Projects
In addition to providing bioinformatics
support to the BCCDC community, the Genome Research Lab leads a number
of our own initiatives.
Genomic Surveillance of Pandemic H1N1 Influenza
- BCCDC Project Leads: Dr. Robert Brunham, Dr. Judith Isaac-Renton, Dr. Jennifer Gardy, Dr. Patrick Tang
- Participating Institutions: BC Centre for Disease Control, Canada’s Michael Smith Genome Sciences Centre, UBC Centre for Health Evaluation and Outcome Sciences, First Nations and Inuit Health
- Funding: $350,000 from Genome British Columbia, $350,000 from BCCDC
- Term: November 1, 2009 – October 31, 2010
The influenza A genome exhibits remarkable plasticity, with both rapid accumulation of point mutations (drift) and complete and frequent replacement of viral genome segments within and between strains (reassortment) shaping the evolution of the virus. This mutability engenders continued frustration in the public health community, with officials forced to direct their intervention efforts at a constantly moving target. Mutation, recombination, and reassortment frequently give rise to influenza isolates resistant to antivirals, as well as multiple incidences of vaccine mismatch. Periodically, reassortment across species boundaries can also result in the emergence of a novel pandemic virus. Once firmly established in the human population, the pandemic virus is then further subject to drift and reassortment as well as adaptation to its new host.
The 2009 pH1N1 outbreak is the first pandemic for which real-time sequencing of the virus is feasible, allowing us to monitor the evolution of the virus as it drifts, reassorts, and adapts. Thus, the first goal of our proposed program of research is to combine targeted sentinel sequencing of specific viral segments with whole genome sequencing of selected isolates to monitor the emergence of mutations associated with antiviral resistance, vaccine efficacy and influenza pathogenesis and the dynamics of viral evolution over the course of the 2009-2010 influenza season in British Columbia. We are also undertaking a metagenomics project, profiling the respiratory microbiome of patients with mild and severe H1N1 to identify co-infecting bacteria and viruses, as well as a social sciences project examining social and ethical issues surrounding the pandemic.
40 TB Genomes
- BCCDC Project Lead: Dr. Patrick Tang (Co-leads: Dr. Brunham, BCCDC; Dr. Fiona Brinkman, Simon Fraser University; Dr. Steven Jones, Genome Sciences Centre)
- Participating Institutions: BC Centre for Disease Control, Canada’s Michael Smith Genome Sciences Centre, Simon Fraser University
- Funding: $150,000 from Genome British Columbia, $100,000 from First Nations and Inuit Health, $155,000 from BCCDC
- Term: September 1, 2008 – May 27, 2010
Mycobacterium tuberculosis infects a third of the world’s population, and multidrug-resistant TB is a growing problem worldwide. Although many advances in TB diagnosis, prevention, and treatment have been made throughout the 20th century, if we are to reduce the impact of this re-emerging disease globally, new directions are needed. By examining an outbreak of tuberculosis in a British Columbia population at the genomic level, we hope to gain more insight into biology of this organism and how small changes in its genome may have larger impacts on its pathogenesis and transmission.
S. pneumoniae Genome Sequencing
- BCCDC Project Leads: Dr. Linda Hoang, Dr. Patrick Tang (Co-lead: Dr. Fiona Brinkman, Simon Fraser University)
- Participating Institutions: BC Centre for Disease Control, Simon Fraser University, Canada’s Michael Smith Genome Sciences Centre, St. Paul’s Hospital
- Funding: Internal
From 2006-2007, an impoverished Vancouver neighbourhood was the focal point of an outbreak of invasive pneumococcal disease caused by serotype 5 S. pneumoniae. Together with the St. Paul’s Hospital researchers who led the outbreak investigation, a team of researchers at BCCDC and Simon Fraser University have sequenced the genome of the outbreak organism and are in the process of examining genomic correlates of IPD severity.