 Wrth iawn, siarad. Grifitho gilydd â'r 28 mlynedd yn gweinidol arol. Wrth i. Fyliciaeth i chi, ddim o ddwylliant y gwaedd i'r Gweinidol, msp. Wrth i erioedu Brynach, Siarad Dfynod Gweiniad, fydd efallai i chi'n ei ffwg, ond mor fydd oedd ei pot i gydag arlu gwellfaeth yr oedden. Yr 1rhyw gweinidol yn oethefn i gydag ar laelio 4 ar yr agenda, ac mae'r ddifrif i gyfegiwyr ar yr eich ystyried o'r cyfieithiaid ym Mhwyfyrir Covid-19. Mae'r ddifrif i gyfegiwyr ym Mhwyfyrir Covid-19 yn perffwyr. Dwi'n credu i gyfegiwyr ym Mhwyfyrir Covid-19 yn perffwyr. Yn gyfegiwyr ym Mhwyfyrir Covid-19, ydw i ddim yn gwybod i gwaith yn cyfegiwyr ym Mhwyfyrir Covid-19. Mae'n gwybod i gyd wedi gwyr ym Mhwyfyrir Covid-19. I would like to welcome to the meeting joining us remotely Dr Rachel Hellowell, who is director centre of expertise for waters and the hydro nation international centre, George Ponton, head of research and innovation at Scottish Water and Peter Singleton, research, innovation and evidence manager at the Scottish Environment Protection Agency. Thank you for giving us your time this morning and thank you also for your written submissions. So we're allowing perhaps an hour for this particular session and I'm going to start with some questions. I'll ask my colleagues to come in. If you would like to respond to a question that's not directed specifically to you, just put an R in the chat box and then we can bring you in as a question and I'm keen that everybody gets as much of an opportunity to speak as possible. So I wonder if I could just start maybe just by asking you all in turn, maybe start with you Mr Ponton from Scottish Water. If you could just tell us a little bit about the experience you've had at Scottish Water with wastewater testing, how that worked in practice, what were the challenges and what you've learned from that for the future? Good morning everybody. From a Scottish Water perspective, the wastewater sampling programme was set up initially to support a piece of research that the Rosalyn Institute wanted to instigate and we worked closely with Rachel Steeck-McCrew to set that initial project up. I think that some of the experience of the wastewater sampling programme was but initially it was a lot of risk assessments to be set out because when this kind of initially started we were all in a bit of an information vacuum, didn't know what the transmissivity of Covid was, a lot of concern amongst our wastewater operatives as to whether there was transmission from the wastewater and that was partly why we could have commissioned or joined the research project initially with the Rosalyn Institute. But once we could have established that there wasn't any risk and had the necessary risk assessments carried out and made sure our operatives had the right protective equipment, sampling at the wastewater treatment works was relatively straightforward. We do operational self-monitoring and we do regulatory sampling at our wastewater treatment works. The access to the wastewater at the inlet of the wastewater treatment works, which is where we were targeting for this surveillance programme, was relatively easy to set up. What we learned was that as part of the wider, once we had the programme up and running, that in discussion with some of the health boards we started looking at the opportunity to sample in the networks and that became a little bit more challenging. The wastewater networks are obviously designed to drain foul and surface water from communities and it's not really designed in a way that allows you to sample discreetly in communities. So, through that initial discussion with some of the local authorities who wanted to perhaps get better information in areas where they weren't getting the clinical testing coming through or the people reporting on PCR testing, that became a little bit more challenging. It was also took a longer lead time to set that sampling programme up because we had to do a lot of desk work to identify what areas were drained into different parts of the network, what cross flows were coming from other parts of networks that perhaps weren't under surveillance. Then we also got the health and safety aspects of sampling in sewers. We basically established anything deeper than about three metres was unsafe because you're effectively, whilst you're on the surface, you're effectively working at a great height. So, sampling anything deeper than about three metres became problematic. The other issue with, or again the learning in this space is that you've got a very consistent flow at wastewater treatment works and you can also set up auto sampling, which gives you a composite sample over 24 hours. You take a sample every 15 minutes, every hour, and then you get a combined sample for a 24-hour period, so that gives you a better sample. In the wastewater, you're dependent on what flows in the sewer at any given time, because you're just taking a grab sample. As the sampler turns up, it drops a container into the sewer flow, whatever is there, and that's what you get, so you just get a snapshot of what's there. There are a number of challenges in that, but overall, the programme worked well. We'd like to commend our staff across scientific services, wastewater networks and operators for the efforts that they've put in on their challenges and circumstances during the Covid pandemic. Okay, thanks very much, Mr Pawnton. Before I bring in the others, can I just ask a couple of follow-ups from what you've said? Can you give us an idea of how many test points there were across the country and what was the resourcing implication for Scottish Water to undertake this work? So, in the initial stages, I think we sampled, I can't remember the exact number, but we sampled it. The initial programme that was set up covered 50 per cent of the population, so working with SIPA-identified target wastewater treatment works to sample that would give a representative sample of 50 per cent of the population. That was quite a small number of wastewater treatment works initially. I've not got the exact number to hand, but I can get it while you're asking other questions and submit that afterwards. Would it be in the hundreds, that sort of level, or fewer? No, fewer works, because some of our works are quite large areas of population, so if you take something like Defield and Edinburgh, that does over 600,000 population. We sampled some of the smaller works in West Llorien, some of the smaller works in Tayside, Perthinc and Norse. Once you started getting out into the island communities and some of the more remote communities, you're then almost sampling out a wastewater treatment works that tells you what level of infection there is in that local community. Some of the bigger urban systems are draining quite large geographical areas, so if you take something like Dalmure, that is draining almost the whole of the Kelkin Valley from Kilside, Cymru and all the way down through that kind of vicinity, so you're draining quite large areas to get on. Sampling one site gives you a very large population of coverage. We're sampling up to 300 samples a week. In terms of resourcing, initially, because a lot of operational activity with the lockdown was stopped, we could utilise our existing sampling resource, that as we got back to normal operational sampling and other activities, we had to recruit extra resource. That, in particular, was when we were doing the network sampling, where we were utilising a couple of sewer network contractors, one in the west and one in the east, to do some of the sampling as well. That's no longer happening because the network sampling isn't included in the Government Surveillance programme. Those are some of the challenges that I started early on. Okay, thanks very much. Can I move on to Peter Singleton? Maybe ask you, Mr Singleton, a similar question to my original question to Mr Ponton. What was your experience of the programme and what lessons have been learned from it for the future? Thanks and good morning everyone. I think my greatest learning lesson was what you can do in an emergency. I have been involved in this business for 30 plus years or something, and I have never seen the barriers between different organisations come down in the way that they did. It was an incredibly positive experience of, yes, we can do that. I don't have a bit of kit, but that's okay. Someone else can lend you a bit of kit. Across the board, it was a really, really positive experience. As George said, it grew out of a worry about keeping people safe in terms of Scottish Water staff. Then, very quickly, we realised that we had all the kit that Roslyn was using, that we could mirror what they were doing as an academic exercise as a monitoring programme. There's quite a big difference between putting a few samples through a lab to putting a monitoring programme in place. As George explained, we had that great opportunity that they had most of the kit already in place. The speed at which we could react was fundamentally supported by the fact that we already had monitoring programmes in place. They had sampling kit in most of the right places. We had a lab that was set up to put multiple samples through. If we tried to do it from a standing start, it would have been a very different experience. We started off doing 24 sites, 28 sites, 40 samples in May 21. We went up to just under 300 samples. We went back down to 200 samples a week. I just checked 120 sites. That's giving us a coverage of about 80 per cent of the sewered population, given that there are parts of Scotland with lots of private wastewater systems. My other learning is that there is a really interesting opportunity here in wastewater-based epidemiology. As I've sat on calls with various people from different walks of life that I wouldn't normally interact with, it is really interesting that there is a data source here, but the question always in the back of my mind is data for data sakes no use. It's about how can we turn that information into something that helps people do their job better or differently or have knowledge that they don't have at the moment. Okay, thanks very much. Just on that last point, do you have a view on how valuable the whole exercise was to the Scottish Government and health advisers in terms of formulation of Covid policies? I've often struggled with that. Effectively, we crunch a bunch of numbers and we stick them on a website that was available to everybody who needed it. It was really heartening to see the data going into things like the Covid muddling reports, so I could point out to my chief executive, this is what we're doing, and here's that information being used in a report to support the decision-making. Whether decisions would have been made differently if that information wasn't there is really difficult to know. Anecdotally, it's quite interesting that, again, as the world returns to semi-normal and you start to talk to people, I literally bumped into someone at a conference who said, I was using your data in Orkney to decide how many tests and trace people to put on that week, because they said, if your data matched our data, then, broadly speaking, we assumed we knew most of the people who had Covid. If your data had a spike and ours didn't, then we guessed that maybe we should do a bit more phoning round to find. I only knew that because I literally bumped into somebody who had been doing that job for six months. Thank you, that's really interesting. I'll move on to Rachel Healywell. Please, maybe just ask you again, as did with the others, just to reflect on your experience of the whole process. Morning, yes, thanks very much. My role is very much working at the science policy interface. I work very closely with the Scottish Government and its agencies. The Centre of Expertise provides that link to the Scottish research community to respond when there is an issue such as this that needs urgent attention. From my perspective, I was asked to prioritise this particular piece of work ahead of everything. I concur with George and Peter in that what was amazing in this space is that when we have a crisis, everybody jumps on board to try to work together to find a way through the issues. From a cruise perspective, we were fortunate because we had established relationships with the key who were required to address the pandemic and respond accordingly to the wastewater surveillance. Working with SEPA and understanding the research community in Scotland, you had the skills to come on board to respond to that. We had four projects within Crew all related to wastewater-based epidemiology, and we could work with them very efficiently. We had processes in place to ensure that projects could be set up, fuelment could be followed quickly and effectively. My budget that we had for this work, the first project that we funded entirely from our existing crew funding, but as the work progressed and as we could see there was promise and we had successes in terms of identifying the virus in wastewater and so on, the Scottish Government provided more funding through Crew to support the activities. It was a very stressful, exciting time. I think everybody got a real buzz from working together and just seeing what could be done. As Peter said, with no barriers we really did work at pace and it was very effective. For me we also drew very much on staff at a UK level from the DHSS and the Joint Bias Security Centre as well. They were engaging with the Scottish team very much and sharing protocols, sharing learnings, sharing samples and I think that was really crucial as well. I think that we all very much appreciated their input and then through Crew we connected internationally as well to other discussions. That was a very positive experience from my perspective. In terms of learning, I think in terms of communication with some sectors that could have been improved to help us make decisions, we were very keen that the outputs from the wastewater surveillance had impact and made a change and I think from what George and Peter of both said, there were changes that happened as a result of the work. There's definitely been a lot of discussions within the Scottish Government and more wider about process and practice and operations that I think have been very beneficial. From my perspective, the lessons learned from this is that going forward we do need to work more closely together. We need to bring interdisciplinary and cross-sector teams more closely together and have a more formal platform to liaise and collaborate. From my perspective, that's a summary of where I come from but from the Centre for Expertise for Waters, I really feel that we are the enabler, we bring people together, we organise the meetings, we take actions and we try to make a difference. I think that was successfully achieved in this particular area. Thank you for that. Do you have a reflection on the value your work was in terms of driving government policy? Like Peter said, this is a really difficult one to answer. In terms of the value, it's incredibly important what has been delivered and there have been changes in certain areas of Scottish policy. We essentially provide the evidence and the information to help decision makers. Those decisions are made at a level above me. I know within the Scottish Government that there are all sorts of committees where the information from this work has been used and discussed to influence various policy areas. Within CREW, we are running a project to try to understand the impact and what happens to some of that evidence once it leaves our responsibility and our involvement there. I would say that it has influence changed in how waste water surveillance is used and interpreted within various Government departments. George Pontot, do you want to come back in? The only other thing that I would, in response to that question, I think that I don't have visibility how it was influencing policy, but certainly during the pandemic, it was the information that we were providing through this programme was helping the health boards and the local authorities in their planning around where they were putting out the mobile test facilities or test units. That certainly drove some of that activity, so it was definitely valued from that perspective. I think that it's still, myself and Peter, are still involved. There is a stakeholder group that is looking at I suppose some of the policy questions that you're referring to. There is a much more broader discussion on what else waste water-based epidemiology can and can't be used for, so I think that it's raised the visibility of what the potential is for future policy. Okay, thank you. I'll bring in Jim Fairlie. Thank you, convener, and thank you, tech. That's the stuff that you're saying just now. I find it really interesting, but one of the things that has absolutely come out of the results of Covid has been how people said, oh, the barriers came down, not just in your sector, right across society. The bit that bothers me is the fact that they weren't down in the first place. However, have you gone back into your silos? You've all said that this co-operative working is very good and we should do it. Are you not still doing it? Have you all gone back into your own silos and now working independently of each other? I thought that that level of co-operation could be used across huge areas of disciplines, whether it's surveying for other diseases and all sorts of other public health issues. So where are you in terms of your co-operation just now? Anybody can chip in with that. Put your hand up. Peter, there you go, you're first. There are always slight barriers, aren't there? So SEPA regulates Scottish Water. George and I are both effectively our heads of research, so there's less of a barrier between us in a way, if you know what I mean, because we're looking in that innovative space. Scotland was the first place to get a programme up and running in the UK and I think that reflects the fact that there was fewer people involved. There was SEPA and Scottish Water and the Scottish Government and we could react more quickly. The biggest barriers that came down, if I'm really honest, were across the UK. I've never had such positive conversations across the whole of the UK. There was a call set up by DEFRA every week with 40 folk on it and it was just what can we do and really open communication and learning and I suppose the other barrier that didn't exist was resource because, as George said, both of the organisations were pretty much in a sort of emergency multiple state so as long as, you know, I didn't have to fight to find people who could do the work because the lab was shut so we opened the lab to do this and that was it. I did definitely notice the UK's barriers coming back up as living in a pandemic became a more normal thing. There was an issue about do we have funding to do this, do we have funding to do that and people were slightly less open. Again, because we live in the research world, actually we worked our way around that really successfully. We were allowed to have more open conversations and I think it would have been if it was seen as an operational permanent thing. I think you're right to question why there are barriers and how can we live in a more open world than maybe we did. It's also a little bit about relationships, isn't it? Yeah, and I think that's really probably important but Rachel, did you want to come in there? I was just agreeing with Peter but, you know, in terms of where this work is going and the future, there are so many opportunities in this space and we've been developing methods to detect Covid in wastewater but wastewater can be used for a whole range of other purposes as well. There are a lot of applications, whether it's using wastewater to detect community-wide use of elicit drugs or lifestyle chemicals such as nicotine, caffeine or alcohol. I mean, there's all sorts of things there but there's, and I think that going forward, we do need to, you need to think about how we can work more closely together to re-engage. You're right, after the initial surge of activity and possibly after the finish of the last crew project in my eyes, I feel that I've become kind of disengaged from that process just because the funding stopped and it's awful that, you know, through that that should be the situation but we do need to keep this dialogue going and getting the right people in the room to think more strategically about where we need to go in this space because there are so many opportunities and that resource and the sampling is all in place. You know, the hard work has almost been done so, you know, let's think about those opportunities moving forward. I wasn't going to come on to that but, George, if you want to come in first, I'm going to come back to that last point that Rich was just made. Yeah, I think just to your original point about kind of the barriers coming down and why we're not down in the first place, I think it depends where you're sitting. I think what was clear and it came out in some of the earlier comments is that it wasn't so much that there are barriers, it's just that it's conflicting priorities. It was a slightly simpler time during the Covid because there was one priority and it was almost survival so everybody kind of focused on on the issue at hand so that kind of meant that it was easier to get resources, it was easier to focus your time on this particular topic. I mean, I've got a very, as I'm sure Peter has, a very broad portfolio of areas that we're working in so it's sometimes very difficult to to carve out the time but what I would say is that the, just picking up on the point that Rachel said there, I think there is still discussion on going and collaboration on going on this whole issue about wastewater-based epidemiology, there is a group in Scottish Government that is running a kind of a trying to lead to kind of the policy development in this space and there's people from Kate Dempsey and the Olympics in your mean later on from kind of epidemiology, there's people from genomic sequencing, there's people from Public Health Scotland, there's people from different parts of Scottish Government, Scottish Water and SIPA as well so I think there is still collaboration going on but I think it's about kind of focusing and agreeing what the priorities are. I know that you want to come back in, Peter, but I'm going to put two more questions to you, two more thoughts to you just before you do. First of all, do you now have a resource that can be upscaled if needed? George, I'll come back to you again. How do you get community, as in small community, sampling done? If we've often heard that areas of deprivation are the hardest hitting with Covid or because there hasn't been enough uptake of vaccination, etc. Are you in a position to be able to go to specific areas to be able to find out whether that community is in trouble or not? Peter, I'll come to you first and then you can come back into these other two points. Thank you very much. I'm just going to give you an example of a co-operation that already existed. SIPA had from Scottish Water their entire GIS system of both their network but also where they had sampling. We could design the original sampling programme based on the equipment that we knew Scottish Water had. We'd already done that bit of co-operation between the organisations that allowed us to move. I think it's probably the thing that allowed us to move faster than the rest of the UK because we literally built a tool that would allow us to design a network and we've just continuously used that tool to adapt the network as we go, which actually allows me slightly to answer your second question. I think the smallest community with a sewage works example of about 2,000 people was somewhere on the borders. As George said, the alternative if you want to break out parts of Livingston or parts of Glasgow is you need their guys to go to their sewer network and literally break out housing estates or whatever, which they did really well. However, as George said, no-one built it with that in mind, so you may get to a point and discover that it's not what you think it is or you can't get the sample from there or it's the middle of a motorway. George, do you want to come back in again? Yes, thanks. In terms of the resource that can be upscaled and the sampling of the streets or smaller communities or deprived communities, the answer to the second question is yes. We've got a nationwide resource that samples from the remotest islands in Shetland to the biggest cities in Scotland. We've got a national logistics network that transports those samples. On the drinking waterside, that's very well-established, and it's been in for a number of years. More recently, we've moved to operational self-monitoring on the waste waterside, so there is an established sampler network, so we can sample the very small works across the country. In terms of the resource that can be upscaled, which sounds slightly contradictory, in terms of availability of resource in some of the smaller communities, remote communities, it's difficult to get people beyond our core operational team. I said earlier that the resource that we're using currently for the wastewater programme, because it's a bit—the funding is only coming in on an annual basis—we're using additional resources rather than our core resource. We've got agency resource and temporary resource in doing the wastewater sampling, just slightly more inefficient than if we were using our core resource because we can combine sampling programmes. However, what we're finding in some of the more remote areas, particularly in the island communities, is the availability of people to do the work, because there are lots of vacancies in those areas, so I think that that becomes a little bit more challenging. However, by and large, the resources are there. We can upscale it. We demonstrated that during the pandemic that we did upscale. In one of our earlier sessions, we heard about how the PPE system was established. What we quickly learned was that we can't stick PPE in a cupboard and wait five years until we might need it. It's got to be on a continuous rolling stock kind of a basis. Where would you collectively see your ability to be able to say to the Scottish Government in a funding term, we need to keep this going, and there are other things that we can develop into it, because the PPE system has grown into almost like its own industry. How do you collectively say, right, well, we can provide this, this and this as part of the funding that you can give us, and then we can use that if we are in another emergency situation? I'm trying to find the quid pro quo for making sure that it keeps going, because we might wait another 50 years for a pandemic, and we might wait another five years, and we just don't know. So how do you do that, or are you looking at that already? Anybody? Right, George, on you go. I can come in initially. There is a conversation that we're having with Scottish Government about the funding that we have for the Covid wastewater monitoring programme is done on a grant basis. It's not part of our co-regulatory funding. The conversation that we're having with the Scottish Government is that if the funding for that was secured for, say, a rolling three-year, five-year period, that would allow us to then build the Covid wastewater surveillance programme into our operational and other regulatory sampling programmes, which would then mean that the resource is more built into business as usual at the moment, because it's almost an ad hoc programme and an additional programme to what we're required to do under normal operational conditions. It's almost been run as a separate project, so if we're running an incident or we're running a capital delivery project where we need additional resources, we're almost running Covid wastewater surveillance on the same basis. I think that if you also had additional funding in place or a commitment to continue with the programme beyond any given financial year, that would bring in the opportunity to drive innovation into the way that the samples are gathered, perhaps the way that the analysis is done. At the moment it's a take a sample, transport it to a central lab, do some analysis on it. One of the things that we're working on within the wider water industry is how do we move some of the analysis and the data gathering from the labs into the field. If you had that longer-term commitment that this was something that people wanted to talk about value and wanted to do into the future, that would create the space for people to innovate into. At the moment people are going to be reluctant to innovate because they can't see what's the longevity of the programme. You could develop an instrument today and then next year we decide that Covid's no longer an issue and we're not going to bother with it. I think that that longer-term view gives you the opportunity to look at different things because you can see a longer-term benefit going forward. Your answer is to give me a question to go to the next panel with Sophie and I'll leave that for them. Peter, do you want to come back in? Yeah, thanks. It's the killer question. I absolutely agree with George if you've got sort of long-term funding you can see coming in it allows you to establish a permanent solution to what you're trying to do and it allows you to innovate. I think I go back to what I said before. I think it needs to be a pull from the user community. To me it doesn't seem terribly intelligent to keep doing what we're doing just in case we've proved that we can ramp it up. However, I can see that there very conceivably is some really useful information that would be usable on a day-to-day basis going forwards and it then gives you those samples that you can analyze for anything. So we've got a freezer full of two years worth of samples and every so often we get a request from either academia or from PHS going have you got a sample from this sewage work this month because somebody's reported with an unusual and they can actually go back and look at that sample and so I think it needs to be a pull from the user community and I 100% agree with George. I think the direction of gravel is to try and take the analysis into the field and there is quite a lot of work going on in there. So I think academically people are on this case now, wastewater-based epidemiology is not going back in the bag. It's out and the academics are going to be working at it. Okay, thank you very much. Do you want to add anything to that, Rachel? No, I don't think there's anything more for me to add there. I think George and Peter have covered it. Grant, looks to me like you all need to have a conversation with each other on a regular basis. Thank you. I'll bring in John Mason. Thanks very much, convener. Rhea, really interesting so far I have to say I'm not an expert on sewage or related matters. Maybe to start with Mr Pontyn, if I can. Before Covid then, what wastewater surveillance was going on, particularly in relation to diseases or whatever, what were you actually looking for, how much what wastewater surveillance was happening at that point? From a Scottish Water perspective, specifically around diseases, we don't look for that at all. That's not part of our general analysis. Wastewater surveillance goes on, on the basis of general sampling for regulatory compliance, for understanding of what's coming into our wastewater treatment works and how our wastewater treatment works are performing, but in terms of actual analysis that we do, we weren't doing any in this space. I believe that there was, as part of a UK monitoring programme, samples taken from a site in Glasgow that was feeding into a UK national monitoring programme around polio, but other than that, I'm not aware of any other wastewater virology surveillance that was ongoing. Certainly, it's not something that Scottish Water undertakes. Our role in this whole programme was to facilitate the access to the wastewater for others to see what we're doing, the analysis in this space. Dr Healywell, were other countries doing that? Did that all just really start this idea of testing the water with Covid? Scotland was leading in terms of how quickly and efficiently it mobilised its teams to respond to the crisis, but there has been a number of projects internationally in the Netherlands, and more widely, where research teams have been developing the methods and the approaches to determine the scope to RNA and the virus in general from wastewater. One of the activities that I was involved with, with the chief scientific advisor at the time, was to engage with the Rockefeller Centre in the US, and we were talking about international activities and partnerships in this area, where we're trying to consolidate progress and information and samples and protocols to try and move forward at pace in this area. But it was not only on a practical level, it was also drawing on experiences from airport sampling of wastewater to try and target new methods for detecting and sampling at airports to try and reduce spread and so on. So there's all sorts of different angles that were taken in this international dimension, but this is very much something of that activity, but the beauty of what the work that happened in Scotland, I think Scotland is relatively small, and just those existing partnerships and networks allowed us to take a lead on how to work together from an environmental regulator and industry perspective and bring in public health of course. Thanks, and I think Mr Singleton wanted to say something. Yeah, so if I can just convert George's right as the UK at a polio programme and the WHO monitor for polio using wastewater, but they're using quite, but I called old-fashioned technology, so they're culturing it. So the big shift here was the fact that we could use genomics as opposed to culture technology, so we can get a result much faster. So to a large extent it was just a question of where the science was at the moment that the pandemic hit. So most other uses of wastewater are actually looking, tend to be chemical methods rather than looking for viruses and things, but I think now we know what we can do than the world's oyster. Okay, seeing you there, I'll ask you that some of the technical stuff we were given I totally don't understand, and so for example it says from in November wastewater COVID-19 levels were in the range of 21 to 32 million gene copies per person per day. Can you explain or, one of your colleagues, even roughly what that means? It literally means what it says in the sense that it's the number of gene that we measured, but it's a number and what we managed to do for a long period of time was match the results we were getting out of the back end of our PCR machine with the case data that was being currently reported, so we had a very good relationship between the wastewater data and the local case data. So we didn't worry too much as to what our number meant, what was good and useful was that it appeared to track the case data. The real challenge particularly with a Scottish wastewater system is that it's not just sewage in your pipe, there's a lot of runoff in the pipe. So if there's been a lot of rain, your signal is diluted by the fact that you've got fresh water in the system, it's not just sewage. So we needed to have some measure that tried to say you know if it's rained, we're adjusting the value for the fact that we know there's some infiltration into the system. Right, so one day it might have been, if there was less rain, the concentration would be greater, for as if there's more rain in the effect that it's diluted. Yeah, yeah, yeah, yeah. Right, so that's an interesting point because I think where I live they're trying now to separate out the rainwater from the sewage. Is that important? Would that be helpful going forward? Well, yes it would be helpful, but it's not. We can work around it. Okay, so we used ammonia as a signal for the constant strength of the proportion of sewage in the sample and that seemed to work really well. But yes, absolutely clear, it's neater if the two, you know, the run-off stream and the foul stream are separate and it makes the job easier for Scottish Water to treat. Okay, thanks. And you made the point there that, you know, there was this correlation between testing the wastewater and the samples that health boards or whatever were getting directly from people. So when it came to new variants, who was picking that up first? Was that yourself or was that the testing? No, that was testing in the sense that if you, so the medics will keep, I hope my understanding's right here. If you take a swab from a person, there's only one variant in that person. It is what it is. Right. If you take a sample from sewage, it might have 200 people's COVID in it, so you'll have multiple variants in your sewage. So in the sewage, we were always looking for known variants, whereas in a human being, you could literally just look at the COVID and say, what is it? Right. Okay. So you needed to know in the sewage what you're looking for. Okay. Thank you. That's helpful. I think I picked up that we're currently playing 200 samples per week, which is less than previously. Can you or can Scottish Water explain why 200 is that good? Is that bad? Should we do more? How long should we keep that 200 going? I guess that was a, you know, a negotiation or a discussion in the group as to what's about right in terms of the resource we're putting into stuff. The throughput, the lab can handle the levels that we're detecting. So it just seemed to be about the right number. You know, it allowed us to maintain a sampling network of the 120 sewage works, but also didn't mean that our lab was solely concentrating on COVID. Okay. Thanks. I don't know, Dr Heliwell, if you want to add anything to that. And I'm interested to going forward. I mean, we've already mentioned that polio can be picked up, and we've talked about alcohol and drugs. I mean, is that just purely, all of these things could be analysed or sampled. So it's really purely a question of resources and political will as to whether we actually want to do these things? Yes, and the need and the requirement from public health as well. As I mentioned, the investment in the infrastructure, the methods resources, you know, that's all there. And I think from the samples, you know, there's so, so there's a diverse range of like information from like the chemistry biology of these samples that, you know, I think it's essential that we do look at these wider applications. And, yeah, I mean, at the moment, yeah, these 200 samples, I mean, obviously that's dictated by the resource and the finance and capacity of the labs and obviously the labs in terms of how busy they are change over time. And so, you know, all these things are all needing to be considered moving forward in any strategy. But, you know, we talk about, you know, antimicrobial resistance, for example. And that is one thing where I think wastewater-based epidemiology could really make significant inroads in that area. There are so many possibilities in this space. Yeah, I kind of mentioned the illicit drugs and the lifestyle chemical and infectious diseases and just how, you know, wastewater can be used just to estimate disease prevalence based on pharmaceutical usage, for example. So, the opportunities are just fast. I don't know whether, you know, George or Peter want to just come back in on that at all. But, yeah, from my perspective, yeah, the future is quite exciting in this area. Okay. Well, can I ask you one more question, then, if they want to come back in, they can. And that is being suggested that we should have a chief scientist for public health. And I don't know if you've got a view on that. And because we already have a chief scientist for health and we've got a chief medical officer, I'm personally reluctant to just keep creating more posts. But is that something you think might be helpful? It was certainly a recommendation from the Covid crew report that we had from the social science team. And from their interviews, it was clear that public health expertise spans a wide range of skills and expertise wider than just human medicine. And the recommendation to appoint a chief scientist for public health sense sends very much from the recognition to bring that kind of greater breadth of knowledge and expertise into a kind of complex and multifaceted policy area. So, obviously, that feedback from the interviews during the crew project was quite clear. And I think increasingly in the future, public health challenges will require this more multidisciplinary approach. And that kind of goes very much beyond just that understanding of medicine and human health. So, that's more or less where that recommendation came from. I know that the report has definitely instigated quite in-depth discussion across departments within Scottish Government. And like you say, there are a number of chief scientists and advisors working at a senior level. But I do think that to implement change, we do need to get these people working more closely together and engaging relatively regularly on subjects such as this. No, that's very helpful. That's excellent. Thank you. Mr Pontyn, did you want to say something else? Yeah, I'm just going back to your point earlier on about what else can waste water-based epidemiology be used for. So, there are—and I sometimes try and put the voice of reason into this a little bit, just in the sense of there's lots of things we can do, but there are practicalities of where you can do it within the waste water network. I think that's the key element of this. And that was one of the biggest learning points in this whole, from a sampling perspective, was that if you want to take a sample at a waste water treatment works relatively easy to do, relatively easy to set up, if you want to do it in the waste water network, that's a lot more challenging. It's a lot more resource intensive from the health and safety perspective, and it's also the way that the network is configured doesn't always allow you to achieve the objective that you initially set out to do, and that was certainly clear from the discussions that we had with the health boards, whether we're trying to get discrete samples in different parts of communities. That was quite challenging. No, that's very helpful as well. That's great. Thank you so much. Okay, thank you. I'd like to welcome Sean Brown and Sean. Thank you, thank you, convener. I apologise everybody for my late arrival, something beyond something I had to deal with, but thank you so much, and apologies if I'm going to repeat a question here. One of the things that I did want to bring up this morning, and thank you for the written evidence from Dr Isabel Fletcher, which was from research conducted by Dr Fletcher and Professor Catherine Lann. I thought it was quite really interesting that some of the things that were noted was in crisis situations people initially turned to their existing networks for assistance with unexpected and urgent tasks, and it also highlights the climate crisis will result in increasing threats to human health, including future pandemics, demanding responses that span public health, animal health and the environment. This in turn will require more joined-up approaches with effective day-to-day working relationships with the Scottish Government and other agencies, and I know that my colleague John Mason mentioned that it was suggested to the benefits of creating a chief scientist for public health posts, but I would like to ask the panel, is there any other ways you think this could be coordinated by the Government moving forward? Can I bring in Rachel? Well, I think as part of that report they also mentioned that as a recommendation that some secretariat should be brought in at that level to help coordinate responses. From my perspective, I think that we need to consider some centre or secretariat along the lines of role that the crew has played in the past within this space, a centre to facilitate engagement, but to work with the Government to understand what the priorities are, but also to think about how to enhance the resilience in this space going forward. Isabelle mentioned that climate change is all sorts of unknowns there, and I do think that the Government needs to have some committee centre that is there to plan and take action, work together to know who is operating in this space. One of the things that was brought out is this lack of understanding of who is who in the Government departments and so on, who to draw on and bring into that space. Some register of experts or whatever it might be would be really helpful just to understand who we need to engage where it's going forwards. I don't know if that's the answer to your question. That's helpful, thank you. Can I bring in Peter, please? Thanks. Really interesting and tricky space to unravel. As we said earlier, part of the success of what happened, I think, is that it was led from the research end of the businesses and in essence, therefore, two of our key contacts in the Government were the chief scientists for health and the chief scientists for the environment, because they were effectively that, you know, the use of shorthand head of research. Therefore, we didn't need to understand that knowledge of the rest of the system that Rachel was just explaining. You know, we could just go to them and they had the understanding of which department the Government was doing whatever. So they became our sales force to an extent. So I think that was definitely one of the success points. I think it's much more difficult to work out what is the right solution going forwards. I think I come back to, to me, it's all about pool. There was an environmental scientist, for most of my life, I've been in a box looking after the environment, but over the last 10 to 15 years, that there's been a much greater acknowledgement of the impact of the environment on human health. And I think that's, that's growing. So I think there is, there is now a much more wider understanding of what people tend to call one health. So we're using a lot of the same drugs in agricultural culture, you know, veterinary medicines are not that dissimilar to human medicines. So there is a wider acknowledgement of the overlap in that space. Okay, thank you very much for that. That is really helpful. And I know I've missed most of this session and I really do apologise for that because reading the papers, it was really fascinating all the work that's been going on. And I just want to like commend you for all your work, because I think with the dark cloud of Covid this is something, the bit of silver lining in groundbreaking work. So no, thank you. Well thank you all. I appreciate the panel taking the time this morning to come and speak to us. And if you have any follow-up evidence you want to submit, please feel free to submit that in writing. There's been a lot of talk of sewage for this early time of the day. I know John Mason is delighted with that, but for the rest of us it's been a bit of a challenge. But thank you very much. And we will now have a brief suspension to allow a change over. Thank you. Good morning and welcome back. And apologies for myself for being late this morning and we've also received apologies from Alex Rowley. We will now continue to take evidence on the Covid-19 surveillance and our second panel will be giving evidence on genomic sequencing. I'd like to welcome our second panel to the meeting. We've got Professor Sharon Peacock, CBE, Executive Director and Chair of Covid-19 Genomics UK Consortium, who joins us remotely. We've got Mike Gray, Service Manager at Laboratory Medicine, NHS Lothian, who joins us in person. Dr Kate Templeton, Head Molecular Diagnostics, Microbiology, Veralogy and Molecular Pathology. Director, STI and Viral, Genotyping Reference Laboratory, Royal Infirmatory Edinburgh. That's a mouthful. And we've got Professor Rory Gunson, Consultant Clinical Scientist and Veralogy, Clinical Lead and Laboratory Director of the Western Scotland Specialist Veralogy Centre, Glasgow Royal Infirmary, who joins us remotely as well. And Professor Matthew Holden, COG UK Principal Investigator, Public Health Scotland. Welcome everybody. Thank you for giving us your time this morning and for your written submissions. We estimate this session will run up to about 20 past 11 and each member should probably have about 12 to 15 minutes each to speak to the panel last year questions. For those witnesses who are attending remotely this morning, if you'd like to respond to an issue being discussed, if you could just type R in the chat box and I'll try to bring you in. I'm keen to ensure that everybody gets an opportunity to speak but I apologise in advance therefore if time runs on too much I might have to interrupt members or witness in the interests of gravity. Can I invite witnesses to briefly introduce themselves and I will start with Professor Sharon Peacock who's joining us remotely. Thank you very much and good morning everybody. My name is Sharon Peacock. I'm Professor of Public Health and Microbiology at the University of Cambridge and I'm also the director of the Covid-19 Genomics UK consortium that was stood up in March 2020 to provide genome sequence data to the pandemic and public health agencies. Thank you very much. Mike Gray. Hello. My name is Mike Gray. I'm the service manager for laboratory medicine in NHS Lothian which I guess is the organisation within which one of the Scottish systems sat. I'm a part scientist, part manager to trade. Thank you very much. Dr Kate Templeton. Hi, I'm Dr Kate Templeton. I am consultant clinical scientist in Edinburgh and I was part of the consortium led by Sharon Peacock at sequence Covid-19 from March 2020 and then has transferred that service into NHS Lothian as part of the network with Rory and with Matt. Okay, thank you very much. No, it should be done for us. Thank you. Can I bring in Professor Rory Gunson who's joining us remotely? Hi there. I'm Rory Gunson, clinical lead for virology in NHS, you can see, and like Kate said, my host, the virology and typing service for the west which feeds into the service that Matt and Kate also contributed to. Thank you very much and Professor Matthew Ordon. Morning, I'm Matt Holden. I'm a professor of pathogenomics at the University of St Andrews and I've been working as a genomics adviser in Public Health Scotland. Since the beginning of the pandemic, I've been seconded to Public Health Scotland, helping them to firstly work with COG to integrate the data into the response but more luckily helping to establish and build up the genome sequencing capacity. Thank you very much. If I can start with questions and I'll turn to the first question and it's very simple. Can you please explain to me how genomic sequencing works and what it is? I don't know who wants to come in. Matt, did you want to come in? Yes, I can be in and others can chip in. Genomic sequencing, every living organism and indeed sort of infectious agents such as a virus has genetic material inside it and as you know it's a sort of blueprint for life and the sort of instructions to how it works. So what genome sequencing is is effectively taking that and decoding it and turning it into sort of a genetic sequence. Why do we want that information? Well actually each genome has as you say the set of instructions that gives us clues as to how it behaves so for example how whether an organism is going to be resistant to an antibiotic or potentially cause a more severe disease but also each genome is a historical record because it comes from its ancestors so by comparing genomes we can understand if two separate microorganisms or viruses are very closely related share a common ancestor and then can be perhaps traced back to a transmission or an outbreak so we can use genome sequencing to do that and what we do with genome sequencing is we take our organism or our virus we harvest in the laboratory the genetic material from that so in effect it's a big polymer it's a chemical chain and we use a series of molecular techniques to effectively fragment fragment it break it up into tiny fragments and read the sequencing the sequence of those fragments using sequencing technologies the technologies that are now in Kate's and Rory's labs and Sharon's labs in in Cambridge and that will effectively decode that the bases as you know the G's the C's the A's and the T's and that can be turned into a digitised information that we can analyse with computers and decode and extract all that useful information about the sort of template of the of the microorganism that gives us the clues as to how it behaves or do the genetic fingerprinting to help us understand the sort of origins and spread of pathogens. Thank you. Can I ask were you were you working together as a team were you all brought together when Covid came in March 2020? I did we were all working together but whether we were as much we we're definitely more of a team now than we were and certainly within the cog framework which Sharon can speak about more there was a lot of different academic institutions that maybe wouldn't have necessarily worked together before but definitely all came together very much under under that umbrella but there's always been a close working relationship in Scotland with with all the labs there and within Public Health Scotland there was a predating programme that had been set up to do genomic sequencing already for Nigeria, meningitis, Salmonella, estec and that that basis had already been set up so there was already something in existence. Thank you. Can I bring in Professor Pickup please who wants to come in? Yes, thank you. So back in March 2020 there were a large number of people universities at the four public health agencies that were capable of doing genome sequencing of pathogens but that the system wasn't connected together and we didn't at that point have the scale that we needed to sequence the number of genomes that we anticipated we would need to sequence to track the genetic changes that would occur over time. And so in March 2020 there was a kind of coming together of 16 individual academic institutions, universities, the four public health agencies in the United Kingdom and the Welcome Sanya Institute and we got together around a room we were based in a meeting with The Welcome in Euston Road and in mid March we decided that we would get together all our ideas, develop a plan to provide the sequencing capability that was really connected across the country and it was really key that because this was going to travel across the country and not respect borders that it was a four nation approach and so that's what we set about to do to create a country-wide sequencing network and so we we're all familiar with each other but we've never had the opportunity to work in such a cohesive way before. Thank you that's really helpful. If I can move on to my next question in Scotland, do you feel at the moment that we are well placed for any future pandemics as well as any other threats such as maybe antibiotic resistance? I don't know if someone wants to come in. I mean we've set up what the great thing is that as a result of the money that we've received from Scottish Government to set up the sequencing service we are now in the best position possible to be able to sequence more of the pathogens but at the moment we only have this guaranteed till March 2023 but we have that legacy there ready to be evolved and enacted but at the moment we're focusing on COVID but we have already within this time period done sequence monkeypox there was an outbreak of monkeypox and we were able to sequence that using exactly the same sort of techniques exactly the same templates that we were able we'd set up as part of COVID and and that's the idea around this and the infrastructure with PHS having the sort of bioinformatics turning all of these G's and C's as Matt was talking about into something that then can become data that's understood by people is the sort of key parts that we've set all of this up? I don't know if Matt will say any more on this. Yeah I don't want to follow on from that I think a lot of work's gone into sort of upscaling building capacity on the back of COVID I think was sort of very nicely illustrating the session before in terms of the sort of COVID turbo charge what we could do and that definitely had an impact on pathogenomics before COVID arrived we were implementing whole genome sequencing in the reference labs but albeit at a smaller scale on a more limited budget what we've now managed to achieve is to have a capacity that can contribute and has been responsive to the COVID pandemic but now that's there to help going forward and it's not just about the sequencing I think this is against a backdrop of also alongside that it's introducing whole genome sequencing into an organisation and thinking about the other components to make genome sequencing effective that's a really important consideration you can genome sequence but if you can't translate that into useful information that people can action and make decisions on then it's potentially not effective and so there's been a lot of work that's built around linking data creating databases creating bioinformatic resources and even actually just getting genome data into the the everyday vocabularies that people understand it politicians understand it the public understand it the sort of notion that the population would have detailed sort of interest in genetic variants and variants and it's because it had such an impact on our lives so it's now become part of our sort of understanding and consciousness and even when you look in the organisation genome data is now just feeding through on a regular basis of that understanding and that knowledge that has given an understanding of what we can do with genome sequencing so I think we're very well placed to capitalise on that and actually as you say apply it to other threats indeed I think you mentioned antimicrobial resistance arguably that's the the hidden pandemic if you will in the background it's not going to go away so we're now well placed to capitalise on that so it's not just the investment it's all the other work that's gone around that to support it and integrate it into into public health into our into the NHS and indeed into government thank you can I bring in Professor Gunson please yeah actually Matt's just covered it very eloquently I was going to say we're well placed with all the infrastructure the users are aware of how to use this technology but as Kate said the biggest worry at the moment is funding which at the moment goes to march next year so if we're going to build on what we've put in place we really need that clarified thank you Mike Gray did you want to come in yeah I was just going to come in briefly basically to back up from an operational standpoint working in the healthcare system in Scotland and the test being done of course within NHS boards it's a difficult position to find yourself in if that accumulated skillset that's been built over say the last 18 months possibly is on the precipice of falling off the cliff and it's a fairly standard trope to say that without the workforce and the skillset and a sustainable plan for the future is we can talk about legacy all you like but if it's stopped tomorrow it might take quite an effort to restart and that's always a fear that we hold operationally in our systems thank you thank you for that can I bring in Murdo thank you thank you convener good morning to the panel just to follow up on that last question from the convener I mean it does sound like what you've done is very successfully very quickly been able to scale up in terms of addressing the issue and providing the capacity that's required but I suppose my question is and you've already identified the risk of that continuing how essential is it in your view that we maintain that level that we're now at and what are the risks to that in terms of future funding maybe Mr Gray seeing as you address that I can start from a non scientific basis and then I'll hand you over to my professorial colleagues just from a basic workforce perspective if you put an advert out for genomic scientists and all those particular skillsets say two years ago these things didn't really exist they weren't out there in large numbers and one of the legacy and benefits of what we've just been through been the mind that we had a bit of a hot start for sequencing because we'd already been in team mode for PCR routine testing for laboratories across Scotland systems across the UK so we were we were well versed in in putting that operational team in on the ground however this endeavour required a completely new skill set and whilst it might be easier now to put an advert out and accumulate people if it dwindles you'll find that the marketplace there to supply those type of people just isn't there and you kind of want to avoid I think in terms of pandemic preparedness this peak and and trough element of workforce this is a great asset with a great skill set now which we think there is a true legacy for and on the science I'm going to pass you over to professor doctor I mean just to answer the question directly what difference would it make at the moment for the Covid so there's various reports that are produced on a regular basis that are used by our infection control team in NHS Lothian so something called a cluster report which basically tells the infection control team that where they've got maybe one or two cases in award and they're not related or where they've got 10 cases on award and they are all related and then they're able to then infer the sort of practice and policy around making sure we keep as many hospital beds open as possible and every bed open is is at this time or any time probably is completely crucial so that is a really valuable report and without the sequencing that stops and then the other part of the data that we're producing is understanding what is going on with Covid and that's essentially informing the vaccination policy how often we may be seeing reinfections linked in with the siren study which is another wealth funded study from Scotland that's obviously UK led but that again has hugely influenced our vaccination policy but sequencing is completely crucial of Covid genomic sequencing in that to inform that and vaccination is as we all seen is the way that Covid remains that we're not all sitting here with masks on essentially so those are just two two main examples and those are regular reports that are produced on a weekly basis and for the legacy I think we're always seeing another new threat coming along and when we've right now got group A strep which has hit the headlines there's all sorts of unknown questions there sequencing could absolutely be a tool to basically gas us to the point that we're where we understand more about what's going on whenever we have an outbreak on award we always try to sequence it in Lothian and we always find out something new in any time that we we do that so it's a it's a vital tool right at the front line of the NHS and it's also understanding sort of from a more of a legacy basis I could never somebody else see no I think Kate very eloquently illustrated some of the examples again just to say where we are in terms of Covid at the moment beyond the examples that Kate mentioned there it just provides the intelligence that we know what are the variants that are circulating Scotland as you as you're probably aware Covid just does change we see the emergence sort of on a regular basis of new variants at the moment we've got bq1 which has just appeared and has effectively become the dominant strain in Scotland and as part of planning for that and understanding responding to that we need to know if we have a new variant and then actually be able to identify it so we can look back at the sort of patient information and make assessments at a population level public health level as to how it's behaving and again make assessments about vaccine escape or severity of disease to help us plan for the future so again a lot of the data we're generating from genome sequencing is providing that genomic intelligence that is going into just as you say the sort of the response in terms of NHS but also the future planning in terms of modelling as well to project how these things won't perhaps behave in the coming months when the pressures on the NHS are greatest sure okay thanks for that I mean just follow that up and go back to this point about funding I mean is there funding in place to maintain this capacity that's been built up I mean Mr Gray you're suggesting it wasn't yeah that's what needs to happen I mean there are people in Scottish Government who are trying to source the funding but it's not clear there is no clarity on that at the moment again the funding that supported the the expansion genome sequencing I think was from test and protect as you're aware obviously budgets have changed as we've moved over and I think one of the the questions for the service we had a year's budget from that and the funding going forward has not been part of a sort of a centralized core stream so it's identifying firstly the source of the funding as we shift from the the Covid response funding but also looking at the the potential for longer term I think as Mike has indicated a lot of the sort of support whilst we can we have funding that can keep the service going but we need to be able to invest in the skills and the personnel and offer the contracts and it's very difficult to offer contracts when you don't have the projected funding going forward at the moment currently our funding ends at the end of March and because of that and I think maybe colleagues can speak about the impact that that's had in terms of just staff retention because there's an uncertainty we are working hard with colleagues in Scottish Government and PHS and obviously they're the labs this is something that's very much on our mind at the moment but it does pose potential sort of threat in the future going forward okay thank you um professor um peacock that you wanted to come in um no I didn't put I think it might have been Rory but um perhaps I'm sorry is that I think that I think that's yeah okay um yeah that's right Rory Gunson yeah thank you yeah just just to follow on from from what Matt was saying and to build on what Mike was saying so what we've experienced in Glasgow is we've employed people trained them up there's been very little sequencing experience in the NHS and we've we've got these people to the quite level of of experience that we could build on in future but because of the temporary nature of the funding the people have jumped to permanent posts as we've come nearer the end of the contract so what we need is long term funding so we can actually build on that experience and those people can then be used to to do the sequencing and turn their attention towards some of the other pathogens that Kate has talked about or to look at what we're currently doing and see how we do it better so it's it's we have a plan that's been in place for a while but the funding needs to be aligned to that plan um so we can build on it rather than start again in a in a few months time which is my current concern okay okay all right thank you thank you Jim fairly please um guys you keep throwing up more questions than answers uh ffessor mathews holding if you don't mind i want to come to you first and there's got absolutely nothing to do with inquiry but you just sparked an interest to me um you talked to ancestor genomes what time range does that ancestry work in or does that depend on the particular genome this is purely for my interests so um as you know sort of organisms evolve and their genomes pick up mutations so it's the the sort of rate at which they accumulate mutations is what we can use as a sort of like almost like a clock to to sort of work backwards in time so something like SARS-CoV-2 and correct me if i'm wrong i think it mutates about uh two every um eight weeks yeah two mutations every eight weeks so you've got a sort of like a clock rate so you can work back to the the ancestry so when we sequence genomes we can effectively build what we call phylogenes or family trees that you can reconstruct the evolutionary history and those are the those are really informative in identifying sort of groups of very closely related strains that may be part of an outbreak or a successful lineage but other organisms can that allow you to forward plan um in you can there is information you can get from the mutations that can tell you um the sort of potential evolutionary trajectory about how much scope there is for variation now that's a it's a really interesting question at the moment we've seen omicron come in and omicron has just effectively settled and become the dominant strain but the way it's now evolving in contrast to previous variants where we've seen these sort of like an alpha and a beta and a delta very different omicron seems to be throwing off these sort of smaller sub variants with with mutations they're actually cropping up independently in the same population so from that perspective we can people are looking at that and saying well is that predicting what we're now going to face in terms of future threats is it going to be small reinventions of the same thing or are we going to have big jumps frankly that's something for research i think it's very difficult to use that in effective way to to plan because there's so much uncertainty about it but you can use the information we we get from looking backwards to also think about what's possible in in the future right okay we can probably within a month we can make predictions because we see a variant increasing like the bq1 that you talked about you can see the rate of change that has over one week and then suddenly it's popping up and it's like way in front of all the others and then and then with the epidemiological information on whether all those bq1s are in icu or if they're all hospitalized with requiring oxygen which the epi team and phs are able to add to that if you can see that in the first week you then know for your next three four weeks you're hitting a time where you'll have more icu admissions so it's maybe not right now it's not a long-term thing but it's a short-term prediction tool that we're able to infer just to follow on from that that's the sort of basis of the the varying technical reports that uk hsa produce and public health scotland contribute into they're looking at what is the current behavior patterns of a new variant that seems to be on that way up to make predictions about potentially how severe the infections will be or how it will escape when i can give you information to pass on to health boards that this is what it looks like this is what we think is coming fantastic right i've got a whole lot of e-questions i'll bear with me in terms of the all working together one of the questions i put to the to the early panel i don't know if you heard it was were you working in silos before and are you now working now but the signs of it yous have all had a reasonably good working relationship it's grown into this team effort do you as we heard from the lad from sepa he now begins to feel barriers coming back up at a uk level do you have that same concern and are you still working as a team absolutely still working as a team but it's and and the i mean even from the cog perspective there are still talks and things there so we're still connected with that as well which and it's given us a fantastic connection with other academic groups going going forward but from the sort of link between roaring myself and matt we're very much you know we are basically going forward for a an accreditation as a single service we might all not be in the same building but whereas we see ourselves as a single service together okay one of the things that concerns me is the fact that you're all talking about is the fact the lack of funding coming up next year now my backland is in sheet famine and antimicrobial resistance is a major problem in sheet famine because there's been you know overuse antibiotics and warmers and all that sort of stuff what work are you guys already doing on that and is that the kind of thing that you can put it sounds like you're selling something but effectively that's what it is is that the kind of thing that you guys can put to government to say we're working on this and if we can keep this genome servicing going we can you know put something more in place adding it sounds ridiculous to say this but adding value to what you're already doing in order to maintain the funding that is there yeah do you want to expand on that i mean just to give maybe a matt and i recently had a phd student together on an organism called fferee bankomise and resistant enterococci which is is by its very name has resistance in there because of the vancomycin bit and this scotland unfortunately we are we have the worst rates in the whole of europe but the moment we're not it is a bacteria right and what does it do um so it it's i mean it's it's a sort of a um it it causes um infection but it's not as bad as staph aureus um as some of the bacterial infections but it can cause nasty infections in the hospital um it particularly gets into those areas where you've got lots of um plastics and stuff like that so you know units like that are a problem um your hematology your cancer patients those kind of places are other so you know very vulnerable patients and for whatever reason we in scotland have the highest rate in europe and we would like to be able to do a lot more work on understanding this one of the ways to understand this is um is to do the whole genome sequencing and well at the moment you can treat the vancomycin with another drug call and there's a need but if that goes you then lose your last line antibiotic for this infection and matt will probably say more on this because he's been involved in it but that's just one example of something we're not doing anything about it's in research projects at the moment and it it should be something that says scotland that we're doing something about okay matt yeah and just to follow up on that i think when we are making the case for the sort of extension and support for future support we're always making the case that other threats such as amr and particularly amr are ones that it's this this technology is very applicable to and in fact it can probably add more value than we've done so far because of the detail you get from it and again just to give you an illustration that the work that cape mentions currently phsr i've had requests to develop a service for this using existing capacity we have a governance structure in place to looking at the development of a pathogen genomic strategy going forward and actually the expansion of the service utilising the the capacity that we've built so um there's a paper that has gone forward to that for consideration for recommendation of whether to develop a service to support the use of the whole genome sequencing to characterise all these strains that are coming from hospital acquired infections so we get a better intelligence of what's circulating in scotland and how it's spreading excellent professor peacock you wanted to go in yes thank you i wanted to build on the amr story and then extend that into other areas where we we definitely need to be sequencing so for amr i completely concur with colleagues about the importance of building up our capacity for antimicrobial resistance and it will detect the emergence of new resistance it will detect the tracking of that resistance in the same way that we've done with SARS-CoV-2 in particular amr can be very impactful for patient outcomes in hospitals when you have multi-drog resistant outbreaks we've already heard that being able to do outbreak investigations for multi-drog resistant pathogens say in intensive care units that is a capability that's not available in most places and i think that's really important to try and bring those outbreaks to under control but the other areas we need to just think about when we're thinking about a sustainable country wide sequencing capability are areas such as foodborne pathogens and foodborne associated outbreaks and so there is an increasing trend now to automatically sequence all pathogens associated with potentially with that could be associated with a foodborne outbreak and then use the sequence data to detect outbreaks rather than the other way round so traditionally two-letter epidemiology would mean that you'd need to look for clusters of people with a foodborne disease foodborne associated disease in an outbreak and then go and sequence the organism to see if they're related it's really flipping on its head now to say if you sequence all the pathogens you can detect the outbreaks really early and actually be guided by the genome data rather than the epidemiology and the advantage of that is that foodborne outbreaks with the food production that we had globally the food production means that the food is all across the country all across the world from a single source so that allows you to detect where that might be coming from and there's a really good example a few years ago where a neuroblissin called Listeria had got into a food production at sandwich sandwich sandwich preparation actually and the sandwiches were sent to hospitals all across england and it was only the sequencing that captured that there was an outbreak way before there was an exceeding number so I think foodborne and colleagues in the room may want to extend on that but foodborne detection of foodborne outbreaks using sequencing as a kind of a very powerful detection tool I think is important the other area that's important is such as tuberculosis and so you know the UK developed one of the first TB sequencing capabilities for TB sequencing capabilities for TB and there's two reasons why you want to do that first is that sequencing can detect multi-drug resistance in TB much faster than lab methodology so you can get to that answer in you know a day or so whereas the culture methods can take weeks or months to to detect them you want to know if TB is multi-drug resistant or not before it starts to spread and you can also look at how it's spreading in the community so you can as Matt said you can connect to two cases together because of the relativness of the genome and see whether there is an outbreak occurring so I think that AMR is really important but we need to think about the much wider piece and where sequencing is already established but really needs to be consolidated actually in the national service. That's what I've got time for. Yes. The foodborne one you've just raised a whole new load of questions and given the global food supply chain that we have I think that's absolutely right because obviously we know we had the E. coli outbreak a number of years ago which killed quite a number of people. Is there any work being done by yourselves to to work in the in the food industry to do that kind of thing because you've kind of confused me with seeing your flipping that on its head I don't know where you go for the first to catch it in the first place if you don't know there's a problem where do you go so we already all s tech so all the E. coli with the shiga toxin are all ready all sequenced in Scotland also all the TB cases are all sequenced which is now giving us great opportunity to put people on the right drugs so it's doing the full linked up full nation response together for for doing the TB work and as is the s tech and salmonella is all sequenced already in Scotland from the pre-existing work and again that is linked together has to be across the across the four nations to understand that but not there are gaps within that it could it definitely has has a role to be improved and make sure that we are always connecting all the dots but yeah we we would like to build on that as well definitely. Yeah just I think to follow up on your point in terms of there is work that's ongoing to try and bring together the domains of what is sort of clinical health in terms of animal health and also food health there's currently a gap analysis underway that Public Health Scotland are leading that's looking at involving stakeholders to have this discussion about where genome sequencing fits in that and supporting that recognising just the way the infrastructure is that the microbiology for food goes on in different labs than say animals and clinicals that is an area of development just to pick up your point about the flipping it on its head and what what Sharon was saying I think often if we're going to detect an outbreak we're reliant on effectively looking and looking at the numbers of cases and seeing that's been an increase in cases and then from that going and investigating those and and it's often then looking for links between them for like a common food source doing an epidemiological investigation I think what Sharon's is suggesting and what I think the aim is is if you routinely sequence all clinical isolate so if somebody presents with a salmonella infection you just sequence it and you automatically just look to see if any samples are closely related and if you see that they are you know that they've probably got common source so then you can go straight in to then investigate the epidemiology without waiting for the cases to kind of pop up and somebody somewhere to say hang on a minute we've got 10 cases in Lanarkshire we should do something about that excellent thank you thank you can I bring in John Mason please thanks very much convener it's been very interesting so far everyone's mentioned funding so far but we haven't had a lot of numbers I don't know if this is your area Mr Gray would you like to put a figure on how much money we need I'll pass again pass over to the experts in terms of what was original and then proposed so the original bid we had was £14 million was what we originally asked for we haven't actually spent anything like that because we were imagining a lot more covid so I think we're closer to sort of eight million and then sorry that you've actually spent we've actually spent okay but I you know that is we're not at the end of the financial year yet um and then um and the end of that and that was that was for the whole programme that wasn't for just one year and then we um we then um we've putting together bids um and I think the final the one which we would prefer is I think around the five million um pound mark I think per year per year and that's for Scotland that's for Scotland yeah I mean you've all made the point that it's been good to work together in the UK so presumably there should be UK funding for work right across the UK as well so some of them funding would be coming from Westminster perhaps I don't um I don't think for this because the whole health is devolved in Scotland so I think this is something that um is up the road and comes back down the road again so it comes here I think the UK funding and then decisions are made here on pass out to the Scottish system as we understand it okay okay for now you guys will know more than we do yes I mean yeah I'm asking for financial side because that's my kind of background um but yes every part of this works differently so I was just wondering but that's been that's helpful that clarifies things a bit um looking at the report um especially Professor Peacock your report it's all very glowing about how it all went and Cog UK seems to have been a total success there's nothing negative in the report at all um and Rand I think it's Rand Europe had done a kind of overview and everything they say is positive as well but I mean surely something went wrong um I mean are the things are the things that could have been done better uh you know did did people not join up as quickly as they should have you know is there anything that we can that didn't go right well I think you're right it is glowing but that's because it was largely glowing it was quite remarkable that 21 different organisations could sign a legal agreement have a data sharing agreement have everything working together was remarkable day to day there were bumps and and I would say a couple of things first of all um we we uh we had to work in an imperfect situation to be really focused on outcomes over process but but people have often likened it to trying to take off in an airplane before the wings are quite fixed on so we were constantly working very hard to um uh to kind of close any gaps that we had and the system at the time was changing very quickly so overnight we might realise that a whole new testing centre had opened up a new lighthouse had opened up we then had to connect that to our sequencing capability so we had the sequencing capability is connected to a hundred and five hundred and five NHS testing labs and all of the lighthouse labs that that are fed into our sequencing so I'm not suggesting that it was altogether easy it was it was really tough going but overall it was glowing if I would if I could change one thing from the very beginning I wish that data connectivity and integration was much better and and I think that that was a function of of testing being stood up very large-scale testing being stood up across the country and the data flows from them was was really actually quite challenging initially and we need that that limited amount of data of who whereas the sample come from what date was it taken actually who is the person that gave that sample because we needed their match to their genome and then provide that data to the public health agencies and so for me the biggest problem was constantly data connectivity and data integration and trying to make that run very smoothly and often that was a barrier in terms of getting the data available very fast so we can sequence very quickly but until we connected it to the person's data we it's of no value to anybody and so data connectivity it got faster but that was really quite problematic in the at the outset and is that because we're too fanatical about privacy in the UK there are several reasons the systems the systems of connectivity were not necessarily in place in the first instance and it could be that that in part that was driven by privacy issues but also we had new systems being built from scratch which had no data connectivity so the major lighthouse labs for example they had to build their data connectivity systems and plug it into the rest of a highly complex data system and so I think it was inevitable that you would start with somebody collecting information on a piece of paper you know the first day that the lighthouse lab was open and that had to rapidly integrate that data into into the wider UK picture but I don't think it was just about privacy I think that we saw a lot of changes about how data could be shared during pandemic which I think really helped with the data integration and data sharing so I think it was largely the system that we had when we went into the pandemic and the fact that so much of so many new things came in that were not connected to that original system okay and I mean we've mentioned the UK mainly so far and connectivity within the UK but what about the international scene I mean how are other countries have how have they been doing with genome sequencing how are they planning to go forward I mean we tend to think of America as the leader often you know where are they and all this of the rest of Europe well I can start that and other people may want to come in the first thing I would say is that all of our data was shared immediately into a an international database called gizade and so as soon as we had the data we would share that and so we had a very much an open access policy to our methods as well and our protocols so we were leading leading in many ways in terms of the analysis of genomes and developing methods that people could analyse their own genomes to everything was made public and and at one point in time the UK was producing 50% of all global genomes in that database and so we're very ahead of the curve there were many other countries that did an excellent job too actually um for example Canada had a very similar initiative was uh there had very good sequencing in many European countries them up and so on I think that the US were um were hampered in the pace at which they stood up their sequencing because it's a very large country and every state has kind of its own uh own kind of system of sequencing or testing and so on and so I think joining that up together was actually quite a challenge for them but other people may have um have something to say on this matter to you yes I mean I wonder that universities tend to have good relationships often with other universities around the world I don't know of Dr Templeton or Professor Gunson has experience of working internationally on this so I could mention the monkeypox as an example so this was a you know it was known about pathogen but sequencing whole genome sequence the whole virus hadn't been sequenced or at scale much before it arrived as the outbreak and so we were able to connect up with Yale University who provided us with the primer sequences and then we've sequenced the virus using the same techniques that we had there and then we've published the the work and that's all come through connections through from the cog sort of way of then you have connections beyond that and so that connections you you're always trying to find out what what other people are doing and having those connections but they it's definitely helped by having these connections built up from from cog to be able to do that and that was a really good example I mean how would some of the developing countries be coping because they were very slow to get the vaccines off and would this be an area that they'd be struggling in some of them I mean there have been various initiatives again through cog I mean I've done various things in Uganda which is a we have a Fleming fund through University of Edinburgh where we we are trying to train up fellows in Uganda around AMR and then through that we're setting up processes in their labs and this this is a UK funded initiative the Fleming fund and then through that there have been connections to get them trained up in whole genome sequencing as well and some of the beauty of of the techniques that we were actually using for Covid was first of all employed in for Ebola in the outbreak that happened in 2014 so it was and that all they most of these countries don't want the samples to move outside they want the sequencing to be done locally and that's how it was set up was to be a technique that you could actually do locally in the country and for Ebola that the sequencing for the Arctic protocol that we used was actually used there so I mean all of this requires you to basically go out and find you know whether it's a Fleming fund or other funds it's difficult to you know with our money that we hope we get we would be very much focused on delivering the service that we're asked to buy the Scottish government but if part of that was to have connections to other countries then that can be part of it but at the moment we're really doing that under an academic hat or under my university hat kind of thing. Professor Gunson did you have anything about a kind of international relationship? It's very much the same as Kate described so that I'm aware of things through the university of glass I'm not directly involved in where they've been training people and then trying to push the technology back into to those countries so they can do it locally and I'm also aware of the things that Sharon alluded to in terms of what Cog UK have done as well and the sharing of data which is probably the key part in terms of all rapid responses if people have complete access to what's going on in other countries you can respond much more quickly and that's been a great benefit of Covid and Cog UK I have to say. Okay thanks and I think the final point I wanted to raise was something that came up at the previous panel which was the desire for a chief scientist for public health I don't know if that's something that any of you would have an opinion on. I think the only thing that we find difficult is who do we go to to ask for this money that's and Matt has already alluded to that we would like to be able to um go to one person who we know is responsible for that um and they have that responsibility hat on their head but uh the reason it isn't clear because the test and protect thing has stopped um and so there are various different departments probably and there's also national services Scotland but there also they get their funding for a different route so it's that's probably if that made that easier then that would be good. Okay Mr Gray and then I'll come to Professor Peacock. I would I would probably advocate for it um if if that job could start to make the connections and this sounds like a broken record in terms of what workforce is required to deliver that for Scotland because it's it's not an equal it's not an equal set of four countries in terms of the development of healthcare science in in England, Wales, Scotland Scotland's fairly poorly apportioned in terms of the development of all healthcare science training posts so if a chief scientist for public health was involved in the conversations about sustainability contingency planning um I mean I wrote down here genomic fire brigade can you believe it because because while while colleagues were talking about antimicrobial resistance in sheep flocks etc is is there are two parts to this when you think about it when you're asking for cash are you adding value absolutely but the second part is business continuity is you wouldn't hire your fire brigade on a temporary contract to switch it off in March and we don't know what the next thing over the horizon is so even a coherent small amount of money would allow us to develop a coherent workforce so if the chief scientist for public health could help with that that'd be fabulous yeah I'm tempted to get into debate on some of that because as you probably know in the political field everybody wants the money to go into a and e and to to deal with the actual issue and what you would probably be seen as preventative spend has a little bit of pressure I think Professor Peacock and then Professor Gunson thank you I'm going back to your previous question actually about about our involvement overseas two quick points one is that pog UK was very plugged into the foreign comworth and development office and they would often put us into various meetings and interactions with people the other is that that we there was there was huge inequity actually in access to sequencing capability in the same way as there was for access to vaccines and given that we only had a limited budget we spun out a training arm called cog train and that developed online courses which took you through every step for how you do sequencing it did virtual classrooms and trained the trainer courses we felt that training underpinned we couldn't provide the funding or the equipment for countries to do sequencing but we could provide support for training and that's where we invested our time for the amount of money that we had which we thought would give us the best outcome that sounds very positive a professor Gunson to comment on the chief scientist for public health I think I think it'd be a good idea if and it's a big if it brings together all these these separate streams that do seem to be working in silos at the moment such as pandemic planning you know we talked about animals and and food as well and if it could be all brought together under one strategy under one person it would make things a lot simpler there does seem to be a lot of separate planning at the moment that doesn't take into account what is happening and I think Mike's points clear as well because if you have a long-term strategy that brings all these things together we can actually plan the staffing which at the moment is is you know we know what we want to do but there hasn't been any long-term planning around staffing for labs for the scientific side of things for the bioinformatic analysis as well all these things need to be built up alongside the lab plan to make sure that we can actually deliver at the end of this because there's so much potential with this technology as we've alluded to but we just need to make sure that we have the people in place to be able to deliver it okay well thanks that's helpful I'm sure the government's watching this but we can maybe raise some of these points with them as well thank you thank you very much if I can just just on one point I know that there's no workforce development strategy in place at the moment and I take of the genome sequencing it seems quite specialised is there any challenges with training staff or staffing issues if you'd were to develop a workforce strategy moving forward I mean we've shown that we can do it I mean it's we've had I know we've recruited sort of 20 probably people in Edinburgh and we have trained them up over the last year 18 months to be able to deliver this big capacity I think all that happens is if you get rid of that you're then two years down the line and then having to re-go real two years or whatever I mean whether we find the same level of people but probably you would but it's two years that you're all suddenly going back to square one and doing that and and it is the train the trainers the the experts to be able to then train them they may go and find some other role and so then you don't have the expertise to be able to cascade the training down so it's not impossible if we lose the funding but it definitely sets us a long way back okay thank you can I bring in Professor Gunson I'm sorry we've got only a couple more minutes before we're going to have to finish okay yep very quickly as Kate says we can train them I think what I would like to see is it the training built into some of the core preliminary training for biomedical staff clinical scientist staff as well so we're bringing more of those people into laboratories who already have that experience that that we can retain and then build upon we also need to look at the management side of things so so we can look at how we manage these these laboratories and also how we address the quality process too so we can and then not to forget bioinformatics which which Matt maybe wants to talk to because there's also a need there to develop people and have those positions available to recruit to so so we can definitely do it but we do need that needs to pay additional funding into some of these core training groups okay thank you I'm going to bring in Jim Felly very quickly I'm going back to Mike's analogy of the the fire service the fire effectively what you're looking for is a to keep the analogy a retained fire service within the scientific community who can very quickly start to keep or to keep that information flowing is that effectively what you're asking for you know absolute worst case scenario yes I mean I don't think we we want to look at a worst case scenario and you want what colleagues have described here today which is a well trained workforce and but if there was 50 quid left in the budget is what would you do is yes you would you would work towards some sort of business continuity but that doesn't deliver any of the benefits we've talked about today you said that the scotland is poorly served in terms of that the workforce why if you look at it so at the moment because well clearly healthcare is devolved but if you look at bair numbers in and this is for healthcare science across all disciplines in in in healthcare so that could be physics genomics bacteriology chemistry etc in england next year there are 600 funded places in wales i think there are 60 funded places and in scotland there are four funded places and that's information from national education scotland nhs nes okay thank you okay thank you very much that's a time today i'd like to thank all the witnesses for their evidence and giving us your time this morning if witnesses would like to raise any further evidence with the committee they can do so in writing with the clerks and we'll be happy to liaise with you on how to do that the committee's next meeting will be in the new year and the details will be published on our website in due course that concludes the public part of our meeting this morning and i suspend the meeting to allow the witnesses to leave and for the meeting to move into private thank you