COVID-19 Briefing for 7th April 2020

Notes from a conversation held by Lara Marks with Stephen Baker, professor of molecular microbiology, Jeffrey Cheah Biomedical Centre, Cambridge University on Friday 3rd April 2020

Challenges of converting a research laboratory into a diagnostic centre

What we have been doing has been trying to set up our research laboratory to be able to run the diagnostic PCR for COVID-19. The issues that we confront in research laboratories are that they are not set up to do diagnostics. This is because research laboratories have different sample flows, different equipment and differently trained staff. Moreover, they have different PCR machines depending on the supplier. We also need different reagents for the new processes. So, what we have done is take the conventional coronavirus diagnostic PCR from Addenbrooke's Hospital and adapted it to run on our machine to try to detect coronavirus nucleic acid in nasal/oral swabs.

Challenges of virus preparation

Another challenge with it is the coronavirus virus preparation method that most places use needs to be done in a containment 3 level laboratory, which is the second most top level safety laboratory. This is because the virus is not deactivated in traditional media when the swab is taken from the patient. What we have done is adapt a method to take the swab and put it into a different type of transport media which deactivates the virus the moment it enters the medium. This means then that, with appropriate care, we can then process those in a level 2 safety containment laboratory which improves the turnaround time because we don’t need such specified equipment and we have more space to do it. This means that theoretically our turnaround time is a lot quicker; 4 hours from swab to result.

Validating the process

After a week of effort, we got everything established, validated and found our limit of infection. As of yesterday (April 2nd) we got access to 20 theoretically known positives and 20 known negative swabs from the hospital that were blinded when we received them. We processed them using our new approach. This involves receiving the samples, unpacking them, extracting them and then amplifying the nucleic acid.

This morning (April 3) we found out that we got the exactly the right number of positives and negatives. Now that we have got the process working to identify viruses in biological samples, we have to ensure we do not get false positives or false negatives results.

Accessing enough reagents and other raw materials

Now the issue is making sure we get enough reagents. We are finding a means to work around the reagent shortages so that we are not dependent on supply issues. We have essentially done this by getting access to ones from around the university and the few we have in the laboratory which we have adapted to work on our equipment. This takes away the demand on particular types of extraction, machinery, equipment. We have some suppliers to keep us going, but we are trying to order more to make sure we can do the testing longitudinally.

We also need raw materials for doing extraction. This is something which we are fine tuning because we are making them ourselves, rather than buying them, to relieve stress on suppliers as they might be required by other places. We also need primers and probes. There is a bit of an issue getting those because everybody currently requires primers as probes. We also need plasticware, plates and other disposable items like filter tips, pipette tips to prevent things getting contaminated.

We also need to adapt our sample flow so that we have enough of the required equipment. This is to ensure we can do everything safely for the people doing the laboratory work. It is also important to make sure we can report back results that are correct and that we can be certain are not cross-contaminated.

We are also working on getting access to enough tubes and raw material liquids so that we can provide a kit to hospitals to put the swabs they collect into the desirable media. We need to make sure that this works. We are in the process of ordering enough reagents to longitudinally do the extractions of the nucleic acids and the reactions in the coming weeks and months.

System to track samples

Another thing we need to work on is how to communicate and coordinate with the hospital so that its staff understand how we process the samples. They also need to know how to swab patients, how information is recorded on the databases, and what the system is for checking who has been swabbed - each person swabbed has an individual identifier. All of this needs to be logged on our laboratory system. We need to extract and follow each person swabbed all the way through the process so that when we get results at the end they can be uploaded into a similar database system with a cross reference with the original sample identification number.

We are not yet set up to track each sample and it is something and we have to work on in the coming days. We need to make sure that a swab coming from someone in the hospital to us is reporting back appropriate information within the designated time.

We are already talking about swabs coming from the hospital on Monday, 6th April, and then we can start amplifying the virus technically on Tuesday, 7th April.