RJ GIFFORD

Recent Publications

Retroviruses and ERVs

Hron T, Elleder D, and RJ Gifford (2019)
Deltaretroviruses have circulated since at least the Paleogene and infected a broad range of mammalian species.
Retrovirology [view]

Halo JV, Pendleton AL, Jarosz AS, Gifford RJ, Day ML, and JM Kidd (2019)
Origin and recent expansion of an endogenous gammaretroviral lineage in canids.
Retrovirology [view]

Zhu H, Gifford RJ*, and Murcia PR* (2018)
Distribution, diversity and evolution of endogenous retroviruses in perissodactyl genomes.
Journal of Virology
* co-corresponding authors [view]

Gifford RJ, Blomberg B, Coffin JM, Fan H, Heidmann T, Mayer J, Stoye J, Tristem M, and WE Johnson (2018)
Nomenclature for endogenous retrovirus (ERV) loci.
Retrovirology [view]

Hron T, Farkašová H, Gifford RJ, Benda P, Hulva P, Tamás Görföl, Pačes J, and D. Elleder (2018)
Remnants of an ancient deltaretrovirus in the genomes of horshoe bats (Rhinolophidae). Virus Research [view]

Krupovic M, Blomberg J, Coffin JM, Dasgupta I, Fan H, Geering AD, Gifford RJ, Harrach B, Hull R, Johnson W, Kreuze JF, Lindemann D, Llorens C, Lockhart B, Mayer J, Muller E, Olszewski N, Pappu HR, Pooggin M, Richert-Pöggeler KR, Sabanadzovic S, Sanfaçon H, Schoelz JE, Seal S, Stavolone L, Stoye JP, Teycheney P, Tristem M, Koonin KV, and JH Kuhn (2018)
Ortervirales: A new viral order unifying five families of reverse-transcribing viruses.
Journal of Virology [view]

Farkašová H, Hron T, Pačes J, Hulva P, Benda P, Gifford RJ*, Elleder D*. (2017)
Discovery of an endogenous Deltaretrovirus in the genome of long-fingered bats (Chiroptera: Miniopteridae).
Proc Natl Acad Sci U S A. [view]
* co-corresponding authors

RNA Viruses

Konno Y, Kimura I, Uriu K, Fukush M, Irie T, Koyanagi Y, Gifford RJ, USFQ-COVID19 consortium, Nakagawa S, and K Sato* (2020)
SARS-CoV-2 ORF3b is a potent interferon antagonist whose activity is further increased by a naturally occurring elongation variant. Cell reports

Ho JSY, Angel M, Ma Y, Sloan E, Wang G, Martinez-Romero C, Alenquer M, Roudko V, Chung K, Zheng S, Chang M, Fstkchyan Y, Clohisey S, Dinan AM, Gibbs J, Gifford RJ, Shen R, Gu Q , Nerea I, Campisi L, Cheng H, Nan Z, Jones JD, van Knippenberg I, Zhu Z, Moshkina N, Meyer L, Noel J, Peralta Z, Rezelj V, Kaake R, Rosenberg B , Wang Bo, Wei J, Paessler S, Wise HM, Johnson J, Vannini A, João Amorim M, Baillie KJ, Miraldi ER, Benner C, Brierley I, Digard P, Łuksza M, Firth AE, Nevan Krogan, Greenbaum BD, MacLeod MK, van Bakel H, Garcìa-Sastre A, Yewdell JW, Hutchinson E, and Ivan Marazzi (2020)
Hybrid gene origination creates human-virus chimeric proteins during infection.
Cell [view]

Small DNA Viruses

Hildebrandt E, Penzes J, Gifford RJ, Agbandje-Mckenna M, and R Kotin (2020)
Evolution of dependoparvoviruses across geological timescales – implications for design of AAV-based gene therapy vectors. Virus Evolution [view]

Pénzes JJ, de Souza WM, Agbandje-Mckenna M, and RJ Gifford (2019)
An ancient lineage of highly divergent parvoviruses infects both vertebrate and invertebrate hosts.
Viruses [view]

Pénzes JJ, Marsile-Medun S, Agbandje-McKenna M, and RJ Gifford (2018)
Endogenous amdoparvovirus-related elements reveal insights into the biology and evolution of vertebrate parvoviruses.
Virus Evolution [view]

de Souza WM, Tristan TPW, Fumagalli MJ, Araujo J, Sabino-Santos Jr. G, Maia FGM, Acrani GO, Carrasco AOT, Romeiro MF, Modha S, Vieira LC, Ometto TL, Queiroz LH, Durigon EL, Nunes MRT, Figueiredo LTM, and RJ Gifford (2018)
Whole-genome sequencing of parvoviruses from wild and domestic animals in Brazil provides new insights into parvovirus distribution and diversity.
Viruses [view]

Dennis TPW, Flynn PJ, de Souza WM, Singer JB, Moreau CS, Wilson SJ, and RJ Gifford (2018)
Insights into circovirus host range from the genomic fossil record.
Journal of Virology [view]

Dennis TPW, de Souza WM, Marsile-Medun S, Singer JB, Wilson SJ, and RJ Gifford (2018)
The evolution, distribution and diversity of endogenous circoviral elements in vertebrate genomes.
Virus Research [view]

Souza WM, Romeiro MF, Fumagalli MJ, Modha S, de Araujo J, Queiroz LH, Durigon EL, Figueiredo LT, Murcia PR, Gifford RJ. (2017)
Chapparvoviruses occur in at least three vertebrate classes and have a broad biogeographic distribution.
J Gen Virol. [view]

Genomic Epidemiology & Virus Surveillance

Brunker K, Gurdeep G, Thumbi SM, Lushasi K, Lugelo A, Czupryna AM, Ade F, Wambura G, Chuchu V, Steenson R, Ngeleja C, Bautista C, Gomez MRR, Chu MYJV, Manalo DL, Miranda MA, Kamat KT, Rysava K, Espineda J, Silo EAV, Aringo AM, Bernales RP, Adonay FF, Tildesley MJ, Marston DA, Jennings DL, Zhu W, Meredith LW, Gifford RJ, B. Singer JB, Muturi M, Mwatondo A, Biek R, and K Hampson (2019)
Rapid in-country sequencing of virus genomes to inform rabies elimination programmes. Wellcome Open Research [view]

Cowton VM, Singer JB, Gifford RJ, and AJ Patel (2018)
Predicting the Effectiveness of Hepatitis C Virus Neutralizing Antibodies by Bioinformatic Analysis of Conserved Epitope Residues Using Public Sequence Data.
Frontiers in Immunology [view]

Niebel M, Singer JB, Nickbakhsh S, Gifford RJ and EC Thomson (2017)
Hepatitis C and the absence of genomic data in low-income countries: a barrier on the road to elimination?
Lancet Gastroenterol Hepatol. [view]

Carrozza MJ, Niewiadomska AM, Mazzei M, Abi-Said MR, Hué S, Singer JB, Hughes J, and RJ Gifford (2018)
Emergence of pandemic lentivirus infection in small ruminants. [preprint]

Paleovirology

Callaway HM, Subramanian S, Urbina C, Barnard K, Dick R, Hafentein SL, Gifford RJ, and CR Parrish (2019)
Examination and reconstruction of three ancient endogenous parvovirus capsid proteins in rodent genomes.
Journal of Virology [view]

Blanco Melo D, Gifford RJ, and P. Bieniasz (2018)
Reconstruction of a replication-competent ancestral murine endogenous retrovirus-L.
Retrovirology [view]

Blanco-Melo D, Gifford RJ, and PD Bieniasz (2017)
Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors.
Elife [view]

Host-Virus Interface

Jumpei Ito, Robert J. Gifford, Kei Sato (2019)
Retroviruses drive the rapid evolution of mammalian APOBEC3 genes.
PNAS [view]

Schmidt F, Keele BF, Del Prete GQ, Voronin D, Fennessey CM, Soll S, Kane M, Raymond A, Gifford RJ, KewalRamani V, Lifson JD, Bieniasz P, and T Hatziioannou (2019)
Derivation of simian tropic HIV-1 infectious clone reveals virus adaptation to a new host.
PNAS [view]

Valencia-Herrera I, Cena-Ahumada E, Faunes F, Ibarra-Karmy R, Gifford RJ*, and G Arriagada* (2019) *co-corresponding authors
Molecular properties and evolutionary origins of a parvovirus-derived myosin fusion gene in guinea pigs.
Journal of Virology [view]

Tie C, Fernandes L, Conde L, Robbez-Masson L, Sumner R, Peacock T, Rodriguez-Plata MT, Mickute G, Gifford RJ, Towers G, Herrero J, and H Rowe (2018)
KAP1 regulates ERVs in adult human cells and contributes to innate immune control.
EMBO Reports [view]

Shaw AE, Hughes J, Gu Q, Behdenna A, Singer J, Dennis T, Orton RJ, Varela M, Gifford RJ, Wilson SJ and M Palmarini (2017)
Fundamental properties of the mammalian innate immune system revealed by multi-species comparison of type I interferon responses.
Plos Biology [view]

Bioinformatics / Software Development

Singer JB, Gifford RJ, Cotten M, and D Robertson (2020)
CoV-GLUE: A Web Application for Tracking SARS-CoV-2 Genomic Variation.
Preprints [preprint]

Singer JB, Thomson EC, Hughes J, Aranday-Cortes E, McLauchlan J, da Silva Felipe A, Tong L, Manso CF, Gifford RJ, Mbsisa JL, Bibby DF, Bradshaw D, and D Smith (2019)
Interpreting Viral Deep Sequencing Data with GLUE.
Viruses [view]

Singer JB, Thomson EC, McLauchlan J, Hughes J, and RJ Gifford (2018)
GLUE: A flexible software system for virus sequence data.
BMC Bioinformatics [view]

Zhu H, Dennis T, Hughes J, and RJ Gifford (2018)
Database-integrated genome screening (DIGS): exploring genomes heuristically using sequence similarity search tools and a relational database. [preprint]

Publications prior to 2017

Jacobs M, Rodger A, Bell DJ, Bhagani S, Cropley I, Filipe A, Gifford RJ, Hopkins S, Hughes J, Jabeen F, Johannessen I, Karageorgopoulos D, Lackenby A, Lester R, Liu RS, MacConnachie A, Mahungu T, Martin D, Marshall N, Mepham S, Orton R, Palmarini M, Patel M, Perry C, Peters SE, Porter D, Ritchie D, Ritchie ND, Seaton RA, Sreenu VB, Templeton K, Warren S, Wilkie GS, Zambon M, Gopal R, Thomson EC. (2016)
Late Ebola virus relapse causing meningoencephalitis: a case report.
Lancet [view]

Ng M, Ndungo E, Kaczmarek ME, Herbert AS, Binger T, Kuehne AI, Jangra RK, Hawkins JA, Gifford RJ, Biswas R, Demogines A, James RM, Yu M, Brummelkamp TR, Drosten C, Wang LF, Kuhn JH, Müller MA, Dye JM, Sawyer SL, Chandran K. (2015)
Filovirus receptor NPC1 contributes to species-specific patterns of ebolavirus susceptibility in bats.
Elife. [view]

Katzourakis A, Magiorkinis G, Aaron G. Lim, Sunetra Gupta, Robert Belshaw, and RJ Gifford (2014) Larger mammalian body size selects for lower retroviral activity.
PLoS Pathogens [view]

Henzy JE, Gifford RJ, Johnson WE, and JM Coffin (2014)
A novel recombinant retrovirus in the genomes of modern birds combines features of avian and mammalian retroviruses.
J. Virol. [view]

Gloria Arriagada and RJ Gifford (2014)
Parvovirus-derived endogenous viral elements in two South American rodent genomes.
J. Virol. [view]

Wu HL, Léon EJ, Wallace LT, Nimiyongskul FA, Buechler MB, Newman LP, Castrovinci PA, Paul Johnson R, Gifford RJ, Brad Jones R, Sacha JB. (2014)
Identification and spontaneous immune targeting of an endogenous retrovirus K envelope protein in the Indian rhesus macaque model of human disease.
Retrovirology. [view]

Niewiadomska AM and RJ Gifford (2013)
The extraordinary evolutionary history of the reticuloendotheliosis viruses.
PLoS Biology [view]

Rihn, SJ, Wilson SJ, Loman NJ, Alim M, Bakker SE, Bhella D, Gifford RJ, Rixon FJ, and PD. Bieniasz. (2013)
Extreme genetic fragility of the HIV-1 capsid.
PLoS Pathogens [view]

Magiorkinis G, Gifford RJ, Katzourakis A, de Ranter J, and R Belshaw (2012)
Env-less endogenous retroviruses are genomic superspreaders.
PNAS [view]

Capomaccio S, Cappelli K, Cook RF, Nardi F, Gifford R, Marenzoni ML, and F. Passamonti (2011)
Geographic structuring of global EIAV isolates: A single origin for New World strains?
Virus Research [view]

Gifford RJ (2012)
Viral evolution in deep time - Lentiviruses and mammals.
Trends in Genetics [view]

Katzourakis A. and RJ. Gifford (2010)
Endogenous viral elements in animal genomes.
PLoS Genetics [view]

de Oliveira T, Pillay D and RJ. Gifford (2010)
The HIV-1 subtype C epidemic in South America is linked to the United Kingdom.
PLoS ONE [view]

Katzourakis A*, Gifford RJ*, Tristem M, Gilbert MTP, and OG. Pybus (2009)
Macroevolution of complex retroviruses.
Science [view]
* co-corresponding authors

Gifford RJ, Liu TF, Rhee SY, Kiuchi M, Hue S, Pillay D, Shafer RW. (2009).
The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance.
Bioinformatics [view]

Hue S, Gifford RJ, Dunn D, Fearnhill E, and D. Pillay. (2009)
Demonstration of sustained drug-resistant HIV-1 lineages circulating amongst drug-naive individuals.
J. Virol. [view]

Gifford RJ, Katzourakis A, Tristem M, Pybus, OG, Winters M, and RW. Shafer. (2008) A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution.
PNAS [view]

Katzourakis A, Tristem M, Pybus OG, and RJ. Gifford (2007) Discovery and analysis of the first endogenous lentivirus. PNAS [view]

Gifford RJ, de Oliveira T, Rambaut A, Pybus OG, Dunn D, Vandamme A, Kellam P, and D. Pillay. (2007) Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of HIV-1. J. Virol. [view]

Gifford RJ, Kabat P, Martin J, Lynch C, and M. Tristem. (2005)
Evolution and distribution of class II-related endogenous retroviruses.
J. Virol. [view]

Gifford RJ and M Tristem. (2003).
The evolution, distribution and diversity of endogenous retroviruses.
Virus Genes [view]