Diagnosing Ebola – A day in the life of a diagnostics lab in Sierra Leone

It’s hot, it’s humid and you’re tasked with setting up a diagnostics lab ready to process samples that could contain a deadly virus. You’re far away from home, in a country struggling to contain Ebola. How do you cope? Leaving his lab in Cambridge, Professor Ian Goodfellow headed to Sierra Leone with the NGO International Medical Corps, to join a team putting together a diagnostic lab in Makeni. In the second of this two-part series, he explains the challenges the team had to overcome and talks us through an average day in an Ebola diagnostics lab…

During the first two weeks in Makeni, Sierra Leone, our focus was very much on getting the diagnostics lab operational as fast as possible. There was a real lack of diagnostic capacity in this area of the country the lab facility needed to go live prior to the opening of the treatment centre.

With no existing diagnostics facility, all samples were being driven (or sometimes flown on a UN helicopter) to a Centre of Disease Control (CDC) lab based in Bo. They were fantastic, but although they had a very quick turn around time for testing samples, the logistics of physically getting the samples to them meant the process was slowed down significantly. Creating a diagnostic facility in this area was key to speeding up diagnoses.

Opening a molecular diagnostic lab in the conditions we faced was not straightforward. There was a lot of waiting around for deliveries of equipment, loading the kit by hand and then shifting boxes around the camp. One of my lasting memories is having to ask the entire team to move a huge tent’s worth of equipment across the building site by hand, because the clinical staff needed the tent to store their personal protective equipment (PPE).

With the heat, humidity and the sheer volume of equipment we had to move across a live building site, it was a real challenge. What I hadn’t really factored in was that the first half of the team had already unloaded all the same boxes the previous two days into the first tent. Needless to say they were less than thrilled when we had to relocate them, but after a little discussion, the team did a fantastic job and all the kit got moved. A few days later (after the blisters had healed), this rather surreal situation became a source of amusement for us.

When the diagnostic lab opened, the rota was set up to stagger the number of people in lab, making sure we could cover the 6am-10pm opening times. Team members would start their shifts at 6am, 8am, 11am and 2pm, with the late shift staying until everything had been completed. A typical shift lasted around eight hours.

If you were working the early shift, an average day would be something like this:

5:30 am:

Wake up and brave a cold shower. Try to find something for breakfast (the guest house didn’t serve breakfast until 7am). Don’t forget to take anti-malarial, take temperature (36.3C).

~5:45 am:

Wait and hope that the driver remembers to pick you up to take you to the treatment centre.

(Logistics and transport were typically good but there were times when we had to wait around for transport.)

~6:00 am:

Arrive at Ebola Treatment Centre (ETC). (Outside the gates, three rather cold looking members of the national ETC staff would greet us.)

Wash hands with bleach, have temperature taken and answer questions to check health status. (“Do you have any bruises?”, “Did you sleep well?” etc).

Boots sprayed with bleach before entry to the ETC. Pass through changing room, don scrubs and wellington boots (I often spent 10 minutes trying, and usually failing, to find two that fit!) in order to move into the lab in the “green zone”.

(The temperature in the mornings was similar to a typical British summer, but much colder than the local staff were used to. They would find ingenious ways of keeping warm – including huddling around the open doors of the industrial clothes driers!)

~6:10 am:

Arrive at the lab and unlock it, change footwear clogs and have a quick general look around the lab to make sure power is still on and nothing has leaked.

Put on cloth gown, two pairs of gloves and goggles. Time to make up the bleach – 10,000 ppm for the dunk buckets and isolators, 5000 ppm for everything else. Mop floors, swab benches and empty buckets from the previous day.

Inspect the isolators, which are used to work with Ebola positive samples, clean them out and set up for the day ahead. Check all the stock items in the lab – do we have enough aliquots of the various reagents? Where are the 1.5ml tubes in that huge tent again? Do we have enough EDTA blood tubes prepared for the Driver?

(The one thing I will not miss is the intense smell of chlorine, we used higher concentrations in the lab than they use in the rest of the ETC and in a confined environment the chlorine fumes got rather overpowering. Even the clinical staff at the ETC commented that outside the lab the smell of chlorine was strong.)

~8:00 am:

The second shift arrives. Discuss the results from the previous day – How many positives were there? Did anything go wrong? Did all the reagents behave as they should?

(The heat and dust had all kinds of effects on the equipment and reagents. The lack of a reliable Internet connection also meant we were unable to access troubleshooting guides so relied heavily on the experience and ingenuity of team members to solve any problems.)

~8:30-11:00 am:

The first set of the day’s samples turn up. “Major” (probably not his real name) drives them in.

(Major is a locally employed member of staff who has done a heroic job over the course of the outbreak. Until the Makeni Lab opened, he was driving samples to Bo, some five hours away, everyday – an example of the sheer dedication of the locals to controlling the epidemic. All the Sierra Leonean members of staff were very proud to be able to help in any way they could.)

Don additional plastic aprons and face shields for handing and sorting incoming samples. The paperwork is brought into the lab and wiped down with bleach. Samples are put into the large isolator (named the ‘BFG’) to be opened. One of the team opens the sample pots in the isolator and inspects the bags without touching anything inside– has anything leaked? Are there are any sharps in there.

(We had been warned that during the early stages of the epidemic samples would turn up in all kinds of containers, sometimes with the needles still in the bags. Thankfully we never experienced this.)

Count the total number of samples and compare to the number of sample request forms received. One by one carefully remove each sample from its packaging and wipe it down with bleach inside the isolator. Check details of sample against the sample request forms.

Label samples with a unique lab identifier and arrange into batches of samples for processing. Samples are wrapped in two individually sealed bags, wiped down with bleach and after 10 minutes they can be moved to a second isolator where the nucleic acid extraction takes place.

~11:00am-1:00pm:

Inside the second isolator (we had two, named “Kate” and “Wills”), carefully extract nucleic acid from an aliquot of the patient’s blood or swab. Run malaria tests if required. (This work is done with the help of a buddy to check every step is performed correctly and to record the various steps on the sample record forms.

Once the samples have been inactivated with extraction buffer and ethanol, wipe down the tubes with bleach and wait ten minutes before bringing them out.

(Working in the isolators is a skill on its own as due to the two pairs of gloves, one of which is similar to dishwashing gloves, you lose a lot of dexterity. Despite the fact that most of us had no experience working in an isolator, the team did a fantastic job and picked it up quickly.) 

~1:00pm-2:00pm:

Bring inactivated samples out of the isolator and carry out final checks to ensure the inactivation times are correct. Extract nucleic acid on the bench.

Purify viral RNA genome from other things present in samples. This process takes ~40 minutes and the final product is a small amount of purified nucleic acid.

Coordinate with other team members to set up tubes containing the Mastermix so that they are ready to go as soon as the extracts are ready.

~2:00-4:00pm:

Once the extracts are ready, add to the Mastermix in a separate room and take the samples into the PCR room. Analyse the samples using the Polymerase Chain Reaction (PCR) on one of the three PCR machines (called ‘Alvin’, ‘Simon’ and ‘Theodore’).

The PCR takes just under two hours to complete, after which the results are analysed and checked by two members of the team. Complete the paperwork and enter the results into a database.

(Depending on where the samples had come from, the results would either be reported later that night or immediately phoned through to clinical staff. The typical turnaround times were 4-5 hours from sample reception to results, which – given the critical safety steps that had to be followed – was pretty quick.)

~8:30pm:

One of the team leaders to send out a report of the day to the various agencies involved.

(This  “simply” entailed sending an email – yet it was one of many challenges we faced during a typical day. We had satellite based internet but it was somewhat temperamental and very slow. We also had mobile internet “dongles” but reception at the treatment centre was somewhere between poor and non-existent. I did, after an hour of snooping around, find a single spot in one tent where I could get a single bar 3G signal.) One particular evening it took almost two hours to send the report out due to these connectivity problems.)

~9:00-10:00 pm:

The late shift team (2pm onwards) close down the lab at the end of the day (~10pm), cleaning out all the isolators (“BFG”, “Kate and Wills”), discarding all the waste, swabbing down the benches with bleach and generally trying to prepare the lab for the team in the morning.

~10:00pm:

Meet colleagues at the end of the day in the dining room of the hotel (Makama Lodge) for a chat and a drink.

(These periods were very important, not only for airing any issues that had come up during the day (practical or personal), but also for the overall morale of the team. Working in that environment with the same people for long periods of time can be quite stressful (kind of a lab-based “Big Brother” experience) so its essential the team has rest time together.)

Team Makeni. From left to right; Stanley Ko (University of Central Lancashire), Ian Goodfellow (University of Cambridge), Cristina Leggio (PHE Porton Down), Stephanie Leung (PHE Porton Down), Lisa Hodges (CWPS UHCW, NHS), Steve Diggle (PHE, Manchester), Laura Grice (PHE, Manchester), Catherine Moore (Public Health Wales, Cardiff), Kate Baldwin (North Bristol NHS Trust), Angela Short (PHE, Bristol).

We were all tired, missing our families and many were ill due to gastroenteritis. Despite this morale was always high. The saying “laughter is the best medicine” held very true. “Makeni Team One” was a fantastic bunch of people and they were always there to support each other. It was a real honour to have been part of the team.