Edited transcript of interview with Professor Jonathan Heeney* by Dr Lara Marks and Dr Ankur Mutreja, 6th July 2021

* head of the Laboratory of Viral Zoonotics, Department of Veterinary Medicine, Cambridge University

(this transcript has been edited for clarity and brevity)

Lara

Can you tell us a bit about your background?

Jonathan

I'm a veterinarian by training and studied viral pathology in Canada and then went to the National Institutes of Health. During my PhD there was an outbreak of coronaviruses in cheetahs in a captive Safari Park in Oregon, and I was sent to confirm the cause of this small outbreak. I think it had at that time a 30% more mortality in that cheetah population. So I characterised that virus. That was a long time ago.

Then I went to Stanford and did human pathology, where I got involved in viruses that jump from animals to humans. And after I'd say 18 years in the Netherlands, where I worked at a vaccine Institute. I then took up this professorship in comparative pathology here [Cambridge University] where I set up the lab of viral zoonotic which studies viruses that go from animals to humans. We have a spin out company [DIOSynVax], based on genomics and structural biology that we use to make novel vaccines. And this is sort of the background as to how we got into [developing a vaccine for coronaviruses].

Professor Jonathan Heeney

Professor Jonathan Heeney.

After the big Ebola outbreak in West Africa, in 2014/15, we started to work on making better hemorrhagic fever vaccines. You may or may not know that the Zaire ebolavirus, which was the cause then of the West African Ebola outbreak, is just one of five different distinct genomic groups of filoviruses. They all cause a disease that is distinct. Then there's the Marburg subfamily which is yet further genomically distinct, and that causes hemorrhagic disease, more in central East Africa. And then overlaid on these hemorrhagic fevers, called filoviruses, there is Lassa fever, which has a five to seven, depending on how you count them, lineages also distinct genomic groups of filoviruses. Lassa fever is more endemic than Ebola because Ebola flares up [every now and then].

Anyway, so we set out to build a trivalent hemorrhagic fever vaccine, one that would protect against the different filoviruses: Marburg, as well as Lassa fever, which [by Sept 2018] was about to be launched and is in stage four for GMP production (Quested). Then we got this big award from the Bill and Melinda Gates Foundation [in Aug 2019] to make a universal flu vaccine (Brackley). So that set us up for this pandemic, really, because we were working on that. And then we got another award from Innovate UK to build a different kind of universal flu vaccine (Cambridge University Enterprise).

We had those two technologies and we had a team of structural biologists and bioinformaticists working away on flu when in December 2019 we saw these cases on the radar of acute respiratory disease fatality in Wuhan province. We thought ‘wow this is flu’ and we watched and watched and kept reading, thinking a little bit differently. Anyway, finally when the sequence was released in early 2020 [and] it turned out to be a coronavirus, I said to the team, ‘Oh, I know this virus. We can do this’ and away we went.

At that moment we were focused on making vaccines to prevent pandemics. That is where our technology is placed, in that we build structures that cover these large family groups. Of course, nothing's bigger than the diverse influenza family. So we then dove into the coronavirus literature and decided we could start with the sarbecco coronaviruses.

Lara

It would be helpful to have a bit of background about the sarbecco coronaviruses.

Jonathan

So coronaviruses are a hugely diverse group of viruses, a family of viruses. They are extremely well known to veterinarians. It is one of the important causes of gastrointestinal and sometimes respiratory diseases in domestic cats. You have an enteric coronavirus that if it shifts and loses parts of its genome causes a disease called ‘feline infectious peritonitis’. And as a young pathologist, that was one of the viruses that I wrote up and studied and did case reports on. In fact I still use it when I lecture to veterinary students because it causes vasculitis. But it causes it in a slightly different way than with SARS CoV-2. It is more like SARS. And being from Toronto [I know this virus because] SARS hit our city hard in 2002.

Knowing the coronaviruses we were very concerned about what's called antibody dependent enhancement (ADE) or how vaccines can actually backfire. From [the] earliest efforts to try and make a feline infectious peritonitis vaccine, we knew that vaccines could make the disease more severe.

Lara

When you say antibody dependent enhancement what happens.

Jonathan

What happens is you make antibodies to the spike protein that are neutralising, and instead of the antibodies binding to the outside of the virus they're taken up by antigen presenting cells, like alveolar macrophages or peritoneal macrophages or whatever. This causes a pro-inflammatory response, which we also see in COVID disease.

When vaccines were made against SARS, they never made it into the clinic because the epidemic was successfully treated by quarantine. So by the time they got the vaccines ready a year and a half, two years later, it wasn't an issue. In fact, nobody pursued them anymore. But when they did the studies in animal models, where they challenged the virus with SARS vaccines, they made the animals ill in many of the cases.

There are two coronavirus proteins involved in antibody dependent enhancement, this immunopathology: the spike protein and the end protein. Now why this is important is if you're going to build a pan-coronavirus vaccine you need to have this knowledge. You cannot treat it like SARS-CoV2 which is a very different beast, which is why we've had trouble controlling it. [It is alo] why some of us were very pleased when the spike protein vaccines worked [because] it could have been a disaster. That sort of [developed] on the back of [knowledge about] MERS, which is a camel transmitted coronavirus and fortunately isn't as contagious as going from human to human to human. It's more caused by camel to human transmission and maybe some nosocomial infections. But you can easily contain it.

What's different about SARS CoV-2 is that it acquired a furin cleavage site between the S1 and the S2 proteins. So the spike protein is a trimer. The trimer is like two scoops of ice cream on three ice cream cones held together by an elastic band. The two scoops of ice cream are S1 and S2. The top scoop has a little cherry on the top called the receptor binding domain (RBD) which is the business end of the spike protein that binds to the ACE2 receptor.

Lara

That's a great description. Thank you.

Jonathan

What is different from SARS and all these other coronaviruses is this furin cleavage site between the two scoops of ice cream, which [gets cleaved when it comes to contact with] serum proteases [which are in our lungs]. It's like splitting the lunar module off the capsule. [This process] allows the virus to properly engage [with] the ACE2 receptor and enter the virus.

Lara

So our body is working with the virus to open the virus up to infect the body is what you're saying?

Jonathan

Let's just say the viruses use, as all viruses do, human or animal attributes that allow them to have the best possible lifestyle.

Ankur

That's how evolution works. They've evolved in a way to engage the sort of host mechanisms to flourish more.

Jonathan

So this furin cleavage site is an important acquisition of this coronavirus in its evolutionary history. Whether it acquired it in pangolins or it came from a species of bat that we have yet to identify. It is one of the remaining questions. But, suffice it to say that all these bat coronaviruses use the ACE2 receptor that we have in our lungs and in our blood vessels. Don't forget this is a systemic disease. We acquire it through our respiratory tract. The ACE2 receptor is amenable to virus entry and because of this furin cleavage [site] you get such a high affinity attachment that there's no time for the antibodies to drag the virus off elsewhere. So in many ways, it's much more contagious. And the delta variant has changes not just to it's RBD, but the whole spike protein is what makes it much more contagious than the other variants that have gone before.

Lara

Can I just ask, how does that compare with HIV which equally manages to escape the immune system very quickly, as I understand within days of you catching it.

Jonathan

I studied HIV for 20 years, and again that has animal origins. It came from monkeys, infected chimpanzees, recombined with another monkey virus and evolved within chimpanzees to become adapted. It just moved up the food chain to humans. Essentially HIV is a retrovirus, so it's able to persist within cells longer because it has a DNA intermediate [and] it is able to go into a sort of a quiescent state. And because it stays within the body, while it's replicating quietly, it is transmitted in stealth. That means that people can have it for up to eight years and not know it before they see the CD4 cells decline and they get immunosuppressive disease. What that means is that the virus is within that individual adapting. You have what's called ‘within host adaptation’, which then creates another dimension of variability. And because of this slow, persistent infection, the degree of variation that you get with HIV is incomparable to a coronavirus.

Lara

But the coronavirus at the moment, the Delta variant, is very worrying from what you're saying?

Jonathan

Yes, because it's highly, highly contagious. The R factor, which is really important for monitoring transmissibility or contagiousness, is much higher than the original Wuhan virus.

How I bring this all back together is the sarbecoviruses are defined by the fact that they're bat viruses, but also the fact that they use the ACE2 receptor. They are a group within the beta coronaviruses. The beta coronaviruses include MERS, the camel to human respiratory disease, but that uses a completely different receptor. .. So you can see that within the Alpha, Beta, Gamma, Delta coronaviruses you already have this complexity because even within the beta coronaviruses you've got there sarbeccos that use the respiratory ACE2 entry route, MERS, which uses a different receptor to cause respiratory disease. And then you've got the common cold coronaviruses, of which we know at least four that have been around [for a long time], that pop up every six to eight years and cause seasonal infections.

Lara

So when you started developing a vaccine for SARS-CoV-2, did you originally say ‘right I'm going to go off the pan coronavirus vaccine to start with’? How did you start? What was your thinking?

Jonathan

We said ‘okay, listen, we've had SARS, [and now] SARS CoV-2, and we're building a universal flu vaccine so let's do the same thing for coronaviruses before we get a SARS-3 pandemic. We started off doing that from the beginning. And to do that, as I told you, we had to avoid these antibody dependent types of immune pathologies. That means that very carefully, structurally, you need to avoid these elements that can cause that immunopathology. Because the last thing you want to do is vaccinate the population and say that this will protect you from the next pandemic and then if something like SARS came along everybody dies of adverse effects from the vaccine that's not good. That's why individuals who are trying to create a pan coronavirus vaccine, if they don't take these observations from history into account, then they're destined for bad press.

Lara

How did you get going?

Jonathan

[From the beginning] our goal was to make this very broadly protective vaccine that would protect against SARS, SARS-CoV-2, and all the other sarbecco viruses that may spill over in the future. To do this we took a broad family of genes and looked at what's common amongst them and what can't be changed. That means that the virus is using a particular pathway that is essential for its life cycle. And we retain those common elements. We looked at the structure that they must maintain to keep that structural integrity, because that defines what a common antigen or conserved antigen will be. Then we removed the variable parts, or the parts that can cause immunopathology. That took some doing, but by June [2019], we had our first generation of sarbecco (Cambridge University Enterprise). That's when we won a grant from the UK Government. We were the so-called third vaccine out there.

So we had this candidate and we had a facility lined up in Europe [but the government put it to the back of the queue once the Oxford/AstraZeneca vaccine started to do well]. Anyway, that was a good thing because it gave us a chance to reconfigure and improve the candidate we had and to do the preclinical work.

The great news is that we [now] have a GMP product that is in all the freezers ready for the clinical trial. [It has gone] through toxicology assessment, which every vaccine has to do, just for safety. What you do is you take a little bit of the final human prepared product, and you test it on animals [to make sure there is no pathology associated with it]. When we collected the serum from the rabbits …. and did our viral tests ….the exciting news is that it was very potent, not just against SARS-CoV2, but against SARS and many of the viruses in between. And last week, on Friday afternoon [July 1], after a very positive meeting about a clinical trial, we got data back that it looks like it neutralises the delta variant as well. So we're delighted with that. The only challenge we have now is getting the right population in the UK to immunise with our vaccine.

Lara

Why is that a challenge?

Jonathan

Because they've accelerated the immunisation protocol in such a way that there actually won't be any immunologically naive people by the time we get our trial started. So what we're going to do is boost one of the commercial vaccines, because that's the population we have. But that's fine. Our work in mice shows that if we boost one of the licenced vaccines that we can get a broader response that protects against SARS, as well SARS-CoV-2. That is the format and this is just our first generation vaccine.

We are now in discussion with manufacturers, RNA manufacturers for scale-up. Because as you know, nothing can be manufactured quite so quickly now, as mRNA vaccines.

Lara

And is yours a DNA based vaccine?

Jonathan

That's what ours is. The only reason it is, is because it's a proprietary technology that we have. The vector that we had made [can be] used to quickly insert these structures. And we make libraries of synthetic genes, and then screen them in vitro and in vivo, and take the ones that produce the best types of immune response. That is in what we call a DNA plasmid effector.

Lara

Can you just explain [a bit more].

Jonathan

We make hundreds of iterations of the protein structure that we're trying to create or recreate, modify, and then we put them into our vector system. So the gene is synthesised, put into our vector system and then we screen that in cell lines. Then we take the best in class of those and we put them into small animals, mice. Then we choose the mice that have the best immune responses and take that plasmid and then forward it for clinical development.

Lara

Okay.

Jonathan

That allows us to screen out any badly reactive proteins, etc. So what we did is simply just use our plasmid system as a DNA vector.

Ankur

What's the origin of the plasmid system that you're using?

Jonathan

It's a modified plasmid that we have derived, synthesised. It has a history of being successfully used as a DNA vaccine in SARS clinical trials and in HIV clinical trials. But we modified it so that we could quickly take this insert in that vector and easily just click it out and put it into adenovirus, mRNA, and any other vector systems.

Lara

And is that patented? Is that what DiosynVax has a patent on so I'd be able to find it in the patent literature.

Jonathan

You would, yes.

Ankur

Out of curiosity, what's your insights for this sarbecco vaccine progressing to clinical trials?

Jonathan

It is a subunit of S for which we've taken away the domains that could possibly cause ADE.

Ankur

Right. But it still has the RBD?

Jonathan

Yes. It's a chimeric molecule that has epitopes that give it that immunological breadth. So it's a chimeric antigen. And to give us greater breadth, we're now taking forward in animal studies another component, which is another structural protein. That is being evaluated so that we can add in greater breadth through multiple antigens.

Ankur

So in a way, it's a multivalent antigen that you have?

Jonathan

Well, the single antigen that we have right now in itself is broad coverage.

Ankur

Interesting.

Jonathan

But by adding multiple targets to it decreases the risk that there'll be vaccine escape and increases the robust immune response to different targets.

Ankur

Right, it's very interesting. So this is all a synthetically modified antigen that was presumably initially picked from SARS-CoV-2.

Jonathan

Well we actually took not just the SARS-CoV-2 genomes. When we designed this, we looked at all the beta coronaviruses, including and focused really on the sarbeccos.

Ankur

Right. And then you made an insert on your computer, ordered a gene synthesis of that and then that you inserted in your DNA plug in vector.

Jonathan

Yes. In fact, we ordered multiple inserts and made a library.

Lara

And is that what you then screened across this plasmid library?

Jonathan

That's right. So then we put that through our cell lines and through our animal screens, and came out with our best in class antigen. So with this first trial and with subsequent generations, that will increase the breadth across the whole beta coronaviruses. Once we're convinced that we have got protection in the betas, then we'll see if we can go broader.

Lara

Okay.

Jonathan

I'll be happy when we get all the betas covered.

Lara

That would be amazing. So at this stage, you've put it into mice and you've got the results from mice. Is that right?

Jonathan

Well, not only mice. We've used it in four different species now. We've confirmed it in hamsters, guinea pigs, and rabbits. That's part of screening it broadly.

Lara

At what point do you think it might go into humans?

Jonathan

It will go into humans at the end of the summer?

Lara

Wow, okay. So what feeling do you have about it in terms of it being helpful as a pan coronavirus vaccine? How realistic do you think it is?

Jonathan

I think it's a fantastic start. If I was in an area where there were lots of bats with endemic sarbecco viruses, I would give it to everybody, in Wu Han, Guangdong Province and in any other risk areas in Southeast Asia.

Lara

So for future emergent coronaviruses it could be protective against those?

Jonathan

I think the issue now is simply finding the best way to scale up, to make millions of doses. This is why we're talking to different mRNA manufacturers, Big Pharma, to partner with. But at the same time, we are going to head with our phase I and possibly phase II trials this fall.

Lara

Who's sponsoring that? Is that still the UK Research Innovate?

Jonathan

Yes.

Lara

And to make the vaccine, the GMP product, how are you doing that? Is that being done in Cambridge or who's doing it? Is it academic?

Jonathan

That’s being done by industry. It’s being done by a biotech endeavour.

Lara

Could you have got to this point, if you had not formed the spin out company DiosVax [(Digitally designed, Immune Optimised Selected and Synthesized Vaccines]? Is that what actually helped to get to this process?

Jonathan

It's been critical to get to this process. Yeah.

Lara

In what way?

Jonathan

We really couldn't have done it academically. The same is true for Oxford who formed Vaccitech to commercialise their vaccine vector. Vaccitech was established, I think three, two or three years ago, also for a universal flu vaccine. A T-cell based vaccine immunity.

Lara

Are you also looking at T-cell as well as antibody immunity?

Jonathan

Yes, definitely. We believe that the whole immune system is really important for robust vaccine protection. So we're firm believers in T and B cell immunity. It's very difficult to get good protection with just one rather than the other.

Lara

And that's partly where Oxford was going with the malaria vaccine.

Jonathan

Yeah, that's right. Both B and T cells. Of course, Adrian Hill and his colleagues were trying to get a better way of making it more broadly reactive. They've got a B and T cell malaria vaccine.

Lara

And is this what you're now doing with your vaccine, you're able to get both antibody and T cell responses?

Jonathan

That's right.

Lara

How are you measuring the T cell responses?

Jonathan

Everybody tends to do it the same way - it is high throughput, quite high tech, T-spot. It's sort of a routine standard now for many vaccine trials. Oxford have used it as a benchmark for their T cell based models.

Lara

You were talking about having structural biologists on your team. How important has that been to pushing this project forward?

Jonathan

It's a cornerstone of our technology.

Lara

Would you have been able to do that without cryo EM?

Jonathan

Cryo EM informs the structures. You know, the beautiful work done here at the LMB and around the world has really informed what these structures look like. And we were well set up for influenza. There's a lot of good structural information about the hemagglutinin and neuraminidase from diverse influenza viruses and now for different spikes of different coronaviruses. All that information has been very powerful for our technology.

Lara

Is there anything else you feel that would be important to include in the article?

Jonathan

Just that this is the first of multiple waves of candidates that we are generating. The key thing now is for us to find that large scale manufacturer to partner with to be able to provide not just 1000s of doses, but the millions of doses that are needed.

Lara

And is it a slightly different process with the DNA vector rather than using mRNA?

Jonathan

Yes. So until 2020, when mRNA stormed on stage, most of the vaccines have been biological systems. Meaning you need to have a living organism to produce it. Whether it's a DNA plasmid, or a viral vector, you need to grow these in cells. I don't know, if you've ever been inside a brewery [where there are] big vats of stainless steel pipe going everywhere. And this all has to be sterile. Of course, if you're making these in a biological system, you need to extract the vaccine, whether it's an adenovirus [or something else], you need to separate it from all the cells; the serum proteins or whatever is involved in growing these to scale. But mRNA is different in that as long as you have a cleanroom you don't need to have big vats, growing bacteria, or cells growing viruses. You simply put them in a wave bag with the enzymes, the RNA part dependent enzymes that make RNA copies. It's just really adding the enzymes and the ingredients needed to get a massive replication and duplication of the mRNA. And that's done now synthetically.

Lara

And for your technology, how would you produce it?

Jonathan

Well with DNA it is traditionally made by bacteria. These are all synthetic processes that are done with utmost safety in mind.

Ankur

It would also be useful to know about the delivery technology. I noticed that you were talking about powder forms that you can inject in the skin.

Jonathan

We have an agreement with a company called Pharmajet (Lille). This is really cool. You can go on our website and see the video of how Pharmajet delivers [the vaccine]. It is without a needle. It is just a jet of air that goes into your dermis (BBC). Outside of our GI tract, the second biggest immune system in our body is our skin.

The technology works extremely well with DNA. Because, unlike RNA, DNA is pretty sturdy. In fact, DNA is great for places like Africa where there's no cold chain. It can be lyophilized, freeze dried, and it doesn't break down like mRNA does. So that is another advantage of it.

Lara

Did you DiosynVax develop the delivery technology itself?

Jonathan

DiosynVax contacted Pharmajet because we knew that intradermal delivery of DNA is probably the best way to deliver DNA.

Ankur

And with your clinical trial is that delivery device incorporated or not?

Jonathan

Yes. Definitely. It is going to be administered to Southampton volunteers without a needle. So anybody who's got a needle phobia, will I think want to have this vaccine.

Ankur

I think it's incredible that there is a candidate for the sarbecco virus that's progressing into clinical trials .That really gives some hope that a beta coronavirus vaccine is not really unthinkable going forward.

References

Brackley, P (25 Sept 2018) ‘University of Cambridge’s Prof Jonathan Heeney answers a call from Bill Gates to transform flu vaccine', Cambridge Independent. Back

BBC (26 Aug 2020) ‘The Covid vaccine that won't need needles!’Back

Cambridge University Enterprise (April 2019) ‘Casestudy: DiosSynVax’, Cambridge Independent. Back

Back

Lille, N (27 Oct 2020) ‘University of Cambridge Receives Multi-million Dollar Funding for Clinical Trial Using PharmaJet’s Needle-free System to Deliver Vaccine to Prevent COVID-19‘.Back

Quested, T (20 Sept 2018) ‘Cambridge scientists win millions to trial new vaccine against Ebola and other killer viruses’, Business Weekly.Back

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