Wednesday, 27 May 2020

Unexpected science in 2020

What a half-year it’s been. Having kept myself broadly out of Addenbrookes Hospital for 20 years, I spent 5 weeks in the neonatal intensive care last December, thankful for some extraordinary NHS care to our premature child (who is now doing great!). This had put me in a very “clinical/medical” mindset. I became aware of the COVID-19 disease around Christmas time, my parents had come over from Italy, and we were looking together at the news coming out of China, commenting how unthinkable the lockdown of a large city and the loss of freedoms would be anywhere here in the “West”. Surely something like this (at some level, we were thinking both the disease and the response to it) could only happen in China?!  My parents flew over again, late February, and stayed here for a week. A small (and then not so small) number of cases had being found close to Bergamo, and treated in highly specialised units in Milan. It still seemed something that would have no impact on the broad population. However things moved so fast that the day after they flew back to Milan the whole Lombardy region became red zone, and within a few days all of Italy was in lockdown, as it essentially remains to date. 

Early March, I realised that what was happening in Italy would almost for sure very quickly happen in the other European countries, because we are just so similar in our ways of life and societies, and so connected. I was also very worried, because the health system in Lombardy is better than almost anywhere else in the world, and the disease was straining it. With a delay of roughly two weeks, there was a similar trend of cases in Spain, Germany and France. Still, at that point, cases in the UK was surprisingly (given the degree of international mobility here) few. There was in the UK news reporting a sense of disbelief and displacement, which reminded me very much of what I had in mind back the previous December, when looking at the news coming out of China.    COVID-19 then did pick up in the UK, and it was clear from the number of cases and then shortly afterwards the number of deaths, that the curve of the epidemics was at least as bad as in Italy and Spain. Is it so difficult to learn from each other’s experience?

It was quite clear to me that also the measures that would have to be taken, in terms of emergency lockdown would have to be similar, since any opportunity for a more reasoned control strategy was not being pursued. I was not very surprised when on the 20th of March the university, rather abruptly, decided to lock down completely. Students were encouraged to find their way “home”, if they could, causing significant distress and confusion. For the first time in my lifetime the departments closed down to the point that even faculty were not able to access their labs and their offices. This was quite shocking. My thoughts during the week heading to shutdown were conflicted, between the desire to keep everyone safe and infection rates as low as possible, but also to react to this threat by doing something useful. After all, Universities contain a lot of creative people, many of whom are great problem solvers. Shutting down was an extreme reaction, I felt it was not the optimal solution. 

Researchers were being forced out of their labs when perhaps they could have something useful to do. From then on, research in the University has only been allowed on projects very strictly related to COVID. This in practice has meant only very few biology labs, working directly on the virus biology, have remained active. Other groups hoping to do relevant work, for example investigating aerosol dispersal or mask materials, have found it difficult to work. One project that did manage to go ahead has been based in engineering, aimed at designing robust and cheap ventilators. Everybody else has had to reshape their work from home.

I could see it was not clear to everyone around me that this disease was really going to be life changing, in the short, medium and long terms. I thought it was a good idea to urgently stimulate people to think about what they could do. So, in the in the days just before the shutdown, I set up an online bulletin system using a software called Slack. I defined various initial topics to focus on, and I allowed access to all the academics from Cambridge and their collaborators. Very quickly we grew to have about 1000 researchers, contributing knowledge and sharing ideas in a structured way.  This was very useful, it served for example to rapidly coordinate efforts around the ventilator designs that various teams had started thinking about, and also to share instructions on how to make various kinds of cheap masks, and we shared information about modelling approaches for the epidemics. This Slack platform served as a remarkable bottom-up community, and is still useful now two months on - the “mainstream” University offices are using it to see what researchers think might be possible in various themes and directions.

Between complex shopping adventures and dipping into various other jobs normally entrusted to professionals (schooling, babysitting, housecleaning, DIY) I of course still had to run my day to day job. Luckily for me, this did not involve online teaching because I had done my course and examining in Michealmas. I could just focus on talking to my graduate students and postdocs, and keeping their research going as much as possible, helping them to transition to things that they could do at home, such as data analysis and writing up results and preparing plans for the future.    I got involved in two new COVID-19 related projects.  In a very minor way, I tried to help the open source ventilator, which was built in the Whittle lab, part of the engineering department. My interest in that project is connected to work that we do with bio/medical technology developing countries, I wanted to see if simple designs could really be taken all the way to medical instruments. It’s certainly become clear to us that there are huge challenges in certifying instruments for medical use, and we are still in the process of understanding how what has been developed so far I can be licenced and produced locally in a safe and legitimate way.

I had a more significant involvement and in another project, together with Prof. Cecilia Mascolo in the computer science lab, where the idea was to see if the sounds of voice, cough and breathing,  recorded in a simple way through smartphones, could be enough to diagnose the COVID-19 condition, its severity, and perhaps even distinguish it from other types of airway diseases like the common cold or flu. This project  is going well -  we are still in the initial phase of data gathering sound samples.  We are still looking for more people to join!  Having promoted the idea through social media and our personal networks, we also managed to get this concept on many newspapers and I ended up on mainstream television. We have so far 7000 people who have donated their sounds, the largest such data set globally, and we're in the process to see to what extent these sounds can be used to diagnose the disease using signal detection and machine learning algorithms. If this project turns out to be successful it could serve as an automated filter, perhaps as part of an NHS 111 response, helping the health system manage the demand for advice, and to work out who should go to hospital and who should safely wait at home. Working on this project has been a great learning experience! For the first time in a while I've actually myself had data to work on, and I enjoyed working out procedures for data analysis. I made figures and reports to other team members – it felt like being a student again!  Being active in research at the level of “raw data” is something I had lost, as many people do, when growing into a group leader. In my main established projects there are very competent people in the lab doing almost everything. Suddenly having to face an entirely new challenge allows everybody to input, including senior people like me!

I am based in Physics but I work on biological systems. One of the main thrusts of research in my group is around understanding malaria disease, which includes creating affordable technologies to help tackle malaria diagnosis in developing countries. I usually begin my talks by reminding the audience that malaria currently kills around half a million people per year, every year, mostly children, concentrated in few countries of the world. The COVID-19 pandemic is causing huge problems to us, with loss of life and socio-economic problems. And yet -thankfully- it is such a small thing compared to malaria. (COVID-19 deaths have reached about 285,000 globally accessed 11th May 2020 and are shared between many different countries). This really brought home to me what terrible impact an endemic infectious disease can have on everyday life.  We have to invest enough to sort out these problems, it should be within our ability to find scientific solutions to both these infectious diseases.

The pandemic has already caused lots of changes, many are obviously simply bad and we hope to revert them. It has sped up, for good or for worse, many trends that were perhaps about to happen anyway. By changing our daily life and our habits so suddenly, and by preventing us from doing a whole set of things, it has opened up for some people a window of free time. For me despite being busier than ever it's certainly allowed a chance to consider, with a little bit of detachment, how to use my time and my expertise in order to try and do something immediately useful.

Monday, 31 August 2009

First Post

Hi. This is a blog relating to the research of Dr Pietro Cicuta and his students and collaborators at the Cavendish Lab, University of Cambridge.

I aim to update regularly with our work progress and possibly other info !

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