Presentation given at Genome Science 2015 about the use of MinION sequencing in Guinea to provide real-time sequencing results of new Ebola cases

1. Sequencing Ebola in the field
1 Sequencing Ebola in the field
Lauren Cowley @laurencowley4

2. 2 Sequencing Ebola in the field
• 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

3. 3 Sequencing Ebola in the field

4. 4 Sequencing Ebola in the field
• 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

5. 5 Sequencing Ebola in the field
Sequencer: Lauren
Cowley
Receive RNA extraction
of new
positive 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

6. 6 Sequencing Ebola in the field
Data also available on virological.org and
ebola.nextflu.org

7. Transmission chain merging
7 Sequencing Ebola in the field
Tamaranssy
chain
Filima chain

8. 8

9. 9 Sequencing Ebola in the field
ebola.nextflu.org

10. 10 Sequencing Ebola in the field
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

11. 11 Sequencing Ebola in the field
Challenges of sequencing in the field
• Coordinating receiving RNA from other labs is difficult as are all
logistical issues in West Africa

12. 12 Sequencing Ebola in the field
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

13. 13 Sequencing Ebola in the field
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.

14. 14 Sequencing Ebola in the field
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

15. 15 Sequencing Ebola in the field
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.

16. 16 Sequencing Ebola in the field
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

17. 17 Sequencing Ebola in the field
Challenges of sequencing in the field
• Unwelcome rodent lab assistants, that probably carry Lassa
fever…

18. 18 Sequencing Ebola in the field
Benefits of sequencing in the field
• Guinea is a stunning location and I got to enjoy that every morning on
the ride into work

19. 19 Sequencing Ebola in the field
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.

20. 20 Sequencing Ebola in the field
Second time in WestAfrica 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.

21. 21 Sequencing Ebola in the field
The Struggle goes on
We need 0
cases + 42
days before
we can
breathe
easy

22. 22 Sequencing Ebola in the field
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