Dr Robert Gifford

Affiliate (School of Infection & Immunity)

MRC-University of Glasgow Centre for Virus Research (CVR), Garscube Campus,, Sir Michael Stoker Building, 464 Bearsden Road

Import to contacts

https://orcid.org/0000-0003-4028-9884

Biography

I study virus evolution - the problems and opportunities that it creates.

Research interests

My research addresses general themes in virus evolution.

I develop computational tools and methods for studying virus evolution.

I use these tools and methods to conduct my research.

My research has addressed a diverse range of viruses including retroviruses, filoviruses, parvoviruses and rhabdoviruses, to name a few.

Publications

List by: Type | Date

Jump to: 2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2009 | 2008

Number of items: 57.

2024

Blanco-Melo, D., Campbell, M. A., Zhu, H., Dennis, T. P., Modha, S., Lytras, S., Hughes, J. , Gatseva, A. and Gifford, R. J. (2024) A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record. Genome Biology, (Accepted for Publication)

Blanco-Melo, D., Campbell, M. A., Zhu, H., Dennis, T. P. W., Modha, S. , Lytras, S., Hughes, J. , Gatseva, A. and Gifford, R. J. (2024) A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record. Genome Biology, (Accepted for Publication)

2023

Bautista, C., Jaswant, G., French, H., Campbell, K., Durrant, R. , Gifford, R. , Kia, G. S.N., Ogoti, B., Hampson, K. and Brunker, K. (2023) Whole genome sequencing for rapid characterization of rabies virus using nanopore technology. Journal of Visualized Experiments(191), e65414. (doi: 10.3791/65414) (PMID:37677046)

Bravo, A., Fernández-García, L., Ibarra-Karmy, R., Mardones, G. A., Mercado, L., Bustos, F. J., Gifford, R. J. and Arriagada, G. (2023) Antiviral activity of an endogenous parvoviral element. Viruses, 15(7), 1420. (doi: 10.3390/v15071420) (PMID:37515112) (PMCID:PMC10384997)

Oliver, M. R. , Toon, K. , Lewis, C. B., Devlin, S., Gifford, R. J. and Grove, J. (2023) Structures of the Hepaci-, Pegi-, and Pestiviruses envelope proteins suggest a novel membrane fusion mechanism. PLoS Biology, 21(7), e3002174. (doi: 10.1371/journal.pbio.3002174) (PMID:37432947) (PMCID:PMC10335668)

Carrozza, M.-L., Niewiadomska, A.-M., Mazzei, M., Abi-Said, M. R., Hue, S., Hughes, J. , Gatseva, A. and Gifford, R. J. (2023) Emergence and pandemic spread of small ruminant lentiviruses. Virus Evolution, 9(1), vead005. (doi: 10.1093/ve/vead005) (PMID:36793939) (PMCID:PMC9924038)

2022

Kambol, R., Gatseva, A. and Gifford, R. J. (2022) An endogenous lentivirus in the germline of a rodent. Retrovirology, 19, 30. (doi: 10.1186/s12977-022-00615-2) (PMID:36539757) (PMCID:PMC9768972)

Campbell, M. A., Loncar, S., Kotin, R. M. and Gifford, R. J. (2022) Comparative analysis reveals the long-term coevolutionary history of parvoviruses and vertebrates. PLoS Biology, 20(11), e3001867. (doi: 10.1371/journal.pbio.3001867) (PMID:36445931) (PMCID:PMC9707805)

Fernandes, L. P. et al. (2022) A satellite DNA array barcodes chromosome 7 and regulates totipotency via ZFP819. Science Advances, 8(43), eabp8085. (doi: 10.1126/sciadv.abp8085) (PMID:36306355) (PMCID:PMC9616502)

Shema Mugisha, C., Dinh, T., Kumar, A., Tenneti, K., Eschbach, J. E., Davis, K., Gifford, R. , Kvaratskhelia, M. and Kutluay, S. B. (2022) Emergence of compensatory mutations reveals the importance of electrostatic interactions between HIV-1 integrase and genomic RNA. mBio, 13(5), e0043122. (doi: 10.1128/mbio.00431-22) (PMID:35975921) (PMCID:PMC9601147)

Campbell, K., Gifford, R. J. , Singer, J., Hill, V., O'Toole, A., Rambaut, A., Hampson, K. and Brunker, K. (2022) Making genomic surveillance deliver: a lineage classification and nomenclature system to inform rabies elimination. PLoS Pathogens, 18(5), e1010023. (doi: 10.1371/journal.ppat.1010023) (PMID:35500026) (PMCID:PMC9162366)

Bamford, C. G.G., de Souza, W. M., Parry, R. and Gifford, R. J. (2022) Comparative analysis of genome-encoded viral sequences reveals the evolutionary history of flavivirids (family Flaviviridae). Virus Evolution, 8(2), veac085. (doi: 10.1093/ve/veac085) (PMID:36533146) (PMCID:PMC9752770)

2021

Zafferani, M. et al. (2021) Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures. Science Advances, 7(48), eabl6096. (doi: 10.1126/sciadv.abl6096) (PMID:34826236)

Parry, R., Gifford, R. J. , Lytras, S., Ray, S. C. and Coin, L. J.M. (2021) No evidence of SARS-CoV-2 reverse transcription and integration as the origin of chimeric transcripts in patient tissues. Proceedings of the National Academy of Sciences of the United States of America, 118(33), e2109066118. (doi: 10.1073/pnas.2109066118) (PMID:34344759)

Gifford, R. J. (2021) Mapping the evolution of bornaviruses across geological timescales. Proceedings of the National Academy of Sciences of the United States of America, 118(26), e2108123118. (doi: 10.1073/pnas.2108123118) (PMID:34088856) (PMCID:PMC8256053)

Lytras, S., Arriagada, G. and Gifford, R. J. (2021) Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes. Virus Evolution, 7(1), veab012. (doi: 10.1093/ve/veab012) (PMID:33747544) (PMCID:PMC7955980)

2020

Konno, Y. et al. (2020) SARS-CoV-2 ORF3b is a potent interferon antagonist whose activity is increased by a naturally occurring elongation variant. Cell Reports, 32(12), 108185. (doi: 10.1016/j.celrep.2020.108185) (PMID:32941788) (PMCID:PMC7473339)

Hildebrandt, E., Penzes, J. J., Gifford, R. J. , Agbandje-Mckenna, M. and Kotin, R. M. (2020) Evolution of dependoparvoviruses across geological timescales – implications for design of AAV-based gene therapy vectors. Virus Evolution, 6(2), veaa043. (doi: 10.1093/ve/veaa043) (PMID:32913662) (PMCID:PMC7474932)

Sook Yuin Ho, J. et al. (2020) Hybrid gene origination creates human-virus chimeric proteins during infection. Cell, 181(7), 1502-1517.e23. (doi: 10.1016/j.cell.2020.05.035) (PMID:32559462) (PMCID:PMC7323901)

Brunker, K. et al. (2020) Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes. Wellcome Open Research, 5, 3. (doi: 10.12688/wellcomeopenres.15518.2) (PMID:32090172) (PMCID:PMC7001756)

Ito, J., Gifford, R. J. and Sato, K. (2020) Retroviruses drive the rapid evolution of mammalian APOBEC3 genes. Proceedings of the National Academy of Sciences of the United States of America, 117(1), pp. 610-618. (doi: 10.1073/pnas.1914183116) (PMID:31843890) (PMCID:PMC6955324)

2019

Hron, T., Elleder, D. and Gifford, R. J. (2019) Deltaretroviruses infect a broad range of mammalian species and have circulated since the Paleogene. Retrovirology, 16, 33. (doi: 10.1186/s12977-019-0495-9) (PMID:31775783) (PMCID:PMC6882180)

Valencia-Herrera, I., Faunes, F., Cena-Ahumada, E., Ibarra-Karmy, R., Gifford, R. J. and Arriagada, G. (2019) Molecular properties and evolutionary origins of a parvovirus-derived myosin fusion gene in guinea pigs. Journal of Virology, 93(17), e00404-19. (doi: 10.1128/JVI.00404-19) (PMID:31217242)

Pénzes, J. J., de Souza, W. M., Agbandje-McKenna, M. and Gifford, R. J. (2019) An ancient lineage of highly divergent parvoviruses infects both vertebrate and invertebrate hosts. Viruses, 11(6), 525. (doi: 10.3390/v11060525) (PMID:31174309) (PMCID:PMC6631224)

Schmidt, F. et al. (2019) 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(21), pp. 10504-10509. (doi: 10.1073/pnas.1818059116) (PMID:31048506) (PMCID:PMC6535013)

Singer, J. B. et al. (2019) Interpreting viral deep sequencing data with GLUE. Viruses, 11(4), 323. (doi: 10.3390/v11040323) (PMID:30987147) (PMCID:PMC6520954)

Callaway, H. M., Subramanian, S., Urbina, C., Barnard, K., Dick, R., Bator, C. M., Hafentein, S. L., Gifford, R. J. and Parrish, C. R. (2019) Examination and reconstruction of three ancient endogenous parvovirus capsid protein gene remnants found in rodent genomes. Journal of Virology, 93(6), e01542-18. (doi: 10.1128/JVI.01542-18) (PMID:30626673) (PMCID:PMC6401472)

Halo, J. V., Pendleton, A. L., Jarosz, A. S., Gifford, R. J. , Day, M. L. and Kidd, J. M. (2019) Origin and recent expansion of an endogenous gammaretroviral lineage in domestic and wild canids. Retrovirology, 16, 6. (doi: 10.1186/s12977-019-0468-z) (PMID:30845962) (PMCID:PMC6407205)

Dennis, T. P.W., Souza, W. M. d., Marsile-Medun, S., Singer, J. B., Wilson, S. J. and Gifford, R. J. (2019) The evolution, distribution and diversity of endogenous circoviral elements in vertebrate genomes. Virus Research, 262, pp. 15-23. (doi: 10.1016/j.virusres.2018.03.014) (PMID:29601845) (PMCID:PMC6372831)

2018

Singer, J. B., Thomson, E. C. , McLauchlan, J. , Hughes, J. and Gifford, R. J. (2018) GLUE: a flexible software system for virus sequence data. BMC Bioinformatics, 19, 532. (doi: 10.1186/s12859-018-2459-9) (PMID:30563445) (PMCID:PMC6299651)

Zhu, H., Gifford, R. and Murcia, P. R. (2018) Distribution, diversity and evolution of endogenous retroviruses in perissodactyl genomes. Journal of Virology, 92(23), e00927-18. (doi: 10.1128/JVI.00927-18) (PMID:30209175) (PMCID:PMC6232481)

Tie, C. H.C. et al. (2018) KAP1 regulates endogenous retroviruses in adult human cells and contributes to innate immune control. EMBO Reports, 19(10), e45000. (doi: 10.15252/embr.201745000) (PMID:30061100) (PMCID:PMC6172469)

Gifford, R. J. , Blomberg, J., Coffin, J. M., Fan, H., Heidmann, T., Mayer, J., Stoye, J., Tristem, M. and Johnson, W. E. (2018) Nomenclature for endogenous retrovirus (ERV) loci. Retrovirology, 15, 59. (doi: 10.1186/s12977-018-0442-1) (PMID:30153831) (PMCID:PMC6114882)

Dennis, T. P.W., Flynn, P. J., Souza, W. M. d., Singer, J. B., Moreau, C. S., Wilson, S. J. and Gifford, R. J. (2018) Insights into circovirus host range from the genomic fossil record. Journal of Virology, 92(16), e00145-18. (doi: 10.1128/JVI.00145-18) (PMID:29875243) (PMCID:PMC6069186)

Pénzes, J. J., Marsile-Medun, S., Agbandje-McKenna, M. and Gifford, R. J. (2018) Endogenous amdoparvovirus-related elements reveal insights into the biology and evolution of vertebrate parvoviruses. Virus Evolution, 4(2), vey026. (doi: 10.1093/ve/vey026) (PMID:30443409) (PMCID:PMC6232428)

Cowton, V. M., Singer, J. B., Gifford, R. J. and Patel, A. H. (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. (doi: 10.3389/fimmu.2018.01470) (PMID:30013555) (PMCID:PMC6036255)

Krupovic, M. et al. (2018) Ortervirales: a new viral order unifying five families of reverse-transcribing viruses. Journal of Virology, 92(12), e00515-18. (doi: 10.1128/JVI.00515-18) (PMID:29618642)

Blanco-Melo, D., Gifford, R. J. and Bieniasz, P. D. (2018) Reconstruction of a replication-competent ancestral murine endogenous retrovirus-L. Retrovirology, 15, 34. (doi: 10.1186/s12977-018-0416-3) (PMID:29716624) (PMCID:PMC5930517)

Hron, T., Farkašová, H., Gifford, R. J. , Benda, P., Hulva, P., Görföl, T., Pačes, J. and Elleder, D. (2018) Remnants of an ancient deltaretrovirus in the genomes of horseshoe aats (Rhinolophidae). Viruses, 10(4), 185. (doi: 10.3390/v10040185) (PMID:29642581) (PMCID:PMC5923479)

de Souza, W. M. et al. (2018) Novel parvoviruses from wild and domestic animals in Brazil provide new insights into parvovirus distribution and diversity. Viruses, 10(4), 143. (doi: 10.3390/v10040143) (PMID:29565808) (PMCID:PMC5923437)

2017

Shaw, A. E. et al. (2017) Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses. PLoS Biology, 15(12), e2004086. (doi: 10.1371/journal.pbio.2004086) (PMID:29253856) (PMCID:PMC574750)

Niebel, M. , Singer, J. B., Nickbakhsh, S. , Gifford, R. J. and Thomson, E. C. (2017) Hepatitis C and the absence of genomic data in low-income countries: a barrier on the road to elimination? Lancet Gastroenterology and Hepatology, 2(10), pp. 700-701. (doi: 10.1016/S2468-1253(17)30257-1) (PMID:28895545)

Blanco-Melo, D., Gifford, R. J. and Bieniasz, P. D. (2017) Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors. eLife, 6, e22519. (doi: 10.7554/eLife.22519) (PMID:28397686) (PMCID:PMC5388530)

Farkašová, H., Hron, T., Pačes, J., Hulva, P., Benda, P., Gifford, R. J. and Elleder, D. (2017) 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(12), pp. 3145-3150. (doi: 10.1073/pnas.1621224114) (PMID:28280099) (PMCID:PMC5373376)

Henzy, J. E., Gifford, R. J. , Kenaley, C. P. and Johnson, W. E. (2017) An intact retroviral gene conserved in spiny-rayed fishes for over 100 My. Molecular Biology and Evolution, 34(3), pp. 634-639. (doi: 10.1093/molbev/msw262) (PMID:28039384)

de Souza, W. M., Romeiro, M. F., Modha, S. , de Araujo, J., Queiroz, L. H., Durigon, E. L., Moraes Figueiredo, L. T., Murcia, P. R. and Gifford, R. (2017) Chapparvoviruses occur in at least three vertebrate classes and have a broad biogeographic distribution. Journal of General Virology, 98(2), pp. 225-229. (doi: 10.1099/jgv.0.000671) (PMID:28284244) (PMCID:PMC5646239)

2016

Jacobs, M. et al. (2016) Late Ebola virus relapse causing meningoencephalitis: a case report. Lancet, 388(10043), pp. 498-503. (doi: 10.1016/S0140-6736(16)30386-5) (PMID:27209148) (PMCID:PMC4967715)

Wu, H. L. et al. (2016) Identification and spontaneous immune targeting of an endogenous retrovirus K envelope protein in the Indian rhesus macaque model of human disease. Retrovirology, 13, 6. (doi: 10.1186/s12977-016-0238-0) (PMID:26767784) (PMCID:PMC4714462)

2015

Ng, M. et al. (2015) Filovirus receptor NPC1 contributes to species-specific patterns of ebolavirus susceptibility in bats. eLife, 4, e11785. (doi: 10.7554/eLife.11785) (PMID:26698106) (PMCID:PMC4709267)

2014

Henzy, J.E., Gifford, R.J. , Johnson, W.E. and Coffin, J. M. (2014) A novel recombinant retrovirus in the genomes of modern birds combines features of avian and mammalian retroviruses. Journal of Virology, 88(5), pp. 2398-2405. (doi: 10.1128/JVI.02863-13)

Arriagada, G. and Gifford, R. J. (2014) Parvovirus-derived endogenous viral elements in two South American rodent genomes. Journal of Virology, 89(20), pp. 12158-12162. (doi: 10.1128/JVI.01173-14) (PMID:25078696)

Katzourakis, A., Magiorkinis, G., Lim, A. G., Gupta, S., Belshaw, R. and Gifford, R. (2014) Larger mammalian body size leads to lower retroviral activity. PLoS Pathogens, 10(7), e1004214. (doi: 10.1371/journal.ppat.1004214)

2013

Niewiadomska, A.M. and Gifford, R.J. (2013) The extraordinary evolutionary history of the reticuloendotheliosis viruses. PLoS Biology, 11(8), e1001642. (doi: 10.1371/journal.pbio.1001642)

Rihn, S.J. , Wilson, S.J. , Loman, N.J., Alim, M., Bakker, S.E., Bhella, D. , Gifford, R.J., Rixon, F.J. and Bieniasz, P.D. (2013) Extreme genetic fragility of the HIV-1 capsid. PLoS Pathogens, 9(6), e1003461. (doi: 10.1371/journal.ppat.1003461) (PMID:23818857) (PMCID:PMC3688543)

2012

Magiorkinis, G., Gifford, R.J., Katzourakis, A., De Ranter, J. and Belshaw, R. (2012) Env-less endogenous retroviruses are genomic superspreaders. Proceedings of the National Academy of Sciences of the United States of America, 109(19), pp. 7385-7390. (doi: 10.1073/pnas.1200913109)

2009

Katzourakis, A., Gifford, R.J., Tristem, M., Gilbert, M.T.P. and Pybus, O.G. (2009) Macroevolution of complex retroviruses. Science, 325(5947), p. 1512. (doi: 10.1126/science.1174149)

2008

Gifford, R.J., Katzourakis, A., Tristem, M., Pybus, O.G., Winters, M. and Shafer, R.W. (2008) A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution. Proceedings of the National Academy of Sciences of the United States of America, 105(51), pp. 20362-20367. (doi: 10.1073/pnas.0807873105)

This list was generated on Thu May 2 15:32:48 2024 BST.

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