Siobain Duffy Assistant Professor Rutgers University Dept. of Ecology, Evolution & Natural Resources Foran Hall, Room 316 School of Env & Biol Sciences New Brunswick. NJ 08903 (732) 932-8165. Ext. 318 FAX- 0312 duffy@aesop.rutgers.edu Visit the Duffy Lab

Emerging viruses, experimental evolution, bioinformatics, bacteriophage

Experimental evolution of emerging viruses

Most viruses require a host range mutation to enter a novel host. Once able to enter, they fix additional mutations to adapt to the novel host, and to increase their transmission between hosts. While the exact mutations that are beneficial for a particular virus on a particular host are highly individual and dependent on the virus’ ecology, there may be general properties of adaptive mutations in emerging viruses that we can study in model systems. For instance, RNA viruses seem much more likely than DNA viruses to host-shift into humans -- is this because host range mutations have a lower cost in RNA viruses? Or is it because RNA viruses have higher mutation rates, and therefore more frequently sample host range mutations? Is it simply because there are many RNA viruses infecting other mammals, and it is easier for viruses to host-shift between closely related hosts?

We use experimental evolution to simulate viral emergence events on novel hosts. This allows us to study the frequency and effects of adaptive mutations in a wide variety of viruses (RNA and DNA, single- and double-stranded, segmented and monopartite). Longer evolution experiments also allow us to study the adaptive walks of these viruses as they adapt to the novel host.

Understanding viral genetic variation

As natural selection can only act on variation within a population, we also study the mechanisms by which viruses create and maintain variation: mutation, recombination, reassortment. This work spans the gamut from field work to molecular microbial genetics, and often relies on intensive sequencing of viral populations. Currently, we are focused on understanding the forces shaping diversity in natural populations of geminiviruses, which are frequently emerging pathogens of plants.Our wet lab work uses a number of bacteriophage systems, such as the highly unusual phage phi6, and the ssDNA phage phiX174. We also work on/collaborate with labs that work on circular ssDNA viruses of plants and animals (anelloviruses, geminiviruses, circoviruses, nanoviruses).

Viral Phylogenetics

We also use a variety of bioinformatic methods, including Bayesian coalescent approaches, to assess how, and how quickly, viruses are evolving. Our interests range from the theory-laden (do segmented viruses evolve more quickly than monopartite viruses?) to applied molecular epidemiology (how quickly are emerging plant pathogens spreading in North America?)

Selected Publications

Firth C, Charleston MA, Duffy S, Shapiro B, Holmes EC. (2009) Insights into the evolutionary history of an emerging livestock pathogen: Porcine Circovirus 2. J Virol. Oct 7. [Epub ahead of print]

Harkins GW, Martin DP, Duffy S, Monjane AL, Shepherd DN, Windram OP, Owor BE, Donaldson L, van Antwerpen T, Sayed RA, Flett B, Ramusi M, Rybicki EP, Peterschmitt M, Varsani A. (2009) Dating the origins of the maize-adapted strain of maize streak virus, MSV-A. J Gen Virol. Aug 19. [Epub ahead of print]

Cuevas JM, Duffy S, Sanjuán R. Point Mutation Rate of Bacteriophage {Phi}X174. (2009) Genetics. 183(2):747-9.

Harkins GW, Delport W, Duffy S, Wood N, Monjane AL, Owor BE, Donaldson L, Saumtally S, Triton G, Briddon RW, Shepherd DN, Rybicki EP, Martin DP, Varsani A. (2009) Experimental evidence indicating that mastreviruses probably did not co-diverge with their hosts. Virol J. 6:104.

Rosario K, Duffy S, Breitbart M. (2009) Diverse circovirus-like genome architectures revealed by environmental metagenomics. J Gen Virol. Jul 1. [Epub ahead of print]

Duffy S, Holmes EC. (2009) Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses. J Gen Virol. 90(Pt 6):1539-47.

Duffy S, Shackelton LA, Holmes EC. Rates of evolutionary change in viruses: patterns and determinants.(2008) Nat Rev Genet. 9(4):267-76.

Duffy S, Holmes EC. (2008) Phylogenetic evidence for rapid rates of molecular evolution in the single-stranded DNA begomovirus tomato yellow leaf curl virus. Virol. 82(2):957-65.

Duffy S, Burch CL, Turner PE. (2007) Evolution of host specificity drives reproductive isolation among RNA viruses. Evolution. 61(11):2614-22.

Duffy S, Holmes EC. (2007) Multiple introductions of the Old World begomovirus Tomato yellow leaf curl virus into the New World. Appl Environ Microbiol. 73(21):7114-7.

Duffy S, Turner PE, Burch CL. (2006) Pleiotropic costs of niche expansion in the RNA bacteriophage phi 6. Genetics. 172(2):751-7.

Duffy S, Schaffner DW. (2002) Monte Carlo simulation of the risk of contamination of apples with Escherichia coli O157:H7. Int J Food Microbiol. 78(3):245-55.

Duffy S, Tsao KL, Waugh DS. (1998) Site-specific, enzymatic biotinylation of recombinant proteins in Spodoptera frugiperda cells using biotin acceptor peptides. Anal Biochem. 262:122-128.