My research focuses on viral pathogens and mechanisms of virulence. Two virus groups are studied in my laboratory, Poxviruses (relatives of smallpox), and Coronaviruses, which include the human Severe Acute Respiratory Syndrome (SARS) virus. Both virus groups are of concern in human and veterinary health.
Poxvirus - Smallpox is a Category A biological disease agent which has been identified by the US Government as the primary bioterrorism/biowarfare threat. In addition, other poxviral diseases are evolving and emerging anew. In South America, a vaccinia virus derived from the smallpox vaccine strain is spreading in the human population, thus far causing mild disease. In Africa and more recently in North American, monkeypox has entered the human population, sometimes causing fatality rates similar to smallpox.
Coronavirus - The emergence of SARS represents the most significant viral evolution event in infectious disease since HIV. Previously coronaviruses had received little research attention and caused no significant human disease. When we sequenced and analyzed the SARS genome (Science 2003) we discovered this virus belongs to a new, previously unrecognized, group of coronaviruses. While the initial outbreak was controlled, the continuing transfer of SARS from animals to humans in Asia suggests that it may only be a matter of time before another important mutation occurs releasing a new virulent and transmissible 'SARS 2'.

My lab pursues three main areas of research:
Bioinformatics- Bioinformatics is the use of computers to analyze biological information and is essential to genome analysis of poxviruses and coronaviruses, which have some of the largest genomes of all viruses. We use bioinformatic analysis to mine the genomes of these pathogens for information and to form hypotheses about viral virulence mechanisms. My lab has been involved in the development and use of bioinformatics software and databases for the analysis of viral genomes. These software suites can be viewed at www.poxvirus.org and www.sarsresearch.ca. With these programs, we have grouped poxvirus and coronavirus genes into homologous families or orthologous clusters, identified conserved protein motifs and structural features, and identified conserved genes, which likely form the minimum essential genome. These analyses highlight genes of interest for further biochemical and biological characterization.
Virulence factors - Why are some viruses so virulent, while closely related viruses are not? Bioinformatic analysis indicates that the large linear viral genomes of these pathogens encode a number of unique gene sequences compared to less virulent relatives. In addition putative genes of unknown function have been identified, some of which have interesting motifs or homologies that are suggestive of a particular function. These hypotheses can then be tested directly to elucidate the role of these proteins in the ability of the virus to cause disease. For many of these genes it has not even been documented whether the predicted protein is made. Our lab works to determine the expression and timing of various interesting proteins, the function of the protein in the virus life cycle and in controlling host anti-viral responses. Many of these target proteins are likely to be useful for therapeutic drug and vaccine design. I am working in collaboration with the SARS Accelerated Vaccine Initiative of Canada to develop and test SARS vaccines.
Virion morphogenesis - Spread of a virus within an individual, or transmission during an epidemic, requires viral replication and formation of complete virus particles with surface proteins that bind to host cell receptors. Poxviruses and Coronaviruses both display viral attachment proteins on membranous viral envelope that has been usurped from host cell membranes. The formation of the nascent virus particle and the interactions of viral proteins with host membranes in order to facilitate this essential membrane wrapping process is also a focus of my lab.

N. Chen, G. Li, M. K. Liszewski, J. Atkinson, P. Jarhling, Z. Feng, J. Schriewer, C. Buck, C. Wang, E. J. Lefkowitz, J. J. Esposito, T. Harms, I. K. Damon, R. L. Roper, C. Upton, and R. M. L. Buller. 2005. Virulence differences between monkeypox virus isolates from West Africa and the Congo basin. Virology. 340;46-63, July.

Li, G., N. Chen, R. L. Roper, Z. Feng, A. Hunter, M. Danila, C. Upton and R. M. L. Buller. 2005. Complete Coding Sequences of the Rabbitpox Virus Genome. J. Gen. Vir; 86:2969-77.)

D. M. Skowronski, C. Astell, R. C. Brunham, D. E. Low, M. Petric, R. L. Roper, P. J. Talbot, T. Tam, L. Babiuk. 2005. Severe Acute Respiratory Syndrome (SARS): A Year in Review. Annual Review of Medicine, 56:357-381.

R. Brodie, R.L. Roper, A.J. Smith, V. Tcherepanov,and C. Upton. 2004. Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments. BMC Bioinformatics. 5:96.

Roper, R. L. ³Rapid Preparation of Vaccinia Virus DNA Template for Analysis and Cloning by PCR² in Methods in Molecular Biology, S. Isaacs Ed. 2004. 269:113-8.

M. A. Marra, S. J. M. Jones, C. R. Astell, R. A.Holt , A. Brooks-Wilson, Y. S. N. Butterfield , J. Khattra, J. K. Asano, S. A. Barber, S. Y. Chan, A. Cloutier, S. M. Coughlin, D. Freeman, N. Girn, O. L.Griffith, S. R. Leach, M. Mayo, H. McDonald, S. B.Montgomery, P. K. Pandoh, A. S. Petrescu, A. G. Robertson, J. E. Schein, A. Siddiqui, D. E. Smailus, J. M. Stott, G. S. Yang, F. Plummer, A. Andonov, H. Artsob,N. Bastien, K. Bernard, T. F. Booth, D. Bowness, M. Drebot, L. Fernando, R. Flick, M. Garbutt, M.Gray, A. Grolla, S. Jones, H. Feldmann, A. Meyers, A. Kabani, Y. Li, S. Normand, U. Stroher, G. A. Tipples, S. Tyler, R. Vogrig, D. Ward, B. Watson, R. C.Brunham, M. Krajden, M. Petric, D. M. Skowronski, C.Upton, R. L. Roper. 2003. The Genome Sequence of the SARS-Associated Coronavirus. Science. 300(5624):1399-404.

Upton C, Slack S, Hunter AL, Ehlers A, Roper RL. Poxvirus Orthologous Clusters: Toward Defining the Minimum Essential Poxvirus Genome. Journal of Virology. 2003 Jul; 77(13):7590-600.

Brodie, R, R. L. Roper, and C. Upton. 2004 JDotter: A Java Interface to Multiple DotPlots Generated by Dotter. Bioinformatics. 20:279-281.

Roper, R. L., B. Graf, and R. P. Phipps. 2002. Prostaglandin E2 and cAMP Promote B Lymphocyte Isotype Switching to IgG1. Immunology Letters. 84(3):191-198.

Ehlers, A., J. Osborne, R. L. Roper, S. Slack, and C. Upton. 2002. Poxvirus Orthologous Clusters. Bioinformatics 18:1544-1545.

Roper, R. L. and B. Moss. 1999. Envelope Formation is Blocked by Mutation of a Sequence Related to the HKD Phospholipid Metabolism Motif in the Vaccinia Virus F13L Protein. Journal of Virology. 73:1108-1117.