SEP 14, 2017 12:00 PM PDT

How to deploy a portable lab for the surveillance of emerging infectious diseases

Speaker
  • Research Fellow, University of Birmingham
    Biography
      Josh is a molecular biologist finishing up his PhD at the University of Birmingham. He is a member of Nick Loman's lab which explores the use of cutting-edge genomics and metagenomics approaches to the diagnosis, treatment and surveillance of infectious disease. In 2015 during the West-African Ebola virus outbreak he travelled to Guinea with a 'lab-in-a-suitcase' to establish a sequencing laboratory to perform genome sequencing of new cases in a matter of days. Last year, over the course of three trips to Brazil, he developed a multiplex version of the tiling-amplicon approach used previously leading to the first successful sequencing of Zika virus genomes directly from clinical samples. This was successfully used by the ZiBRA consortium and other groups investigating the origins of Zika virus in the Americas. Most recently, as part of a group of developers known as the Nanopore WGS consortium, he showed it was possible to sequence extremely long reads on the MinION using optimized extraction and rapid sequencing protocols. Generating runs with read N50's over 100 kilobases it demonstrated MinION is likely to be the platform of choice for those seeking highly contiguous assemblies for complex genomes.

    Abstract

    Genome sequencing can be used to discover new pathogens but it can also be used to monitor known ones. This is known as genomic surveillance and it becoming an increasingly important tool in the response to viral outbreaks. We have demonstrated that a portable laboratory for virus sequencing can be flown to the epicentre of an ongoing outbreak and provide rapid, actionable results from the field. This avoids the delays associated with shipping samples out the country for sequencing elsewhere. We have set up mobile labs in Guinea during the 2014 West African Ebola outbreak and to Brazil during the 2015 Zika outbreak. I will talk about what goes into building a mobile lab and the ways in which they can be of use in an ongoing outbreak.


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