Speech - ASID Annual Scientific Meeting
Kia ora koutou katoa.
Thank you Professor Rhonda Stuart & Professor Tania Sorrell for the kind introduction and thank you to ASID for the invitation to speak today.
It is an honour to speak alongside so many knowledgeable and dedicated colleagues, including Dr Fauci and Professor Sutton, who have both demonstrated effective and consistent leadership throughout the pandemic.
I would like to acknowledge the great work that ASID does and has done in Australia and New Zealand over the 45 years since it was founded. ASID members have been at the forefront of the COVID-19 responses in Australia and New Zealand, as hospital specialists, infection control practitioners, clinical trial scientists and experts informing policy on public health measures and vaccines.
As many of you will know, until my election to the New Zealand Parliament late last year and my appointment as Associate Minister of Health, I was an infectious diseases physician in Wellington, and clinical epidemiologist.
I wish we were meeting in person, as there are many friends and former colleagues to catch up with. I was a registrar at Capital and Coast District Health Board in Wellington, where Doctors Tim Blackmore and Nigel Raymond inspired me to train in infectious diseases.
I was also fortunate to do my fellowship at the National University of Singapore, studying under Professor Dale Fisher, Professor Paul Tambayh and Associate Professor Sophia Archuleta. Training of the next generation of physicians is really important. I’m so grateful to those that trained, encouraged and challenged me.
As a trainee I was also grateful for those seniors who shared how they got to where they were.
After my fellowship, I undertook a study of tuberculosis case contacts in Bandung, Indonesia. I sought to understand why some contacts remain persistently uninfected despite prolonged and intense exposure to tuberculosis.
To do this a team of nurses identified x-ray and smear positive cases at community clinics and I got consent to visit their homes to recruit their contacts.
M. tuberculosis isolates from the cases were cultured. Contacts were assessed for M. tuberculosis infection by interferon gamma release assay performed at baseline and 14 weeks. Contacts’ exposure to the case was quantified by sleep proximity to the case, hours spent at with the case, smear grade of the case and the presence of cavities.
Like other investigators using IGRA we found BCG vaccination was protective against M. tuberculosis infection (45% reduction), and that the strength of that association was dose dependant. For contacts exposed to the lowest dose of M. tuberculosis BCG was associated with the highest protection against infection, whereas those exposed to the highest dose, BCG was not as protective.
We also found a significant interaction with BCG protection and M. tuberculosis genotype. In other words, BCG protection was not significant when a contact was exposed to a Beijing strain of M. tuberculosis but was when exposed to any other strain (mostly lineage 4). In brief this and other studies supports the hypothesis that the Beijing strain of M. tuberculosis has evolved in East Asia to evade BCG.
I’ll come back to the specifics of vaccine escape mutants later, but for now it is enough to say that, as with every PhD journey, what ends up in your thesis is only half of your experience. In Indonesia I learnt to manage a high-quality contact tracing operation. I needed to manage linked case and contact data, and for my analysis I needed to grasp the relationships between variables that influenced transmission. As it turns out this proved to be very useful.
Pandemic recap summary
The COVID-19 pandemic is unprecedented, and while each country is working to its own strategy and goal, it is heartening to see scientific and health co-operation on COVID - and more - between Australia and New Zealand. The scientific progress we have made is a credit to the collaborative efforts from all involved.
Today, I will talk about New Zealand’s COVID-19 response from my perspective as an Associate Minister for Health. I’ll talk you through the development of our elimination strategy and highlight some of the scientific contributions New Zealanders have made.
Events and early pandemic
While I wasn’t part of the Government early last year, I know New Zealand’s response was based on science. However, science alone was not enough.
Science couldn’t answer the question, “how important are the lives of our sick or our seniors?” That is a question of values.
Science can’t predict, “will people stay home if the Government asks them to?” That is a question of leadership. And ultimately, the collective will of the community.
It’s worth bearing this in mind as we go over the timeline of events.
It was a year ago yesterday that the Prime Minister of New Zealand announced that the entire country would be moving into ‘Alert Level Four’ - lockdown - where we would stay for more than a month in an attempt to eliminate COVID-19.
This report by Sarah Jefferies and colleagues at our surveillance centre ESR details our early response to the pandemic. This is a graph of cases over time, with the background shading representing the intensity of social distancing measures.
We introduced travel restrictions for foreign nationals coming to New Zealand from Wuhan at midnight on 2 February. We recommended self-isolation for 14 days for anyone travelling from mainland China, and encouraged these returnees to voluntarily register through the telehealth service “Healthline”.
We developed the capacity for diagnostic testing on February 2 and our first case was confirmed on February 28.
That same day, we placed temporary border restrictions on incoming travellers from Iran, which was at that time experiencing high case numbers.
On 4 March, we confirmed our second COVID-19 case – this time a woman in her 30s who had returned to New Zealand from Italy. Our border grew progressively tighter as the pandemic spread internationally, with travel restrictions extending to Italy and South Korea.
From 14 March, everyone entering New Zealand from anywhere in the world, excluding the Pacific Islands, had to self-isolate for 14 days.
On 17 March, the Government announced a $12.1 billion business continuity package and two days later, we closed our border to all travellers except New Zealand citizens and residents. New Zealanders were advised to not travel overseas. This slide shows international passenger arrivals falling away following escalating travel restrictions from February through to May.
This border closure remains in place today.
Social distancing and the alert level system.
Origins of the alert level system
A crucial part of our COVID response has been our alert levels. These levels represent increasingly stringent social distancing measures.
We sought an easy to understand framework, as we had seen developed in Singapore. This was to help people understand the current level of risk and the restrictions that legally must be followed. However, we designed it for an elimination approach. The goal of social distancing measures is not merely to reduce the R0 to <1, but to keep it there and extinguish transmission.
- Alert level 4 – Lockdown (likely the disease is not contained). People are instructed to stay home in their bubble for all but essential movements. Non-essential movements outside the home are limited (e.g. for exercise once a day and must be local).
- Alert level 3 – Restrict (high risk the disease is not contained). Parts of the economy are open such as construction and primary production, but retail and hospitality are not.
- Alert level 2 – Reduce (the disease is contained, but the risk of community transmission remains). People are allowed to move outside their bubble, working from home is encouraged and gatherings can be up to 100 people.
- Alert level 1 – Prepare (the disease is contained in New Zealand) but hygiene measures including masks on public transport and completion of contact tracing registers (manually or digitally) is required.
As part of lockdown, the ‘bubble’ proved to be a powerful concept that resonated well with New Zealanders. ‘Stay in your bubble, don’t burst your bubble’ was a positive way of framing what the team of 5 million Kiwis needed to do to keep themselves, their families and their community safe from COVID-19 and it worked.
We introduced our alert levels to the New Zealand public on 21 March with a move to ‘Alert Level 2’.
On 23 March 2020, New Zealand committed to an elimination strategy in response to the pandemic.
It was determined that the only way to control the pandemic was to move to Alert Level 4.
Prime Minister Jacinda Ardern announced that on 26 March, NZ would commence an intense lockdown of the country (Alert Level 4). Our lockdown was among the most stringent in the world, with close to 60% reduction in movement measured by cell phone tower data collected by Statistics NZ.
At the time, NZ had just over 100 COVID‐19 cases and no deaths so this approach surprised many. However, there were compelling reasons for NZ to pursue elimination.
In addition to widespread mortality and hospitalisations, we feared the impacts would be greater on Māori and Pacific communities, as in previous pandemics. Whatsmore we wished to avoid exporting COVID to neighbouring Pacific countries, as had recently happened during a measles outbreak.
Our nation would stay in lockdown for almost 5 weeks.
Development of the Elimination Strategy
Until early March 2020, the NZ response to COVID‐19 followed the existing pandemic plan, which was based on a mitigation approach for managing pandemic influenza. The plan had four key phases: keep it out (border controls), stamp it out (through case based measures like isolation and contact tracing) and manage it (through social distancing to minimize the impact on health services) and recovery. These were intended to be applied sequentially.
By early March the evidence base for elimination was growing, with the increasing realisation that COVID‐19 was markedly different to pandemic influenza in terms of its transmission dynamics.
Early reports found COVID-19 has a longer incubation period than influenza. The report of the WHO joint mission to China also suggested asymptomatic transmission was less frequent than for influenza. Both these observations suggest case isolation and contact tracing measures were likely to be more effective against COVID-19 than influenza.
Consistent with this, at the population level, the WHO report also confirmed that an outbreak can be contained even after widespread community transmission had commenced. Again, this contrasts with influenza where community transmission cannot be contained and the response needs to rapidly change to mitigation. Indeed that was our experience with H1N1 influenza.
These observations, and the early success of the elimination approach in Taiwan, Hong Kong and South Korea supported the feasibility of an elimination strategy.
Countries pursuing an elimination strategy use similar tools to those pursuing a mitigation or suppression strategy, but they differ in terms of their intensity and timing.
This table, from a paper I wrote with Infectious Diseases Epidemiologist Michael Baker and others sets out the key differences. Specifically, very strong border management keeps the virus out, intensive and rapid case contact management stamps out transmission, and intensive surveillance must be performed to identify cases.
An elimination approach also applies physical distancing or lockdowns early to extinguish community transmission. Whereas a suppression approach keeps them in reserve to “flatten the curve” when health systems are threatened.
Our Prime Minister explained this strategy to New Zealanders in a manner fit for a nation of sports enthusiasts as “going hard and early”.
Operationalising the Elimination Strategy
Of course, a theoretical framework is one thing, operationalising it required extensive work to strengthen our response.
In the next section I want to give credit to the monumental work done by officials in the public sector and health professionals to operationalise the elimination strategy.
We have set up quarantine facilities when we had none, established a multifaceted surveillance system and developed a system of rapid case and contact management. I will discuss these in turn.
New Zealand’s borders are, with a few exceptions, closed to overseas visitors, and a quarantine system has been developed to accommodate New Zealanders returning from overseas. Or in public health terms our interventions at the border are both exclusion and quarantine.
Since 9 April 2020, we have required all new arrivals into New Zealand to go into quarantine or isolation in an approved facility, usually a hotel, for a minimum of 14 days. That continues today.
During their stay, people are subject to daily health and wellbeing checks and at least 3 tests – a negative result from the final test (taken on around day 11/12 of their stay) is one of the requirements for exit. While in quarantine and isolation facilities, people have access to a full range of clinical and psycho-social support.
Unlike comparative models of border quarantine overseas, to support the mental wellbeing of guests, our model allows for guests to leave their hotel room for outdoor exercise and/or smoking under supervision and adherence to infection prevention and control measures. For those coming from ‘high risk’ countries, this is only permitted following receipt of a negative day 0/1 test result.
As hospital doctors you will know preventing COVID-19 transmission in purpose built facilities is hard enough. Doing so in hotels staffed by a mix of health care and other workers is even harder.
We have had a suite of infection control measures and audit cycle in isolation and quarantine facilities, but specific measures have had to change as our understanding of SARS-CoV2 transmission has evolved.
Transmission in quarantine or isolation facilities
However, instances of in facility transmission have occurred as documented in this report by Dr Nick Eichler and others.
On September 18 case G, a recent arrival from India was identified.
He was part of a cohort of 149 NZ citizens or permanent residents returning from India on August 27, of these 8 showed positive results in quarantine. Three were gnomically linked (cases A, B, and C) – all sat within 2 rows of each other on their flight. Case C’s onset of symptoms was consistent with infection during this flight, from either case A or B.
Case C tested positive on day 12 of their quarantine and was relocated to an isolation facility. Before their relocation an adult and child were in the adjacent room (case D and E) who had also arrived on the same flight from India. Both were negative on routine day 3 and 12 tests, but later tested positive in the community, consistent with infection in the quarantine facility.
Review of hotel closed circuit TV footage shows there were no instances where the three people were outside their room at the same time. But, when day 12 testing was performed in the doorway of the hotel rooms there was a 50 second period between the closing of the door to patient C and the opening of the door to case D and E. The authors hypothesize that suspended aerosol particles were probably the mode of transmission. A review of the ventilation system found that the rooms in question had a net positive pressure relative to the corridor.
Following completion of their 14 days quarantine cases D and E travelled with case G on a domestic chartered flight from Christchurch to Auckland. Case G sat directly in front of case D and E. There was also onwards transmission to their household contacts.
Measures to prevent aerosol spread in quarantine and isolation facilities.
All community cases are investigated in this level of detail, including with WGS, so that lessons can be learnt and improvements implemented across the system.
We have implemented a range of measures to prevent aerosol spread of covid-19 in quarantine and isolation facilities in response to cases like this, and the increasing international evidence regarding the aerosolisation of SARS-CoV-2.
Requiring the use of N95/P2 particulate respirators by staff for specific activities and during close interactions with hotel guests (irrespective of COVID status). This is contrary to international IPC guidelines but we justify it on the basis of the poor ventilation of hotels relative to purpose built facilities.
We have assessed the ventilation systems of the hotels to identify potential risks for aerosol transmission and implement practical remediation to improve air flow. This includes deploying portable HEPA filtration units for use in poorly ventilated, shared indoor spaces within the facilities, such as corridors and lifts.
Since April 2020, the isolation and quarantine system has housed 125,128 people, identified 759 imported cases of COVID-19 and 7 instances of COVID-19 transmission in isolation or quarantine facilities.
The robust IPC measures in place in isolation and quarantine facilities has been critical to their success in largely preventing cross-infection within the facility, as well as instances of transmission to staff.
Surveillance and testing
Surveillance for community COVID-19 cases has been an essential part of NZ’s elimination strategy from the beginning. After all, cases can’t be isolated nor contacts traced unless the cases are identified.
Consistent with this, countries with an elimination strategy have a low test positivity rate. We’re looking for a needle in a haystack.
Whereas rapid tests may have public health impact in high transmission settings, in elimination context highly sensitive tests are required. That’s why nasopharyngeal swabs is the only sample type used for community surveillance in NZ.
I wrote this paper with colleagues Nick Wilson and others. In it we model the rate of community testing required to detect SARS-CoV-2 transmission in the community. We suggest a rate of approximately 5,500 tests per day. This has proved very hard to achieve because people are less likely to present for testing between outbreaks.
Instead our surveillance system routinely tests people in managed isolation and quarantine staff in these facilities or other border facing roles. We encourage community testing at all times, but in practice when community cases are detected testing surges. Pragmatically we support ramping up testing through targeted communications, pop-up community testing facilities and a laboratory network in which 14 laboratories have a combined surge capacity of 32,000 tests per day.
During the recent Papatoetoe cluster 90,362 tests were performed in Auckland consistent with 5% of the resident population being tested in 28 days.
Our network of clinical laboratories have proven themselves to be agile and willing to come together nationally. Clinicians, scientists and operational teams have collaborated locally and nationally to build resilience into the system. This involved using different platforms and reagents, optimising use of existing resources, redeploying and training staff, reorganising teams and rosters, extending hours of work, and using other laboratories to undertake testing.
In overseas jurisdictions the amount of viral RNA in a wastewater sample provides an accurate proxy of the disease burden within a catchment. Screening wastewater has, in some cases, provided advanced warning of COVID-19 in the community. The method has been successfully trialled at 18 locations across New Zealand.
The primary strength of wastewater lies in the fact that samples can be collected that are representative of a large number of people.
The key limitations of wastewater is the lack of certainty around the sensitivity of detection (thought to be 1-10 people in a population of ~100,000) and the fact that historical cases can trigger a positive PCR result. The former factor is an important limitation from the perspective of an elimination strategy, where test sensitivity is key.
We have recently used wastewater testing in response to two community outbreaks, where it provides some level of assurance that there are not a large number of unidentified cases.
We continue to work on how waste water testing might be incorporated into our strategy. Currently we plan to use it routinely in 18 housing communities near ports or quarantine facilities through-out the country.
It maybe that we use waste water testing more when borders open (without quarantine). Here the fact that waste water testing can be performed independent of community testing behaviour may be an advantage.
Case Management and Contact Tracing
When New Zealand went in to lockdown our contact tracing capacity was 10 cases per day. Contact tracing and other communicable disease functions are heavily devolved to 12 public health units. Lead by public health medicine specialists who are designated medical officers of health in the Health Act.
While we enjoy strong professional relationships between practitioners and Government, formal accountabilities were poorly defined. The system was highly fragmented and processes were not consistent or interoperable. Resources were limited meaning, for example, DOTs couldn’t be provided to all tuberculosis patients pre pandemic.
I was asked to perform a rapid audit of NZ’s contact tracing system in April.
I drew on a couple of important experiences in my training to perform that report. I had learnt a structured approach to performing rapid reviews of health systems during outbreaks when Prof Dale Fisher sent me on the GOARN training. I also returned to a conceptual model of contact tracing I developed during my studies on tuberculosis case contacts in Indonesia.
Essentially contact tracing is a clinical pathway – it begins with a symptomatic case who must present for testing, be tested, have a positive test reported to public health authorities, their contacts identified and isolated.
Conceptualised this way we see, firstly, that contact tracing needs to be viewed as an ‘end to end process’. Timeliness of contact tracing will always depend on timeliness of self-referral for testing and laboratory turnaround times, as well as public health system performance.
Secondly, modelling studies tell us that contact tracing needs to be fast and complete to achieve R0<1.
This means that each step must be performed quickly and with a high degree of completion.
The progress of each contact through the clinical pathway can be traced through a cloud hosted client relationship management software package called the national contact tracing solution. This forms the backbone of our data management system and it allows the development of key performance indicators to track performance, and identify where system improvement is required.
I recommended this platform was extended to every PHU, enabling contact tracing across geographic regions, but more importantly, also connecting a national public health workforce that provides surge capacity for local outbreaks.
This replaced the 12 different information systems used in each public health unit with a single national system.
Clarity on the underlying process assists us in developing common SOPs for public health units across the country.
However there are other aspects of contact tracing it doesn’t capture. Good contact tracing must also be acceptable to the community, integrate disease control and welfare objectives and be equitable in its outcomes.
We have also elevated the role of the Ministry of Health in formally co-ordinating the outbreak response.
Change towards a “preparedness” mind-set that focuses on building capacity, stress testing and planning for particular scenarios.
Digital contact tracing for smartphone users has also been implemented through both Bluetooth and QR code scanning at public venues.
The improvements in our contact tracing system over time can be illustrated by this slide. In August 2020 a cool store outbreak in South Auckland led to 179 cases with 2643 close contacts traced, 60% within 48 hours. In February 2021 for 15 cases we traced over 6000 contacts i.e. 400 contacts per case, although this included many casual contacts. Nonetheless 88% were isolated within 48 hours.
We have pre-ordered four different vaccine candidates for New Zealand and most recently have purchased full population coverage of the Pfizer/BioNTech vaccine.
We chose to make Pfizer our primary vaccine for its high efficacy, and because using a single vaccine would be equitable and easier logistically.
The sequencing framework is a targeted roll-out plan.
As recommended for countries with low transmission we aim to minimize the risk of future transmission and protect the most vulnerable.
The sequencing framework has four key groups:
Group 1: consists of border and MIQ workers, their household contacts and people they live with. This group is approximately 50,000 people and we expect most people in this group to receive their first dose by the end of March.
Group 2: includes approximately 480,000 frontline workers and people living in high-risk settings. This group started receiving vaccinations in February and will continue through to May.
Group 3: is made up of priority populations of people who are at higher risk if they catch COVID-19: seniors and those with underlying conditions. This group includes approximately 1.7 million people and is planned to start in May.
Group 4: includes the remaining population, which is approximately 2 million New Zealanders. Vaccinations for this group are planned to start from July.
Constrained vaccine supply and the need to develop all the delivery logistics mean our vaccination rate increases gradually across the year.
How the COVID-19 vaccination programme will leave a legacy for the future
The COVID-19 immunisation programme is being designed to leave a legacy that is bigger than just the response to COVID-19.
A COVID-19 Immunisation Register (CIR) has been created, which is the authoritative source for information on every COVID-19 vaccination. Over time, the register will be built upon to become the new National Immunisation Solution so that it has the ability to track and support delivery of other vaccinations in New Zealand, beyond COVID-19. The programme will also enable health consumers to view their own vaccine records and information.
The future of the Elimination Strategy
Compared to countries with large outbreaks, New Zealand and Australia face a tricky set of questions about reopening after the vaccination campaign.
One of the most challenging questions is how and when we open our borders.
To do so safely we need a vaccine that blocks transmission, and vaccine coverage above the herd immunity threshold.
I’m encouraged by reports that show the Pfizer vaccine to have similar efficacy against infection as disease.
We haven’t set a coverage target in New Zealand but are pursuing a number of related questions with modellers.
What worries me is the possibility of vaccine escape mutants.
As I mentioned BCG has probably selected for the Beijing strain that evades BCG protection. This could be because BCG induced immunity is only partially protective, non-sterilising, as I found, overcome by high exposure to M. tuberculosis.
One might also expect that escape mutants would be more likely when transmission intensity is high, as is the case for pandemic diseases, and in contrast with the endemic diseases prevented by vaccines we routinely use.
In any case they pose a challenge. What occupies me now is how we maintain a surveillance system that will detect them in a timely way.
This raises the question what our ongoing public health controls should be, given we may need to reactivate them following reopening of our borders.
What the threat of new variants should remind us is the adage that nobody is safe until everyone is safe. We must continue efforts to assist in global control of the pandemic.
That’s why New Zealand, like Australia, participates in the COVAX facility and is purchasing enough vaccines across for full eligible population coverage of six Polynesian countries.
Strengthening Public Health Capacity
Looking ahead I want to ensure New Zealand has the public health capacity to continue to respond to this pandemic, and the next one. New Zealand went into this pandemic poorly prepared – we scored 30 out of 60 high income countries in the Global Health and Security index. COVID-19 comes on top of long-standing under-resourcing, fragmentation and health inequities across the public health system.
While responding to the pandemic Public Health Units have been strengthened to enhance leadership and coordination, local relationships and coordination of public health intelligence. They have also stepped up processes for incorporating scientific and community voices into strategy and policy and considering equity in their response. The process of building meaningful relationships between the Ministry of Health, iwi and other communities is critical and requires our ongoing effort.
I am leading the development of a national public health service that includes improving system leadership and coordination. This includes strengthening the relationship with the 12 PHUs A national public health service will have a critical mass of technical, operational and policy expertise to lead health protection, promotion and prevention.
At the peak of the initial outbreak, we had 90 cases in one day. But our rate fell quickly after the first two weeks in lockdown.
So far, New Zealand has among the world’s lowest rate of cases and deaths.
Our strong public health response has also enabled a strong economic recovery.
Science and strong leadership have been at the heart of the New Zealand response. The delivery of clear, open, empathetic communication assisted with a high level of cooperation – people understood the ‘why’ and ‘how’, not just the ‘what’ – stay home, save lives, be kind.
Decisions strongly informed by epidemiology, infectious disease and immunology expertise from across the science sector and implemented at pace have meant that New Zealand’s response to the pandemic resulted in a much lower impact on the country and the initial elimination of COVID-19.
Every step of the way, the New Zealand Government has put science at the front and centre of the decision-making process. Whether it’s our border management, the design and operation of our managed isolation and quarantine facilities, guidance and requirements in relation to the use of PPE, or the nature and extent of restrictions on personal movement and business operations.
I’d like to thank all the scientists listening today and the rest of the medical community for all the research you’ve carried out over the last 14 months and your ongoing commitment to building our understanding of the virus and how it spreads. I can assure you the New Zealand Ministry of Health closely monitors the work you’re doing and I trust you see this reflected every day in our public health response.
Thank you so much for helping us keep our people safe.