherer D. 2010 Oct. The Little Ice Age and the emergence of influenza A. Medical hypotheses 75:359-62
  78. Stanton RJ, Baluchova K, Dargan DJ, Cunningham C, Sheehy O, Seirafian S, McSharry BP, Neale ML, Davies JA, Tomasec P, Davison AJ, Wilkinson GW. 2010 Sep. Reconstruction of the complete human cytomegalovirus genome in a BAC reveals RL13 to be a potent inhibitor of replication. The Journal of clinical investigation 120:3191-208