Genome science talk

Sequencing Ebola in the field

1 Sequencing Ebola in the field

Lauren Cowley @laurencowley4


• From June 2nd – July 10th 2015 I was deployed to Coyah, Guinea to use the MinION to provide real-time sequencing analysis of new positive cases of Ebola

• This was a collaboration of the University of Birmingham, Public Health England, the European Mobile Lab and the World Health Organisation


• The epidemiologist’s work to intercept transmission chains was essential

• We fed back our sequencing results in regular reports that would rule new cases into known clusters of cases or not

• The speed of MinION sequencing usually allowed us to feedback to epidemiologists within ~48hours of receiving the RNA

Working hand in hand with epidemiologists


Sequencer: Lauren Cowley

Receive RNA extraction of newpositive Ebola case from diagnostic lab

Sequencing undertaken

Working hand in hand with epidemiologists

Epidemiologist: Amy Mikhail

National coordination is made aware of new positive lab diagnosis

Transmission chain investigation and contact tracing

Case of interest is enquired about, suspected to be part of transmission chain x or new case with no known contacts

Phylogenetic tree and report fed back

Suspicions about transmission confirmed or new clustering and possible contacts elucidated

~48 hours


Data also available on virological.org and ebola.nextflu.org

Transmission chain merging


Tamaranssy chain

Filima chain


ebola.nextflu.org


Challenges of sequencing in the field• Intermittent electricity supply so have to back everything up with UPS

power to prevent a sequencing run failing just as it is starting• head torches are a godsend


Challenges of sequencing in the field• Coordinating receiving RNA from other labs is difficult as are all

logistical issues in West Africa


Challenges of sequencing in the field• The humidity caused the magnets on my MagnaRack to come unstuck

so I had magnets flying all over the room towards metal whenever it was jolted, I was therefore probably more likely to die from a flying magnet than Ebola


Challenges of sequencing in the field• The internet was absolutely appalling which made responding to critical

emails impossible and the upload of reads for bioinformatic analysis in the UK was a daily challenge that usually filled my swear jar right to the top. The only thing that seemed to reliably work was whatsapp but that doesn’t have a MinION raw reads attachment button… yet.


Challenges of sequencing in the field• There is no running water in the house where we stayed so cold

bucket showers it was every morning


Challenges of sequencing in the field• There are annoying amounts of insects everywhere and I have

very frustratingly got to the end of a library prep before only to witness a mosquito land directly in it before I could stop it.


Challenges of sequencing in the field• I have also had a 6cm long praying mantis land on my face

during a critical pipetting stage so couldn’t move


Challenges of sequencing in the field• Unwelcome rodent lab assistants, that probably carry Lassa

fever…


Benefits of sequencing in the field• Guinea is a stunning location and I got to enjoy that every morning on

the ride into work


Benefits of sequencing in the field• It was great to get the opportunity to collaborate with epidemiologists

and understand their processes in looking at chains of transmission and intercepting them

• I hope that this project will be an example for future large scale outbreaks and the use of real time sequencing to cut chains of transmission and the spread and evolution of a pathogen quickly

• The portability and ease of setup of the MinION has enabled this here.


Second time in West Africa working on the Ebola Response

• I was out in Sierra Leone in December last year working in the PHE diagnostic labs then right at the peak of the outbreak, so for me this is a huge advance in the fight against Ebola.

• I saw first hand epidemiologists being able to track transmission routes accurately with phylogenetic data in real time and then attempting to intercept the chain this time.

• This is exciting and could be the key to the end of this outbreak, and we’ve seen huge advances towards it in the last few weeks.


The Struggle goes on

We need 0 cases + 42 days before we can breathe easy


Thanks to:• Sophie Duraffour, Josh Quick and Nick Loman• European Mobile Laboratory (Stephan Gunther)• World Health Organisation• Public Health England (Miles Carroll)• Amy Mikhail, Pierre Formenty, Ettore Severi• Andrew Rambaut, Trevor Bedford

Lauren Cowley @laurencowley4

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