COVID-19: From Zero to 6,000 in Eight Weeks

Hidden Health Workers

Medical scientists are unique healthcare professionals. We play a pivotal role in the diagnosis of disease and treatment of patients. Yet, we never meet them, in fact, most don’t even know we exist.

Although we don’t see the faces behind the samples, the patients are in the forefront of our minds in every step of our testing procedure. This remains the case during this pandemic where we must ensure we can stand over and trace every aspect of the process, from sample collection through analysis and results.

Starting from Scratch

When we made the decision to introduce in-house testing for SARS-CoV-2, we didn’t have the existing equipment required or enough staff to maintain the service. Thankfully, close links to UCD provided us with both equipment and scientists to help get us off the ground. Our medical scientists welcomed that assistance and worked round-the-clock to validate all the necessary components. 

The procedure for SARS-CoV-2 involves a number of different steps. When samples are received, as with all samples, they are checked to ensure identifiers on swab and form match. A lysis step is next, where buffer is added to some of the liquid media from the patient’s swab. This lyses cells and inactivates the virus making the sample safe for further processing. 

An extraction procedure follows, to isolate and purify the viral RNA (genetic material), if present, from the patient sample/lysis buffer mix. The final step in the pathway is RT-PCR. Viral RNA, is converted to DNA and this DNA is amplified and measured by the PCR instrument. 

All procedures along the way need to be validated and internal controls are included in every step, in every run. Despite the enormity of the task, less than a week after the decision to start testing, we reported our first results.  

Dealing with Rapid Change

The first few weeks went by in a blur. Everyday brought new challenges and as soon as one issue was resolved, another arose; reagent shortages, consumable shortages, equipment issues.

Throughout this eight-week period we have used four different lysis buffers, four different extraction methods and four different Real-time PCR methods, each needing validation before tests results can be released. Results were sometimes delayed as we battled uncooperative equipment or technical issues. I stumbled out of work in tears after some very late nights.

Challenges during Challenging Times

I expected the validation of a brand new test to be challenging. A challenge that I hadn’t anticipated was the public perception of medical scientists. From being a largely unknown profession outside of hospitals, suddenly we were in the spotlight.  Sampling and testing were commonly confused. 

Everyone was demanding to know what was taking us so long. Why couldn’t we just make reagents/get analysers/test faster? After working countless hours to validate new systems to ensure quality of results, it sometimes felt like a personal attack, even though the situation was out of our control. 

Currently our supply chains seem robust and our orders are maintained through a centralised HSE network where reagents/consumables are allocated depending on test capacity.

Teamwork in a time of crisis

A whole new section in our department was created in a week, and we still had to process all our normal microbiology specimens. We had to divide staff into teams to allow social distancing and limit contacts. 

Staff also had to contend with the same issues that face front-line workers throughout the country including childcare and worry of possibly infecting family members at home. Despite these difficulties, the laboratory staff came together to make it work.

As a team, both in St. Vincent’s University hospital and in the Medical Scientist community as a whole, we have grown closer and stronger. A network, between hospitals and departments, which luckily always existed, was now called upon more than ever to share experience and loan/swap reagents. 

Staff members have driven reagents to different hospitals and another hospital allowed us to use their equipment when one of ours broke down. Staff at the National Virus Reference Lab (NVRL) have helped provide materials to use for validation and have shared validation procedures, despite being incredibly busy.

Amazing Achievement

Less than two months after that first test, we have now tested over 6,000 samples. We have the capacity to test 200 samples/day seven days a week and our turnaround time for results after receipt of samples into the laboratory is between 8 and 30 hours. 

We also have a one-hour RT-PCR assay for urgent samples. We have come a long way in eight weeks and we are aware that there is a long way to go but we will continue to test, test, test; always remembering that behind every sample is a patient.

This Blog was written by Deirdre Keating  (dkeating@svhg.ie), Specialist Medical Scientist, St. Vincent’s University Hospital.

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