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Mar - Jeff Joy

Speaker: Jeff Joy

Talk Title: “Evolutionary genetic applications to disease analysis and monitoring: from science to public health benefit”

Event Details


Thursday, March 14, 2019 5:30 – 6:30 PM


Location: Room 2314, AMS Student Nest, 6133 University Blvd, University of British Columbia, Vancouver

Organized in conjunction with BIG19 Research Day

Affiliation: Research Scientist, BC Centre for Excellence in HIV/AIDS (BCCfE)

Web-site: Jeff Joy


Viral pathogens diversify rapidly both within individual hosts and among populations of hosts. The resulting hierarchies of viral genetic diversity present challenges for clinical care and public health and unparalleled opportunities to study evolution. Evolutionary genetic thinking, methods, and tools when integrated with clinical characteristics and molecular sequence data derived from viral pathogens lead to strong inferences. In my laboratory we apply such integrative analyses to studies of a variety of viral pathogens including HIV and HCV at all levels of epidemic hierarchies: from population to patient. A key problem at the population level is that it is becoming increasingly difficult to both 1) identify new diagnoses and 2) identify remaining pockets of ongoing viral transmission, particularly in well-managed epidemics in the developed world. One approach to this is through phylogenetic monitoring – the process by which in near real time clusters of diagnoses are identified through harnessing of large, rapidly growing, sequence databases with bioinformatic and computational tools. A second key problem at the patient level is the analysis of next generation sequencing data derived from individual infections when the viral population is composed of a mixture of lineages derived from different sources. In this seminar I will first discuss methods and applications of phylogenetic monitoring of HIV at the population level within BC and Canada; second at the patient level I will discuss analyses of individual infections of HCV derived from multiple infections with different lineages.

Introductory Speaker: Kevin Kuchinski (MSc student, Prystajecky Lab, BC Centre for Disease Control)

Title: “A pipeline for designing hybridization probes against highly diverse viral pathogens”


Diagnosis and surveillance of viral pathogens using next-generation sequencing is hindered by vast size differences between the genomes of viruses and their hosts. To overcome excessive genomic background introduced by the host and reduce the sequencing depth required to recover viral genome sequences, hybridization probe enrichment is often used to increase the proportion of viral material in the sequencing library. In this method, synthetic DNA oligomers complementary to the viral genome are used to capture target material while background material is washed away. The design of these probe sequences presents a bioinformatic challenge for viral species with extensive genomic diversity and rapid mutation rates. This talk will discuss a pipeline for designing probe sequences against highly diverse viral pathogens. It will also demonstrate how these tools were used to recover avian influenza virus genomes in sediment from wild bird habitats in the Fraser Valley and Lower Mainland.

Webcast Link:

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