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Items: 45

1.

Examination and reconstruction of three ancient endogenous parvovirus capsid protein gene remnants found in rodent genomes.

Callaway HM, Subramanian S, Urbina C, Barnard K, Dick R, Bator CM, Hafentein SL, Gifford RJ, Parrish CR.

J Virol. 2019 Jan 9. pii: JVI.01542-18. doi: 10.1128/JVI.01542-18. [Epub ahead of print]

PMID:
30626673
2.

GLUE: a flexible software system for virus sequence data.

Singer JB, Thomson EC, McLauchlan J, Hughes J, Gifford RJ.

BMC Bioinformatics. 2018 Dec 18;19(1):532. doi: 10.1186/s12859-018-2459-9.

3.

Endogenous amdoparvovirus-related elements reveal insights into the biology and evolution of vertebrate parvoviruses.

Pénzes JJ, Marsile-Medun S, Agbandje-McKenna M, Gifford RJ.

Virus Evol. 2018 Nov 12;4(2):vey026. doi: 10.1093/ve/vey026. eCollection 2018 Jul.

4.

Distribution, Diversity, and Evolution of Endogenous Retroviruses in Perissodactyl Genomes.

Zhu H, Gifford RJ, Murcia PR.

J Virol. 2018 Nov 12;92(23). pii: e00927-18. doi: 10.1128/JVI.00927-18. Print 2018 Dec 1.

PMID:
30209175
5.

Nomenclature for endogenous retrovirus (ERV) loci.

Gifford RJ, Blomberg J, Coffin JM, Fan H, Heidmann T, Mayer J, Stoye J, Tristem M, Johnson WE.

Retrovirology. 2018 Aug 28;15(1):59. doi: 10.1186/s12977-018-0442-1. Review.

6.

Predicting the Effectiveness of Hepatitis C Virus Neutralizing Antibodies by Bioinformatic Analysis of Conserved Epitope Residues Using Public Sequence Data.

Cowton VM, Singer JB, Gifford RJ, Patel AH.

Front Immunol. 2018 Jun 27;9:1470. doi: 10.3389/fimmu.2018.01470. eCollection 2018.

7.

Insights into Circovirus Host Range from the Genomic Fossil Record.

Dennis TPW, Flynn PJ, de Souza WM, Singer JB, Moreau CS, Wilson SJ, Gifford RJ.

J Virol. 2018 Jul 31;92(16). pii: e00145-18. doi: 10.1128/JVI.00145-18. Print 2018 Aug 15.

8.

Reconstruction of a replication-competent ancestral murine endogenous retrovirus-L.

Blanco-Melo D, Gifford RJ, Bieniasz PD.

Retrovirology. 2018 May 2;15(1):34. doi: 10.1186/s12977-018-0416-3.

9.

Remnants of an Ancient Deltaretrovirus in the Genomes of Horseshoe Bats (Rhinolophidae).

Hron T, Farkašová H, Gifford RJ, Benda P, Hulva P, Görföl T, Pačes J, Elleder D.

Viruses. 2018 Apr 10;10(4). pii: E185. doi: 10.3390/v10040185.

10.

The evolution, distribution and diversity of endogenous circoviral elements in vertebrate genomes.

Dennis TPW, de Souza WM, Marsile-Medun S, Singer JB, Wilson SJ, Gifford RJ.

Virus Res. 2019 Mar;262:15-23. doi: 10.1016/j.virusres.2018.03.014. Epub 2018 Mar 27.

11.

Novel Parvoviruses from Wild and Domestic Animals in Brazil Provide New Insights into Parvovirus Distribution and Diversity.

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.

Viruses. 2018 Mar 22;10(4). pii: E143. doi: 10.3390/v10040143.

12.

Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses.

Shaw AE, Hughes J, Gu Q, Behdenna A, Singer JB, Dennis T, Orton RJ, Varela M, Gifford RJ, Wilson SJ, Palmarini M.

PLoS Biol. 2017 Dec 18;15(12):e2004086. doi: 10.1371/journal.pbio.2004086. eCollection 2017 Dec.

13.

Hepatitis C and the absence of genomic data in low-income countries: a barrier on the road to elimination?

Niebel M, Singer JB, Nickbakhsh S, Gifford RJ, Thomson EC.

Lancet Gastroenterol Hepatol. 2017 Oct;2(10):700-701. doi: 10.1016/S2468-1253(17)30257-1. No abstract available.

PMID:
28895545
14.

A14 Comprehensive characterisation and evolutionary analysis of endogenous retroviruses in the mouse genome.

Dennis TPW, Zhu H, Wilson SJ, Gifford RJ.

Virus Evol. 2017 Mar 5;3(Suppl 1). pii: vew036.013. doi: 10.1093/ve/vew036.013. eCollection 2017 Mar. No abstract available.

15.

Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors.

Blanco-Melo D, Gifford RJ, Bieniasz PD.

Elife. 2017 Apr 11;6. pii: e22519. doi: 10.7554/eLife.22519.

16.

Chapparvoviruses occur in at least three vertebrate classes and have a broad biogeographic distribution.

Souza WM, Romeiro MF, Fumagalli MJ, Modha S, de Araujo J, Queiroz LH, Durigon EL, Figueiredo LT, Murcia PR, Gifford RJ.

J Gen Virol. 2017 Feb;98(2):225-229. doi: 10.1099/jgv.0.000671.

17.

Discovery of an endogenous Deltaretrovirus in the genome of long-fingered bats (Chiroptera: Miniopteridae).

Farkašová H, Hron T, Pačes J, Hulva P, Benda P, Gifford RJ, Elleder D.

Proc Natl Acad Sci U S A. 2017 Mar 21;114(12):3145-3150. doi: 10.1073/pnas.1621224114. Epub 2017 Mar 9.

18.

An Intact Retroviral Gene Conserved in Spiny-Rayed Fishes for over 100 My.

Henzy JE, Gifford RJ, Kenaley CP, Johnson WE.

Mol Biol Evol. 2017 Mar 1;34(3):634-639. doi: 10.1093/molbev/msw262.

19.

Late Ebola virus relapse causing meningoencephalitis: a case report.

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.

Lancet. 2016 Jul 30;388(10043):498-503. doi: 10.1016/S0140-6736(16)30386-5. Epub 2016 May 18.

20.

Identification and spontaneous immune targeting of an endogenous retrovirus K envelope protein in the Indian rhesus macaque model of human disease.

Wu HL, Léon EJ, Wallace LT, Nimiyongskul FA, Buechler MB, Newman LP, Castrovinci PA, Paul Johnson R, Gifford RJ, Brad Jones R, Sacha JB.

Retrovirology. 2016 Jan 15;13:6. doi: 10.1186/s12977-016-0238-0.

21.

Filovirus receptor NPC1 contributes to species-specific patterns of ebolavirus susceptibility in bats.

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.

Elife. 2015 Dec 23;4. pii: e11785. doi: 10.7554/eLife.11785.

22.

Parvovirus-derived endogenous viral elements in two South American rodent genomes.

Arriagada G, Gifford RJ.

J Virol. 2014 Oct;88(20):12158-62. doi: 10.1128/JVI.01173-14. Epub 2014 Jul 30.

23.

A novel recombinant retrovirus in the genomes of modern birds combines features of avian and mammalian retroviruses.

Henzy JE, Gifford RJ, Johnson WE, Coffin JM.

J Virol. 2014 Mar;88(5):2398-405. doi: 10.1128/JVI.02863-13. Epub 2013 Dec 18.

24.

The extraordinary evolutionary history of the reticuloendotheliosis viruses.

Niewiadomska AM, Gifford RJ.

PLoS Biol. 2013;11(8):e1001642. doi: 10.1371/journal.pbio.1001642. Epub 2013 Aug 27.

25.

Extreme genetic fragility of the HIV-1 capsid.

Rihn SJ, Wilson SJ, Loman NJ, Alim M, Bakker SE, Bhella D, Gifford RJ, Rixon FJ, Bieniasz PD.

PLoS Pathog. 2013;9(6):e1003461. doi: 10.1371/journal.ppat.1003461. Epub 2013 Jun 20.

26.

Characterisation of a group of endogenous gammaretroviruses in the canine genome.

Tarlinton RE, Barfoot HK, Allen CE, Brown K, Gifford RJ, Emes RD.

Vet J. 2013 Apr;196(1):28-33. doi: 10.1016/j.tvjl.2012.08.011. Epub 2012 Sep 27.

27.

Vaccination with cancer- and HIV infection-associated endogenous retrotransposable elements is safe and immunogenic.

Sacha JB, Kim IJ, Chen L, Ullah JH, Goodwin DA, Simmons HA, Schenkman DI, von Pelchrzim F, Gifford RJ, Nimityongskul FA, Newman LP, Wildeboer S, Lappin PB, Hammond D, Castrovinci P, Piaskowski SM, Reed JS, Beheler KA, Tharmanathan T, Zhang N, Muscat-King S, Rieger M, Fernandes C, Rumpel K, Gardner JP 2nd, Gebhard DH, Janies J, Shoieb A, Pierce BG, Trajkovic D, Rakasz E, Rong S, McCluskie M, Christy C, Merson JR, Jones RB, Nixon DF, Ostrowski MA, Loudon PT, Pruimboom-Brees IM, Sheppard NC.

J Immunol. 2012 Aug 1;189(3):1467-79. doi: 10.4049/jimmunol.1200079. Epub 2012 Jun 27.

28.

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.

29.

Viral evolution in deep time: lentiviruses and mammals.

Gifford RJ.

Trends Genet. 2012 Feb;28(2):89-100. doi: 10.1016/j.tig.2011.11.003. Epub 2011 Dec 22. Review.

PMID:
22197521
30.

No trespassing: ancient BST2 deletion confers protection against simian immunodeficiency virus infection of humans.

Gifford RJ.

Hum Mutat. 2011 Nov;32(11):v. doi: 10.1002/humu.21619. No abstract available.

PMID:
22006663
31.

Endogenous viral elements in animal genomes.

Katzourakis A, Gifford RJ.

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

32.
33.

The HIV-1 subtype C epidemic in South America is linked to the United Kingdom.

de Oliveira T, Pillay D, Gifford RJ; UK Collaborative Group on HIV Drug Resistance.

PLoS One. 2010 Feb 19;5(2):e9311. doi: 10.1371/journal.pone.0009311.

34.

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.

35.

The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance.

Gifford RJ, Liu TF, Rhee SY, Kiuchi M, Hue S, Pillay D, Shafer RW.

Bioinformatics. 2009 May 1;25(9):1197-8. doi: 10.1093/bioinformatics/btp134. Epub 2009 Mar 20.

36.

Demonstration of sustained drug-resistant human immunodeficiency virus type 1 lineages circulating among treatment-naïve individuals.

Hué S, Gifford RJ, Dunn D, Fernhill E, Pillay D; UK Collaborative Group on HIV Drug Resistance.

J Virol. 2009 Mar;83(6):2645-54. doi: 10.1128/JVI.01556-08. Epub 2009 Jan 21.

37.

Phylogenetic reconstruction of transmission events from individuals with acute HIV infection: toward more-rigorous epidemiological definitions.

Brown AE, Gifford RJ, Clewley JP, Kucherer C, Masquelier B, Porter K, Balotta C, Back NK, Jorgensen LB, de Mendoza C, Bhaskaran K, Gill ON, Johnson AM, Pillay D; Concerted Action on Seroconversion to AIDS and Death in Europe (CASCADE) Collaboration.

J Infect Dis. 2009 Feb 1;199(3):427-31. doi: 10.1086/596049.

PMID:
19133810
38.

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.

39.

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.

40.

Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors.

Rhee SY, Liu TF, Kiuchi M, Zioni R, Gifford RJ, Holmes SP, Shafer RW.

Retrovirology. 2008 Aug 7;5:74. doi: 10.1186/1742-4690-5-74.

41.

Sequence editing by Apolipoprotein B RNA-editing catalytic component [corrected] and epidemiological surveillance of transmitted HIV-1 drug resistance.

Gifford RJ, Rhee SY, Eriksson N, Liu TF, Kiuchi M, Das AK, Shafer RW.

AIDS. 2008 Mar 30;22(6):717-25. doi: 10.1097/QAD.0b013e3282f5e07a. Erratum in: AIDS. 2008 Oct 18;22(16):2225.

42.

Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1.

Gifford RJ, de Oliveira T, Rambaut A, Pybus OG, Dunn D, Vandamme AM, Kellam P, Pillay D; UK Collaborative Group on HIV Drug Resistance.

J Virol. 2007 Dec;81(23):13050-6. Epub 2007 Sep 26.

43.

Discovery and analysis of the first endogenous lentivirus.

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

Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6261-5. Epub 2007 Mar 23.

44.

Evolution at the host-retrovirus interface.

Gifford RJ.

Bioessays. 2006 Dec;28(12):1153-6. Review.

PMID:
17117481
45.

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