Publications

  1. Brunker K, Jaswant G, Thumbi SM, Lushasi K, Lugelo A, Czupryna AM, Ade F, Wambura G, Chuchu V, Steenson R, Ngeleja C, Bautista C, Manalo DL, Gomez MRR, Chu MYJV, Miranda ME, Kamat M, Rysava K, Espineda J, Silo EAV, Aringo AM, Bernales RP, Adonay FF, Tildesley MJ, Marston DA, Jennings DL, Fooks AR, Zhu W, Meredith LW, Hill SC, Poplawski R, Gifford RJ, Singer JB, Maturi M, Mwatondo A, Biek R, Hampson K. 2020. Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes. Wellcome open research 5:3
  2. de Souza WM, Fumagalli MJ, Martin MC, de Araujo J, Orsi MA, Sanfilippo LF, Modha S, Durigon EL, Proença-Módena JL, Arns CW, Murcia PR, Figueiredo LTM. 2019 Jul. Pingu virus: A new picornavirus in penguins from Antarctica. Virus evolution 5:vez047
  3. Fotiou E, Williams S, Martin-Geary A, Robertson DL, Tenin G, Hentges KE, Keavney B. 2019 Oct. Integration of Large-Scale Genomic Data Sources With Evolutionary History Reveals Novel Genetic Loci for Congenital Heart Disease. Circulation. Genomic and precision medicine 12:442-451
  4. Fumagalli MJ, de Souza WM, de Araujo J, Modha S, Queiroz LH, Durigon EL, Murcia PR, Figueiredo LTM. 2019 Nov. Krykféie dicistrovirus: A novel dicistrovirus in velvety free-tailed bats from Brazil. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 75:104036
  5. Ansari MA, Aranday-Cortes E, Ip CL, da Silva Filipe A, Lau SH, Bamford C, Bonsall D, Trebes A, Piazza P, Sreenu V, Cowton VM, Ball J, Barnes E, Burgess G, Cooke G, Dillon J, Foster G, Gore C, Guha N, Halford R, Holmes C, Hudson E, Hutchinson S, Irving W, Khakoo S, Klenerman P, Martin N, Mbisa T, McKeating J, McLauchlan J, Miners A, Murray A, Shaw P, Simmonds P, Smith S, Spencer C, Thomson E, Troke P, Vickerman P, Zitzmann N, Hudson E, Bowden R, Patel AH, Foster GR, Irving WL, Agarwal K, Thomson EC, Simmonds P, Klenerman P, Holmes C, Barnes E, Spencer CC, McLauchlan J, Pedergnana V. 2019 Sep 3. Interferon lambda 4 impacts the genetic diversity of hepatitis C virus. eLife 8:
  6. Yen PS, Chen CH, Sreenu V, Kohl A, Failloux AB. 2019 Jun 10. Assessing the Potential Interactions between Cellular miRNA and Arboviral Genomic RNA in the Yellow Fever Mosquito, <i>Aedes aegypti</i>. Viruses 11:
  7. Ankcorn M, Gallacher J, Ijaz S, Taha Y, Harvala H, Maclennan S, Thomson EC, Davis C, Singer JB, da Silva Filipe A, Smollett K, Niebel M, Semple MG, Tedder RS, McPherson S. 2019 Aug. Convalescent plasma therapy for persistent hepatitis E virus infection. Journal of hepatology 71:434-438
  8. Hufsky F, Ibrahim B, Modha S, Clokie MRJ, Deinhardt-Emmer S, Dutilh BE, Lycett S, Simmonds P, Thiel V, Abroi A, Adriaenssens EM, Escalera-Zamudio M, Kelly JN, Lamkiewicz K, Lu L, Susat J, Sicheritz T, Robertson DL, Marz M. 2019 May 5. The Third Annual Meeting of the European Virus Bioinformatics Center. Viruses 11:
  9. Tapinos A, Constantinides B, Phan MVT, Kouchaki S, Cotten M, Robertson DL. 2019 Apr 26. The Utility of Data Transformation for Alignment, De Novo Assembly and Classification of Short Read Virus Sequences. Viruses 11:
  10. Zhang J, Chai H. 2019. Recent In Silico Research in High-Throughput Drug Discovery and Molecular Biochemistry. Current topics in medicinal chemistry 19:103-104
  11. de Souza WM, Fumagalli MJ, de Araujo J, Ometto T, Modha S, Thomazelli LM, Durigon EL, Murcia PR, Figueiredo LTM. 2019 Apr 3. Discovery of novel astrovirus and calicivirus identified in ruddy turnstones in Brazil. Scientific reports 9:5556
  12. de Souza WM, Fumagalli MJ, Sabino-Santos G Jr, Motta Maia FG, Modha S, Teixeira Nunes MR, Murcia PR, Moraes Figueiredo LT. 2019 Mar 24. A Novel Hepacivirus in Wild Rodents from South America. Viruses 11:
  13. McFarlane S, Orr A, Roberts APE, Conn KL, Iliev V, Loney C, da Silva Filipe A, Smollett K, Gu Q, Robertson N, Adams PD, Rai TS, Boutell C. 2019 Mar. The histone chaperone HIRA promotes the induction of host innate immune defences in response to HSV-1 infection. PLoS pathogens 15:e1007667
  14. Kouchaki S, Tapinos A, Robertson DL. 2019 Feb 15. A signal processing method for alignment-free metagenomic binning: multi-resolution genomic binary patterns. Scientific reports 9:2159
  15. Ravindran V, Nacher JC, Akutsu T, Ishitsuka M, Osadcenco A, Sunitha V, Bagler G, Schwartz JM, Robertson DL. 2019 Feb 14. Network controllability analysis of intracellular signalling reveals viruses are actively controlling molecular systems. Scientific reports 9:2066
  16. Bergner LM, Orton RJ, da Silva Filipe A, Shaw AE, Becker DJ, Tello C, Biek R, Streicker DG. 2019 Jan. Using noninvasive metagenomics to characterize viral communities from wildlife. Molecular ecology resources 19:128-143
  17. Ito J, Gifford RJ, Sato K. 2020 Jan 7. Retroviruses drive the rapid evolution of mammalian <i>APOBEC3</i> genes. Proceedings of the National Academy of Sciences of the United States of America 117:610-618
  18. Hron T, Elleder D, Gifford RJ. 2019 Nov 27. Deltaretroviruses have circulated since at least the Paleogene and infected a broad range of mammalian species. Retrovirology 16:33
  19. Valencia-Herrera I, Faunes F, Cena-Ahumada E, Ibarra-Karmy R, Gifford RJ, Arriagada G. 2019 Sep 1. Molecular Properties and Evolutionary Origins of a Parvovirus-Derived Myosin Fusion Gene in Guinea Pigs. Journal of virology 93:
  20. Pénzes JJ, de Souza WM, Agbandje-McKenna M, Gifford RJ. 2019 Jun 6. An Ancient Lineage of Highly Divergent Parvoviruses Infects both Vertebrate and Invertebrate Hosts. Viruses 11:
  21. Schmidt F, Keele BF, Del Prete GQ, Voronin D, Fennessey CM, Soll S, Kane M, Raymond A, Gifford RJ, KewalRamani V, Lifson JD, Bieniasz PD, Hatziioannou T. 2019 May 21. Derivation of simian tropic HIV-1 infectious clone reveals virus adaptation to a new host. Proceedings of the National Academy of Sciences of the United States of America 116:10504-10509
  22. Halo JV, Pendleton AL, Jarosz AS, Gifford RJ, Day ML, Kidd JM. 2019 Mar 7. Origin and recent expansion of an endogenous gammaretroviral lineage in domestic and wild canids. Retrovirology 16:6
  23. Callaway HM, Subramanian S, Urbina CA, Barnard KN, Dick RA, Bator CM, Hafenstein SL, Gifford RJ, Parrish CR. 2019 Mar 15. Examination and Reconstruction of Three Ancient Endogenous Parvovirus Capsid Protein Gene Remnants Found in Rodent Genomes. Journal of virology 93:
  24. Pénzes JJ, Marsile-Medun S, Agbandje-McKenna M, Gifford RJ. 2018 Jul. Endogenous amdoparvovirus-related elements reveal insights into the biology and evolution of vertebrate parvoviruses. Virus evolution 4:vey026
  25. Orton RJ, Wright CF, King DP, Haydon DT. 2020 Feb 6. Estimating viral bottleneck sizes for FMDV transmission within and between hosts and implications for the rate of viral evolution. Interface focus 10:20190066
  26. Fahnøe U, Pedersen AG, Johnston CM, Orton RJ, Höper D, Beer M, Bukh J, Belsham GJ, Rasmussen TB. 2019 Oct 10. Virus Adaptation and Selection Following Challenge of Animals Vaccinated against Classical Swine Fever Virus. Viruses 11:
  27. Bergner LM, Orton RJ, Benavides JA, Becker DJ, Tello C, Biek R, Streicker DG. 2020 Jan. Demographic and environmental drivers of metagenomic viral diversity in vampire bats. Molecular ecology 29:26-39
  28. Oade MS, Keep S, Freimanis GL, Orton RJ, Britton P, Hammond JA, Bickerton E. 2019 Jul 15. Attenuation of Infectious Bronchitis Virus in Eggs Results in Different Patterns of Genomic Variation across Multiple Replicates. Journal of virology 93:
  29. Dagleish MP, Clark JJ, Robson C, Tucker M, Orton RJ, Rocchi MS. 2018 Nov. A Fatal Case of Louping-ill in a Dog: Immunolocalization and Full Genome Sequencing of the Virus. Journal of comparative pathology 165:23-32
  30. Jerome H, Taylor C, Sreenu VB, Klymenko T, Filipe ADS, Jackson C, Davis C, Ashraf S, Wilson-Davies E, Jesudason N, Devine K, Harder L, Aitken C, Gunson R, Thomson EC. 2019 Oct. Metagenomic next-generation sequencing aids the diagnosis of viral infections in febrile returning travellers. The Journal of infection 79:383-388
  31. Bamford C, Wignall-Fleming E, Sreenu VB, Randall R, Duprex P, Rima B. 2019. Unusual, stable replicating viruses generated from mumps virus cDNA clones. PloS one 14:e0219168
  32. Donald CL, Varjak M, Aguiar ERGR, Marques JT, Sreenu VB, Schnettler E, Kohl A. 2018 Dec 6. Antiviral RNA Interference Activity in Cells of the Predatory Mosquito, <i>Toxorhynchites amboinensis</i>. Viruses 10:
  33. Nobre LV, Nightingale K, Ravenhill BJ, Antrobus R, Soday L, Nichols J, Davies JA, Seirafian S, Wang EC, Davison AJ, Wilkinson GW, Stanton RJ, Huttlin EL, Weekes MP. 2019 Dec 24. Human cytomegalovirus interactome analysis identifies degradation hubs, domain associations and viral protein functions. eLife 8:
  34. Siddell SG, Walker PJ, Lefkowitz EJ, Mushegian AR, Dutilh BE, Harrach B, Harrison RL, Junglen S, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Nibert ML, Rubino L, Sabanadzovic S, Simmonds P, Varsani A, Zerbini FM, Davison AJ. 2020 Feb. Binomial nomenclature for virus species: a consultation. Archives of virology 165:519-525
  35. Dhingra A, Ganzenmueller T, Hage E, Suárez NM, Mätz-Rensing K, Widmer D, Pöhlmann S, Davison AJ, Schulz TF, Kaul A. 2019 Aug. Novel Virus Related to Kaposi’s Sarcoma-Associated Herpesvirus from Colobus Monkey. Emerging infectious diseases 25:1548-1551
  36. Wignall-Fleming EB, Hughes DJ, Vattipally S, Modha S, Goodbourn S, Davison AJ, Randall RE. 2019 Sep 1. Analysis of Paramyxovirus Transcription and Replication by High-Throughput Sequencing. Journal of virology 93:
  37. Walker PJ, Siddell SG, Lefkowitz EJ, Mushegian AR, Dempsey DM, Dutilh BE, Harrach B, Harrison RL, Hendrickson RC, Junglen S, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Nibert M, Rubino L, Sabanadzovic S, Simmonds P, Varsani A, Zerbini FM, Davison AJ. 2019 Sep. Changes to virus taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2019). Archives of virology 164:2417-2429
  38. Suárez NM, Musonda KG, Escriva E, Njenga M, Agbueze A, Camiolo S, Davison AJ, Gompels UA. 2019 Jul 31. Multiple-Strain Infections of Human Cytomegalovirus With High Genomic Diversity Are Common in Breast Milk From Human Immunodeficiency Virus-Infected Women in Zambia. The Journal of infectious diseases 220:792-801
  39. Subramaniam K, Venugopalan A, Davison AJ, Griffin MJ, Ford L, Waltzek TB, Hanson L. 2019 Apr 11. Complete Genome Sequence of an Ictalurid Herpesvirus 1 Strain Isolated from Blue Catfish (Ictalurus furcatus). Microbiology resource announcements 8:
  40. Young DF, Wignall-Fleming EB, Busse DC, Pickin MJ, Hankinson J, Randall EM, Tavendale A, Davison AJ, Lamont D, Tregoning JS, Goodbourn S, Randall RE. 2019 Feb. The switch between acute and persistent paramyxovirus infection caused by single amino acid substitutions in the RNA polymerase P subunit. PLoS pathogens 15:e1007561
  41. Masembe C, Sreenu VB, Da Silva Filipe A, Wilkie GS, Ogweng P, Mayega FJ, Muwanika VB, Biek R, Palmarini M, Davison AJ. 2018 Oct. Genome Sequences of Five African Swine Fever Virus Genotype IX Isolates from Domestic Pigs in Uganda. Microbiology resource announcements 7:
  42. Modha S, Hughes J, Bianco G, Ferguson HM, Helm B, Tong L, Wilkie GS, Kohl A, Schnettler E. 2019 Sep 17. Metaviromics Reveals Unknown Viral Diversity in the Biting Midge <i>Culicoides impunctatus</i>. Viruses 11:
  43. Maabar M, Davison AJ, Vučak M, Thorburn F, Murcia PR, Gunson R, Palmarini M, Hughes J. 2019 Jul. DisCVR: Rapid viral diagnosis from high-throughput sequencing data. Virus evolution 5:vez033
  44. Rihn SJ, Aziz MA, Stewart DG, Hughes J, Turnbull ML, Varela M, Sugrue E, Herd CS, Stanifer M, Sinkins SP, Palmarini M, Wilson SJ. 2019 Oct 15. TRIM69 Inhibits Vesicular Stomatitis Indiana Virus. Journal of virology 93:
  45. Alamil M, Hughes J, Berthier K, Desbiez C, Thébaud G, Soubeyrand S. 2019 Jun 24. Inferring epidemiological links from deep sequencing data: a statistical learning approach for human, animal and plant diseases. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 374:20180258
  46. Suárez NM, Wilkie GS, Hage E, Camiolo S, Holton M, Hughes J, Maabar M, Vattipally SB, Dhingra A, Gompels UA, Wilkinson GWG, Baldanti F, Furione M, Lilleri D, Arossa A, Ganzenmueller T, Gerna G, Hubáček P, Schulz TF, Wolf D, Zavattoni M, Davison AJ. 2019 Jul 31. Human Cytomegalovirus Genomes Sequenced Directly From Clinical Material: Variation, Multiple-Strain Infection, Recombination, and Gene Loss. The Journal of infectious diseases 220:781-791
  47. Singer JB, Thomson EC, Hughes J, Aranday-Cortes E, McLauchlan J, da Silva Filipe A, Tong L, Manso CF, Gifford RJ, Robertson DL, Barnes E, Ansari MA, Mbisa JL, Bibby DF, Bradshaw D, Smith D. 2019 Apr 3. Interpreting Viral Deep Sequencing Data with GLUE. Viruses 11:
  48. Halo JV, Pendleton AL, Jarosz AS, Gifford RJ, Day ML, Kidd JM. 2019 Mar 7. Origin and recent expansion of an endogenous gammaretroviral lineage in domestic and wild canids. Retrovirology 16:6
  49. Callaway HM, Subramanian S, Urbina CA, Barnard KN, Dick RA, Bator CM, Hafenstein SL, Gifford RJ, Parrish CR. 2019 Mar 15. Examination and Reconstruction of Three Ancient Endogenous Parvovirus Capsid Protein Gene Remnants Found in Rodent Genomes. Journal of virology 93:
  50. Zhu H, Damdinjav B, Gonzalez G, Patrono LV, Ramirez-Mendoza H, Amat JAR, Crispell J, Parr YA, Hammond TA, Shiilegdamba E, Leung YHC, Peiris M, Marshall JF, Hughes J, Gilbert M, Murcia PR. 2019 Feb. Absence of adaptive evolution is the main barrier against influenza emergence in horses in Asia despite frequent virus interspecies transmission from wild birds. PLoS pathogens 15:e1007531
  51. Cotmore SF, Agbandje-McKenna M, Canuti M, Chiorini JA, Eis-Hubinger AM, Hughes J, Mietzsch M, Modha S, Ogliastro M, Pénzes JJ, Pintel DJ, Qiu J, Soderlund-Venermo M, Tattersall P, Tijssen P, Ictv Report Consortium. 2019 Mar. ICTV Virus Taxonomy Profile: Parvoviridae. The Journal of general virology 100:367-368
  52. Rezelj VV, Mottram TJ, Hughes J, Elliott RM, Kohl A, Brennan B. 2019 Mar 15. M Segment-Based Minigenomes and Virus-Like Particle Assays as an Approach To Assess the Potential of Tick-Borne <i>Phlebovirus</i> Genome Reassortment. Journal of virology 93:
  53. Callaway HM, Subramanian S, Urbina CA, Barnard KN, Dick RA, Bator CM, Hafenstein SL, Gifford RJ, Parrish CR. 2019 Mar 15. Examination and Reconstruction of Three Ancient Endogenous Parvovirus Capsid Protein Gene Remnants Found in Rodent Genomes. Journal of virology 93:
  54. Dennis TPW, de Souza WM, Marsile-Medun S, Singer JB, Wilson SJ, Gifford RJ. 2019 Mar. The evolution, distribution and diversity of endogenous circoviral elements in vertebrate genomes. Virus research 262:15-23
  55. Pénzes JJ, Marsile-Medun S, Agbandje-McKenna M, Gifford RJ. 2018 Jul. Endogenous amdoparvovirus-related elements reveal insights into the biology and evolution of vertebrate parvoviruses. Virus evolution 4:vey026
  56. Zhu H, Gifford RJ, Murcia PR. 2018 Dec 1. Distribution, Diversity, and Evolution of Endogenous Retroviruses in Perissodactyl Genomes. Journal of virology 92:
  57. Gifford RJ, Blomberg J, Coffin JM, Fan H, Heidmann T, Mayer J, Stoye J, Tristem M, Johnson WE. 2018 Aug 28. Nomenclature for endogenous retrovirus (ERV) loci. Retrovirology 15:59
  58. Cowton VM, Singer JB, Gifford RJ, Patel AH. 2018. Predicting the Effectiveness of Hepatitis C Virus Neutralizing Antibodies by Bioinformatic Analysis of Conserved Epitope Residues Using Public Sequence Data. Frontiers in immunology 9:1470
  59. Dennis TPW, Flynn PJ, de Souza WM, Singer JB, Moreau CS, Wilson SJ, Gifford RJ. 2018 Aug 15. Insights into Circovirus Host Range from the Genomic Fossil Record. Journal of virology 92:
  60. Donald CL, Varjak M, Aguiar ERGR, Marques JT, Sreenu VB, Schnettler E, Kohl A. 2018 Dec 6. Antiviral RNA Interference Activity in Cells of the Predatory Mosquito, <i>Toxorhynchites amboinensis</i>. Viruses 10:
  61. Blanco-Melo D, Gifford RJ, Bieniasz PD. 2018 May 2. Reconstruction of a replication-competent ancestral murine endogenous retrovirus-L. Retrovirology 15:34
  62. Masembe C, Sreenu VB, Da Silva Filipe A, Wilkie GS, Ogweng P, Mayega FJ, Muwanika VB, Biek R, Palmarini M, Davison AJ. 2018 Oct. Genome Sequences of Five African Swine Fever Virus Genotype IX Isolates from Domestic Pigs in Uganda. Microbiology resource announcements 7:
  63. Hron T, Farkašová H, Gifford RJ, Benda P, Hulva P, Görföl T, Pačes J, Elleder D. 2018 Apr 10. Remnants of an Ancient Deltaretrovirus in the Genomes of Horseshoe Bats (Rhinolophidae). Viruses 10:
  64. Gu Q, Veselkov K. 2018 Dec 1. Bi-clustering of metabolic data using matrix factorization tools. Methods (San Diego, Calif.) 151:12-20
  65. Franzke K, Leggewie M, Sreenu VB, Jansen S, Heitmann A, Welch SR, Brennan B, Elliott RM, Tannich E, Becker SC, Schnettler E. 2018 Dec. Detection, infection dynamics and small RNA response against Culex Y virus in mosquito-derived cells. The Journal of general virology 99:1739-1745
  66. Varjak M, Dietrich I, Sreenu VB, Till BE, Merits A, Kohl A, Schnettler E. 2018 Feb 18. Spindle-E Acts Antivirally Against Alphaviruses in Mosquito Cells. Viruses 10:
  67. Singer JB, Thomson EC, McLauchlan J, Hughes J, Gifford RJ. 2018 Dec 18. GLUE: a flexible software system for virus sequence data. BMC bioinformatics 19:532
  68. Mercuri L, Thomson EC, Hughes J, Karayiannis P. 2018. Quasispecies Changes with Distinctive Point Mutations in the Hepatitis C Virus Internal Ribosome Entry Site (IRES) Derived from PBMCs and Plasma. Advances in virology 2018:4835252
  69. Babayan SA, Orton RJ, Streicker DG. 2018 Nov 2. Predicting reservoir hosts and arthropod vectors from evolutionary signatures in RNA virus genomes. Science (New York, N.Y.) 362:577-580
  70. Becker DJ, Bergner LM, Bentz AB, Orton RJ, Altizer S, Streicker DG. 2018 Sep. Genetic diversity, infection prevalence, and possible transmission routes of Bartonella spp. in vampire bats. PLoS neglected tropical diseases 12:e0006786
  71. Davis C, Mgomella GS, da Silva Filipe A, 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. 2019 Apr. Highly Diverse Hepatitis C Strains Detected in Sub-Saharan Africa Have Unknown Susceptibility to Direct-Acting Antiviral Treatments. Hepatology (Baltimore, Md.) 69:1426-1441
  72. 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. 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
  73. Maia FGM, de Souza WM, Sabino-Santos G Jr, Fumagalli MJ, Modha S, Murcia PR, Figueiredo LTM. 2018 Oct. A novel polyomavirus in sigmodontine rodents from São Paulo State, Brazil. Archives of virology 163:2913-2915
  74. 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
  75. 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:
  76. 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
  77. 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
  78. 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
  79. 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 Apr. 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 68:864-866
  80. 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
  81. 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
  82. 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
  83. 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
  84. 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
  85. 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:
  86. 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
  87. 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
  88. 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:
  89. 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
  90. 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:
  91. Davison AJ. 2017 Jan. Journal of General Virology – Introduction to ‘ICTV Virus Taxonomy Profiles’. The Journal of general virology 98:1
  92. 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
  93. Souza WM, Romeiro MF, Fumagalli MJ, Modha S, de Araujo J, Queiroz LH, Durigon EL, Figueiredo LTM, 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
  94. 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
  95. 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
  96. 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:
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  157. 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
  158. Rihn SJ, Hughes J, Wilson SJ, Bieniasz PD. 2015 Jan. Uneven genetic robustness of HIV-1 integrase. Journal of virology 89:552-67
  159. 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
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  161. 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
  162. 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:
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  164. 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
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  171. 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
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  182. Gatherer D, Galpin V. 2013 Nov 17. Rosen’s (M,R) system in process algebra. BMC systems biology 7:128
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  193. Kaján GL, Davison AJ, Palya V, Harrach B, Benkő M. 2012 Nov. Genome sequence of a waterfowl aviadenovirus, goose adenovirus 4. The Journal of general virology 93:2457-2465
  194. 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
  195. 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
  196. 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
  197. 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 93:1046-1058
  198. 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
  199. 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
  200. 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
  201. 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
  202. 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
  203. 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
  204. 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
  205. Davison AJ. 2011 Aug. Evolution of sexually transmitted and sexually transmissible human herpesviruses. Annals of the New York Academy of Sciences 1230:E37-49
  206. 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
  207. 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
  208. 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
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  210. Gatherer D. 2010 Oct. The Little Ice Age and the emergence of influenza A. Medical hypotheses 75:359-62
  211. 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