Location:
Level 6, Seminar Room Wallace Wurth Building UNSW Australia Sydney NSW 2052
Open to
All
Contact for enquiries
Rata Joseph +61 (0)2 9385 0900 rjoseph@kirby.unsw.edu.au
The Kirby Institute is pleased to present:
Dr Matthew Scotch -Assistant Professor, Department of Biomedical Informatics
Assistant Director, Center for Environmental Security, Biodesign Institute
Arizona State University
“Population health surveillance of RNA viruses through phylogeography.”
Lunch will be served from 12.30 in the foyer of level 6, Wallace Wurth Building.
Please RSVP to rjoseph@kirby.unsw.edu.au for catering purposes at COB Wednesday 8th June 2016.
Abstract:
There is now a greater need to integrate virus sequence data into public health surveillance. This is particularly relevant for zoonotic viruses that are transmittable between animals and humans such as influenza, rabies, and West Nile Virus. This talk will cover two United States NIH-funded projects related to virus phylogeography and phylodynamics that aim to address complex public health issues through analysis of virus sequences.
Tracking evolutionary changes and virus spread requires the geospatial assignment of taxa, which is often obtained from GenBank (NCBI/NIH) metadata. Unfortunately, geospatial metadata such as host location is often uncertain in GenBank entries, with only 36% containing a precise location such as a county, town, or region within a state. For example, information such as “China” or “USA” is more often indicated instead of “Beijing” or “Bedford, NH, USA”. While town or county might be included in the corresponding journal article, this valuable information is not available for immediate use unless it is extracted and then linked back to the appropriate sequence. The goal of the first study is to enable health agencies and other researchers to automatically generate phylogeographic models that incorporate enhanced geospatial data for better estimates of virus spread. This project focuses on developing and applying information extraction and statistical phylogeography approaches to enhance models that track evolutionary changes in viral genomes and their spread. We are developing a framework that uses natural language processing (NLP) for the automatic extraction of relevant geospatial data from the literature, and assigns a confidence between such geospatial mentions and the GenBank record.
The goal of the second project is to develop and evaluate a bioinformatics system that merges virus sequence data with climate, population, and travel data to study spread of zoonotic viruses. Here we note that there are many potential drivers of virus transmission that need to be considered including climate, population and travel, and ultimately, genetic polymorphisms in the virus itself. We are developing an online portal for generating sophisticated models of virus spread so that health agencies can prioritize control measures and reduce morbidity and mortality from zoonotic viruses.
Bio:
Dr. Matthew Scotch is an Assistant Professor in the Department of Biomedical Informatics and Assistant Director of the Biodesign Center for Environmental Security at Arizona State University. His research focuses on the theory and application of phylogeography to study the migration of zoonotic RNA viruses with a particular interest in influenza A viruses. Work in his lab includes the integration, analysis, and presentation of viral genetics for public health/animal health surveillance.
Current projects include studying approaches to advance:
* Phylogeography models in order to identify climate, population, and genetic factors that support viral spread. Funding: NIH/NLM R01LM012080
* Geospatial metadata in virus sequence databases and approaches to include observation error for virus phylogeography. Funding: NIH/NIAID R01AI117011
Dr. Scotch’s lab is also interested in the molecular epidemiology of zoonotic viruses including the amplification and sequencing of influenza A genes for studying spread among avian and human hosts.
Dr. Scotch received a Masters in Biomedical Informatics from Columbia University, a PhD in Biomedical Informatics from the University of Pittsburgh, and a Masters of Public Health (MPH) from Yale University. He also did his postdoctoral training at Yale University.