Digital Pathogen Surveillance: a new paradigm for outbreak detection and response?

Portable genome sequencing, coupled to digital platforms for epidemiological surveillance and data-sharing, could change the way we respond to outbreaks of infectious disease. But are we ready for this new model of public health response?

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The paper in Nature Reviews Genetics is here:

This review was a long time coming…

If you want to go right back to the beginning, I suppose it would be around 2009/10. I’d just started my first “grown-up scientist” job at the BC Centre for Disease Control, and was messing around with data that ended up being the first paper to use whole genome sequencing to characterize multiple person-to-person transmission events in a large outbreak of a bacterial infectious disease (Gardy et al, NEJM, 2011). At the same time, my co-author Nick Loman was a Research Associate (and PhD student!) at the University of Birmingham and was working on similar problems – how could bacterial genome sequencing be deployed to understand outbreaks of infectious disease? The community of researchers who would eventually unite under the banner of “genomic epidemiology” was small at that point, but many of us were active on Twitter. We used the digital platform as a way to share papers, pipelines, and data and just banter back forth about all things microbial WGS. Little did we know that our research interests and our penchant for digital communication would one day lead to this article.

Over the next five years or so, genomic epidemiology for bacterial infectious diseases took off. At the same time, the viral evolutionary genomics and the bacterial genomics communities started mixing to a degree they hadn’t before, aided in no small part by Twitter. Coupled to in-person meetings at conferences, by 2015 there was quite a network of friends and colleagues with an interest in using sequencing as a tool to respond to outbreaks, viral or bacterial, and in practicing open science, using digital platforms to share sequences and analysis in real time. Three of us – myself, Nick, and Andrew Rambaut – wrote a short editorial on this emerging notion of digital pathogen surveillance, and Nick’s team found themselves putting portable sequencers to the test in the later stages of the West African Ebola outbreak, with Andrew and other colleagues contributing much to the data-sharing and analytical efforts.

In March 2016, Nature Reviews Genetics approached Nick about an extended review of portable sequencing in outbreak scenarios and we agreed to take on the task. We had most of a draft ready to go and then…. Zika.

The virus had been on public health’s radar for a few months and was about to be declared a Public Health Emergency of International Concern by the WHO. It was too much for Nick to resist, who managed to obtain some emergency grant funding from the Medical Research Council and Wellcome Trust, and so together with many friends from our digitally-connected community, he set off for Brazil and the ZIBRA project, using portable sequencers to track the virus in patient and mosquito samples.


The ZIBRA mobile lab, watercolour by Matthew Cotten.


While the trip delayed our writing process by a year, it really changed the direction of the review and helped us flesh out our vision of digital pathogen surveillance. It revealed many of the challenges associated with in situ sequencing for diagnosis and outbreak response – challenges which hadn’t been as apparent in the Ebola outbreak, and it got our community thinking about the One Health ethos to a degree we hadn’t before – how could we include vector, veterinary, and environmental samples to better understand disease ecology? It also suggested that digital platforms weren’t just good for sharing information during an outbreak response, but that they could also be signals of the start of an outbreak – WhatsApp played a critical role in the early detection of cases of microcepahly in Brazil, for example.

The new perspective that Zika afforded us ended up making for a much stronger article in which we present (what we think is) a compelling vision for bringing in country genomic epidemiology together with digital epidemiology, all informed by the One Health ethos. We know that this is just a starting point, though – there will be another Ebola, another Zika, and with those events, our take on digital pathogen surveillance will undoubtedly evolve even further. We can’t predict where or when that next event will occur, but we can confidently say one thing – that when it does, it will be sequenced and it will be tweeted. Follow us (@jennifergardy and @pathogenomenick) and join in!

Jennifer Gardy

Senior Scientist, BC Centre for Disease Control

Jennifer is interested in how genomics can be used to answer questions in communicable disease epidemiology. When not tracking outbreaks with sequencing, she can be found presenting science TV programs in her native Canada.