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Towards a genomics-informed, real-time, global pathogen surveillance system

Nature Reviews Genetics volume 19, pages 920 (2018) | Download Citation


The recent Ebola and Zika epidemics demonstrate the need for the continuous surveillance, rapid diagnosis and real-time tracking of emerging infectious diseases. Fast, affordable sequencing of pathogen genomes — now a staple of the public health microbiology laboratory in well-resourced settings — can affect each of these areas. Coupling genomic diagnostics and epidemiology to innovative digital disease detection platforms raises the possibility of an open, global, digital pathogen surveillance system. When informed by a One Health approach, in which human, animal and environmental health are considered together, such a genomics-based system has profound potential to improve public health in settings lacking robust laboratory capacity.

Key points

  • Despite the recommendations of many expert groups, public health surveillance systems have not yet improved to the point where emerging infectious threats can be better anticipated. The Ebola and Zika epidemics are the latest to demonstrate that pathogens often spread undetected for some time before being diagnosed in a population.

  • Next-generation sequencing, particularly the use of portable genomic sequencers, offers an intriguing solution to the diagnosis and surveillance problems — it enables rapid in situ diagnostics through amplicon-based or metagenomics approaches and creates a stream of genomic data that can reveal critical epidemiological aspects of an outbreak or epidemic's dynamics.

  • Genomic epidemiology for rapid outbreak response has demonstrated some early successes in Ebola and Zika, but there are a number of challenges to overcome — some technical and some cultural. Data sharing is one of these, but other ethical and legal issues must be considered.

  • The power of a genomic epidemiology approach could be extended by incorporating concepts from digital disease detection and One Health. By coupling sequencing to an enhanced surveillance and response platform, we could take a more anticipatory approach to outbreak prevention and control.

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J.L.G. is funded by the Canada Research Chairs and Michael Smith Foundation for Health Research programmes.

Author information


  1. British Columbia Centre for Disease Control, Vancouver, British Columbia V5Z 4R4, Canada.

    • Jennifer L. Gardy
  2. School of Population and Public Health, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.

    • Jennifer L. Gardy
  3. Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK.

    • Nicholas J. Loman


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Both authors contributed equally to all aspects of the article.

Competing interests

J.L.G. declares no competing interests. N.J.L. has received travel expenses and accommodation and an honorarium payment from Oxford Nanopore Technologies to speak at organized symposia. N.J.L. is a member of the Oxford Nanopore MinION Access Programme and has received reagents for nanopore sequencing free of charge.

Corresponding author

Correspondence to Jennifer L. Gardy.


Public health surveillance

The systematic collection, analysis and dissemination of health-related data to support planning, implementation and evaluation of public health practices and response.


Outbreaks and epidemics are both defined as increases in the number of cases of a particular disease beyond what is expected in a given setting. In outbreaks, the affected settings are smaller geographic regions; epidemics can span larger areas.


An epidemic that has grown to span multiple countries or continents, often with many affected individuals.


A group of epidemiologically related cases defined by their relationship in space and time or via molecular methods.


The sequencing of genetic material recovered directly from a sample, whether environmental or clinical, permitting the identification of all organisms represented in the sample.

Bait probes

Nucleic acid probes designed to recognize and capture specific DNA sequences, allowing for the enrichment of DNA from a specific organism of interest.

Emerging infectious diseases

(EIDs). Diseases that have recently appeared in a population or that have transitioned from a small number of isolated cases to many cases.


The event through which a pathogen is transferred from one entity to another. Transmission can be person-to-person, as in the case of Ebola, vector-to-person, as with Zika, or environment-to-person via routes including food, water and contact with a contaminated object or surface.

Genomic epidemiology

The use of genome sequencing to understand infectious disease transmission and epidemiology. See Fig. 3.

Basic reproductive number R0

The average number of secondary cases of an infectious disease produced by a single infectious case, given a completely susceptible population.


A term describing infectious diseases that typically exist in an animal reservoir but that can be transmitted to humans.

Survivor transmission

The transmission of an infectious disease, such as Ebola, from a survivor of that disease who has recovered from their symptoms.


A term describing infectious diseases that are transmitted to humans through contact with a non-human species, particularly those diseases spread through insect bites. An example is the Zika virus, which is carried by mosquitos.

Hot spots

Geographical settings where a variety of factors converge to create the social and environmental conditions that promote disease transmission.


The process by which an infectious disease changes from existing exclusively in animals to being able to infect, then transmit between, humans. See Fig. 4.

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