Dr Robert Gifford

  • Bioinformatician (Virology)
  • Affiliate (School of Infection & Immunity)

Research interests

CVR logo 

Viral Genomics & Bioinformatics
Paleovirology

My research addresses the ecology and evolution of viruses. Viruses typically have high mutation rates and can evolve extremely rapidly, yet may be the oldest of all kingdoms of life. We are still only just beginning to comprehend the extent and complexity of viral biodiversity, and to appreciate the myriad roles that viruses play as dynamic components of ecosystems. Over recent years, however, revolutionary advances in DNA sequencing and related information technologies have radically transformed the research landscape. As well as facilitating the use of genetic approaches to track viral evolution within and spread between infected hosts, explosive progress in genomics is allowing unprecedented insight into the longer-term history of viral evolution.

My principal contention is that understanding the long-term evolution and origins of viral species will allow the threat posed by contemporary viruses to be assessed and countered more effectively. A central theme in my research is the development of theories that link our growing understanding of contemporary viruses with ecological and evolutionary phenomena that took place over timescales ranging from hundreds to millions of years.

Publications

List by: Type | Date

Jump to: 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2009 | 2008
Number of items: 49.

2022

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)

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 Tue Nov 29 07:52:40 2022 GMT.
Jump to: Articles
Number of items: 49.

Articles

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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 Tue Nov 29 07:52:40 2022 GMT.

Grants

Grants and Awards listed are those received whilst working with the University of Glasgow.

  • The center for HIV/AIDS-related structural biology
    National Institutes of Health
    2017 - 2020
     
  • Quinquennial Core Funds
    Medical Research Council
    2016 - 2021
     

Visit the Gifford Group webpage

MRC, University of Glasgow and CVR logos