Publications

  1. Davis C, Mgomella GS, Filipe ADS, Frost EH, Giroux G, Hughes J, Hogan C, Kaleebu P, Asiki G, McLauchlan J, Niebel M, Ocama P, Pomila C, Pybus OG, Pépin J, Simmonds P, Singer JB, Sreenu VB, Wekesa C, Young EH, Murphy DG, Sandhu M, Thomson EC. 2018 Nov 2. New highly diverse hepatitis C strains detected in sub-Saharan Africa have unknown susceptibility to direct-acting antiviral treatments. Hepatology (Baltimore, Md.) :
  2. Dunlop JI, Szemiel AM, Navarro A, Wilkie GS, Tong L, Modha S, Mair D, Sreenu VB, Da Silva Filipe A, Li P, Huang YS, Brennan B, Hughes J, Vanlandingham DL, Higgs S, Elliott RM, Kohl A. 2018 Oct 29. Development of reverse genetics systems and investigation of host response antagonism and reassortment potential for Cache Valley and Kairi viruses, two emerging orthobunyaviruses of the Americas. PLoS neglected tropical diseases 12:e0006884
  3. Maia FGM, de Souza WM, Sabino-Santos G Jr, Fumagalli MJ, Modha S, Murcia PR, Figueiredo LTM. 2018 Jun 21. A novel polyomavirus in sigmodontine rodents from São Paulo State, Brazil. Archives of virology :
  4. de Souza WM, Romeiro MF, Sabino-Santos G Jr, Maia FGM, Fumagalli MJ, Modha S, Nunes MRT, Murcia PR, Figueiredo LTM. 2018 Jun. Novel orthohepeviruses in wild rodents from São Paulo State, Brazil. Virology 519:12-16
  5. de Souza WM, Dennis T, Fumagalli MJ, Araujo J, Sabino-Santos G, Maia FGM, Acrani GO, Carrasco AOT, Romeiro MF, Modha S, Vieira LC, Ometto T, Queiroz LH, Durigon EL, Nunes MRT, Figueiredo LTM, Gifford RJ. 2018 Mar 22. Novel Parvoviruses from Wild and Domestic Animals in Brazil Provide New Insights into Parvovirus Distribution and Diversity. Viruses 10:
  6. de Souza WM, Fumagalli MJ, de Araujo J, Sabino-Santos G Jr, Maia FGM, Romeiro MF, Modha S, Nardi MS, Queiroz LH, Durigon EL, Nunes MRT, Murcia PR, Figueiredo LTM. 2018 Jan 15. Discovery of novel anelloviruses in small mammals expands the host range and diversity of the Anelloviridae. Virology 514:9-17
  7. Saucedo B, Hughes J, Spitzen-van der Sluijs A, Kruithof N, Schills M, Rijks JM, Jacinto-Maldonado M, Suarez N, Haenen OLM, Voorbergen-Laarman M, van den Broek J, Gilbert M, Gröne A, van Beurden SJ, Verheije MH. 2018 Apr 4. Ranavirus genotypes in the Netherlands and their potential association with virulence in water frogs (Pelophylax spp.). Emerging microbes & infections 7:56
  8. Modha S, Thanki AS, Cotmore SF, Davison AJ, Hughes J. 2018 Jul 1. ViCTree: an automated framework for taxonomic classification from protein sequences. Bioinformatics (Oxford, England) 34:2195-2200
  9. da Silva Filipe A, Sreenu V, Hughes J, Aranday-Cortes E, Irving WL, Foster GR, Agarwal K, Rosenberg W, Macdonald D, Richardson P, Aldersley MA, Wiselka M, Ustianowski A, McLauchlan J, Thomson EC. 2018 Jan 12. Reply to: "Reply to: 'Response to DAA therapy in the NHS England Early Access Programme for rare HCV subtypes from low and middle income countries'". Journal of hepatology :
  10. McNaughton AL, Sreenu VB, Wilkie G, Gunson R, Templeton K, Leitch ECM. 2018 May. Prevalence of mixed genotype hepatitis C virus infections in the UK as determined by genotype-specific PCR and deep sequencing. Journal of viral hepatitis 25:524-534
  11. Marston DA, Horton DL, Nunez J, Ellis RJ, Orton RJ, Johnson N, Banyard AC, McElhinney LM, Freuling CM, Fırat M, Ünal N, Müller T, de Lamballerie X, Fooks AR. 2017 Jul. Genetic analysis of a rabies virus host shift event reveals within-host viral dynamics in a new host. Virus evolution 3:vex038
  12. 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
  13. 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
  14. Lourenço-de-Oliveira R, Marques JT, Sreenu VB, Atyame Nten C, Aguiar ERGR, Varjak M, Kohl A, Failloux AB. 2018 Feb. Culex quinquefasciatus mosquitoes do not support replication of Zika virus. The Journal of general virology 99:258-264
  15. Chauché C, Nogales A, Zhu H, Goldfarb D, Ahmad Shanizza AI, Gu Q, Parrish CR, Martínez-Sobrido L, Marshall JF, Murcia PR. 2018 Mar 1. Mammalian Adaptation of an Avian Influenza A Virus Involves Stepwise Changes in NS1. Journal of virology 92:
  16. Lefkowitz EJ, Dempsey DM, Hendrickson RC, Orton RJ, Siddell SG, Smith DB. 2018 Jan 4. Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV). Nucleic acids research 46:D708-D717
  17. Jiang X, Feyertag F, Robertson DL. 2017. Protein structural disorder of the envelope V3 loop contributes to the switch in human immunodeficiency virus type 1 cell tropism. PloS one 12:e0185790
  18. Davison AJ, Nielsen O, Subramaniam K, Jacob JM, Romero CH, Burek-Huntington KA, Waltzek TB. 2017 Oct 19. Genome Sequence of an Alphaherpesvirus from a Beluga Whale (<i>Delphinapterus leucas</i>). Genome announcements 5:
  19. Rakus K, Ronsmans M, Forlenza M, Boutier M, Piazzon MC, Jazowiecka-Rakus J, Gatherer D, Athanasiadis A, Farnir F, Davison AJ, Boudinot P, Michiels T, Wiegertjes GF, Vanderplasschen A. 2017 Feb 8. Conserved Fever Pathways across Vertebrates: A Herpesvirus Expressed Decoy TNF-α Receptor Delays Behavioral Fever in Fish. Cell host & microbe 21:244-253
  20. Fielding CA, Weekes MP, Nobre LV, Ruckova E, Wilkie GS, Paulo JA, Chang C, Suárez NM, Davies JA, Antrobus R, Stanton RJ, Aicheler RJ, Nichols H, Vojtesek B, Trowsdale J, Davison AJ, Gygi SP, Tomasec P, Lehner PJ, Wilkinson GW. 2017 Feb 10. Control of immune ligands by members of a cytomegalovirus gene expansion suppresses natural killer cell activation. eLife 6:
  21. Davison AJ. 2017 Jan. Journal of General Virology - Introduction to 'ICTV Virus Taxonomy Profiles'. The Journal of general virology 98:1
  22. Farkašová H, Hron T, Pačes J, Hulva P, Benda P, Gifford RJ, Elleder D. 2017 Mar 21. Discovery of an endogenous Deltaretrovirus in the genome of long-fingered bats (Chiroptera: Miniopteridae). Proceedings of the National Academy of Sciences of the United States of America 114:3145-3150
  23. Souza WM, Romeiro MF, Fumagalli MJ, Modha S, de Araujo J, Queiroz LH, Durigon EL, Figueiredo LT, Murcia PR, Gifford RJ. 2017 Feb. Chapparvoviruses occur in at least three vertebrate classes and have a broad biogeographic distribution. The Journal of general virology 98:225-229
  24. Hage E, Wilkie GS, Linnenweber-Held S, Dhingra A, Suárez NM, Schmidt JJ, Kay-Fedorov PC, Mischak-Weissinger E, Heim A, Schwarz A, Schulz TF, Davison AJ, Ganzenmueller T. 2017 Jun 1. Characterization of Human Cytomegalovirus Genome Diversity in Immunocompromised Hosts by Whole-Genome Sequencing Directly From Clinical Specimens. The Journal of infectious diseases 215:1673-1683
  25. Sumner T, Orton RJ, Green DM, Kao RR, Gubbins S. 2017 Apr. Quantifying the roles of host movement and vector dispersal in the transmission of vector-borne diseases of livestock. PLoS computational biology 13:e1005470
  26. Suárez NM, Lau B, Kemble GM, Lee R, Mocarski ES, Wilkinson GWG, Adler SP, McVoy MA, Davison AJ. 2017 Aug. Genomic analysis of chimeric human cytomegalovirus vaccine candidates derived from strains Towne and Toledo. Virus genes 53:650-655
  27. Blanco-Melo D, Gifford RJ, Bieniasz PD. 2017 Apr 11. Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors. eLife 6:
  28. Adams MJ, Lefkowitz EJ, King AMQ, Harrach B, Harrison RL, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Mushegian AR, Nibert M, Sabanadzovic S, Sanfaçon H, Siddell SG, Simmonds P, Varsani A, Zerbini FM, Gorbalenya AE, Davison AJ. 2017 Aug. Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2017). Archives of virology 162:2505-2538
  29. Varjak M, Maringer K, Watson M, Sreenu VB, Fredericks AC, Pondeville E, Donald CL, Sterk J, Kean J, Vazeille M, Failloux AB, Kohl A, Schnettler E. 2017 May-Jun. <i>Aedes aegypti</i> Piwi4 Is a Noncanonical PIWI Protein Involved in Antiviral Responses. mSphere 2:
  30. Milani A, Fusaro A, Bonfante F, Zamperin G, Salviato A, Mancin M, Mastrorilli E, Hughes J, Hussein HA, Hassan M, Mundt E, Terregino C, Cattoli G, Monne I. 2017 May. Vaccine immune pressure influences viral population complexity of avian influenza virus during infection. Veterinary microbiology 203:88-94
  31. Boutier M, Gao Y, Vancsok C, Suárez NM, Davison AJ, Vanderplasschen A. 2017 Sep. Identification of an essential virulence gene of cyprinid herpesvirus 3. Antiviral research 145:60-69
  32. Davison AJ, Subramaniam K, Kerr K, Jacob JM, Landrau-Giovannetti N, Walsh MT, Wells RS, Waltzek TB. 2017 Aug 3. Genome Sequence of a Gammaherpesvirus from a Common Bottlenose Dolphin (<i>Tursiops truncatus</i>). Genome announcements 5:
  33. Selinger M, Wilkie GS, Tong L, Gu Q, Schnettler E, Grubhoffer L, Kohl A. 2017 Aug. Analysis of tick-borne encephalitis virus-induced host responses in human cells of neuronal origin and interferon-mediated protection. The Journal of general virology 98:2043-2060
  34. da Silva Filipe A, Sreenu V, Hughes J, Aranday-Cortes E, Irving WL, Foster GR, Agarwal K, Rosenberg W, Macdonald D, Richardson P, Aldersley MA, Wiselka M, Ustianowski A, McLauchlan J, Thomson EC. 2017 Dec. Response to DAA therapy in the NHS England Early Access Programme for rare HCV subtypes from low and middle income countries. Journal of hepatology 67:1348-1350
  35. Zeuzem S, Dvory-Sobol H, Brainard DM. 2017 Dec. Reply to: "Response to DAA therapy in the NHS England Early Access Programme for rare HCV subtypes from low and middle income countries". Journal of hepatology 67:1350-1352
  36. Vancsok C, Peñaranda MMD, Raj VS, Leroy B, Jazowiecka-Rakus J, Boutier M, Gao Y, Wilkie GS, Suárez NM, Wattiez R, Gillet L, Davison AJ, Vanderplasschen AFC. 2017 Nov 1. Proteomic and Functional Analyses of the Virion Transmembrane Proteome of Cyprinid Herpesvirus 3. Journal of virology 91:
  37. Zhang E, Bell AJ, Wilkie GS, Suárez NM, Batini C, Veal CD, Armendáriz-Castillo I, Neumann R, Cotton VE, Huang Y, Porteous DJ, Jarrett RF, Davison AJ, Royle NJ. 2017 Nov 15. Inherited Chromosomally Integrated Human Herpesvirus 6 Genomes Are Ancient, Intact, and Potentially Able To Reactivate from Telomeres. Journal of virology 91:
  38. Dennis TPW, Zhu H, Wilson SJ, Gifford RJ. 2017 Mar. A14 Comprehensive characterisation and evolutionary analysis of endogenous retroviruses in the mouse genome. Virus evolution 3:
  39. Saucedo B, Hughes J, van Beurden SJ, Suárez NM, Haenen OLM, Voorbergen-Laarman M, Gröne A, Kik MJL. 2017 Aug 31. Complete Genome Sequence of <i>Frog virus 3</i>, Isolated from a Strawberry Poison Frog (<i>Oophaga pumilio</i>) Imported from Nicaragua into the Netherlands. Genome announcements 5:
  40. Niebel M, Singer JB, Nickbakhsh S, Gifford RJ, Thomson EC. 2017 Oct. Hepatitis C and the absence of genomic data in low-income countries: a barrier on the road to elimination? The lancet. Gastroenterology & hepatology 2:700-701
  41. Klymenko T, Gu Q, Herbert I, Stevenson A, Iliev V, Watkins G, Pollock C, Bhatia R, Cuschieri K, Herzyk P, Gatherer D, Graham SV. 2017 Oct 11. RNASeq analysis of differentiated keratinocytes reveals a massive response to late events during human papillomavirus type 16 infection, including loss of epithelial barrier function. Journal of virology :
  42. Varjak M, Donald CL, Mottram TJ, Sreenu VB, Merits A, Maringer K, Schnettler E, Kohl A. 2017 Oct. Characterization of the Zika virus induced small RNA response in Aedes aegypti cells. PLoS neglected tropical diseases 11:e0006010
  43. 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
  44. 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
  45. Rihn SJ, Foster TL, Busnadiego I, Aziz MA, Hughes J, Neil SJ, Wilson SJ. 2017 Apr 1. The Envelope Gene of Transmitted HIV-1 Resists a Late Interferon Gamma-Induced Block. Journal of virology 91:
  46. 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
  47. Myster F, van Beurden SJ, Sorel O, Suárez NM, Vanderplasschen A, Davison AJ, Dewals BG. 2016 Dec 7. Genomic duplication and translocation of reactivation transactivator and bZIP-homolog genes is a conserved event in alcelaphine herpesvirus 1. Scientific reports 6:38607
  48. Beelontally R, Wilkie GS, Lau B, Goodmaker CJ, Ho CMK, Swanson CM, Deng X, Wang J, Gray NS, Davison AJ, Strang BL. 2017 Feb. Identification of compounds with anti-human cytomegalovirus activity that inhibit production of IE2 proteins. Antiviral research 138:61-67
  49. Henzy JE, Gifford RJ, Kenaley CP, Johnson WE. 2017 Mar 1. An Intact Retroviral Gene Conserved in Spiny-Rayed Fishes for over 100 My. Molecular biology and evolution 34:634-639
  50. 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
  51. Rijks JM, Saucedo B, Spitzen-van der Sluijs A, Wilkie GS, van Asten AJ, van den Broek J, Boonyarittichaikij R, Stege M, van der Sterren F, Martel A, Pasmans F, Hughes J, Gröne A, van Beurden SJ, Kik MJ. 2016. Investigation of Amphibian Mortality Events in Wildlife Reveals an On-Going Ranavirus Epidemic in the North of the Netherlands. PloS one 11:e0157473
  52. Thomson E, Ip CL, Badhan A, Christiansen MT, Adamson W, Ansari MA, Bibby D, Breuer J, Brown A, Bowden R, Bryant J, Bonsall D, Da Silva Filipe A, Hinds C, Hudson E, Klenerman P, Lythgow K, Mbisa JL, McLauchlan J, Myers R, Piazza P, Roy S, Trebes A, Sreenu VB, Witteveldt J, Barnes E, Simmonds P. 2016 Oct. Comparison of Next-Generation Sequencing Technologies for Comprehensive Assessment of Full-Length Hepatitis C Viral Genomes. Journal of clinical microbiology 54:2470-84
  53. Polachek WS, Moshrif HF, Franti M, Coen DM, Sreenu VB, Strang BL. 2016 Sep 15. High-Throughput Small Interfering RNA Screening Identifies Phosphatidylinositol 3-Kinase Class II Alpha as Important for Production of Human Cytomegalovirus Virions. Journal of virology 90:8360-71
  54. 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 44:286-292
  55. Wignall-Fleming E, Young DF, Goodbourn S, Davison AJ, Randall RE. 2016 Jul 21. Genome Sequence of the Parainfluenza Virus 5 Strain That Persistently Infects AGS Cells. Genome announcements 4:
  56. Franzo G, Cortey M, Segalés J, Hughes J, Drigo M. 2016 Sep. Phylodynamic analysis of porcine circovirus type 2: Methodological approach and datasets. Data in brief 8:549-52
  57. Adams MJ, Davison AJ. 2016 Dec. Eric Carstens: new life member of the International Committee on Taxonomy of Viruses (ICTV). Archives of virology 161:3601
  58. Schnettler E, Sreenu VB, Mottram T, McFarlane M. 2016 Nov. Wolbachia restricts insect-specific flavivirus infection in Aedes aegypti cells. The Journal of general virology 97:3024-3029
  59. Donald CL, Brennan B, Cumberworth SL, Rezelj VV, Clark JJ, Cordeiro MT, Freitas de Oliveira França R, Pena LJ, Wilkie GS, Da Silva Filipe A, Davis C, Hughes J, Varjak M, Selinger M, Zuvanov L, Owsianka AM, Patel AH, McLauchlan J, Lindenbach BD, Fall G, Sall AA, Biek R, Rehwinkel J, Schnettler E, Kohl A. 2016 Oct. Full Genome Sequence and sfRNA Interferon Antagonist Activity of Zika Virus from Recife, Brazil. PLoS neglected tropical diseases 10:e0005048
  60. 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
  61. Papageorgiou KV, Suárez NM, Wilkie GS, McDonald M, Graham EM, Davison AJ. 2016. Genome Sequence of Canine Herpesvirus. PloS one 11:e0156015
  62. 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
  63. 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
  64. Ng M, Ndungo E, Kaczmarek ME, Herbert AS, Binger T, Kuehne AI, Jangra RK, Hawkins JA, Gifford RJ, Biswas R, Demogines A, James RM, Yu M, Brummelkamp TR, Drosten C, Wang LF, Kuhn JH, Müller MA, Dye JM, Sawyer SL, Chandran K. 2015 Dec 23. Filovirus receptor NPC1 contributes to species-specific patterns of ebolavirus susceptibility in bats. eLife 4:
  65. Wu HL, Léon EJ, Wallace LT, Nimiyongskul FA, Buechler MB, Newman LP, Castrovinci PA, Paul Johnson R, Gifford RJ, Brad Jones R, Sacha JB. 2016 Jan 15. Identification and spontaneous immune targeting of an endogenous retrovirus K envelope protein in the Indian rhesus macaque model of human disease. Retrovirology 13:6
  66. Papageorgiou KV, Suárez NM, Wilkie GS, Filioussis G, Papaioannou N, Nauwynck HJ, Davison AJ, Kritas SK. 2016 Jan 21. Genome Sequences of Two Pseudorabies Virus Strains Isolated in Greece. Genome announcements 4:
  67. Murrell I, Wilkie GS, Davison AJ, Statkute E, Fielding CA, Tomasec P, Wilkinson GW, Stanton RJ. 2016 Apr. Genetic Stability of Bacterial Artificial Chromosome-Derived Human Cytomegalovirus during Culture In Vitro. Journal of virology 90:3929-43
  68. Zhang E, Cotton VE, Hidalgo-Bravo A, Huang Y, Bell AJ, Jarrett RF, Wilkie GS, Davison AJ, Nacheva EP, Siebert R, Majid A, Kelpanides I, Jayne S, Dyer MJ, Royle NJ. 2016 Mar 7. HHV-8-unrelated primary effusion-like lymphoma associated with clonal loss of inherited chromosomally-integrated human herpesvirus-6A from the telomere of chromosome 19q. Scientific reports 6:22730
  69. Ratinier M, Shaw AE, Barry G, Gu Q, Di Gialleonardo L, Janowicz A, Varela M, Randall RE, Caporale M, Palmarini M. 2016 Jun 1. Bluetongue Virus NS4 Protein Is an Interferon Antagonist and a Determinant of Virus Virulence. Journal of virology 90:5427-39
  70. Robinson MW, Hughes J, Wilkie GS, Swann R, Barclay ST, Mills PR, Patel AH, Thomson EC, McLauchlan J. 2016. Tracking TCRβ Sequence Clonotype Expansions during Antiviral Therapy Using High-Throughput Sequencing of the Hypervariable Region. Frontiers in immunology 7:131
  71. Franzo G, Cortey M, Segalés J, Hughes J, Drigo M. 2016 Jul. Phylodynamic analysis of porcine circovirus type 2 reveals global waves of emerging genotypes and the circulation of recombinant forms. Molecular phylogenetics and evolution 100:269-280
  72. Fusaro A, Tassoni L, Milani A, Hughes J, Salviato A, Murcia PR, Massi P, Zamperin G, Bonfanti L, Marangon S, Cattoli G, Monne I. 2016 Jul 15. Unexpected Interfarm Transmission Dynamics during a Highly Pathogenic Avian Influenza Epidemic. Journal of virology 90:6401-6411
  73. 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
  74. 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
  75. 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
  76. 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
  77. 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
  78. 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
  79. 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
  80. 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
  81. 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
  82. 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
  83. 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
  84. 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
  85. 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
  86. 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
  87. Wilkie GS, Kerr K, Stewart JP, Studdert MJ, Davison AJ. 2015 Mar 12. Genome sequences of equid herpesviruses 2 and 5. Genome announcements 3:
  88. 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
  89. Zhu H, Hughes J, Murcia PR. 2015 May. Origins and Evolutionary Dynamics of H3N2 Canine Influenza Virus. Journal of virology 89:5406-18
  90. 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
  91. 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
  92. 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
  93. Rihn SJ, Hughes J, Wilson SJ, Bieniasz PD. 2015 Jan. Uneven genetic robustness of HIV-1 integrase. Journal of virology 89:552-67
  94. Jombart T, Aanensen DM, Baguelin M, Birrell P, Cauchemez S, Camacho A, Colijn C, Collins C, Cori A, Didelot X, Fraser C, Frost S, Hens N, Hugues J, Höhle M, Opatowski L, Rambaut A, Ratmann O, Soubeyrand S, Suchard MA, Wallinga J, Ypma R, Ferguson N. 2014 Jun. OutbreakTools: a new platform for disease outbreak analysis using the R software. Epidemics 7:28-34
  95. 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
  96. 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
  97. 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:
  98. 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
  99. 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
  100. 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
  101. 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
  102. Arriagada G, Gifford RJ. 2014 Oct. Parvovirus-derived endogenous viral elements in two South American rodent genomes. Journal of virology 88:12158-62
  103. Katzourakis A, Magiorkinis G, Lim AG, Gupta S, Belshaw R, Gifford R. 2014 Jul. Larger mammalian body size leads to lower retroviral activity. PLoS pathogens 10:e1004214
  104. Arriagada G, Gifford RJ. 2014 Oct. Parvovirus-derived endogenous viral elements in two South American rodent genomes. Journal of virology 88:12158-62
  105. 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
  106. 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
  107. 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
  108. 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
  109. 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
  110. 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
  111. 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
  112. 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
  113. 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
  114. 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
  115. 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
  116. 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
  117. Gatherer D, Galpin V. 2013 Nov 17. Rosen's (M,R) system in process algebra. BMC systems biology 7:128
  118. 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
  119. Rihn SJ, Wilson SJ, Loman NJ, Alim M, Bakker SE, Bhella D, Gifford RJ, Rixon FJ, Bieniasz PD. 2013. Extreme genetic fragility of the HIV-1 capsid. PLoS pathogens 9:e1003461
  120. 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
  121. 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
  122. 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
  123. 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
  124. 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
  125. Jarrett RF, Gallagher A, Gatherer D. 2013. Molecular methods of virus detection in lymphoma. Methods in molecular biology (Clifton, N.J.) 971:277-93
  126. 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
  127. 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
  128. 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
  129. Abdel-Moneim AS, Afifi MA, El-Kady MF. 2012 Aug 27. Isolation and mutation trend analysis of influenza A virus subtype H9N2 in Egypt. Virology journal 9:173
  130. 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
  131. 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
  132. 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
  133. 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
  134. 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
  135. 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
  136. 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
  137. 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
  138. 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
  139. 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
  140. Davison AJ. 2011 Aug. Evolution of sexually transmitted and sexually transmissible human herpesviruses. Annals of the New York Academy of Sciences 1230:E37-49
  141. 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
  142. 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
  143. 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
  144. Gatherer D. 2010 Nov 30. Tempo and mode in the molecular evolution of influenza C. PLoS currents 2:RRN1199
  145. Gatherer D. 2010 Oct. The Little Ice Age and the emergence of influenza A. Medical hypotheses 75:359-62
  146. 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

Image
Image
Image