Detection and identification of dangerous pathogens
Using metagenomic surveillance and broad-spectrum diagnostics to detect dangerous pathogens
This profile is tailored towards students studying biological sciences and engineering, however we expect there to be valuable open research questions that could be pursued by students in other disciplines.
Why is this a pressing problem?
Pandemics could pose an increasing threat to humanity’s flourishing in the future. ‘Spillover events’ where pathogens jump from animals to humans are increasing due to factors like habitat destruction and intensive farming; technological advances are increasing the number of people who can synthesise dangerous pathogens; and an increasing number of laboratories are working with pathogens that could cause pandemics if accidentally released. Early detection to limit the spread and allow countermeasures to be taken is key to limiting the harm when a pathogen with pandemic potential next emerges.
This is where biosurveillance – ‘the detection and monitoring of biological agents to prevent biological threats’ – is important. Although still extremely expensive, metagenomic monitoring is one promising approach because it’s pathogen agnostic; it allows the detection of all microorganisms in a sample without prior knowledge of their identities, meaning novel pathogens can be detected. There are three kinds of metagenomic monitoring: environmental surveillance, which involves testing samples from the built environment, such as from wastewater or air filters that aggregate over many people; sentinel surveillance, which involves collecting samples from a pool of the population, potentially those at particularly high risk of exposure to pathogens; and clinical metagenomics, which involves sequencing samples from patients in clinics and hospitals.
In the video below, Dr Pardis Sabeti and Dr Christian Happi discuss SENTINEL, their proposed early warning system that uses CRISPR-based diagnostics and metagenomic sequencing to detect viral threats.
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Contributors: This profile was last updated 5/12/2022. Thanks to Jeff Kaufman, Mike McLaren, Vivian Belenky for helpful feedback. All errors remain our own. Learn more about how we create our profiles.
