Fresh from heading state forecaster MetService, Irish-born Peter Lennox has just started as chief executive of ESR. It comes as the Crown research institute is in the thick of responding to the Covid-19 crisis - and as Lennox's own family has been kept apart by the pandemic. Herald science reporter Jamie Morton put these questions to him.
ESR has received plenty of kudos for its slick genomic sequencing work at the outset of the pandemic, with scientists like Joep de Ligt, Una Ren and Matt Storey helping complete whole genomes by early March. Of course, you weren't leading the organisation then - but was ESR prepared for the Covid-19 challenge at that point - and are you happy with how it's performed?
ESR has stepped up to the challenge.
Not long after joining ESR, I immediately launched into reactive mode to support the response efforts around the resurgence of community transmission.
I've been very impressed with the proficiency and collaboration of the people who are embedded in this response.
We have 400 people working here that stepped up to this response and to many other challenges faced by New Zealand in previous years.
Not to mention what we provide in what we might call "peace time" outside of these crises as ESR provides health intelligence for the country inside and outside of any outbreak or pandemic.
For Covid-19, we maintain the end-to-end system for testing, validating, analysing and reporting on Covid-19, and we are stewards of national public health data on current cases.
To unlock the mysteries of the recent outbreak, ESR has been conducting research across several disciplines – from genome sequencing, wastewater testing, and environmental swabbing, to Covid-19 testing.
ESR's value is in bringing together in one place a number of complimentary disciplines that collectively provide information and intelligence to support response and public advice.
But we're part of a much larger network, working with other researchers in Crown Research Institutes (CRIs), universities and other institutes as well as in the health sector, and supporting tens of thousands of people in the broader public sector.
Whole genome sequencing has been ongoing since the first wave of the pandemic, but it has certainly taken on a more vital role for the Auckland August Cluster in providing vital pieces of the puzzle which add to the notifiable infectious diseases data we collect to allow us to provide a more complete picture of disease transmission dynamics.
As we have always said, genomics is just one tool in the pandemic response that enriches other analyses and directly informs response activities, such as contact tracing.
As of August 3, we have sequenced a total of 855 Covid-19 cases, 93 of which are related to Auckland's August outbreak.
We are thrilled at how useful it has become and the interest that people have had in it.
Prior to the pandemic, ESR and the Ministry of Health invested in sequencing and bioinformatics capability, as we could see the potential for this for multiple areas of our science.
For example, our recent study used our genomic and epidemiological capabilities to estimate the true scale of the campylobacter outbreak that hit Havelock North in 2016.
Genome sequencing allowed us to confirm that cases from people living outside Havelock North were really part of the outbreak and not the result of some other cause.
And more generally genomics has been supporting our surveillance efforts for many infectious diseases as well as tracking antimicrobial resistance, another threat to our healthcare system for which good stewardship and monitoring is crucial.
Just as there's a wider team within ESR producing genomic analyses and putting them into useful epidemiological context, there is also a team of people New Zealand-wide who are able to extract and analyse this data for use in the pandemic response inside and outside ESR.
For example, Massey researchers were asked to help sequence the SARS-CoV-2 genomes from the first cases of the Auckland August Cluster outbreak.
There is a wide collaborative group of New Zealand - and international - scientists who have collaborated to get this work across the line, including our associate scientist Jemma Geoghegan, who works for both ESR and Otago University.
The work is also linked to a collaborative $600,000 research project funded by MBIE.
Above all, we need laboratories to actually test all those cases so they can send in the positive samples and we need a whole team to enable analysis and public health guidance based on results.
It is truly a collaborative endeavour and we continue to explore what more it can offer.
Are there any plans afoot for ESR to now ramp up its work in the sequencing area?
When the pandemic hit, ESR was quick to see what more investment was needed in this area with the purchase of new equipment.
We are currently looking into what investment would best enhance the team's efforts going forward. Further, increasing our resilience to provide this intelligence is a key factor in this.
Another role of ESR has been to help maintain a Covid-19 dashboard, and provide statistics to the Ministry of Health through EpiSurv. Can you tell me about this operation?
ESR deployed the New Zealand Covid-19 intelligence dashboard at the start of New Zealand's first wave in collaboration with Epi-Interactive and for use by the Ministry of Health, public health units and the public.
Put simply, it is the visual representation of some of the critical intelligence that is collected and analysed by the ESR team.
It is pulled from national systems like EpiSurv, which have been developed and run by our team, and analysed and visualised in such a way that is accessible and easy to interpret for its different audiences – the health sector and the New Zealand public.
It is the intelligence that informs the cases that Dr Ashley Bloomfield reports at the 1pm media stand-ups and that is being used to guide the response to the pandemic.
One of the challenges in Covid-19 is the greater public access to information and the expectation not only of information but of informed analysis and interpretation in near real-time to support more rapid response and public advice.
The dashboard has undergone significant upgrades over time, as the needs of the response has evolved.
When it started, it provided the number of cases over time, a map of the cases by district health board, the age, sex and ethnicity of cases; and the source case.
As the pandemic has progressed it has taken on brand-new features.
It now has an outbreak tab that describes each of New Zealand's clusters, including the current one in Auckland and an international tab which shows how New Zealand compares to the rest of the world.
Data hounds can download the intelligence for use in their own visualisations.
ESR's response team has a wealth of specialist expertise that was used to develop the dashboard, including informaticians, epidemiologists, clinicians, public health specialists and staff who are experienced in responding to major national infectious disease threats.
There are so many in the background putting this information together at a rapid rate to support the best-informed response for New Zealand.
It's the way that these activities feed into each other within ESR that allows us to better understand the clusters and the pandemic more generally and to provide analysis and support to the Ministry of Health and, through them, to decision-makers.
It represents a huge amount of work and is a really useful tool for New Zealand to understand the outbreak.
The dashboard is just one part of ESR's health intelligence services for Covid-19 and other diseases, but a part we are very proud of.
ESR continues running diagnostic testing for the virus, along with culturing - or growing - the virus. Lately, we've been hearing a lot more about serology and saliva testing, as ways to improve our regime of predominantly testing through nasal swabs. What are these other types of testing - and can we expect ESR to pick these up?
New Zealand's Covid-19 testing laboratories and ESR are already considering saliva testing and are in communication with various groups, such as the Yale School of Public Health.
However, more investigation is needed to ensure the accuracy and viability of any saliva test before it is offered in New Zealand.
Regarding serology tests - where we look for antibodies from a previous Covid-19 infection - these are becoming more important as the pandemic progresses and we look to find those people who have had the disease but didn't know they were ill.
There are many such tests and understanding the value of various test options will be important in knowing how they can best be applied.
ESR has been evaluating several tests. Additionally, we are awaiting ethics around a study in the serology area, so keep your eyes peeled for this.
There's also the fascinating prospect of testing at scale through wastewater surveillance. This has already turned up traces of the virus through pilot studies this year. Where is ESR looking to take this approach to aid New Zealand's overall Covid-19 strategy?
The message here is our team is going strong on this research project, but it is very much a research project, and it is taking place over 18 months.
There is currently no ongoing active wastewater surveillance programme tool to detect the presence of Covid-19 cases in the community.
ESR recently visited Parliament to discuss the research. We have advised the Government on progress.
The main message is that the research is progressing but the data from the collection of samples are not yet actionable.
But we are working with the Ministry of Health to feed any intelligence from the research in an appropriate way and looking at where we can deploy our limited resources within the research.
For example, If any of these return conclusive positive results, ESR will communicate this to the Ministry of Health with appropriate caveats about the use of these data.
The overall goal long-term is for robust and reliable tools for the detection of SARS-CoV-2 in sewage, that can be used to identify any unrecognised Covid-19 infections in New Zealand.
We also want to gauge how infectious it is in sewage and the persistence of SARS-CoV-2 in sewage.
But before these can be achieved, there is a lot of robust laboratory analysis methodology that needs to be done.
As part of method validation work and following the cluster of new cases in the community, wastewater samples are now being collected from other Auckland locations, and from a range of other regions in New Zealand and being sent to ESR for analysis.
What has the pandemic itself meant for ESR's capacity and capability? Has it had to boost staffing to meet demand? Are there plans for expansion or scaling up operations, directly as a result of Covid-19?
Responding to a pandemic is what we're all about and what we prepare for a response like this in "peace-time".
We're also continuing with our background work in "normal" outbreak management while all of this goes on.
Undoubtedly, we've had to increase our capability and capacity both to cover people who are working on Covid-19 and to add to that workforce.
For example, we've added new information systems and have more informaticians.
Traffic through our laboratories is increasing with Covid-19 testing, bespoke test development, wastewater and environmental testing and research so we're bringing in lab staff and scientists. We're bringing in more medical support for epidemiological analysis.
In fact, it's difficult to keep pace with demand in such a rapidly changing environment, and we will shortly be looking for more people from a variety of backgrounds – from IT and informatics through to science, public health and medicine.
These will be announced in the next few weeks.
If I could ask a little about yourself: you've had a taste of the hardship this pandemic has brought, with your wife having only just arrived in the country - and in managed isolation as we speak - after spending a long lockdown in Scotland. How tough has that been on yourself and your family here? And what added insight has it given you as you oversee an agency at the forefront of our national response?
It gives you a better understanding of what people are going through - not only the pain that there is in dealing with the virus if you have got it, but dealing with the virus if it's in the community, and how that can impact upon families.
Having that affinity with the impacts of the virus certainly does make one aware much more readily of what mood people will be in.
Because lives have been turned upside down in many ways, and it is difficult for some people to grasp that.
My wife and I have been married 38 years and this is by far the longest that we have ever been apart.
She went over [to Scotland] for three weeks at the beginning of March and we talked about it escalating, but nobody knew it would get like this.
Her dad was having a cataract operation, so she went to be with him and she got stuck.
Scotland, compared to the rest of the United Kingdom ... their lockdown was very severe.
By the time that we get together again, if everything goes swimmingly well, it will have been six months since we've been apart. I'm really excited about seeing her again.
ESR seems to fall somewhat into your wheelhouse, given you have experience in science with post-graduate degrees in biochemistry and biological sciences from Queen's University in Northern Ireland and Heriot-Watt University in Edinburgh. Do you think you've finally found your fit?
Over the last 10 years or so, I've been in physical sciences - physics, mathematics, computer science and meteorology - and there are some real clever people there.
I enjoy those different disciplines and how they are applied especially.
It may sound strange and glib, but when I came here to ESR, I started doing tours of the labs, and you got a sense of the smell for the reagents ... and what's going on really did give me a real boost, and the feeling that I was back where I belong.
I didn't realise how much I've missed it. It was just amazing.
It's nice now to have some degree of further knowledge when people are talking to you about realms of science where I have been involved in before ... I am really revelling in that at the moment.
Finally: your last posting was heading MetService, and back in February you faced some questions from MPs at select committee over a forecasting double-up with Niwa. The Commerce Commission has also been investigating possible anti-competitive behaviour between two state-funded organisations. Are you happy with how things have been left, in that regard?
When you leave any business, no matter what it is, there are always things that are going on.
When I left my previous job before MetService, there were lots of things happening then that you always wished that you could have seen through to their conclusion.
As with this, it is the same here.
It is over to MetService to comment on it now, as things will have moved on.
However, the professional way in which it was handled and the professional way it will be handled in the future, I think just reflects the way that MetService does things.
When you move jobs, there are other challenges and that is what is happening here.
I think it would be unfair for me to comment any further, because, one, I'm out of the loop now, and secondly, MetService will have its new leadership and for me to reflect on things probably isn't fair to them.