The science of fighting Covid-19


It has been a baptism of fire for the Chief Medical Scientist of Microbiology at St Vincent’s University Hospital (SVUH) in Dublin.

Abigail Salmon was appointed in December 2018, taking over the role from a predecessor who had an eight-year stint.

Just over one year into the role, she and her team were planning for a possible pandemic.

Like a boxing match, she said, all the sparring and training in the world could not prepare a fighter for a match taking place in the dark, with an unseen opponent jabbing and punching from every angle.

“In non-pandemic times, there is a recruitment crisis in medical lab science across the board. There are a lot of posts not filled. Prior to the pandemic, we were short five positions filled, as well as two maternity leave posts. 

“It is not SVUH Group that is not filling these posts, the hospital administration is enthusiastic and competitively trying to do so, we are trying to recruit but we just couldn’t fill them. Graduates are just not staying in the field,” she said.

With not enough graduates staying in the field, it meant all hands on deck for current SVUH staff from January.

“SVUH started multidisciplinary meetings across the departments back in January – labs, ED, procurements, catering, everyone bought in. We had a whole system in place. But you couldn’t truly plan – it was firefighting from the get go.

Abigail Salmon with Concepta Gallagher, Senior Medical Scientist at the specimen reception area of the microbiology lab in the hospital where swabs for Covid-19 testing are gathered.
Abigail Salmon with Concepta Gallagher, Senior Medical Scientist at the specimen reception area of the microbiology lab in the hospital where swabs for Covid-19 testing are gathered.

“We were having meetings but weren’t certain about what could happen. We were planning how we’d get a patient to the emergency department, and planning to send the Covid-19 samples to the UCD National Virus Reference Laboratory (NVRL). But the pandemic took hold like wildfire and the hospital had to test their own patients and staff.” 

From firefighting to sourcing equipment to maintaining social distancing while testing for a number of hospitals – such as its own patients, St Michael’s in Dun Laoghaire, St Columcille’s Hospital in Loughlinstown, as well as a GP catchment in North Dublin and Wicklow – it has been an all-out team effort, Ms Salmon said.

“The team has really shown what it is made of. They have responded to longer days and manic schedules and lack of equipment with great professionalism and sense of duty. 

“Backed up by the excellent support of the team of consultant microbiologists and admin staff in SVUH, they can always be proud as to how they responded to Ireland when their country needed them.” 

“At the time when we first heard of Covid-19, only the NVRL in UCD was testing for it. We are a bacteriology lab. The only virus we would test for is GeneXpert, a molecular test that detects Influenza A,B and RSV. It can detect those three viruses within 30 minutes.

“Around March 17, we were told we would start testing for Covid-19. You sample the patient, and that sample goes into the Viral Transport Media, which goes to the lab.

“We put a little bit into a lysis buffer, the lysis buffer kills the virus and exposes the RNA – we want to get that RNA pure, so we put that on the Magna Pure 96 in order to be extracted. We then add that to a 96-well plate with the PCR mix and put it onto a Light Cycler 480. We have to turn that RNA back into DNA. That cycling machine does that and it then takes about two hours to get the result. It is not a simple swab-and-see process.” 

“The patient goes to get tested, the nurse takes a swab, down the throat and up the nose, it’s not pleasant. That is why there can be false negatives, if you haven’t tested properly. 

“A quick swab up the nose won’t do. It has to be nasopharyngeal swabs, at the base of the skull and the roof of the mouth. Sputum was thought originally to be better, but sometimes it is very hard to get sputum swabs from a Covid patient.

“The swab is then put into liquid called Viral Transport Media. If there is the virus present in the swab, it should be released into that liquid.The liquid will preserve the virus and prevent degradation.

“We take the sample and need to deactivate it. We add some of that VTM liquid into the tube, and also add lysis buffer. The purpose of the lysis buffer is to deactivate the virus, and also breaks open the protein membrane of the virus. Basically a virus is like an envelope with nucleic acid material inside, either RNA or DNA. Lysis exposes the RNA, that’s what we want.

“After that step, the virus is dead. We want to get the RNA, we’ve got VRM and lysis buffer. It’s like throwing the egg with the shell, and wanting to get the yolk out. That’s what the Magna Pure 96 is for – we want to get the RNA isolated and purified. So if there is RNA present, it is isolated. Magna Pure is fully automated, it will do its job, doing 96 samples in an hour, give or take.” 

Testing times: The science of fighting Covid-19

“Professor Paddy Mallon kindly loaned up his Magna Pure 96 from UCD and pharmaceutical firm Roche, which makes it, had to come in and set us up. Magna Pure 96 is a system that can test 96 samples at a time.

We had a Magna Pure 24 onsite and were only able to run 40 samples a day. Then when Roche came in, they trained us up again, to run more. We now use that twice a day, so we can do 96 and 96, or the capacity to run 192 a day. The training was done in record time.” 

“The initial problem was running out of swabs and VTM, and then there was a huge shortage of lysis buffer. That was a big problem. Some of the academic institutes are now making them, should there be a shortage again. A recipe for lysis buffer has actually been released.

“But when we bring in the commercial lysis buffer, there have been tests done on it, we know it fully deactivates the virus. The ones made in random labs, we have to be really careful. We’d much prefer commercial ones.

“The shortage of reagents was swabs and lysis buffer. Then there were PCR kits. PCR (polymerase chain reaction) basically detects if the virus is there, we amplify the target gene. We put it onto the Light Cycler 480, which heats and cools for around 40 cycles. If the gene is there, and it starts detecting the gene, it doubles, and a fluorescent probe binds to it. That is a positive sample.” 

“PCR kits are commercial kits with fluorescent probes, enzymes and reagents. A reagent is an ingredient, you need lots of reagents in the process, which are usually ready for us in what is called a master mix. You then add the RNA from the Magna Pure 96 onto a plate, the size of a Post It note. There’s 96 little holes, you put one sample per hole, which are called wells.

“You’d put RNA from sample one into a well, then you would add your PCR master mix. You’d put in each well, and then put onto the Light Cycler.

“PCR kits are needed, it’s much better to have CE-IVD kits, which means already approved by the EU. We use CE-IVD equipment, so all we have to do is a verification. But if we make our own, we must then validate our own, which is a huge task and very time consuming. We would not have been able to do our own PCR kits.”

“There was a shortage of swabs, VTM, lysis buffer and then the PCR kits, made by Altona and the only one on the market. The NVRL were using it, so all labs began to use it. Altona couldn’t keep up with the worldwide demand.

“SVUH is a public-voluntary hospital and we order through our own system, but the HSE really stepped up, with conference calls among all the labs about their needs. Then different PCR kits started coming on board.” 

Abigail Salmon with a GeneXpert SARS-CoV-2 cartridge. Using this cartridge a result of a Covid 19 test can be reached in 50 minutes. So lysing, extraction and RT-PCR occurs onboard. However it can only test one at a time. St Vincent's have two GeneXpert instruments to test 20 cartridges at the same time. It is not conducive for high throughput batch testing.
Abigail Salmon with a GeneXpert SARS-CoV-2 cartridge. Using this cartridge a result of a Covid 19 test can be reached in 50 minutes. So lysing, extraction and RT-PCR occurs onboard. However it can only test one at a time. St Vincent’s have two GeneXpert instruments to test 20 cartridges at the same time. It is not conducive for high throughput batch testing.

“Magna Pure is a closed system, it all comes from Roche. It is not just reagents, but a lot of plastic. There is no other company, we can’t just get generic plastic. It’s like an Espresso machine, you use their capsules, and not the wrong ones from the supermarket. Roche won’t cover a breakdown or issue if it’s from a generic company.” 

“When we were really short of swabs, the response from GPs was astounding. They saved the day. I spent a day sorting through it. We are really grateful. That’s the kind of effort and team effort we needed, and we got it.” 

“Because we were so short-staffed, I was working in the lab myself.. This is the first time I have been able to do other real chief work, coordinating how this was to be done.

“We are now getting equipment we never had, that we can keep, and we will be able to use for other tests, which will really improve outcomes. If another pandemic happened, we could hit the ground running. This will save money in the long run, because we will save time and bed days by running tests on this new equipment.

“I’ve been able to network with other chiefs in the system, as well as the HSE so it has been very good that way. That cooperation and coordination can only be a positive.”



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