Okay. Right. So can you just felt like having your name and your position?
So I'm Irish, so I guess I'm a professor of evolution and genomics in the Department of Zoology, and I'm also a tutorial fellow.
So. Hilda's college. That's great. Thank you.
So, first of all, tell me a little about yourself.
Starting from your earliest interest in in world science generally and roughly how your career has developed from that point to where you are now.
Yeah. So I've been working on virus evolution for over 20 years now,
and I started working in this area for my Ph.D. at Central College, um, also where I did my undergraduate degree.
And so I did, I did my Ph.D. in this area. And then I moved to the Department of Zoology in Oxford in around 2004 to start my first postdoc.
Um, again on virus evolution, a thing that I've been working on throughout my research career and have been here ever since,
eventually as a full professor and also as a college tutor.
And it's a it's an area that I've worked on.
I'm particularly interested in the evolutionary biology of viruses and their
interactions with our hosts and how that's played out over various time scales.
So from millennia down to down to a months and years and days,
across across all the different time scales and seeing how how these two types of entity interact.
Mm hmm. So let's start with a really basic question.
What is a virus? Um, so, uh, well, difficult question.
Um, so Peter Medawar famously quipped that it's a piece of bad news wrapped in a protein coat.
Um, they are basically a non cellular replicating entity.
Um. Much debate over whether they're alive or not.
I'm, I'm on the side of yes or it's not that relevant to the question given that they,
they, they, they have all the properties of a living organism in many senses of the word,
um, that all around us we know about them most when they make us sick, but they don't always make the sick.
There's lots of viruses around in the environments in our bodies, many of which are relatively unnoticeable.
Um, there are even viruses that are parts of our life.
For example, our genomes contain domesticated material from ancient viruses that contributes to our, um, biology.
So oh, okay. I get that. So very occasionally viruses will infect a cell from the reproductive tissue of its host, a germline cell, as we call it.
And if that happens, they can be passed down the generations, um, potentially for very, very long periods of time.
Um, and if they're not harmful, they'll just stay there.
Um, or they can just stay there forever. And occasionally, if they do actually contribute to a benefit, natural selection may act to preserve them.
So one of the most famous examples is a gene called Sound System, which is involved in reproduction.
It's involved in protecting the foetus from the maternal immune response, and that's derived from an ancient viral envelope gene.
And I'm taking on that role. Um, so these endogenous viruses, these integrated viruses are a big part of my research.
Mm hmm. Mm hmm. So if I.
Should I jump off this one? I usually do this one first.
If you had to define a single big question, that's the thing that gets you up to bed in the morning.
What would it be? What has.
One question what has been the the role of viruses in the evolution of their hosts?
That's probably the most interesting one. I'm guessing that the viruses have actually driven the way of the species, including ourselves.
Oh, comfortable? Yes. Yes, they have to.
We don't know the extent of and understanding the extent to which they have done that is what interests me.
No. Yeah. So what methods do you use to explore that question?
Related questions. So most of my research until about a few months ago has been primarily computational.
So I because of this process of integration, um, if you read the genome of an animal,
you will find inside it's hundreds of thousands of tiny little fragments of viruses.
And so by reading the genome of an animal like our own genomes or mouse or any other one,
you can find this all these little pieces of DNA and try and piece together the history of
how they go over and the pattern of interactions with their hosts at the genetic level.
You recognise that a piece of DNA is virus derived. So they they.
So if you, if you know what's, um, if you translate DNA into a protein,
you can look for parts of DNA that look like they would encode proteins that resemble contemporary circulating viruses.
So of course, over time there is degradation and you have to account for that and look for things that still resemble
viruses enough given the amount of time that they have degraded and have been in our genomes.
Um. So that would be the way. So.
What is it about viruses that interests you? Particularly, um, aside from that public health concern.
So, so there's a couple of reasons why that they're fascinating to an evolutionary biologist.
One is, um, the speed at which they evolve when we interact with them in the present day.
Um, and that's very useful to an evolutionary biology researcher because you can,
when you, when you're interrogating a contemporary virus, you can actually see it evolve.
Um, so, for example, in addition to the endogenous viruses before COVID came along, I was also working on, on HIV.
Um, on the one side, you have the obvious public health reasons for that.
Um, on the other, you can see the virus picking up resistance mutations to the, to the drugs that we use to combat it.
So the immune systems that, that interacts with, it's, um,
and you can even see these viruses evolve within the time cause of the infection of a single patient.
So it's a very powerful source of data to ask fundamental questions about evolutionary biology.
Um, I'm on the other hand, from a more, in a more general way, this, um,
almost invisible entity that is pervasive throughout life and I believe has shaped the evolution of life in a way that's quite hard to, to get out.
So the challenge of, of unravelling that and understanding that influence is one that intrigues me.
Mm hmm. Um, so it's, as you say, they change very rapidly.
But in order to go on working as viruses, if you like, they also need to have some kind of stability frequently over long periods.
Yeah. So, um, they have a tremendous capacity to mutate.
Um, but, um, evolution picks the mutations that work.
Um, and so there is a disconnect between what mutations happen and what mutations stick around in the long term.
Uh, because a lot of the change that happens in a virus actually breaks the virus, makes it makes it less able to do its job.
Um, and that's that natural selection on, on that variation slows down the long term change of the virus.
Um, I'm actually one of the research questions that I've been most fascinated with over the last
few years is a product of this is the so-called time dependency of evolutionary rates.
It's a kind of viral version of relativity.
Um, so depending on the timescale that you look at the virus, the apparent rate of evolution is very, very different.
So if you examine shallow timescales, you see these very, very rapid rates of evolution.
But if you look over the, the longer term time scales, um, the apparent rates of evolution drop almost to the level of, of the of that host.
Not quite. It's a little bit higher than mass, but, but it drops by several orders of magnitude.
And understanding this this disconnect in rates is a theoretical problem I've been working on.
Mm hmm. Um, so you can recognise virus that's being extracted from very, very ancient sources?
You can, yes. So very. If you interrogate the genome, you can find viruses that are, say, 30, 40 or 50 million years old.
Um, and by rights, they shouldn't be recognisable.
If you consider the short term rates of evolution, they should have changed so much that you wouldn't be able to recognise them.
Um, but as a result of two processes, one is this discrepancy between long term and short term rates, but also, um,
when they get into the genome, they stop evolving at their own rates, then they evolve at the rates that their hosts evolve.
So they essentially freeze in time and that's that preserves them.
So they they are essentially genomic fossils of viruses that were around a really long time ago.
Mm hmm. I'll just put one word here.
Bats? Yeah. So, bats for something you were looking at before we came along.
What? What what's special about bats? So bats are a, um.
They they're a reservoir species for medical important viruses, so, you know,
rabies, Ebola, all sorts of viruses that that trouble us seem to go through bats.
So I was one was also one that when that came along, bats were the first culprits of all that will,
in the end is severe cuts that were eventually identified as being the zoonotic reservoir.
So they seem to be able to carry viruses without consequences for themselves and sealed viral transmissions into other species.
So that's another major current research question of why do viruses transmit between species?
And so we've been very interested in the intersection between these two questions, because viruses are occasionally domesticated by their hosts.
One of the ways in which they're domesticated is by contributing to the immune system of the hosts.
So. So the hosts essentially borrow bits of the viral genome and repurpose them and use them as a as a counter mechanism.
And I'm very interested to determine whether one of the reasons why bats are really good reservoir
species is through this co-option of viral sequences as parts of their own defence mechanism.
And there's also some very interesting viruses in bat genomes, including Filoviruses.
So this is the, the lineage of viruses that includes Zaire, Ebola virus and Marburg.
And we've shown almost a decade ago the bat genomes have got quite a few viruses like this.
So viruses like these Ebola viruses or retroviruses, which are more common,
what we're interested in determining whether they're they have such a role, and I'm close to answering that question.
So on a on a computational level, we've identified a few integrations that appear to bear the characteristic hallmarks of selection that these kinds
of conflicts would engender in terms of actually really determining what properly we need to do some lab work.
And this is a major part of my current research and my research going forwards over the next few years.
Yeah. Okay. So let's, let's turn towards COVID pandemic itself.
Can you remember how you first became aware that it was around?
Was it just appearing in the media like like most people that something's going
on in China or were that kind of internal channels that you were involved with?
So, okay. So my first sort of interest sort of in this came about.
So in January 2020, I was writing only I see grants which I have subsequently been awarded and I'm currently doing.
And Vikram have two questions.
One is this the role of viruses in evolution. The other one is the reconstructing the transmission dynamics of a virus over time.
And as I was writing it and thinking of examples of interesting transmissions,
I saw news reports of an interesting looking virus that seemed to be emerging in Wuhan.
And actually there's a couple of sentences in my ground.
So one thing that might be interesting is seeing what these coronavirus or viral transmissions would do and whether they might be important.
And so it was given as an example. Obviously, I didn't know at the time that quite how impactful it would end up being,
but but it did seem like a quite worrisome and interesting transmission.
I kept an eye on that. Um, beyond that, academically, I didn't turn much further attention to it at the time in January.
Um, it did impact my, my, my, my life more generally.
So the first real sort of impact on me as a, as an individual, I think probably comes from my, my, my trade union activities at the time.
So in, in March, just before the, in early March, um, we were on, on strike, um, in the University of Oxford and in the UK more generally.
I was coordinating the strike in Oxford as president of the of the Oxford branch of UK and.
The last day of the strikes would have been a massive rally in Oxford with speakers, an emotional sort of thing.
But it was in sort of early to mid March and when we were starting to sort of see what
was going on and actually in response to emerging information about the coronavirus,
we decided to cancel that. And so we we pulled off that last day of action as a precaution because although
at the time the government was saying we're not introducing any I mean,
any restrictions on life, it didn't seem like a terribly good idea.
So so that was my first sort of realisation and direct impact on my day to day life from the virus.
And since then, obviously my, my academic interest in it has also increased.
So just to start with the impact on the day to day life, what when the lockdown finally did come into play, the university put measures in across.
How did that affect what you were able to do? So, yeah, so so in a few a few days before lockdown, probably about four,
four or five days before lockdown, I actually told my academic colleagues, you know, nice to see you guys.
I'll see you in however long I'll see you. I don't think I'll be seeing you for a while.
Which elicited slightly puzzled and quizzical responses.
I think a few people thought I was the person talking about it.
So I stopped going to two a few days before, before the lockdown.
At the time, academically, it meant that we shifted our research activities online, which for the kind of work I was doing then was achievable.
I think, you know, we did a lot of computational work can be done at home.
Like it. So did you have to take computers? Yeah, we took you know, everyone took their computers home.
Obviously, it impacts research nonetheless because we were all at home.
I have two small children and, you know, having them in the house is not a terribly conducive way of doing research, although schools didn't close.
So why did they? They closed in April, if I remember correctly. Um, and so so I did carry on my research.
I shifted more of my attention towards Kogan's. Um, but it also my trade union work activity escalated, which diverted me to,
to an extent away from research because I became involved in making representations to the university
on behalf of the trade union to try and ensure that things are as safe as possible for full staff.
Um, so yeah, I think those are the ways in which there was an impact.
Yeah. Yeah. And presumably there was a concern, particularly for short term staff, about them being able to maintain their income.
Yes. Yes, there were there was a lot of worry about about jobs.
So some of these discussions with with the university, um, all the time they were well,
initially for the first month or so, we didn't have much interaction directly with the university.
We were sending them impassioned letters and please and that sort of thing, which initially were probably largely ignored,
but eventually that there was a decision made to to have regular meetings almost weekly between the trade union and the university.
Um, which I think was the right decision.
And in those meetings we talked about things like the application of the furlough scheme, the impacts on this,
on, on short term staff, the impacts on staff with protected characteristics, all that sort of thing.
And trying to make sure that all these things were applied in a way that was as fair as possible,
that protected prospective people out as possible as could be.
Um. Yeah. Mm hmm. So let's go back to your shift.
You said you shifted your research into kind of it. Um, how did that come about?
What what questions? About so many questions?
This, you know, what were the immediate questions that you felt that you were in a good place to to explore?
So as an evolutionary biologist and someone who's been looking at all sorts of different viruses.
Um, I felt in a good place to understand the, the evolution and the interactions of these viruses and the.
Host Um, and so I was interested in trying to see what we could predict, you know, whether,
whether this is something that would run its course, whether it's something that, that would be, would be an escalating threat.
Um. Um, and trying to sort of a lot of people at the time were saying things with incredibly incredible certainty.
Um, and I was interested in interrogating accounts and seeing what really can be said with, with certainty, based on what we know.
I mean, there were no SARS-CoV-2 experts at the beginning of the pandemic because this virus can exist.
Um, but I felt that because I'd looked at viruses broadly, it's something I should think about.
It didn't dominate my research entirely, but it was certainly something I was looking at.
Um, and the genome was available from the end of January, I think it was, yes.
Yeah. Um, and, uh, I mean, over the, the months after that, there were various sort of in a sense,
you kind of had to look around for opportunities to, to say something interesting and see what you can work.
House. Um, and, and for example, one of my Dphil students, um, was,
we were working together on this theoretical question all the time dependency of rights of evolution.
Um, but because of his background's from, um, he's originally from Iran and Iran had an incredibly horrific manifestation of,
of the pandemic and a local manifestation of the pandemic.
Um. He was interested in seeing if we could evaluate the true impact because there was a genuine fear that there was a big undercounting.
And so we were we suddenly turned our attention to seeing if we can measure the impacts and see, you know, how bad is the local wave in Iran?
And because of his contacts and his interest and my role as a supervisor, I said,
Yeah, okay, just divert your research to the lab if that's what you want to do. And I hope you as much as I can.
And so we looked at that, um, another, another thing I got involved in very, very early on was a collaboration with a team in Imperial.
This is the team that involves one of the members of the team was Neil Ferguson, for example,
who we did the paper on, on the initial evaluation of the epidemic that led to the lockdown.
And one of the dominant ideas at the time was that herd immunity would naturally stop the epidemic.
And we did some some theoretical and analytical work with this team to to show that it actually didn't look to be doing a lot at all.
And so, you know, we we put a paper out on that and showing that.
And in Europe, from where we went, where we had data, that there was no evidence of herd immunity, damping, damping these epidemic waves.
Um, so yeah, those were sort of initial things.
I did the around work carried on.
We're still working on, um, undercounting mortality and in reconstructing the,
the dynamics of the epidemic in Iran with, with my students, that's, that's,
you know, operated as a kind of case study that enables you to arrive at particular
insights into the way the virus works and moves and how it affects populations.
Yeah, I mean, one thing we've, we've noticed and we've just, uh, we've,
we've just submitted a paper on this actually and we've put it out as a preprint already.
Is, is that Iran, despite the incredible toll the virus has had, there, doesn't seem to be anywhere near Marinette.
And so you have these peaks coming over time, peak after peak after peak, all of which are very high.
In fact, escalating peaks are higher in Iran relative to previous peaks.
And so we're interested in in the observation that that doesn't seem to be a natural.
And through through past infection, Iran has quite or had quite low vaccination rates.
And so understanding that and what that might mean more, more globally is something that is very interesting to us.
Um, it echoes findings in Manaus, Brazil, for example, where we had this, um, the second wave of the what's now called gamma variants,
which seems to have been higher than the first, um, and of similar things in Southern Africa have been seen.
So, so this, this, this general sort of observation of a lack of natural damping over time is something that I think is very important.
Um, and I mean, you read general statements from time to time about things like the, that as the virus, uh,
evolves through the different letters of the alphabet, not counting over code because that seems to have come from somewhere else.
But the previous ones that affected this country became more transmissible with time.
Is, does that general generalisation stand up? And if so, what would be the evolutionary reason for that?
Yeah. So, um, I believe it does stand up.
I think, um, you know, this is a virus that's, uh, crossed into humans as a sort of general as virus.
It was quite good at replicating in humans, but also not really adapted to human replication, probably quite good at replicating in other animals too.
Um, but what we saw in this first phase of the pandemic is this accumulation of variants that are better at transmitting in humans,
the alpha and then the delta variant being about 50% more transmissible respectively.
Um, like you said, al-Muqrin has a slightly more complicated story.
Um, and this is something that may continue.
It may also change as, as immunity builds up in the population and the dynamics of the.
Do change that. But it's a very important future feature that surprised a lot of people.
I think the idea that transmissibility would increase by 50% shortly after less than a year.
Right. For three of the variants. Trying to do the math in my head, yeah.
I look kind of lost the whole year. So would I try to think back to what happened?
Yeah. The idea that it's pretty much too over years ago now seems like unbelievable.
Yeah. So. So I think that the magnitude of that surprised a lot of people.
And I mean, I at the time was was so taken aback, I thought, okay, if this happens, it might happen again.
So we better take this quite seriously. Mm hmm. Yeah.
So, in general, would you say what you knew about viruses and what you've observed about SARS-CoV-2?
Uh, make you more or less anxious about how it might evolve in the future and, indeed, what other viruses might emerge?
I would say probably more. Um, so, you know, I've spent a lot of my research trying to piece together what an ancient well,
what a viral transmission might have looked like by putting together indirect effects on events that happened millions of years ago.
Here we have something that that's that's playing out in front of our, in front of our very eyes, um,
and things that we've only hypothesised are happening, uh, adaptation and the speed of adaptation is, is happening in a measurable sense.
And that, I don't, I don't think that any of us really thought that the speed of adaptation could be as high as it is,
and that that definitely something that worries me. Yes.
Among your research community, I mean, it's certainly in Oxford as a whole, but there have, you know,
hundreds of people, thousands probably whose research pivoted to some aspect of the of the pandemic.
Did it? Has it felt to you like being a more collaborative exercise than the way you were used to doing research previously?
Um, it's, it's a very strange experience that I think more interactive, certainly.
Um, a more collaborative to an extent. I mean, the speeds or.
Doing research is one that I don't think any any of us has encountered before.
So, for example, you know,
the proliferation of Preprints and the fact that people put out information all the time on what they think might be happening.
And even, you know, even on social media. Right. Likes people will put the plot on Twitter and suddenly that becomes what
everyone is talking about for a few days and trying to work out what it means,
how to debunk it. So, so, so having the scientific community interacting in this intense way is very, very new and very,
very, very challenging, but also also quite fascinating from a, from a research perspective collaborative.
Yeah. I mean, the collaborations are all kind of fishing, a fusion of this in this climate because they're not all lasting.
So you may, you may sort of interact with a few people to try and follow up one question and with a different set of people to follow up another.
So, so certainly collaboration is part of it. I don't think it's academia or academia.
So competition always exists among the collaboration, unfortunately,
but people are more yeah, no, I think it's fair to say people are more collaborative.
I mean, we saw with South Africa, for example, and the data they were putting out now with the Omnicom variant,
for example, potentially to the detriment of their own,
um, their own interest economy, that the idea of putting out data is, is an important one and thankfully is generally upheld by most people.
HM And have you personally felt a sense of responsibility to give advice either formally
through the various committees that have been set up or through using public channels?
Yeah, I have. I think I generally try and respond to queries and requests to to contribute as much as I can constrained by the realities of life.
We don't have, you know, infinite time. But I have done, you know, more media work during the pandemic than I have ever done before.
And how do you feel about it?
Yeah, it's it's a really interesting experience. I think it is challenging and try and trying to work out understandable ways to to explain things.
Um, it's something I feel I should do because I'm in a good position to do it.
And so I do it in terms of committee work and that sort of thing.
I try to contribute through, through, through committees and larger groups when I can.
There's the trade union work, for example, where I do try and use my expertise there in the initial phases of of the pandemic,
I was invited to to be co-opted on to a group called Science Scientists for Labour who were giving scientific advice to the Labour Party.
I initially was quite involved with that. I eventually drifted away for for various reasons.
Um, I'm now most, most recently a few weeks ago, I was asked to get involved in Independent Sage,
which I've gone to two of the briefings so, so far and see, see what I can contribute.
So, so as, as, and when I offer my advice in, you know, in the, in zoology, for example,
which is where I work because I recently published a paper on mitigation in universities with Chris Greenhouse.
Oh, you people bring this up. Yes. Just tell me a bit about that.
So what was that setting up to do? So we we were, you know, because we both work in universities and and also on COVID,
a lot of people were asking us, well, how how do we keep ourselves safe in universities?
So we kept on guessing these personal questions and thought, well, let's okay, well,
let's try and let's try and formalise a response and actually produce a paper
on this to give a general guideline on how to make things as safe as possible.
And this also included a couple of other collaborative collaborators for some Whiteson and Stephen Griffin.
And so we put together this this paper, sent it to two trade unions, to colleagues, to anyone who are interested as well.
We also published it as a, as a, as a paper. Um, and one of the things that came up in.
In zoology, for example, was because we're designing a new building.
The people responsible for that were interested in seeing whether we could incorporate any of
this guidance into the structure of the building in terms of insulation and that sort of thing,
because we were, you know, giving specific suggestions on on the right of our exchange of filtration and that sort of thing,
which are quite hard to add to buildings but are easier to engineer from the start.
So I sort of thought, you know, that's something that came up. But yeah, that's so.
And then there was the yeah, there was an open letter in the BMJ that's quite recently papers that.
Yeah, um, there've been a few open letters over the, over the years.
When. The vaccines plus one. Well, yeah.
So. So that. Yeah, that was. Yeah.
That came about. Just said a couple of months ago, I can't even remember now.
But but the, the, the overarching sort of motivation behind that was to emphasise to the point that,
you know, vaccines are fantastic and we should deploy them as much as possible,
but they may not always be enough to control inflation and everything and that we need to be using all the tools at our disposal in order to,
to to protect ourselves from from the pandemic.
So and this comes we didn't talk about any this case before,
but one of the tricks that the virus viruses in general cover up their sleeve is this notion of it being this great thing.
Phineas, talk a little bit about that. Well, yeah. Um, so.
But not natural selection pushes the evolution of a virus in particular directions, depending on the selective pressures of the virus encounters.
And probably the initial selective pressure SARS-CoV-2 encountered was, um, around transmission.
Um, but as immunity becomes more of a pervasive feature of the landscape for this virus, um,
the need to overcome this immunity is a bigger force in its evolution and has probably,
to a large extent, determined the the emergence and dominance of the home-grown variants.
To an extent, Delta. Delta was a little immune evasive, but nowhere near as much as Almagro.
Um. And so, um.
Vaccines. Vaccines ve low levels of application interact in complex ways with natural selection.
So if replication is very high and you're introducing a bit of immunity into the population,
that can actually escalate the evolutionary pressure and has the likelihood of
of the emergence of immune escape features in the genome of the virus are very,
very high levels of vaccination that probably goes away because of the effects of high levels of application on the vaccine,
on the transmission of the virus. So once you vaccinate everybody, this is probably less of a less of an importance process.
But as you vaccinate the world, the importance of keeping transmission low, both for the public health,
obvious public health benefits of low transmission in an unprotected population,
but also in terms of minimising the risk of the emergence of immune escape variants, is a very important aspect.
And one one we one we emphasised in the open letter.
And, um. Yeah.
Um. On the whole, like, well, I think we'll be able to ask the political question.
To what extent do you think those who are setting the guidelines have paid attention to the
the huge body of scientific research that's gone on about how to manage this outbreak?
Um. They observe it.
I mean, you know, the there is a the the amount of evidence produced here locally in the UK that can guides the pandemic responses is vast.
I mean, there's an incredibly, incredibly alert system by both scientists, but through public health as well.
So we have really, really good data to to inform our response.
I think it's fair to say that the government, while aware of it, has not always acted on it in a timely fashion.
And I think this is this has been a pervasive feature of the response in the UK from the delays involved in in the first lockdown,
from the delays from the lack of of an October circuit breaker in 2020, the delay in acting on on the Delta information, for example.
And, you know, not not restricting the transmission of the virus from India where it emerged to to the UK throughout really I think a now.
So here we are at the end of January 2022.
Yeah. Being told that pretty much all restrictions will be lifted imminently if you think that's too soon.
Yes. Yeah. And, you know, I think we're yeah, it's it's a it's a gamble.
And, you know, it is possible that that after the current wave does pass through,
it is possible that we may have a period of relative quiet, but it is also possible that we will not.
And also the the level of of public health interventions will also shape the that the points at which the the case rate will settle.
Um, and so by, by taking away all restrictions, we are going to determine the number of cases,
hospitalisations and deaths that we will see over the coming months.
And they could be lower if we took a more cautious approach.
So one of your other papers which I got to pick up on,
was also addressing this question of domestic and how that's presented in a somewhat misleading way sometimes.
Can you just walk us through what it means to, you know, it and how it's relative?
Yeah. Um, so so a lot a lot of time,
a lot of the time we have people use the words and the Mr. T and they kind of intermix it with assumptions about
what viruses do in terms of epidemiology and their infection and this sense of an inevitable march towards a calm,
benign, harmless future.
Um, and, you know, you sometimes hear a politician say, oh, well, and the mystery is inevitable, and then the mystery is going to be fine.
And so I sort of wrote this piece to kind of explain what the mystery means in an epidemiological sense.
It just means a relative stability of case rates.
It doesn't mean that that one will be it will be high or low or benign or not benign.
And so I was interested in highlighting that the the effects of our actions will will determine
what that potential and future would look like and whether it's one that is desirable or not.
Um, and I think, you know, an endemic future with the really high case rates is one that will have a lot of death and disease and
also one that will allow the virus more opportunities to to evolve and cause more problems down the line.
And the way to avoid that is to keep the the the non-pharmaceutical interventions going for longer, do you think?
I think until until more of the world is vaccinated in a targeted way.
They do need to be switched on for for longer. Um, and I think we also need to look into structural alterations much more so things,
things that can be going on in the background that disrupt our lives as little as possible,
but can be maintained in perpetuity in order to make sure that and then acceptance as low as possible.
So things things that things like ventilation, for example, and filtration that will require massive investments.
But once they are put in, no longer disrupt our lives in the same way as other things,
I mean, you know, mask wearing, for example, is is a slightly disruptive activity.
But that could potentially be reduced as other aspects of the responses, its strength and isolation as well can be kept as a shorts as possible.
And, you know, deploying the science through through testing and that sort of thing to ensure that it can be as assured but
also as safe as possible is a really important aspect of our public health policy that we could maintain.
Although it is looking like it won't be maintained at all going forwards.
So these kinds of structural alterations, investments in further research,
we're still vaccinating people against the initial strain of the virus that emerged in Wuhan two years ago.
And I think it's about time that we consider updating our vaccines to to to other, newer strains in order to engender broader immune responses.
And obviously, as as the science develops, the hope is that with both the structural interventions,
the the individual level interventions and restrictions will keep going down to the point where they no longer influence our lives.
Mm hmm. So to what extent have you felt personally threatened by the possibility of being infected?
Or have you been afraid? Um, I don't believe I have been infected.
Um, I've. I've never tested positive. Um, it's varied.
Um, I'm probably, I, I worried.
I've worried because of the unknowns. I don't know what's, um, you know, the long term impacts of COVID infection will be I don't think anybody does.
And that's something that concerns me. Um, I'm worried about my.
My family, my kids, my partner. Right. Right.
I think it's a very high it. Yeah, yeah, yeah, yeah.
I mean, my, my school has got cases all the time and it's, you know, it's a, it is a matter of time until she gets is.
Um I was extremely concerned that impacted in October this year I had to go to Greece because my my dad was in hospital and then sadly passed away.
Um, but I was visiting him in ICU every day.
So I had to take a test every single day. And I, you know, I was terrified of the idea that I might also bring him the virus.
Um, I did everything I could to, to minimise that.
Um, direct fear from, for myself is not, it's not the overriding concern.
I think I, I feel.
That I'm personally I mean, this is all subjective, right?
We're talking about feelings. I, I don't fear death from covid.
I, I'm concerned about the possible long term implications because it's a virus that we know so little about know.
Uh. So did you. Did you?
I think you mentioned that. Did you work longer hours than usual during the pandemic?
I think that's. Yeah. Yes.
Whether those hours could all be described as work is another question.
I mean, the experience of of homeschooling to kids.
While while trying to work and talk to the media and be involved in advisory abilities
is one way you would kind of wake up and be involved in things until you went to bed.
How much of that was actual work is another question because my my partner also
has a full time had a full time job through throughout most of the pandemic.
And, um, and we will kind of trying to somehow manage all of all of these activities together.
But it's certainly certainly one where, you know, much of the working day is covered with thoughts of much of the day,
isn't coupled with thoughts about work, although all academics tend to do that for themselves anyway.
Yeah. Um. Yeah. And um.
Besides, yes. I mean, are you normally involved in teaching and how is that impacted by that?
Yeah. So, um, I, yeah, I do teaching in the department, um, in the college.
Um, a lot of that has moved online.
And so getting to grips with the software for moving lectures online and doing that is,
is the paid recording lectures is, is, if it's not, not a trivial activity.
Um, uh, I quite like the products of a recorded lecture, but, but I do obviously enjoy the, the in-person version of it more.
Um, tutorials of course are a massive part of teaching in Oxford that I'm involved in,
that there are periods where that has been online in the last autumn.
Um, some of that I did in person, um, trying to incorporate all the guidance that, that, that we were working on.
So ventilation, masking distancing, keeping numbers low and encouraging people to be safe.
Some of it inevitably moved online because if someone was sick or someone was waiting for tests and then obviously we would go online.
Um, and so it's been a, it's been a, it's been a mix.
It's been, it's been interesting. I, so, for example, on online tutorials, uh, I find.
Draining for a tutor because you you end up doing more of the talking and the work compared to an in-person tutorial, I think.
So it's it's really hard work. It's probably just because the students feel more apprehensive or nervous in an online situation,
they're less forthcoming and they can't interact with each other in the same way.
The contrast is, yeah, that the interactions between them are loads but but also I think, I mean two tutorials are meant to be interactive, right?
It's not meant to be just the tutor talking. And I think non-verbal cues are an important aspect of encouraging participation.
Um, and those are harder to do. You have to, you have to say, you know, you've got two students.
Well, well, you know, Lisa, what do you think? Um, and in a in a real tutorial, I would almost never do that.
I would never call someone by name and tell them to participate.
I would pause and kind of nod and look at them, and it would happen.
Um, and that's, that's difficult to replicate online.
It's, it's, it's a lot more artificial. Um, however, in terms of what you can give them as a tutor, in terms of the delivery of material.
I actually think it's possibly in some, some cases, even even better.
Um, but yeah, in the long run I wouldn't like to see it replace if you think it's good for
the having a balance between the two in future regardless of of infection.
That's right I think a balance yeah.
I think that there are topics that work well online and I the more didactic ones for example to do it quite well,
I wouldn't, I don't, I don't think it's something we should exclude.
Um, obviously, I think, you know, research and feedback is going to be really important in determining whether,
whether there is something new that will stick around.
Um, I don't think the, the, the, I don't think I'd like to see the lectures being be replaced with recordings.
I think that would be a terrible, terrible thing to happen to academia in the long run.
I think the, um, although a lecture does look like it's quite one dimensional, a lecturer is just standing in the front and talking.
Uh, I think the, the feeling and the, the performance element of it is actually quite an important parts of, of learning.
Um, and so I don't. I wouldn't like to see that go away.
Mm hm. So. So we do union hat on.
How would you evaluate how well the university managed, um, that the h or aspects, if you like, of the pandemic as a whole.
It's been a mix. Um, some better than others.
Um. I think locally the University of Oxford has been quite tied in to matching what the government guidance is and because in my
view the government guidance has not always been adequate as a response because of this commitment to matching the Government's,
the university response has not always been, in my view, enough.
I've often found ourselves in meetings saying things and feeling like I haven't been listened to.
This ensued. But then a month later, you know, the university side, they they they do look like they had listened to and they do so.
So there have been cases where the university has gone over and above government guidance, for example, around masking, around testing.
They've had an incredibly proactive approach to vaccination, and these are all really important things that they have done.
But for example, now, you know, the university has is dropping the masking mandates and so much the government's off on the government response.
I don't think that's right. I think we we also brought it into light.
We've had confused guidance around masking for parts of the pandemic.
And there are certainly been been times when I felt more more could have been done.
So do you think? I think I think it's a it's a sort of truism that lockdown was difficult for everybody.
Do you think the fact that you had that your work was directly related to the pandemic and it was something that you could get on with?
Did that support your own wellbeing, do you think? Or was it the fact that you knew so much about the virus make you even more worried?
I think it just the worry. I think a worry in the sense of having to do this.
I don't know. I don't I don't think it's because of my. Well, I think the I mean, the union activity, for example, was very, very hard, actually.
You know, the sense of making representations and feeling like you're not listened to is incredibly draining.
Um, and actually I have, um, I have reduced my, my, my contributions to union work to protect my wellbeing.
Um, and don't tend to as much of it now as I did in the, in the earlier phases,
but because of, of wellbeing reasons, um, and I think the, you know, the kids aspects of this,
um, however much I find my research fascinating, the, the idea of, of compromising their wellbeing because of having to do all this at the same time.
It was not a very pleasant one. So I don't I don't, I don't think I don't think it did make it more more.
More. Yeah, I don't. Certainly didn't make it's harmless to my well-being in terms of comparing that to other people's experience.
I'm not sure I'm necessarily best placed to make that comparison.
Um. Uh.
Okay. I think we would have got to the end. So that that got two final questions.
So has the work that you've been able to do with COVID raised new questions that you're interested in exploring in the future?
Definitely. Definitely. Um, so, um, you know, the, the emergence of variants, for example,
like how and why do these variants emerge within the early stages of a pandemic is something that has never,
never really previously been thought about or seen.
And I'm very interested in understanding that process. Um, what are the forces that, that shape thoughts?
Um, to what extent do you know, you might have heard about this idea of long term immunocompromised,
chronically infected patients, for example, may be the the the space in which these variants arise.
Understanding that. So people who've got HIV, for example, HIV or immunotherapy or certain cancers,
for example, that might be where, where these variants sort of incubates.
Um, I'm trying to understand vaccine obviously to mitigate that as well.
Um, it's going to be a,
it's a really interesting question and also an important public health one to to we need to different have different vaccination strategies.
For example, should we be deploying antiviral drugs in these situations?
And how is how is that going to play out?
Um, there are these fears, for example, around one of the drugs on the market at the moment which mutates the virus.
Um, and certain people, for example, are concerned that this might actually increase the rate of emergence of variants.
I'm less convinced of that. But, but understanding that is an interesting question.
Yes, I see my comments on the press on that. So let's just name it because I can't remember.
Can you read say Molnupiravir? Yeah, they've got these subtle flags.
And so the idea is that it makes the virus mutates so much that it falls to bits essentially.
Yeah, yeah, yeah. I, I, I some people are worried that imperfect applications of that might actually push the virus to, to evolve quicker.
Um, I'm, I'm less convinced around that, but I can't rule it out.
And in the long term immunocompromised patients, that might be a particular risk.
So, so I think, um, studying, you know, sampling the virus over time in isolation, patients who,
who are receiving that drug is going to be a really interesting research question.
And finally, has your experience of Kobe changed your attitude or your approach to your work?
The things you'd like to see change in the future.
It certainly made me a lot more adaptable and trying to observe sort of lateral connections between different data streams.
And, um, my, my research has always been a mix of hypothesis testing and hypothesis generating.
And as an empiricist, I always felt a little bit guilty about the hypothesis generating aspects of the research.
I think the fact that science is always a little sheepish about sort of saying, well,
here's some data and here's some interesting hypotheses that this data might might suggest.
And I think that kind of helps to take some of that guilt away and and sort of enable lateral thinking as long as you're
explicit about it and unclear about the what's happening as a generational hypothesis rather than proposing a fact.
And I think, you know, doing that in a more uninhibited way is is something that I can see happening and what I was.