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, 25(1), 120. (doi: 10.1186/s13059-024-03258-y) (PMID:38741126) (PMCID:PMC11089739)

2023

Blanco-Melo, D., Campbell, M. A., Zhu, H., Dennis, T. P.W., Modha, S. , Lytras, S., Hughes, J. , Gatseva, A. and Gifford, R. J. (2023) A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus ‘fossil record’. bioRxiv, (doi: 10.1101/2023.10.17.562709)

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)

Articles

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, 25(1), 120. (doi: 10.1186/s13059-024-03258-y) (PMID:38741126) (PMCID:PMC11089739)

Blanco-Melo, D., Campbell, M. A., Zhu, H., Dennis, T. P.W., Modha, S. , Lytras, S., Hughes, J. , Gatseva, A. and Gifford, R. J. (2023) A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus ‘fossil record’. bioRxiv, (doi: 10.1101/2023.10.17.562709)

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)

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)

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)