Completed Infection & Immunity Genetics & Molecular Biology

Putting genomic surveillance at the heart of viral epidemic response.

Funder Wellcome Charity-funded
Associated organisations University of Birmingham · University of Cambridge Europe PMC affiliations are not treated as award recipients or mapped locations.
Funding £3.0M
Period Aug 2017 — Sept 2022

In plain English

AI plain-English summary

A portable DNA sequencer, small enough to pack in a suitcase, will be deployed to remote outbreak zones to decode viral genomes in real time. Current epidemic response relies on slow, centralised lab analysis. By the time genomic data arrives, the outbreak may have already shifted. This project builds a complete system—from patient sample to public health action—that works without internet or specialist bioinformaticians. The core innovation is the MinION, a single-molecule sequencer that reads viral RNA directly in the field. New molecular methods will even distinguish individual viruses within a single patient, revealing how the pathogen evolves as it spreads. If successful, public health bodies could track transmission chains, detect new mutations, and link cases within days of sampling, not weeks. This would transform outbreak management for fast-evolving RNA viruses like Ebola, MERS, and influenza, particularly in resource-limited settings where delays are most costly. A web-based visualisation platform will make the resulting epidemiological insights accessible to non-specialists, putting genomic surveillance directly into the hands of those who need it most.

View original technical description
This proposal is to develop an end-to-end system for processing samples from viral outbreaks to generate real-time epidemiological information that is interpretable and actionable by public health bodies. Fast evolving RNA viruses (such as Ebola, MERS, SARS, influenza etc) continually accumulate changes in their genomes that can be used to reconstruct the epidemiological processes that drive the epidemic. Based around a recently developed, single-molecule portable sequencing instrument, the MinION, we will create a 'lab-in-a-suitcase' that will be deployed to remote and resource-limited locations. These will be used to sequence viral genomes from infected patients which will then be uploaded to a central database for rapid analysis. We will develop methods for a wide-range of emerging viral diseases. Novel molecular biology methods will allow us to sequence individual viruses within a patient. Bioinformatics tools will be developed simple enough for non-bioinformaticians to use, without reliance on Internet connectivity. We will develop software to integrate these data and associated epidemiological knowledge to reveal the processes of transmission, virus evolution and epidemiological linkage. Finally we will develop a web-based visualization platform where the outputs of the statistical analyses can be interrogated for epidemiological insights within days of samples being taken from patients.

View the original record at the funder ↗

Researchers

Ian Goodfellow (EPMC Awardee)Nicholas Loman (EPMC Awardee)

Related Research

Grants with similar aims, by meaning.

How can real-time sequencing of viral genomes help inform epidemiology and public health of acute viral epidemics?
Infection response through virus genomics
InfeCtion respONse through vIrus genomiCs (ICONIC)
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Original classification

Collaborative Award in Science

Plain English summaries and category classifications on this site are generated by AI and may not perfectly reflect the original research.