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Robert J. Gifford

Rob Gifford at Tap-o-Noth

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.



Software development

Calibrated Population Resistance Tool: I developed the original version of this tool, which aims to facilitate surveillance of transmitted HIV-1 drug resistance in resource-limited regions, in line with the recommendations of the World Health Organization (WHO).

Database-Integrated Genome Screening Tool: The DIGS-tool facilitates in silico screening of whole genome sequence data. I have used this tool extensively for paleovirological investigations.

Press coverage of my research

National Geographic 2013   The amazing story of a mammal virus that became a bird one.   [view]
The Scientist 2013   Unexpected origin of an avian virus.   [view]
BBC 2012   Ancient virus DNA thrives in us.   [view]
New York Times 2010   Hunting fossil viruses in human DNA.   [view]
The Guardian 2008   HIV's ancestor millions of years older than believed.   [view]
The New Yorker 2008   Darwins Suprise.   [view]


Selected Publications

Viral evolution in deep time (ages, epochs, eras)

Henzy J, Gifford RJ, Johnson W, and J. Coffin (2013) A novel recombinant retrovirus in the genomes of modern birds combines features of avian and mammalian retroviruses. J. Virol.

Niewiadomska AM and RJ Gifford (2013) The extraordinary evolutionary history of the reticuloendotheliosis viruses. PLoS Biology 11 (8): e1001642 [view]

Magiorkinis G, Gifford RJ, Katzourakis A, de Ranter J, and R Belshaw (2012) Env-less endogenous retroviruses are genomic superspreaders. PNAS Apr 23 [view]

Gifford RJ (2012) Viral evolution in deep time - lentiviruses and mammals. Trends in Genetics Feb;28(2):89-100. [view]

Katzourakis A. and RJ. Gifford (2010) Endogenous viral elements in animal genomes. PLoS Genetics 6(11): e1001191. [view]

Katzourakis A*, Gifford RJ*, Tristem M, Gilbert MTP, and OG. Pybus (2009) The macroevolution of complex retroviruses. Science 325:1512 [view]
* co-corresponding authors

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]

Katzourakis A, Tristem M, Pybus OG, and RJ. Gifford (2007) Discovery and analysis of the first endogenous lentivirus. PNAS 104: 6261-5 [view]

Gifford RJ, Kabat P, Martin J, Lynch C, and M. Tristem. (2005) Evolution and distribution of class II-related endogenous retroviruses. J. Virol. 79:6478-86 [view]

Gifford RJ and M Tristem. (2003). The evolution, distribution and diversity of endogenous retroviruses. Virus Genes 26:291-315 [view]

Viral evolution across shallow-intermediate timescales (days, years, centuries, millennia)

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]

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 Res. [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. 5(2):e9311. [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. Mar;83(6):2645-54. [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. 81:13050-6 [view]

Bioinformatics

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]