| Paleovirology  | DIGS Tool 

Robert J. Gifford

Rob Gifford

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.

I think that developing an understanding of the long-term evolution and origins of viral species is an important component of efforts to counter the threat posed by contemporary viruses. 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 / Information & communication technology themes

I am committed to the development of computational innovations that enhance our capacity to share biomedical knowledge and conduct collaborative research. Our research group is currently in the process of deploying bioinformatic tools - developed in the course of our research - as online services on this website. Although the emphasis here will be on providing services associated with paleovirological analysis, our protocols have been developed to facilitate collaborative analysis of sequence data across a wide range of contexts.

Selected Publications

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

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

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 10(7):e1004214 [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. 88 (5), 2398-2405 [view]

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]


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]

Press coverage of my research

National Geographic 2013   The Amazing Story of a Mammal Virus That Became a Bird One   [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]