Investigators' Blog

COVID-19 network modelling trilogy

Elimination, Alert Level 2.5 and other non-pharmaceutical interventions

26 July 2021

The reports ‘Network modelling of elimination strategy pillars: Prepare for it, Stamp it out’; ‘Alert Level 2.5 is insufficient for suppression or elimination of COVID-19 community outbreak’; and ‘Contagion network modelling of effectiveness for a range of non-pharmaceutical interventions for COVID-19 elimination in Aotearoa New Zealand’ were sent to the New Zealand government on 9 December 2020, 15 February 2021, and 16 November 2020 respectively. The reports are presented here as a connected trilogy that are intended to be read in the order above.

Here is some background and context that might be of use to readers:

All three reports deal with the wild type variant of SARS-CoV2 that was common around the world (and in many cases in Aotearoa New Zealand) in the latter half of 2020. The transmissibility of SARS-CoV2 is commonly communicated via an R0 value. This value was around 2-3 for the wild type variant considered in this report.1 More recently a number of more transmissible variants of concern have emerged. The alpha and delta variants that were first noted in the United Kingdom and India, respectively, have R0 values that are around two and four times higher again than the wild type strain of SARS-CoV2. Hence, any control measures and results discussed in these reports will typically no longer apply with the current prevalence of these more transmissible strains.

The ‘Elimination strategy’ report considers the policy settings and possible interventions that can be used to prepare for the emergence of COVID-19 in the community in Aotearoa New Zealand. It then looks at the effectiveness of different Alert Level 3-like interventions in eliminating community transmission once it is detected. Pre-detection, the report focuses primarily on testing rates of symptomatic individuals in the community. Post-detection, a range of measures that could reduce transmission (e.g. closing workplaces, mask wearing) are considered, along with the effect of elevated community testing rates and contact tracing of exposed individuals. Many of the parameters for this report were estimated from the behaviour observed during the August 2020 outbreak in Auckland.

At the end of August 2020, at the tail end of the outbreak, Auckland dropped from Alert Level 3 (AL3) to Alert Level 2.5 (AL2.5), while there were still new cases of COVID-19 being found in the community.2 Despite this, the outbreak remained under control and was eventually eliminated. This raises the question of whether or not the less restrictive AL2.5 could have been used to eliminate a similar outbreak in future, rather than the more disruptive AL3.

The ‘Alert Level 2.5’ report addresses precisely this question. It finds that for a similar community outbreak, AL2.5 is most likely to result in suppression, but not elimination-like behaviour. The probability of elimination under AL2.5 is strongly linked to the outbreak size at initial detection. Outbreaks with ten or fewer total cases (including unknown cases) at the time of alert level elevation have an approximately 60% chance of being eliminated within 150 days of detection, while if the outbreak size is 11 or more at the point when alert levels are elevated, the probability of elimination falls to under 12%.

The fact that a period of AL2.5 did lead to elimination while community cases were still being discovered at the tail-end of the Auckland August outbreak may be explained either by good luck (i.e. a very low probability but successful elimination event) or, more likely, by the preceding period of AL3. During AL3, high levels of contact tracing and testing may have essentially ring-fenced the outbreak. In such a scenario, individuals in the vicinity of the existing cluster would effectively remain at a higher Alert Level while the rest of Auckland moved to level 2.5.

Both the ‘Elimination strategy’ and the ‘Alert Level 2.5’ reports consider a number of different variations of the AL3 and AL2.5 interventions, such as improved contact tracing processes due to increased rates of QR code scanning or adoption of Bluetooth contact tracing.

The final report of this trio, ‘Modelling of effectiveness for a range of non-pharmaceutical interventions’, looks at a large number of combinations of transmission reduction interventions at four levels of strictness (none, partial, increased, and strict) for workplace and community, and three levels (none, partial, and closure) for schools. For example, closing schools but not workplaces, while mandating mask-wearing indoors would approximately match the closure of schools, and ‘partial’ control in workplaces and communities.

The purpose of this report is not so much to design alternative Alert Levels, but rather to provide a sensitivity analysis. This analysis can be used to infer some coarse bounds on the types of behaviour that might be expected in the previous two reports if parameters were adjusted, or if assumptions were modified. Even though this report was produced in advance of its two companions, it is presented here as an add-on that may help to quantify any uncertainty or variation in the more realistic scenarios of the first two reports.

Footnotes

 

  1. We do not directly use R0 to parameterise infectivity or transmissibility in our contagion model. Rather, we characterise transmissibility with the parameter beta – the average number of infections per person per unit time, which is calibrated against the generation time. R0 is related to beta by: R0 = beta/gamma, where gamma is the rate per unit time at which individuals are removed from the infectious state(s).
  2. Covid-19: What happened in New Zealand on 31 August – Radio New Zealand

 

Read the reports

 

Complexity is at the heart of Te Pūnaha Matatini

Complexity is at the heart of Te Pūnaha Matatini

Photo: New director of Te Pūnaha Matatini, Associate Professor Cilla Wehi (R) with new deputy director Dr Mike O’Sullivan (L).

1 July 2021

The next phase of Te Pūnaha Matatini begins today, as Associate Professor Cilla Wehi takes over as our new director.

Cilla has bold aims to build upon the transdisciplinary community that was created under the leadership of founding director Professor Shaun Hendy. “It’s done really well up until now and I think we want to build on that,” she says.

“Our aim is to reimagine what research looks like, and provide a platform to make intellectual leaps that are important here in Aotearoa New Zealand, but also globally.”

Te Pūnaha Matatini is a transdisciplinary Centre of Research Excellence in complex systems that brings together researchers throughout Aotearoa New Zealand.

New deputy director Dr Mike O’Sullivan agrees that “Te Pūnaha Matatini has built a really great community. The value of that community wasn’t well understood until COVID-19 hit, and then its value became quickly apparent at an international level.”

Shaun’s tenure as inaugural director culminated with Te Pūnaha Matatini receiving the 2020 Prime Minister’s Science Prize for our work developing a series of mathematical models, analysing data and communicating the results to inform the New Zealand Government’s world-leading response to the global COVID-19 pandemic.

The success of this work very publicly validated the emphasis that Te Pūnaha Matatini has placed on values, expertise and communication since our establishment in 2015.

Cilla says that she wants to build upon this foundation to continue to contribute to positive societal change. “We’ve got data analytics to create new knowledge for transformative change and we’ve got a vision of the kind of society that we would like to be part of in the future.”

Researchers in Te Pūnaha Matatini’s community often work in the gaps between disciplines, which is where Cilla says the most exciting ideas often emerge.

“Te Pūnaha Matatini has intellectual curiosity, and we’ve got a suite of tools that can be used to address some of the big challenges that New Zealand faces globally, so we really can push out boundaries.”

Mike is excited about supporting Cilla in her leadership role. “Cilla has clear ideas about the things she wants to do,” says Mike. “But she’s good at listening as well.”

“And she’s not afraid to agitate a little bit.”

 

Photo: Te Pūnaha Matatini Kaumātua Associate Professor Tom Roa.

Another fundamental source of support for Cilla in this leadership role is the wisdom and guidance of Te Pūnaha Matatini Kaumātua, Associate Professor Tom Roa.

“I’ve known Tom a long time,” says Cilla. “He’s the most fantastic person to discuss ideas with because he has really deep insight, and brings a wealth of knowledge from Māori contexts that has relevance and can really help us to see the best path forward.”

Tom shared a kōrero from his iwi Ngatī Maniapoto that underpins Te Pūnaha Matatini’s approach. When the kawau (shag or cormorant) flock for flight, they form an arrow shape, which allows them to collectively punch through headwinds. As leaders tire, those behind them move up to the front.

Cilla explains that “if you align yourselves as a group then you can punch through these difficult problems in a way that you could never do as one person alone. But also, when the leading birds get tired they step back and others come forward. So we’re growing people to step up. This is a group effort, and we are in it together.”

One of the key purposes of Te Pūnaha Matatini is to develop new researchers.

Cilla explains that “it’s become really clear over the last few years how important it is to do not only collaborative research but ethical research. There’s a much stronger focus now on working in partnership with our communities, and on our responsibility to communicate evidence. So we want to train researchers who are collaborative and ethical, and are great at both working with data and working with people.”

“It’s about contributing to future research, but also the future of Aotearoa New Zealand.”

“Complexity is at our heart,” concludes Cilla. “We build community across disciplines to solve complex problems.”

A COVID-19 vaccination model for Aotearoa New Zealand

30 June 2021

Executive summary

  • We use a mathematical model to estimate the effect of New Zealand’s vaccine rollout on the potential spread and health impacts of COVID-19 and the implications for controlling border-related outbreaks.
  • The model can be used to estimate the theoretical population immunity threshold, which represents a point in the vaccination rollout at which we could relax border restrictions with few or no controls in place and see only small occasional outbreaks.
  • While there are significant uncertainties in R0 for new variants, for a variant that would have R0=4.5 with no public health measures (e.g. the Alpha variant), the population immunity threshold is estimated to require 83% of the population to be vaccinated under baseline vaccine effectiveness assumptions. For a variant with R0=6.0 (e.g. the Delta variant), this would need to be 97%.
  • While coverage is below this threshold, relaxing controls completely would risk serious health impacts, including thousands of fatalities.
  • Whether or not New Zealand reaches a theoretical population immunity threshold, the higher vaccination coverage is, the more collective protection the population has against adverse health outcomes from COVID-19, and the easier it will become to control outbreaks.
  • Reaching or getting as close as possible to the population immunity threshold is very likely to require vaccinating at least some under-16-year-olds, subject to official approval for the vaccine to be used in these age groups.
  • There remains considerable uncertainty in model outputs, in part because of the potential for the evolution of new variants. If new variants arise that are more transmissible or vaccine resistant, an increase in vaccine coverage will be needed to provide the same level of protection.
  • A second important source of uncertainty arises because not all parts of the population will have equal vaccine coverage. Even if population immunity is achieved at a national level, communities with relatively low vaccine coverage or high contact rates will remain vulnerable to major outbreaks. These thresholds may also vary seasonally.
  • Until the vaccine rollout is complete, retaining the elimination strategy will protect people who have not yet been vaccinated and, by keeping cases to a minimum, decrease the likelihood that the alert level system will be needed to control future outbreaks.

Abstract

We present two implementations of an age-structured model for COVID-19 spread in Aotearoa New Zealand with a partially vaccinated population. The first is a deterministic SEIR model, useful for considering population-level dynamics and questions about population immunity. The second is a stochastic branching process, useful for considering smaller community outbreaks seeded by individual border arrivals. This builds on an earlier model used to inform the response to outbreaks of COVID-19 in New Zealand. The main purpose of this paper is to develop a model that can be used as the basis for policy advice on border restrictions and control measures in response to outbreaks that may occur during the vaccination roll-out. We consider a range of scenarios at different stages in the vaccine roll-out, including an unmitigated epidemic and contained local outbreaks. This work is intended to form a foundation for further COVID-19 vaccination modelling in New Zealand that will account for additional demographic variables.

 


Supplementary information [PDF 2.1MB]

*This paper was updated on 21 September 2021 with an erratum correcting a mistake in the previous version.

Dr Andrea Byrom honoured to accept new role as kairangi

Dr Andrea Byrom honoured to accept new role as kairangi

Ecologist and science leader Dr Andrea Byrom has accepted a role as kairangi in Te Pūnaha Matatini.

Kairangi is a Māori word meaning ‘the finest pounamu’, which can be used to describe a person held in high esteem. This role acknowledges the important contributions of our senior colleagues.

Dr Andrea Byrom has been involved with Te Pūnaha Matatini as an associate investigator since the early days, and has contributed at many hui and supervised several early career researchers. She is currently co-supervising Te Pūnaha Matatini Whānau member Julie Mugford in the final stages of her thesis, alongside Associate Professor Alex James and Professor Michael Plank.

The project that Andrea is most proud of being involved with at Te Pūnaha Matatini was exploring the biodiversity benefits of large-scale pest control regimes with Dr Rachelle Binny. Their work quantified significant benefits for biodiversity from pest control over two decades. Andrea says that “I’m proud to have contributed to that research because it really demonstrated how important science is to the environment, and why we do large-scale conservation efforts like pest control or ecological restoration.”

She also particularly enjoyed collaborating with Professor Shaun Hendy and a group of summer interns on network analyses of the many types of people and organisations involved in environmental protection in Aotearoa. “That was a real introduction to network analyses and some of the things Te Pūnaha Matatini had to offer that I had not previously thought of applying to te taiao the environment.”

Andrea recently resigned from her role as director of Ngā Koiora Tuku Iho New Zealand’s Biological Heritage National Science Challenge. She has been working in the New Zealand science system since joining Manaaki Whenua Landcare Research as a postdoctoral researcher in 1997.

Over two decades working at Manaaki Whenua Andrea moved away from directly doing her own research and into leadership roles, after becoming interested in how science leadership could empower scientists to do their work, rather than add more bureaucracy to their lives.

She says that she “really loved that leadership style”.

“What I liked most about being a director of a National Science Challenge was having a view across all of the amazing talent that we have in the New Zealand science system.”

Her directorial responsibilities meant that Andrea did not have as much time as she would like to devote to Te Pūnaha Matatini in recent years. “I’ve been on a separate journey from Te Pūnaha Matatini for the last wee while, so to come back in as a kairangi now is quite an honour.”

“In the last few years, my interests have broadened to thinking about how we take our Te Tiriti o Waitangi partnership role seriously as scientists, and how we bring mātauranga Māori and kaupapa Māori research methods to the fore. I worked hard to facilitate a lot of that via the National Science Challenge and ended up in a co-director role in that area with Melanie Mark-Shadbolt.”

“I feel like the tide’s turning and that people are starting to listen. But it’s really important to put different perspectives and stories out there.”

After a demanding period as a director, Andrea is focusing on spending more time with her partner, as well as doing environment consultancy work and board roles. “I’m particularly interested in how important governance is to science and the environment. That’s my new passion, and as a kairangi I would like to contribute where I can – particularly around complex environmental research.”

“I love being a sounding board for students and I love coming to hui where there are great minds contributing things that I hadn’t thought of and ideas that I’m interested in.”

Since stepping back as a director, Andrea and her partner have been making the most of their time together by killing of a large amount of lawn on their half-hectare property in mid-Canterbury and replanting it with over 5,000 native plants.

How to kill your lawn with Andrea Byrom

  1. Acquire large quantities of cardboard boxes and flatten them
  2. Lay cardboard over lawn on non-windy day
  3. Cover cardboard with a whole lot of mulch
  4. Water it all down
  5. Leave for two months
  6. Replant with native plants

Links

Long-term biodiversity trajectories for pest-managed ecological restorations: eradication vs. suppression – Ecological Monographs

Fighting COVID-19 with the team of 5 million

Aotearoa New Zealand government communication during the 2020 lockdown

25 May 2021, updated 6 October 2021

Aotearoa New Zealand’s response to the COVID-19 pandemic is considered one of the best in the world. A major component of the government response was the communication of public health measures. In this paper, we approach Prime Minister Jacinda Ardern’s daily press briefings with the Director-General of Health, Ashley Bloomfield as a case study of government communication during a public health crisis.

A reflexive thematic analysis leads us to identify three key themes:

  1. Open, honest and straightforward communication
  2. Distinctive and motivational language
  3. Expressions of care

Situating our findings in the fields of crisis communication, science communication and psychology, we argue that the messages presented in the 2020 daily briefings supported the New Zealand Government’s COVID-19 elimination strategy through building trust with the audience and framing the ‘lockdown’ as an urgent, collective and meaningful cause, mobilising New Zealanders to support public health measures.

 

Prime Minister recognises transformative science

Prime Minister recognises transformative science

The 2020 Prime Minister’s Science Prize has been awarded to Te Pūnaha Matatini for our contribution to Aotearoa New Zealand’s COVID-19 response.

The Prime Minister’s Science Prize is awarded for transformative science which has had a significant economic, health, social or environmental impact.

Te Pūnaha Matatini are being recognised for our work that developed a series of mathematical models, analysed data and communicated the results to inform the New Zealand Government’s world-leading response to the global pandemic.

Te Pūnaha Matatini is a Centre of Research Excellence funded by the Tertiary Education Commission and hosted by the University of Auckland. Over the past six years, Te Pūnaha Matatini has grown from the kernel of an idea into a diverse national network of over a hundred investigators and students who are tackling the interconnected and deeply interdisciplinary challenges of our time. Our values, expertise and focus on communication made us uniquely positioned to grapple with the COVID-19 pandemic in Aotearoa New Zealand.

Te Pūnaha Matatini’s modelling was key in helping the government make good decisions about lockdowns, particularly in April and May when the need to relax Alert Levels arrived, and in August, when a tailored lockdown was used in Auckland to eliminate a large outbreak. These public health interventions have had an immense impact on New Zealanders’ lives, not the least of which was preventing a considerable number of deaths due to COVID-19 if the virus had been allowed to spread unimpeded.

“Even I underestimated the centrality of [science] advice for me, in this time in office, and just how important it would become to us as a government.” – Jacinda Ardern, Prime Minister of New Zealand

The team made sure their models served the health system by working with Orion Health data scientists to ensure information got to where it was needed. Orion Health works with healthcare sector clients to deploy and manage machine learning models, which meant they were able to offer their technology and processes to support the Te Pūnaha Matatini team.

Te Pūnaha Matatini’s work and related research from around the globe was actively communicated to the public throughout 2020, and several of Te Pūnaha Matatini’s researchers were the most prominent science communicators during the crisis.

“I want to thank the many, many, many people in this room who were a part in your own ways in either helping us generate the information we needed to make those decisions, or who helped us communicate those decisions when it mattered most.” – Jacinda Ardern, Prime Minister of New Zealand

The transdisciplinary team working on COVID-19 that received this award brought together researchers from the University of Auckland, University of Canterbury, Victoria University of Wellington, Manaaki Whenua Landcare Research, Market Economics, and Orion Health.

The COVID-19 programme at Te Pūnaha Matatini continues into 2021 with projects focusing on branching process models, complex network models, phylodynamics, and the spread of disinformation and misinformation.

Vaccination and testing of the border workforce for COVID-19 and risk of community outbreaks

A modelling study

22 March 2021

Executive summary

  • Vaccination of New Zealand’s frontline border workforce is a priority in order to protect this high-exposure group from the health impacts of COVID-19.
  • Although vaccines are highly effective in preventing disease, their effectiveness in preventing transmission of COVID-19 is less certain.
  • There is a danger that vaccination could prevent or reduce symptoms of COVID-19 but not prevent transmission. Counterintuitively, this means that vaccinating frontline border workers could increase the risk of a community outbreak.
  • In a scenario where the vaccine reduces transmission by 50%, vaccinating border workers could increase the risk of a significant community outbreak from around 7% per seed case to around 9% per seed case.
  • Until more is known about the effect of the vaccine on transmission, we recommend increasing the routine testing of vaccinated border workers to mitigate this risk. Regular saliva testing may be a good way to achieve this.
  • Careful attention should be paid to any groups, such as frontline workers’ family members, who may be vaccinated but who are not undergoing routine testing to ensure they do not become asymptomatic spreaders.

Abstract

Australia and New Zealand have a strategy to eliminate community transmission of COVID-19 and require overseas arrivals to quarantine in government-managed facilities at the border. In both countries, community outbreaks of COVID-19 have been sparked following infection of a border worker. This workforce is rightly being prioritised for vaccination. However, although vaccines are highly effective in preventing disease, their effectiveness in preventing transmission of COVID-19 is less certain. There is a danger that vaccination could prevent symptoms of COVID-19 but not prevent transmission. Here, we use a stochastic model of COVID-19 transmission and testing to investigate the effect that vaccination of border workers has on the risk of an outbreak in an unvaccinated community. We simulate the model starting with a single infected border worker and measure the number of people who are infected before the first case is detected by testing. We show that if a vaccine reduces transmission by 50%, vaccination of border workers increases the risk of a major outbreak from around 7% per seed case to around 9% per seed case. The lower the vaccine effectiveness against transmission, the higher the risk. The increase in risk as a result of vaccination can be mitigated by increasing the frequency of routine testing for high-exposure vaccinated groups.

 

Estimated inequities in Covid-19 infection fatality rates by ethnicity for Aotearoa New Zealand

4 September 2020

There is limited evidence as to how clinical outcomes of COVID-19 including fatality rates may vary by ethnicity. We aim to estimate inequities in infection fatality rates (IFR) in New Zealand by ethnicity. We combine existing demographic and health data for ethnic groups in New Zealand with international data on COVID-19 IFR for different age groups. We adjust age-specific IFRs for differences in unmet healthcare need, and comorbidities by ethnicity. We also adjust for life expectancy reflecting evidence that COVID-19 amplifies the existing mortality risk of different groups.

The IFR for Māori is estimated to be 50% higher than that of non-Māori, and could be even higher depending on the relative contributions of age and underlying health conditions to mortality risk. There are likely to be significant inequities in the health burden from COVID-19 in New Zealand by ethnicity. These will be exacerbated by racism within the healthcare system and other inequities not reflected in official data. Highest risk communities include those with elderly populations, and Māori and Pacific communities. These factors should be included in future disease incidence and impact modelling.

 

Mathematical modelling to inform New Zealand’s Covid-19 response

Mathematical modelling to inform New Zealand’s Covid-19 response

NEW RESEARCH — LINK TO FULL PDF

22 February 2021

 

Mathematical modelling to inform New Zealand’s COVID-19 response

 


Abstract:

Between February and May 2020, New Zealand recorded 1504 cases of Covid-19 before eliminating community transmission of the virus in June 2020. During this period, a series of control measures were used including population-wide interventions implemented via a four-level alert system, border restrictions, and a test, trace, and isolate system.

Mathematical modelling played a key role in informing the government response and guiding policy development. In this paper, we describe the development of a stochastic mathematical model for the transmission and control of Covid-19 in New Zealand. This includes features such as superspreading, case under-ascertainment, testing and reporting delays, and population-wide and case-targeted control measures.

We show how the model was calibrated to New Zealand and international data. We describe how the model was used to compare the effects of various interventions in reducing spread of the virus and to estimate the probability of elimination. We conclude with a discussion of the policy-modelling interface and preparedness for future epidemic outbreaks.


 

Modelling support for the continued elimination strategy

Modelling support for the continued elimination strategy

NEW RESEARCH — LINK TO FULL PDF 

8 December 2020

 

Modelling support for the continued elimination strategy

 


Executive Summary

  • We model the effects on the risk of COVID-19 border reincursions of a wide variety of different border policies, including changes in managed isolation requirements for travellers as well as different testing regimes for frontline border workers.
  • A more detailed modelling study and risk analysis of a specific policy change would be recommended before any implementation.
  • One potential change in policy that could be considered is to replace the current requirement for 14 days in MIQ with 7 days in MIQ followed by 7 days in home isolation (including a second PCR test) for arrivals from countries with low prevalence of COVID-19 such as Australia.
  • However, any increase in the number of arrivals from high-prevalence countries, for example due to an increase in MIQ capacity or repurposing of existing MIQ capacity, will lead to an increase in the risk of border reincursions.
  • Weekly PCR testing of frontline border workers helps to ensure most border reincursions are detected before they grow too large. Supplementing this with an additional weekly rapid test would be an extra safeguard that decreases the risk of a large outbreak.