Disease Detectives: Taking Whole Genome Sequencing to the field for Ebola surveillance

Dr Lauren Cowley, previously a PhD scholar at PHE and now a postdoctoral researcher at the Harvard T.H. Chan School of Public Health, tells us about her time engaged on the entrance line in West Africa tackling the Ebola outbreak in Sierra Leone and Guinea. All pictures have been taken by Lauren in the areas she labored.

The information of the latest Ebola outbreak in the Democratic Republic of Congo brings again recollections of the  2013-16 Ebola disaster in West Africa which was a shock to the entire world.

It highlighted the significance of investigating and responding to illness outbreaks earlier than they change into a world risk. The international locations affected, particularly Sierra Leone, Guinea and Liberia, suffered main lack of life with a really excessive case fatality charge, in addition to injury to their financial system and infrastructure.

During this time, I used to be in the identical place as most – following the information and feeling helpless as I watched the tragedy unfold and worsen over time. Although I used to be a PhD Student at PHE at the time, the thought of being concerned in tackling this outbreak didn’t cross my thoughts, not to mention travelling to the affected international locations to work in the field.

Soon this grew to become a actuality for me in November 2014, once I utilized to be deployed to Sierra Leone. Suddenly, I used to be now not only a spectator. I went from engaged on nationwide diarrheal outbreaks in the UK, to engaged on the entrance line in Africa, responding to considered one of the largest, most threatening, and most well-known illness outbreaks in modern-day historical past.

My first deployment: Sierra Leone

In November 2014, I went to Sierra Leone for six weeks to work in the diagnostic laboratory, working blood, swab and urine samples to detect the presence of Ebola.

The signs of Ebola, particularly at first, might be very generic as they embrace fever, diarrhoea and vomiting. As such, sickness might usually be mistakenly ascribed to different pathogens which might be much less life threatening. This can have main implications if the pathogen inflicting sickness is, in reality, the Ebola virus.

This is why the diagnostic check was so vital – it was the solely method to categorically determine or exclude circumstances of Ebola. Diagnostic work is the first step that should be carried out to start and form the means of case response and scientific administration of the affected person.

My second deployment: Guinea

My second deployment was to Guinea in June 2015 and was in collaboration with the European Mobile Laboratory and University of Birmingham to present real-time sequencing of recent Ebola circumstances.

This alternative happened via social media. I had been in contact with contacts at the University of Birmingham (Nick Loman and Josh Quick) through Twitter, discussing my experiences throughout my first deployment. At the time, I used to be in the remaining 12 months of my PhD, and was considerably lacking the pleasure and sense of fulfilment from my first journey to West Africa. Therefore, when Miles Carroll, PHE’s Head of Research, contacted me to see if I’d be thinking about a real-time Ebola sequencing venture, it was a right away ‘yes’, and I used to be in Guinea inside three weeks of receiving the first e-mail about it.

Using Whole Genome Sequencing in the field

As the Ebola virus is unfold via human-to-human transmission, Whole Genome Sequencing was a vital method to use in surveillance and case response. The extremely correct method permits the route of transmission to be traced all through a rustic and past, characterises the infectious agent, and offers a high-resolution view of its evolution.

To discover out extra about the means of Whole Genome Sequencing, learn our explainer weblog here.

During the Ebola outbreak, a scarcity of native sequencing capability and the difficulties of transporting samples to sequencing services distant meant that genomic surveillance was inconsistent. However, common genomic surveillance is vital, as the sequence information can be utilized to information management measures, whether it is generated shortly sufficient.

Before being deployed, the staff I labored with devised a genomic surveillance system utilizing a novel nanopore DNA sequencing instrument, which weighed lower than 100 grams. A nanopore is a protein with a really small gap that enables DNA strands to be pushed via it utilizing an electrical present. As every nucleotide passes via the pore, the present is affected and this alteration permits the sequence to be recorded.

All collectively, our system consisted of three of those devices, 4 laptops, a thermocycler, a warmth block, pipettes, and ample reagents and consumables. In April 2015, the staff packed this into common airline baggage and transported it to Guinea, the place they started utilizing the system for real-time genomic surveillance of the Ebola outbreak.

Components of the genomic surveillance system arrange in the laboratory in Guinea

Once I joined the staff in Guinea, I used the surveillance system to perform real-time sequencing and evaluation of all new Ebola circumstances for 5 weeks. We labored in partnership with native Guinean diagnostic laboratories to present the sequencing outcomes to the National Coordination in Guinea, which was offered by the World Health Organisation (WHO). We have been in a position to generate outcomes lower than 24 hours after receiving a constructive pattern, and the sequencing course of itself took as little as 15 to 60 minutes.

Setting up the laboratory

Our laboratory was a small, hut-like delivery container, which we arrange at an Ebola remedy centre in what appeared like the center of nowhere. Despite being in a remedy centre, we weren’t at risk of contracting the virus inside our hut as we have been in a ‘neutral zone of containment’, separate to the place the sufferers have been staying and the different aspect of all containment measures. This meant that the virus was contained and prevented, by a number of measures, from escaping into this zone.

It was fully secure to be dealing with the samples we have been working with, that means we didn’t have to put on private protecting tools. We have been solely working with the uncooked extracted genetic materials of the virus, and never all the viral equipment that’s contained inside the viral cell. The virus requires extra than simply its uncooked genetic materials to successfully infect a human cell.

The delivery container laboratory in Guinea

Advanced applied sciences in resource-limited situations

Working in resource-limited situations and organising our personal laboratory meant that we confronted inevitable obstacles alongside the method.

We encountered a number of logistical points throughout our time in Guinea, with maybe the most difficult being the lack of dependable, steady energy. This meant that we had to rely on unreliable electrical mills and uninterruptable energy provides that present emergency battery energy.

Further to this, web connectivity was persistently poor, which significantly disrupted our skill to ship information again to colleagues at the University of Birmingham for evaluation. I usually couldn’t entry the sequencing software program, and due to this fact had to ship uncooked learn information. Our Birmingham companions would then ship again details about the relatedness of recent circumstances to others already sequenced, and I labored intently with epidemiologists at the WHO to set up transmission chains.

Considering these challenges, I’m happy with the work I did inside this staff, as I feel we demonstrated the risk of conducting such a sophisticated and impactful course of in such resource-limited environments.

How I felt: The variations between the two journeys

It goes with out saying that it’s nerve-racking to be deployed to a rustic the place there’s an energetic, lethal illness outbreak, inflicting lack of life at a speedy charge. Normally, you’d keep away from a spot like this in any respect prices, so on my first journey I used to be cautious and naturally nervous.

I felt extra comfy on my second deployment and I used to be in a position to get pleasure from the work I used to be doing extra. Being the quickest sequencing performed throughout a serious outbreak to date, it felt like I used to be concerned in one thing novel and vital, significantly because it was influencing the scope of future work and choices.

Despite the pleasure of my function, the actuality of the scenario was that there was loss of life, ache and social disarray throughout us. The reminiscence of seeing two docs wearing full protecting fits feeding a dying 8-year-old lady contemporary coconut water, after she had requested it as her final want, won’t ever go away me.

Everything about Ebola and the causes behind why we have been there’s tragic, nonetheless being part of the international effort to battle it was very rewarding and has taught me invaluable life classes.

This programme of labor was awarded the PHE Research Innovation Award in 2016. A present PhD scholar at PHE has not too long ago returned from Nigeria, the place she was part of a staff that efficiently utilized the identical know-how Lauren labored on to the Lassa fever outbreak.

Read extra from Disease Detectives – keeping track of new and emerging infectious diseases.

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