COVID-19 Briefing for 9th May 2020

Notes from a conversation held by Lara Marks with Stephen Baker, professor of molecular microbiology, Jeffrey Cheah Biomedical Centre, Cambridge University on Thursday May 8 2020

Previous project following zoonotic virus transfer in Vietnam

I had the BBC here on Tuesday (May 5) to talk about some previous work I did for a study in Vietnam looking at zoonotic virus transfer from people working in wet markets to people working with wild animals. At the time everyone thought the study was mental, but we predicted that the next pandemic would likely be a respiratory illness caused by a virus that came from an animal. In fact someone remembers I said at the time that it could be a coronavirus that came from bats.

So we launched a project in March 2012. It involved the recruitment of 12000 people in provincial hospitals across Vietnam with diseases of unknown origin, some of whom had respiratory tract infections. We sampled them to try and identify new things that were associated with their disease. We also had a cohort of people working with animals who we sampled together with their animals every year and also when they got sick particularly with flu-like infections. And we tried to work out how much transfer there was between the workers and their animals.

The point that I made was that we now knew that transmission could happen at a small scale, because of what we had demonstrated, it was perfectly possible that it could happen at a big scale but we just didn’t know when it would happen and we didn’t know where it would happen. But we had a good idea about where it was going to come from. It was clear that it was going to be places where people interact with animals and where the likely transfer is going on fairly frequently and suddenly you get one species jump which has catastrophic consequences. So we knew quite a lot about the process but we didn’t know exactly where and when it was going to happen.

The BBC contacted me because they knew I had been involved in the project and they wanted to know what could be done about the problem. I must admit the project was a lot of work and I kind of got burnt out by it. We published a lot of papers from it but nothing really conclusive came out of it.

I must admit I got a bit phased out by the project but everyone else was really impressed by the methods we used. The study used integrated traditional clinical, epidemiological, and medical anthropological methods with new approaches for pathogen detection and discovery. It included novel sequencing techniques combined with phylogenetic analysis to characterise pathogen populations (1). If we had had the same surveillance methods of humans and animals in place while this Covid-19 pandemic was going on then we would have learned so much more by now. We would also know when and how it happened.

Update on screening healthcare workers for COVID-19

We have now screened about 3,000 healthcare workers. It just shows you what a small research laboratory can achieve. Importantly we have gathered what is probably the first asymptomatic healthcare screening data in the world. It is frustrating that we have not yet been able to publish a paper on the data because it has important implications for policy.

One of the interesting things we are beginning to see in the data is that we are getting less positive results and those that we are getting are at the lower limits of detection. I think it means that the people we are testing positive now are probably at the tail end of their infection. What it is probably showing is that because there are less infections in the community there are less individuals in hospital testing positive. And that those who are testing positive were probably infected a couple of weeks ago. That is probably because of lockdown.

Overall the PCR test we are using is pretty much routine now and streamlined. We are happy with the capacity that we have got. Addenbrooke's hospital wants more, but it is still unclear what exactly they want so we need to meet with them to come up with a plan next week. We need to have a discussion about how we carry on the healthcare worker screening which we still want to do for a period of time. What we need is to find a way of offloading some of the workload on to other people.

ICU testing

We are now in a position where we think we are now in a position to write up what we have done in terms of the testing in ICU. We see the testing as important because co-infections with bacteria are probably equally equivalent a problem as the COVID virus itself. Clearly it is not very good that patients already suffering from a severe injury from COVID are getting hit by bacterial infections.

Serology testing for immune response

Having got the safety approval we needed we have now begun to roll out the serological testing. We can now identify antibodies in people that have been exposed to COVID and we’ve got four different antigens that all seem to work quite nicely. So now it is a matter of standardisation. We are going to work with the hospital. They have got an internal test from a different system and we are going to try and link the two together to try and see whether they are overlapping with one another. Then we are going to look at functional responses and neutralisation to see whether antibodies titres do actually appear to correlate with any group immunity.

Scientists in the US are using the same serological test that we are. This will help us get comparable data. Some other people at Cambridge University are collaborating with Florian Crammer’s team at Mount Sinai who has developed a serological assay to detect SARS-CoV-2 seroconversion in humans (2). They have kindly provided us with an antigen from Crammer’s group to develop our test.

References

(1) MA Rabaa, et al, ‘The Vietnam Initiative on Zoonotic Infections (VIZIONS): A Strategic Approach to Studying Emerging Zoonotic Infectious Diseases’, Ecohealth. 2015; 12(4): 726–735.

(2) F Amanat, et al ‘A serological assay to detect SARS-CoV-2 seroconversion in humans’, MedRxiv, 16 April 2020, https://www.medrxiv.org/content/10.1101/2020.03.17.20037713v2.

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