Research in my lab addresses questions about the ecology and evolution of viruses. Like all infectious diseases, viral diseases are underpinned by ecological and evolutionary processes. The interactions between viruses and cells, for example, have been shaped by evolution over millions of years. Across shorter timescales, viral spread between and replication within host organisms are functions of population dynamics and selection. Gaining a better understanding of these processes will advance efforts to anticipate, control and treat outbreaks of viral disease.
Our research focuses on two distinct areas; paleovirology and genetic epidemiology. In our paleovirological research, we seek to infer the long-term evolutionary history of viruses. The genomes of humans and other vertebrates contain the remnants of thousands of sequences derived from ancient viruses. The advance of whole genome sequencing projects is enabling us to explore this 'molecular fossil record' in detail, providing us with novel insights into viral evolution. For example, through the discovery of an ancient retroviral fossil in the mouse lemur (Microcebus murinus) genome, we and our collaborators have shown that lentiviruses - the group of retroviruses that includes HIV - were present in Malagasy primates many millions of years ago. Similarly, our identification of an ancient spumavirus in the genome of the two-toed sloth (Choloepus hoffmanni) indicates that this group of viruses has cospeciated with their mammalian hosts for over 100 million years. By providing information about the background of host and virus evolution, these discoveries complement studies of virus-cell interaction such as those being conducted by other researchers at the Aaron Diamond Center, with whom we work closely.
Our work in genetic epidemiology involves the use of sequence-based strategies to investigate the temporal and spatial characteristics of epidemics. We have developed methods for tracking the spread of viruses using routinely sampled gene sequence data, and have used these methods to investigate how the structuring of the HIV-1 epidemic is changing over time. With our collaborators at Stanford, we have developed software tools to support sequence-based strategies for early detection of transmitted HIV-1 drug resistance in resource-limited countries. Current recent focusses on the development of software and information exchange infrastructure to facilitate the use of viral gene sequence data within public health and research.
We study the evolutionary interactions between viruses and the animals they infect. Viruses can evolve very rapidly, and this underlies their ability to infect new species and to overcome the challenges presented by drugs and vaccines. However, many aspects of the way in which viruses interact with their hosts have remained relatively unchanged over millions of years. In our research, we seek to understand viral diseases by studying the evolution of viruses across both long and short timescales. We use gene sequence data obtained from viruses to investigate genetic changes that occur over the course of an epidemic or an infection. We are also able to explore the long term evolutionary history of viruses because vertebrate genomes contain the remnants of many ancient viral sequences. We use these 'molecular fossils' to investigate the distribution of ancient viruses, and to examine how viruses and their hosts have changed and adapted to one another over the course of their evolution.
NAME: Robert Gifford
POSITION TITLE: Staff Investigator
EDUCATION
| 1997 |
B.Sc. University of Glasgow, Glasgow, UK |
| 1998 |
MSc Imperial College, University of London |
| 2002 |
PhD Imperial College, University of London |
POSITIONS AND HONORS
Positions and Employment
| 2003-2006 |
Postdoctoral Scholar, University College London |
| 2006-2008 |
Postdoctoral Scholar, Stanford University |
| 2009 |
Research Associate. University of Oxford |
| 2009-Present |
Assistant Professor, Aaron Diamond AIDS Research Center |
|
|
Other assignments
| Ad hoc reviewer |
AIDS
AIDS Research and Human Retroviruses
Journal of Acquired Immune Deficiency Syndromes |
PUBLICATIONS (SELECTED)
- Gifford RJ, and M Tristem. 2003. The evolution, distribution and diversity of endogenous retroviruses. Virus Genes 26:291-315
- Gifford RJ, Kabat P, Martin J, Lynch C, and M. Tristem. 2005. Evolution and distribution of class II-related endogenous retroviruses. Journal of Virology 79:6478-86
- Masquelier B, Bhaskaran K, Pillay D, Gifford RJ, Balestre E et al. 2005. Prevalence of Transmitted HIV-1 Drug Resistance and the Role of Resistance Algorithms: Data From Seroconverters in the CASCADE Collaboration From 1987 to 2003. J. Acquir. Immune Defic. Syndr. 40(5):505-11.
- Pillay D, Bhaskaran K, Jurriaans S, Prins M, Masquelier B, Dabis F, Gifford RJ, Nielsen C, Pedersen C, Balotta C, Rezza G, Ortiz M, Mendoza C, Kucherer C, Poggensee G, Gill J and K. Porter on behalf of the CASCADE collaboration. 2005. The impact of transmitted drug resistance on the natural history of HIV infection and response to first-line therapy. AIDS 20:21-28
- Gifford RJ. Evolution at the host-retrovirus Interface. 2006. Bioessays 28:1153-6
- Ylinen LMJ, Keckesova Z, Webb BLJ, Gifford RJ, Smith PLS and GJ Towers. 2006. Isolation of an active Lv1 gene from cattle indicates that tripartite motif protein mediated innate immunity to retroviral infection is widespread among mammals. Journal of Virology 80:7332-8
- Gifford RJ,de Oliveira T, Rambaut A, Myers RE, Gale CV, Dunn D, Shafer R, Vandamme A, Kellam P, and D. Pillay. 2006. Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity. AIDS 20:1521-9
- Bezemer D, de Ronde A, Prins M, Gifford RJ, Pillay D, Masquelier B, Fleury H, Dabis F, Back N, Jurriaans S, and L van der Hoek; CASCADE collaboration. 2006. Evolution of transmitted HIV-1 with drug resistance mutations in the absence of therapy: effects on CD4+ T-cell count and HIV-1 RNA load. Antiviral Therapy 11:173-8
- 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. Journal of Virology 81:13050-6
- Katzourakis A, Tristem M, Pybus OG, and Gifford RJ. 2007. Discovery and analysis of the first endogenous lentivirus. PNAS 104: 6261-5
- UK Collaborative Group on HIV Drug Resistance. 2007. Evidence of a decline in transmitted HIV-1 drug resistance in the United Kingdom. AIDS 21:1035-39
- Gifford RJ,Rhee SY, Eriksson N, Liu TF, Kiuchi M, Das AK, and RW Shafer. 2008. APOBEC-mediated sequence editing and epidemiological surveillance of transmitted HIV-1 drug resistance. AIDS 22:717-725
- 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 105:20362-7
- Rhee SY, Liu TF, Kiuchi M, Zioni R, Gifford RJ, Holmes SP, and RW Shafer. 2008. Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors. Retrovirology 5:74
- Ylinen LMJ, Keckesova Z, Towers GJ, Gifford RJ, and A Katzourakis. 2009. The time scale of lentiviral evolution: identification of a RELIK orthologue in the genome of the European hare (Lepus europaeus). Virology.
- 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. 25:1197-8
- Brown AE, Gifford RJ, Clewley JP, Kucherer C, Masquelier, B, Porter K, Balotta, C, Back, NKT, Jorgensen LB, de Mendoza C, Bhaskaran K, Gill ON, Johnson AM, and D Pillay. 2009. Phylogenetic reconstruction of transmissions from individuals with acute HIV infection: towards more rigorous epidemiological definitions. JID 199:427-431
- 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. 2009 Mar;83(6):2645-54.
- Keckesova Z, Ylinen LM, Towers GJ, Gifford RJ, Katzourakis A. 2009. Identification of a RELIK orthologue in the European hare (Lepus europaeus) reveals a minimum age of 12 million years for the lagomorph lentiviruses. Virology. 5;384(1):7-11.
- Katzourakis A*, Gifford RJ*, Tristem M, Gilbert MTP, Pybus OG. 2009. The macroevolution of complex retroviruses. Science 325:1512
- de Oliveira T, Pillay D, Gifford RJ, For the UK Collaborative Group on HIV Drug Resistance. 2010. The HIV-1 Subtype C Epidemic in South America Is Linked to the United Kingdom. PLoS One. 5(2):e9311.
- Katzourakis A, Gifford RJ, 2010. Endogenous Viral Elements in Animal Genomes. PLoS Genetics. 6(11):e1001191.
- Gifford RJ, 2011. No trespassing: ancient BST2 deletion confers protection against simian immunodeficiency virus infection of humans. Hum Mutat. 2011 Nov;32(11)
- Gifford RJ, 2012. Viral Evolution in Deep Time - Lentiviruses and Mammals. Trends in Genetics. 28(2):89-100.
* co-corresponding authors
- Gifford RJ and M Tristem. 2003. The evolution, distribution and diversity of endogenous retroviruses. Virus Genes 26:291-315
- Gifford RJ, Kabat P, Martin J, Lynch C, and M. Tristem. 2005. Evolution and distribution of class II-related endogenous retroviruses. Journal of Virology 79:6478-86
- Masquelier B, Bhaskaran K, Pillay D, Gifford RJ, Balestre E et al. 2005. Prevalence of Transmitted HIV-1 Drug Resistance and the Role of Resistance Algorithms: Data From Seroconverters in the CASCADE Collaboration From 1987 to 2003. J. Acquir. Immune Defic. Syndr. 40(5):505-11. [view]
- Pillay D, Bhaskaran K, Jurriaans S, Prins M, Masquelier B, Dabis F, Gifford RJ, Nielsen C, Pedersen C, Balotta C, Rezza G, Ortiz M, Mendoza C, Kucherer C, Poggensee G, Gill J and K. Porter on behalf of the CASCADE collaboration. 2005. The impact of transmitted drug resistance on the natural history of HIV infection and response to first-line therapy. AIDS 20:21-8 [view]
- Gifford RJ. Evolution at the host-retrovirus Interface. 2006. Bioessays 28:1153-6 [view]
- Ylinen LMJ, Keckesova Z, Webb BLJ, Gifford RJ, Smith PLS and GJ Towers. 2006. Isolation of an active Lv1 gene from cattle indicates that tripartite motif protein mediated innate immunity to retroviral infection is widespread among mammals. Journal of Virology 80:7332-8 [view]
- Gifford RJ, de Oliveira T, Rambaut A, Myers RE, Gale CV, Dunn D, Shafer R, Vandamme A, Kellam P, and D. Pillay. 2006. Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity. AIDS 20:1521-9 [view]
- Bezemer D, de Ronde A, Prins M, Gifford RJ, Pillay D, Masquelier B, Fleury H, Dabis F, Back N, Jurriaans S, and L van der Hoek; CASCADE collaboration. 2006. Evolution of transmitted HIV-1 with drug resistance mutations in the absence of therapy: effects on CD4+ T-cell count and HIV-1 RNA load. Antiviral Therapy 11:173-8 [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. Journal of Virology 81:13050-6 [view]
- Katzourakis A, Tristem M, Pybus OG, and RJ Gifford. 2007. Discovery and analysis of the first endogenous lentivirus. PNAS 104: 6261-5 [view]
- UK Collaborative Group on HIV Drug Resistance. 2007. Evidence of a decline in transmitted HIV-1 drug resistance in the United Kingdom. AIDS 21:1035-39 [view]
- Gifford RJ, Rhee SY, Eriksson N, Liu TF, Kiuchi M, Das AK, and RW Shafer. 2008. APOBEC-mediated sequence editing and epidemiological surveillance of transmitted HIV-1 drug resistance. AIDS 22:717-725 [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 105:20362-7 [view]
- Rhee SY, Liu TF, Kiuchi M, Zioni R, Gifford RJ, Holmes SP, and RW Shafer. 2008. Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors. Retrovirology 5:74 [view]
- Ylinen LMJ, Keckesova Z, Towers GJ, Gifford RJ, and A Katzourakis. 2009. The time scale of lentiviral evolution: identification of a RELIK orthologue in the genome of the European hare (Lepus europaeus). Virology. [view]
- 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. 25:1197-8 [view]
- Brown AE, Gifford RJ, Clewley JP, Kucherer C, Masquelier, B, Porter K, Balotta, C, Back, NKT, Jorgensen LB, de Mendoza C, Bhaskaran K, Gill ON, Johnson AM, and D Pillay. 2009. Phylogenetic reconstruction of transmissions from individuals with acute HIV infection: towards more rigorous epidemiological definitions. JID 199:427-431 [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. 2009 Mar;83(6):2645-54. [view]
- Keckesova Z, Ylinen LM, Towers GJ, Gifford RJ, Katzourakis A. 2009. Identification of a RELIK orthologue in the European hare (Lepus europaeus) reveals a minimum age of 12 million years for the lagomorph lentiviruses. Virology. 5;384(1):7-11. [view]
- Katzourakis A*, Gifford RJ*, Tristem M, Gilbert MTP, Pybus OG. 2009. The macroevolution of complex retroviruses. Science 325:1512 [view]
- de Oliveira T, Pillay D, Gifford RJ. For the UK Collaborative Group on HIV Drug Resistance. 2010. The HIV-1 Subtype C Epidemic in South America Is Linked to the United Kingdom. PLoS One. 5(2):e9311. [view]
- Katzourakis A, Gifford RJ. 2010. Endogenous viral elements in animal genomes. PLoS Genetics. 6(11):e1001191. [view]
- Gifford RJ, 2011. No trespassing: ancient BST2 deletion confers protection against simian immunodeficiency virus infection of humans. Hum Mutat. 2011 Nov;32(11) [view]
- Gifford RJ, 2012. Viral Evolution in Deep Time - Lentiviruses and Mammals. Trends in Genetics. 28(2):89-100. [view]
* co-corresponding authors
| Robert Gifford |
Staff Investigator |
| Kathryn Evans |
Post Doc |
Paul Bieniasz, Ph.D.
Cecilia Cheng-Mayer, Ph.D. 
Robert Gifford, Ph.D. 
Theodora Hatziioannou, Ph.D.
David D. Ho, M.D.
Yaoxing Huang, Ph.D.
Martin Markowitz, M.D.
Moriya Tsuji, M.D., Ph.D.
Sandhya Vasan, M.D.
Masahiro Yamashita, Ph.D.