COVID-19 Briefing for 9th April 2020
Notes from a conversation held by Lara Marks with Stephen Baker, professor of molecular microbiology, Jeffrey Cheah Biomedical Centre, Cambridge University on Thursday 9th April 2020
In total we have between 6 and 7 people working on turning our research laboratory into a diagnostics centre. Each of us have taken on roles that have evolved over time.
Getting the diagnostic test working
Each day we have confronted different challenges. Getting assays working, getting access to samples and reagents were the first daily challenges. We are no longer facing the technical challenge of getting the machines working and we have all the reagents we need. That is now all organised. Everything is now working. We now have the capability to test 200 samples a day, five days a week, for the next 10-12 weeks.
In order to do the testing we have modified an in-house polymerase chain reaction (PCR) diagnostic test that was developed by Martin Curran in Addenbrooke’s Hospital’s routine diagnostics laboratory. It was validated against a PCR test approved by Public Health England. The test is able to diagnose infection in four hours, much faster than current tests, which on average take 24 hours to provide a result. In order to do the test we extract a tiny amount of RNA from the virus which is then amplified to millions of copies using PCR. This creates enough quantities to confirm the presence of the virus which causes COVID-19.
Importance in inactivating the virus
One of the critical steps in getting the test working was for us to find a way to inactivate the virus. This was crucial to enable us to carry out the testing in our level 2 laboratory which does not have all the containment facilities needed to work with lethal viruses.
Getting the virus inactivated was an obvious thing to do for us. Maybe we had an advantage in doing this because many of us in the team have worked for a long time out in the field with diseases like ebola. The process itself is actually very easy to do. We used a method developed by Professor Ian Goodfellow and colleagues in the Department of Pathology. This has enabled us to inactivate the virus at the point when it is taken from the patient.
Rolling out testing
We have now developed a process for staff testing in collaboration with clinical and occupational health staff at Cambridge University Hospitals Trust (CUH) and the university. Healthcare workers are already being swabbed at Addenbrooke’s Hospital in addition to staff working for other Trust Hospitals who have been asked to isolate themselves because they have been potentially in contact with infected individuals.
Samples are taken using nasal swabs, which are immediately put into a medium to inactivate the virus and then sent to the lab. We are now receiving swabs and we are doing assays on those. The whole process takes four hours.
So we are generating data. The way we are doing this at the moment, however, is a little bit ad hoc. We are getting a consultant virologist to come over to look at the results but that is not possible to do everyday.
Processing the tests and associated information
Now we have got the tests working we face the challenge of processing the data and reporting back. There are a lot of things to handle in terms of handling and processing the associated information. The issue now is how we follow those samples through and put the information streamline so we don’t have people running backwards and forwards with bits of paper.
Today (9 April 2020) we had a conversation that took an hour and a half with Public Health England (PHE) to discuss how we receive the samples, what information we have on the tube and how that goes through our sample processing and how we report that information back to PHE.
The issue is we cannot randomly run around and swab people and then tell them whether they are positive or negative. It is now being offered as a service to healthcare workers. They come in through a special path. They get their own sample number and that goes on to the tube that they get swabbed with. We receive these tubes and labels and have to then log that information in somehow so that it integrates with the database that they have on the hospital computer system. We then have to follow those samples through our process for the detection assay and then generate the result. Then we have to link back those results to the individual identifier and upload the information on to the hospital laboratory servers so they can validate the results. We are using barcoding to track samples and data.
Handling privacy issues
The question is, because we are an academic organisation and not part of PHE, is what information we are entitled to see on the tubes and how much private information we can see on the database?. The issues are privacy, sample handling and also then making sure that there is no potential mechanism for mixing up those samples in any part of the process because we don’t want to report back any false positives or negatives on the wrong people.
Challenge of integrating with PHE system
I must admit I thought getting the test to work was going to be the most complicated bit, but actually the reporting is going to be even more complicated.
If you set up something yourself ad hoc, or you buy it in then it is quite straightforward. But the issue is that if you already have things in place then it is a question of working out how the system at another place, like the PHE, works. The challenge is how we can get on their system to make our system integrate with what they are doing. None of us are PHE or hospital staff so we need to get permission to train on their systems to enter information in the way they want it.
If we were not having to coordinate with PHE and do it just on our own we could probably come up with a process whereby we scan the sample in with our own internal code and then report them back in a certain way. But obviously we can’t do that. We have to follow their regulations. So someone else from the team now has to go off and get training from PHE. My job is to oversee all the information that is reported back is accurate. My job as the principal investigator is to validate the data and make sure it is correct.
Once we know the system it should be pretty straightforward. PHE processes about a million samples a year so they know what they are doing. The thing for us is learning how to work with their system.
At the moment I feel like I will be working on Covid-19 forever. We are not going to be processing samples over the weekend but I think we are going to be busy getting other things ready. There aren’t any weekends at the moment anyway. I can’t remember what day it is. Every day feels the same. It is really weird. It is really full on, but with every challenge we learn how to do things in a different way which is good. So even though it is a bit annoying it is quite a good experience. It will also help us roll out what we have learned in different situations.
Over the past couple of days I have been aiming to write a blueprint on how to convert a research laboratory into a diagnostics lab. But this has been difficult because of the need to do other things.