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Prisoners of war - host adaptation and its constraints on virus evolution.

Simmonds P, Aiewsakun P, Katzourakis A.

Nat Rev Microbiol. 2018 Dec 5. doi: 10.1038/s41579-018-0120-2. [Epub ahead of print] Review.


Human Endogenous Retrovirus-K HML-2 integration within RASGRF2 is associated with intravenous drug abuse and modulates transcription in a cell-line model.

Karamitros T, Hurst T, Marchi E, Karamichali E, Georgopoulou U, Mentis A, Riepsaame J, Lin A, Paraskevis D, Hatzakis A, McLauchlan J, Katzourakis A, Magiorkinis G.

Proc Natl Acad Sci U S A. 2018 Oct 9;115(41):10434-10439. doi: 10.1073/pnas.1811940115. Epub 2018 Sep 24.


Cell-Derived Viral Genes Evolve under Stronger Purifying Selection in Rhadinoviruses.

Aswad A, Katzourakis A.

J Virol. 2018 Sep 12;92(19). pii: e00359-18. doi: 10.1128/JVI.00359-18. Print 2018 Oct 1.


Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat.

Zepeda Mendoza ML, Xiong Z, Escalera-Zamudio M, Runge AK, Thézé J, Streicker D, Frank HK, Loza-Rubio E, Liu S, Ryder OA, Samaniego Castruita JA, Katzourakis A, Pacheco G, Taboada B, Löber U, Pybus OG, Li Y, Rojas-Anaya E, Bohmann K, Carmona Baez A, Arias CF, Liu S, Greenwood AD, Bertelsen MF, White NE, Bunce M, Zhang G, Sicheritz-Pontén T, Gilbert MPT.

Nat Ecol Evol. 2018 Apr;2(4):659-668. doi: 10.1038/s41559-018-0476-8. Epub 2018 Feb 19.


Molecular epidemiology reveals the role of war in the spread of HIV in Ukraine.

Vasylyeva TI, Liulchuk M, Friedman SR, Sazonova I, Faria NR, Katzourakis A, Babii N, Scherbinska A, Thézé J, Pybus OG, Smyrnov P, Mbisa JL, Paraskevis D, Hatzakis A, Magiorkinis G.

Proc Natl Acad Sci U S A. 2018 Jan 30;115(5):1051-1056. doi: 10.1073/pnas.1701447115. Epub 2018 Jan 16.


Roles of Endogenous Retroviruses in Early Life Events.

Magiorkinis G, Katzourakis A, Lagiou P.

Trends Microbiol. 2017 Nov;25(11):876-877. doi: 10.1016/j.tim.2017.09.002. Epub 2017 Sep 29.


STEAK: A specific tool for transposable elements and retrovirus detection in high-throughput sequencing data.

Santander CG, Gambron P, Marchi E, Karamitros T, Katzourakis A, Magiorkinis G.

Virus Evol. 2017 Aug 21;3(2):vex023. doi: 10.1093/ve/vex023. eCollection 2017 Jul.


Editorial overview: Paleovirology: the genomic fossil record, and consequences of ancient viral infections.

Katzourakis A.

Curr Opin Virol. 2017 Aug;25:ix-xi. doi: 10.1016/j.coviro.2017.08.002. Epub 2017 Sep 1. No abstract available.


Disentangling the origins of virophages and polintons.

Campbell S, Aswad A, Katzourakis A.

Curr Opin Virol. 2017 Aug;25:59-65. doi: 10.1016/j.coviro.2017.07.011. Epub 2017 Aug 9. Review.


A novel viral lineage distantly related to herpesviruses discovered within fish genome sequence data.

Aswad A, Katzourakis A.

Virus Evol. 2017 Aug 4;3(2):vex016. doi: 10.1093/ve/vex016. eCollection 2017 Jul.


Marine origin of retroviruses in the early Palaeozoic Era.

Aiewsakun P, Katzourakis A.

Nat Commun. 2017 Jan 10;8:13954. doi: 10.1038/ncomms13954.


Reducing HIV infection in people who inject drugs is impossible without targeting recently-infected subjects.

Vasylyeva TI, Friedman SR, Lourenco J, Gupta S, Hatzakis A, Pybus OG, Katzourakis A, Smyrnov P, Karamitros T, Paraskevis D, Magiorkinis G.

AIDS. 2016 Nov 28;30(18):2885-2890.


A contaminant-free assessment of Endogenous Retroviral RNA in human plasma.

Karamitros T, Paraskevis D, Hatzakis A, Psichogiou M, Elefsiniotis I, Hurst T, Geretti AM, Beloukas A, Frater J, Klenerman P, Katzourakis A, Magiorkinis G.

Sci Rep. 2016 Sep 19;6:33598. doi: 10.1038/srep33598.


De Novo Assembly of Human Herpes Virus Type 1 (HHV-1) Genome, Mining of Non-Canonical Structures and Detection of Novel Drug-Resistance Mutations Using Short- and Long-Read Next Generation Sequencing Technologies.

Karamitros T, Harrison I, Piorkowska R, Katzourakis A, Magiorkinis G, Mbisa JL.

PLoS One. 2016 Jun 16;11(6):e0157600. doi: 10.1371/journal.pone.0157600. eCollection 2016.


Phylogenetic Analysis Reveals That ERVs "Die Young" but HERV-H Is Unusually Conserved.

Gemmell P, Hein J, Katzourakis A.

PLoS Comput Biol. 2016 Jun 13;12(6):e1004964. doi: 10.1371/journal.pcbi.1004964. eCollection 2016 Jun.


The global spread of HIV-1 subtype B epidemic.

Magiorkinis G, Angelis K, Mamais I, Katzourakis A, Hatzakis A, Albert J, Lawyer G, Hamouda O, Struck D, Vercauteren J, Wensing A, Alexiev I, Åsjö B, Balotta C, Gomes P, Camacho RJ, Coughlan S, Griskevicius A, Grossman Z, Horban A, Kostrikis LG, Lepej SJ, Liitsola K, Linka M, Nielsen C, Otelea D, Paredes R, Poljak M, Puchhammer-Stöckl E, Schmit JC, Sönnerborg A, Staneková D, Stanojevic M, Stylianou DC, Boucher CAB; SPREAD program, Nikolopoulos G, Vasylyeva T, Friedman SR, van de Vijver D, Angarano G, Chaix ML, de Luca A, Korn K, Loveday C, Soriano V, Yerly S, Zazzi M, Vandamme AM, Paraskevis D.

Infect Genet Evol. 2016 Dec;46:169-179. doi: 10.1016/j.meegid.2016.05.041. Epub 2016 Jun 2.


Time-Dependent Rate Phenomenon in Viruses.

Aiewsakun P, Katzourakis A.

J Virol. 2016 Jul 27;90(16):7184-95. doi: 10.1128/JVI.00593-16. Print 2016 Aug 15.


Evolution: Endogenous Viruses Provide Shortcuts in Antiviral Immunity.

Katzourakis A, Aswad A.

Curr Biol. 2016 May 23;26(10):R427-9. doi: 10.1016/j.cub.2016.03.072.


Human endogenous retrovirus (HERV) expression is not induced by treatment with the histone deacetylase (HDAC) inhibitors in cellular models of HIV-1 latency.

Hurst T, Pace M, Katzourakis A, Phillips R, Klenerman P, Frater J, Magiorkinis G.

Retrovirology. 2016 Feb 6;13:10. doi: 10.1186/s12977-016-0242-4.


Wide distribution and ancient evolutionary history of simian foamy viruses in New World primates.

Ghersi BM, Jia H, Aiewsakun P, Katzourakis A, Mendoza P, Bausch DG, Kasper MR, Montgomery JM, Switzer WM.

Retrovirology. 2015 Oct 29;12:89. doi: 10.1186/s12977-015-0214-0.


Convergent capture of retroviral superantigens by mammalian herpesviruses.

Aswad A, Katzourakis A.

Nat Commun. 2015 Sep 24;6:8299. doi: 10.1038/ncomms9299.


Endogenous retroviruses.

Hayward A, Katzourakis A.

Curr Biol. 2015 Aug 3;25(15):R644-6. doi: 10.1016/j.cub.2015.05.041.


Time dependency of foamy virus evolutionary rate estimates.

Aiewsakun P, Katzourakis A.

BMC Evol Biol. 2015 Jun 26;15:119. doi: 10.1186/s12862-015-0408-z.


Orthologous endogenous retroviruses exhibit directional selection since the chimp-human split.

Gemmell P, Hein J, Katzourakis A.

Retrovirology. 2015 Jun 20;12:52. doi: 10.1186/s12977-015-0172-6.


HIV-infected sex workers with beneficial HLA-variants are potential hubs for selection of HIV-1 recombinants that may affect disease progression.

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.

Sci Rep. 2015 Jun 17;5:11253. doi: 10.1038/srep11253.


Endogenous viruses: Connecting recent and ancient viral evolution.

Aiewsakun P, Katzourakis A.

Virology. 2015 May;479-480:26-37. doi: 10.1016/j.virol.2015.02.011. Epub 2015 Mar 12. Review.


The origins of giant viruses, virophages and their relatives in host genomes.

Katzourakis A, Aswad A.

BMC Biol. 2014 Jun 30;12:51. doi: 10.1186/s12915-014-0051-y.


Discovery of prosimian and afrotherian foamy viruses and potential cross species transmissions amidst stable and ancient mammalian co-evolution.

Katzourakis A, Aiewsakun P, Jia H, Wolfe ND, LeBreton M, Yoder AD, Switzer WM.

Retrovirology. 2014 Aug 4;11:61. doi: 10.1186/1742-4690-11-61.


Larger mammalian body size leads to lower retroviral activity.

Katzourakis A, Magiorkinis G, Lim AG, Gupta S, Belshaw R, Gifford R.

PLoS Pathog. 2014 Jul 17;10(7):e1004214. doi: 10.1371/journal.ppat.1004214. eCollection 2014 Jul.


The first endogenous herpesvirus, identified in the tarsier genome, and novel sequences from primate rhadinoviruses and lymphocryptoviruses.

Aswad A, Katzourakis A.

PLoS Genet. 2014 Jun 19;10(6):e1004332. doi: 10.1371/journal.pgen.1004332. eCollection 2014 Jun.


Sex-specific aspects of endogenous retroviral insertion and deletion.

Gemmell P, Hein J, Katzourakis A.

BMC Evol Biol. 2013 Nov 7;13:243. doi: 10.1186/1471-2148-13-243.


'There and back again': revisiting the pathophysiological roles of human endogenous retroviruses in the post-genomic era.

Magiorkinis G, Belshaw R, Katzourakis A.

Philos Trans R Soc Lond B Biol Sci. 2013 Aug 12;368(1626):20120504. doi: 10.1098/rstb.2012.0504. Print 2013 Sep 19. Review.


Paleovirology: inferring viral evolution from host genome sequence data.

Katzourakis A.

Philos Trans R Soc Lond B Biol Sci. 2013 Aug 12;368(1626):20120493. doi: 10.1098/rstb.2012.0493. Print 2013 Sep 19. No abstract available.


Paleovirology and virally derived immunity.

Aswad A, Katzourakis A.

Trends Ecol Evol. 2012 Nov;27(11):627-36. doi: 10.1016/j.tree.2012.07.007. Epub 2012 Aug 14. Review.


Env-less endogenous retroviruses are genomic superspreaders.

Magiorkinis G, Gifford RJ, Katzourakis A, De Ranter J, Belshaw R.

Proc Natl Acad Sci U S A. 2012 May 8;109(19):7385-90. doi: 10.1073/pnas.1200913109. Epub 2012 Apr 23.


Phylogenetic analysis of murine leukemia virus sequences from longitudinally sampled chronic fatigue syndrome patients suggests PCR contamination rather than viral evolution.

Katzourakis A, Hué S, Kellam P, Towers GJ.

J Virol. 2011 Oct;85(20):10909-13. doi: 10.1128/JVI.00827-11. Epub 2011 Aug 17.


Phylogenetic analysis consistent with a clinical history of sexual transmission of HIV-1 from a single donor reveals transmission of highly distinct variants.

English S, Katzourakis A, Bonsall D, Flanagan P, Duda A, Fidler S, Weber J, McClure M; SPARTAC Trial Investigators, Phillips R, Frater J.

Retrovirology. 2011 Jul 7;8:54. doi: 10.1186/1742-4690-8-54.


The mode and tempo of hepatitis C virus evolution within and among hosts.

Gray RR, Parker J, Lemey P, Salemi M, Katzourakis A, Pybus OG.

BMC Evol Biol. 2011 May 19;11:131. doi: 10.1186/1471-2148-11-131.


Disease-associated XMRV sequences are consistent with laboratory contamination.

Hué S, Gray ER, Gall A, Katzourakis A, Tan CP, Houldcroft CJ, McLaren S, Pillay D, Futreal A, Garson JA, Pybus OG, Kellam P, Towers GJ.

Retrovirology. 2010 Dec 20;7(1):111. doi: 10.1186/1742-4690-7-111.


Endogenous viral elements in animal genomes.

Katzourakis A, Gifford RJ.

PLoS Genet. 2010 Nov 18;6(11):e1001191. doi: 10.1371/journal.pgen.1001191.


B-cell depletion reveals a role for antibodies in the control of chronic HIV-1 infection.

Huang KH, Bonsall D, Katzourakis A, Thomson EC, Fidler SJ, Main J, Muir D, Weber JN, Frater AJ, Phillips RE, Pybus OG, Goulder PJ, McClure MO, Cooke GS, Klenerman P.

Nat Commun. 2010 Oct 19;1:102. doi: 10.1038/ncomms1100.


Structural and functional analysis of prehistoric lentiviruses uncovers an ancient molecular interface.

Goldstone DC, Yap MW, Robertson LE, Haire LF, Taylor WR, Katzourakis A, Stoye JP, Taylor IA.

Cell Host Microbe. 2010 Sep 16;8(3):248-59. doi: 10.1016/j.chom.2010.08.006.


Prevalence of HIV type-1 drug-associated mutations in pre-therapy patients in the Free State, South Africa.

Huang KH, Goedhals D, Fryer H, van Vuuren C, Katzourakis A, De Oliveira T, Brown H, Cassol S, Seebregts C, McLean A, Klenerman P, Phillips R, Frater J; Bloemfontein-Oxford Collaborative Group.

Antivir Ther. 2009;14(7):975-84. doi: 10.3851/IMP1416.


Macroevolution of complex retroviruses.

Katzourakis A, Gifford RJ, Tristem M, Gilbert MT, Pybus OG.

Science. 2009 Sep 18;325(5947):1512. doi: 10.1126/science.1174149.


Detecting natural selection in RNA virus populations using sequence summary statistics.

Bhatt S, Katzourakis A, Pybus OG.

Infect Genet Evol. 2010 Apr;10(3):421-30. doi: 10.1016/j.meegid.2009.06.001. Epub 2009 Jun 11.


HLA footprints on human immunodeficiency virus type 1 are associated with interclade polymorphisms and intraclade phylogenetic clustering.

Matthews PC, Leslie AJ, Katzourakis A, Crawford H, Payne R, Prendergast A, Power K, Kelleher AD, Klenerman P, Carlson J, Heckerman D, Ndung'u T, Walker BD, Allen TM, Pybus OG, Goulder PJ.

J Virol. 2009 May;83(9):4605-15. doi: 10.1128/JVI.02017-08. Epub 2009 Feb 25. Erratum in: J Virol. 2011 May;85(9):4635.


Ancient, independent evolution and distinct molecular features of the novel human T-lymphotropic virus type 4.

Switzer WM, Salemi M, Qari SH, Jia H, Gray RR, Katzourakis A, Marriott SJ, Pryor KN, Wolfe ND, Burke DS, Folks TM, Heneine W.

Retrovirology. 2009 Feb 2;6:9. doi: 10.1186/1742-4690-6-9.


A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution.

Gifford RJ, Katzourakis A, Tristem M, Pybus OG, Winters M, Shafer RW.

Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20362-7. doi: 10.1073/pnas.0807873105. Epub 2008 Dec 15.


Identification of a RELIK orthologue in the European hare (Lepus europaeus) reveals a minimum age of 12 million years for the lagomorph lentiviruses.

Keckesova Z, Ylinen LM, Towers GJ, Gifford RJ, Katzourakis A.

Virology. 2009 Feb 5;384(1):7-11. doi: 10.1016/j.virol.2008.10.045. Epub 2008 Dec 13.


Conserved footprints of APOBEC3G on Hypermutated human immunodeficiency virus type 1 and human endogenous retrovirus HERV-K(HML2) sequences.

Armitage AE, Katzourakis A, de Oliveira T, Welch JJ, Belshaw R, Bishop KN, Kramer B, McMichael AJ, Rambaut A, Iversen AK.

J Virol. 2008 Sep;82(17):8743-61. doi: 10.1128/JVI.00584-08. Epub 2008 Jun 18.

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