2024

Blanco-Melo, Daniel, Campbell, Matthew A., Zhu, Henan, Dennis, Tristan P., Modha, Sejal ORCID: https://orcid.org/0000-0002-8440-885X, Lytras, Spyros, Hughes, Joseph ORCID: https://orcid.org/0000-0003-2556-2563, Gatseva, Anna ORCID: https://orcid.org/0000-0003-1601-5277 and Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (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, Daniel, Campbell, Matthew A., Zhu, Henan, Dennis, Tristan P.W., Modha, Sejal ORCID: https://orcid.org/0000-0002-8440-885X, Lytras, Spyros, Hughes, Joseph ORCID: https://orcid.org/0000-0003-2556-2563, Gatseva, Anna ORCID: https://orcid.org/0000-0003-1601-5277 and Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (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, Criselda, Jaswant, Gurdeep, French, Hollie, Campbell, Kathryn, Durrant, Rowan ORCID: https://orcid.org/0000-0002-9742-2052, Gifford, Robert ORCID: https://orcid.org/0000-0003-4028-9884, Kia, Grace S.N., Ogoti, Brian, Hampson, Katie ORCID: https://orcid.org/0000-0001-5392-6884 and Brunker, Kirstyn ORCID: https://orcid.org/0000-0001-9990-6299 (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, Angelica, Fernández-García, Leandro, Ibarra-Karmy, Rodrigo, Mardones, Gonzalo A., Mercado, Luis, Bustos, Fernando J., Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 and Arriagada, Gloria (2023) Antiviral activity of an endogenous parvoviral element. Viruses, 15(7), 1420. (doi: 10.3390/v15071420) (PMID:37515112) (PMCID:PMC10384997)

Oliver, Michael R. ORCID: https://orcid.org/0000-0002-1838-8416, Toon, Kamilla ORCID: https://orcid.org/0009-0007-6795-4684, Lewis, Charlotte B., Devlin, Stephen, Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 and Grove, Joe ORCID: https://orcid.org/0000-0001-5390-7579 (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, Maria-Luisa, Niewiadomska, Anna-Maria, Mazzei, Maurizio, Abi-Said, Mounir R., Hue, Stephane, Hughes, Joseph ORCID: https://orcid.org/0000-0003-2556-2563, Gatseva, Anna ORCID: https://orcid.org/0000-0003-1601-5277 and Gifford, Robert James ORCID: https://orcid.org/0000-0003-4028-9884 (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, Roziah, Gatseva, Anna ORCID: https://orcid.org/0000-0003-1601-5277 and Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (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, Matthew A., Loncar, Shannon, Kotin, Robert M. and Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (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, Christian, Dinh, Tung, Kumar, Abhishek, Tenneti, Kasyap, Eschbach, Jenna E., Davis, Keanu, Gifford, Robert ORCID: https://orcid.org/0000-0003-4028-9884, Kvaratskhelia, Mamuka and Kutluay, Sebla 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, Kathryn, Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884, Singer, Joshua, Hill, Verity, O'Toole, Aine, Rambaut, Andrew, Hampson, Katie ORCID: https://orcid.org/0000-0001-5392-6884 and Brunker, Kirstyn ORCID: https://orcid.org/0000-0001-9990-6299 (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, Connor G.G., de Souza, William M., Parry, Rhys and Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (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, Rhys, Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884, Lytras, Spyros, Ray, Stuart C. and Coin, Lachlan 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, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (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, Spyros, Arriagada, Gloria and Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (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, Evin, Penzes, Judit J., Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884, Agbandje-Mckenna, Mavis and Kotin, Robert 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, Jumpei, Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 and Sato, Kei (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, Tomas, Elleder, Daniel and Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (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, Ignacio, Faunes, Fernando, Cena-Ahumada, Eduardo, Ibarra-Karmy, Rodrigo, Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 and Arriagada, Gloria (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, Judit J., de Souza, William Marciel, Agbandje-McKenna, Mavis and Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (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, Heather M., Subramanian, Suriyasri, Urbina, Christian, Barnard, Karen, Dick, Robert, Bator, Carol M., Hafentein, Susan L., Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 and Parrish, Colin 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, Julia V., Pendleton, Amanda L., Jarosz, Abigail S., Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884, Day, Malika L. and Kidd, Jeffrey 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, Tristan P.W., Souza, William Marciel de, Marsile-Medun, Soledad, Singer, Joshua B., Wilson, Sam J. ORCID: https://orcid.org/0000-0002-6065-0895 and Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (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, Joshua B., Thomson, Emma C. ORCID: https://orcid.org/0000-0003-1482-0889, McLauchlan, John ORCID: https://orcid.org/0000-0003-2217-9948, Hughes, Joseph ORCID: https://orcid.org/0000-0003-2556-2563 and Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (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, Henan, Gifford, Robert ORCID: https://orcid.org/0000-0003-4028-9884 and Murcia, Pablo Ramiro ORCID: https://orcid.org/0000-0002-4352-394X (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, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884, Blomberg, Jonas, Coffin, John M., Fan, Hugh, Heidmann, Thierry, Mayer, Jens, Stoye, Jonathan, Tristem, Michael and Johnson, Welkin E. (2018) Nomenclature for endogenous retrovirus (ERV) loci. Retrovirology, 15, 59. (doi: 10.1186/s12977-018-0442-1) (PMID:30153831) (PMCID:PMC6114882)

Dennis, Tristan P.W., Flynn, Peter J., Souza, William Marciel de, Singer, Joshua B., Moreau, Corrie S., Wilson, Sam J. ORCID: https://orcid.org/0000-0002-6065-0895 and Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (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, Judit J., Marsile-Medun, Soledad, Agbandje-McKenna, Mavis and Gifford, Robert James ORCID: https://orcid.org/0000-0003-4028-9884 (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, Vanessa M., Singer, Joshua B., Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 and Patel, Arvind H. ORCID: https://orcid.org/0000-0003-4600-2047 (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, Daniel, Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 and Bieniasz, Paul 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, Tomáš, Farkašová, Helena, Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884, Benda, Petr, Hulva, Pavel, Görföl, Tamás, Pačes, Jan and Elleder, Daniel (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, Marc ORCID: https://orcid.org/0000-0003-2515-6151, Singer, Joshua B., Nickbakhsh, Sema ORCID: https://orcid.org/0000-0001-9543-7536, Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 and Thomson, Emma C. ORCID: https://orcid.org/0000-0003-1482-0889 (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, Daniel, Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 and Bieniasz, Paul 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, Helena, Hron, Tomáš, Pačes, Jan, Hulva, Pavel, Benda, Petr, Gifford, Robert James ORCID: https://orcid.org/0000-0003-4028-9884 and Elleder, Daniel (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, Jamie E., Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884, Kenaley, Christopher P. and Johnson, Welkin 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, William Marciel, Romeiro, Marilia Farignoli, Modha, Sejal ORCID: https://orcid.org/0000-0002-8440-885X, de Araujo, Jansen, Queiroz, Luzia Helena, Durigon, Edison Luiz, Moraes Figueiredo, Luiz Tadeu, Murcia, Pablo Ramiro ORCID: https://orcid.org/0000-0002-4352-394X and Gifford, Robert ORCID: https://orcid.org/0000-0003-4028-9884 (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. ORCID: https://orcid.org/0000-0003-4028-9884, 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, Gloria and Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (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, Aris, Magiorkinis, Gkikas, Lim, Aaron G., Gupta, Sunetra, Belshaw, Robert and Gifford, Robert ORCID: https://orcid.org/0000-0003-4028-9884 (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. ORCID: https://orcid.org/0000-0001-9495-4056, Wilson, S.J. ORCID: https://orcid.org/0000-0002-6065-0895, Loman, N.J., Alim, M., Bakker, S.E., Bhella, D. ORCID: https://orcid.org/0000-0003-2096-8310, 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, Daniel, Campbell, Matthew A., Zhu, Henan, Dennis, Tristan P., Modha, Sejal ORCID: https://orcid.org/0000-0002-8440-885X, Lytras, Spyros, Hughes, Joseph ORCID: https://orcid.org/0000-0003-2556-2563, Gatseva, Anna ORCID: https://orcid.org/0000-0003-1601-5277 and Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (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, Daniel, Campbell, Matthew A., Zhu, Henan, Dennis, Tristan P.W., Modha, Sejal ORCID: https://orcid.org/0000-0002-8440-885X, Lytras, Spyros, Hughes, Joseph ORCID: https://orcid.org/0000-0003-2556-2563, Gatseva, Anna ORCID: https://orcid.org/0000-0003-1601-5277 and Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (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, Criselda, Jaswant, Gurdeep, French, Hollie, Campbell, Kathryn, Durrant, Rowan ORCID: https://orcid.org/0000-0002-9742-2052, Gifford, Robert ORCID: https://orcid.org/0000-0003-4028-9884, Kia, Grace S.N., Ogoti, Brian, Hampson, Katie ORCID: https://orcid.org/0000-0001-5392-6884 and Brunker, Kirstyn ORCID: https://orcid.org/0000-0001-9990-6299 (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, Angelica, Fernández-García, Leandro, Ibarra-Karmy, Rodrigo, Mardones, Gonzalo A., Mercado, Luis, Bustos, Fernando J., Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 and Arriagada, Gloria (2023) Antiviral activity of an endogenous parvoviral element. Viruses, 15(7), 1420. (doi: 10.3390/v15071420) (PMID:37515112) (PMCID:PMC10384997)

Oliver, Michael R. ORCID: https://orcid.org/0000-0002-1838-8416, Toon, Kamilla ORCID: https://orcid.org/0009-0007-6795-4684, Lewis, Charlotte B., Devlin, Stephen, Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 and Grove, Joe ORCID: https://orcid.org/0000-0001-5390-7579 (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, Maria-Luisa, Niewiadomska, Anna-Maria, Mazzei, Maurizio, Abi-Said, Mounir R., Hue, Stephane, Hughes, Joseph ORCID: https://orcid.org/0000-0003-2556-2563, Gatseva, Anna ORCID: https://orcid.org/0000-0003-1601-5277 and Gifford, Robert James ORCID: https://orcid.org/0000-0003-4028-9884 (2023) Emergence and pandemic spread of small ruminant lentiviruses. Virus Evolution, 9(1), vead005. (doi: 10.1093/ve/vead005) (PMID:36793939) (PMCID:PMC9924038)

Kambol, Roziah, Gatseva, Anna ORCID: https://orcid.org/0000-0003-1601-5277 and Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (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, Matthew A., Loncar, Shannon, Kotin, Robert M. and Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (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)

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Shema Mugisha, Christian, Dinh, Tung, Kumar, Abhishek, Tenneti, Kasyap, Eschbach, Jenna E., Davis, Keanu, Gifford, Robert ORCID: https://orcid.org/0000-0003-4028-9884, Kvaratskhelia, Mamuka and Kutluay, Sebla 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, Kathryn, Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884, Singer, Joshua, Hill, Verity, O'Toole, Aine, Rambaut, Andrew, Hampson, Katie ORCID: https://orcid.org/0000-0001-5392-6884 and Brunker, Kirstyn ORCID: https://orcid.org/0000-0001-9990-6299 (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, Connor G.G., de Souza, William M., Parry, Rhys and Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (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)

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Parry, Rhys, Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884, Lytras, Spyros, Ray, Stuart C. and Coin, Lachlan 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, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (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, Spyros, Arriagada, Gloria and Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (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)

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Hildebrandt, Evin, Penzes, Judit J., Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884, Agbandje-Mckenna, Mavis and Kotin, Robert 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)

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Ito, Jumpei, Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 and Sato, Kei (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, Tomas, Elleder, Daniel and Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (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, Ignacio, Faunes, Fernando, Cena-Ahumada, Eduardo, Ibarra-Karmy, Rodrigo, Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 and Arriagada, Gloria (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, Judit J., de Souza, William Marciel, Agbandje-McKenna, Mavis and Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (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)

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Callaway, Heather M., Subramanian, Suriyasri, Urbina, Christian, Barnard, Karen, Dick, Robert, Bator, Carol M., Hafentein, Susan L., Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 and Parrish, Colin 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, Julia V., Pendleton, Amanda L., Jarosz, Abigail S., Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884, Day, Malika L. and Kidd, Jeffrey 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, Tristan P.W., Souza, William Marciel de, Marsile-Medun, Soledad, Singer, Joshua B., Wilson, Sam J. ORCID: https://orcid.org/0000-0002-6065-0895 and Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (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, Joshua B., Thomson, Emma C. ORCID: https://orcid.org/0000-0003-1482-0889, McLauchlan, John ORCID: https://orcid.org/0000-0003-2217-9948, Hughes, Joseph ORCID: https://orcid.org/0000-0003-2556-2563 and Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (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, Henan, Gifford, Robert ORCID: https://orcid.org/0000-0003-4028-9884 and Murcia, Pablo Ramiro ORCID: https://orcid.org/0000-0002-4352-394X (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)

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Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884, Blomberg, Jonas, Coffin, John M., Fan, Hugh, Heidmann, Thierry, Mayer, Jens, Stoye, Jonathan, Tristem, Michael and Johnson, Welkin E. (2018) Nomenclature for endogenous retrovirus (ERV) loci. Retrovirology, 15, 59. (doi: 10.1186/s12977-018-0442-1) (PMID:30153831) (PMCID:PMC6114882)

Dennis, Tristan P.W., Flynn, Peter J., Souza, William Marciel de, Singer, Joshua B., Moreau, Corrie S., Wilson, Sam J. ORCID: https://orcid.org/0000-0002-6065-0895 and Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (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, Judit J., Marsile-Medun, Soledad, Agbandje-McKenna, Mavis and Gifford, Robert James ORCID: https://orcid.org/0000-0003-4028-9884 (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, Vanessa M., Singer, Joshua B., Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 and Patel, Arvind H. ORCID: https://orcid.org/0000-0003-4600-2047 (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)

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Blanco-Melo, Daniel, Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 and Bieniasz, Paul 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, Tomáš, Farkašová, Helena, Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884, Benda, Petr, Hulva, Pavel, Görföl, Tamás, Pačes, Jan and Elleder, Daniel (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)

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Blanco-Melo, Daniel, Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 and Bieniasz, Paul 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, Helena, Hron, Tomáš, Pačes, Jan, Hulva, Pavel, Benda, Petr, Gifford, Robert James ORCID: https://orcid.org/0000-0003-4028-9884 and Elleder, Daniel (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, Jamie E., Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884, Kenaley, Christopher P. and Johnson, Welkin 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)

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Henzy, J.E., Gifford, R.J. ORCID: https://orcid.org/0000-0003-4028-9884, 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, Gloria and Gifford, Robert J. ORCID: https://orcid.org/0000-0003-4028-9884 (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, Aris, Magiorkinis, Gkikas, Lim, Aaron G., Gupta, Sunetra, Belshaw, Robert and Gifford, Robert ORCID: https://orcid.org/0000-0003-4028-9884 (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)

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