NEW RESEARCH — LINK TO FULL PDF
8 December 2020
Modelling support for the continued elimination strategy
- 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.
Study Area(s): science / science communication / design
Scholarship Level: Masters Research (Master of Science in Society / Master of Design)
Closing Date(s): 29 January 2021
Tenure: One year
Number offered: Two (one at the Centre for Science in Society at Victoria University of Wellington, one at the Wellington School of Design at Massey University)
Value: $17,000 each, plus fees.
This unique project combines two Master’s scholarships in order to develop an interdisciplinary response, covering science, science communication, design and community engagement. It is supported by Te Pūnaha Matatini, a Centre of Research Excellence.
The Master’s projects will research, develop and design a tree planting site (as a proof of concept pilot project) that engages visitors about climate mitigation as well as ecology. In line with a design approach the specific outputs are not predetermined, and could include elements such as a custom-designed tree planting area; signage and interpretation integrated across a tree planting location (that contains different species and plantings of different ages and stages); and/or other lateral design responses that help communicate the issues/solutions, both on-site and/or more widely.
This inherently interdisciplinary project has relevance to biodiversity, climate economics, mātauranga Māori, social justice, design and science communication. Across the two candidates (we anticipate there will be extensive peer-to-peer co-learning and knowledge transfer) the project will require an understanding of science (tree ecology, ecosystems, carbon cycle), design (design of spaces, visual communication, community use and engagement), and science (climate) communication (appropriate messaging, audience engagement, politics of communication). This is an exploratory pilot project: while it carries expectations around an on-the-ground experience in-situ, the intention is that the outcomes go beyond that into something that is, or may become, a reusable ‘tool’.
There are many tree planting sites across Aotearoa, often supported by local or regional councils and primarily funded for reasons such as flood protection purposes, with recognition of the beneficial local ecological advantages the planting provides, such as cleaner water and increased biodiversity. At the same time, ‘the public’ are informed that tree planting is a good way to combat climate change, for instance by clicking a climate mitigation button after purchasing air tickets, or in policy discussions about carbon trading. There is, however, little information that connects practical ‘trees in the ground’ to theoretical carbon mitigation – how many trees really need to be planted to absorb the equivalent carbon that is emitted on a flight to Europe? Does it matter what kind of tree is planted? What happens if that tree dies, through natural causes or logging? Do the trees need to stay on dry land? Are native trees better than eucalypts?
These Master’s opportunities have been funded to explore this gap by developing an on-the-ground science communication design output, focused on how trees absorb carbon, and over what time periods (i.e. ten trees may absorb enough carbon for a flight between Auckland and Wellington in 30 years but if we wait long enough, they could cover a flight to London in, say, 150 years). The intention is that this pilot project will provide ‘templates’ or ‘tools’ that could be applied more widely across the country.
The pilot project will be situated in Ōtaki and at least one of the successful applicants will ideally have a connection to the area, through whānau or study, and/or a demonstrated interest and understanding of Mātauranga Māori. The project is a collaboration with Friends of the Ōtaki River, which is providing the pilot site as well as tangible in-kind support. Supervision will come from Dr Rhian Salmon at the Centre for Science in Society (Te Herenga Waka – Victoria University of Wellington), Jo Bailey at the Wellington School of Design (Massey University) and Associate Professor Cate Macinnis-Ng at the University of Auckland, all of whom are investigators with Te Pūnaha Matatini. Though one student will be enrolled at Victoria University of Wellington and one at Massey University School of Design (so will receive independent degrees from those establishments), we hope to use this collaboration to explore cross-institution interdisciplinary collaboration as well. It is vital that the candidates are open to collaborative, interdisciplinary approaches to study, so must be adaptable and responsive to forging a shared body of expertise with their co-candidate (for instance, sharing their expertise and collectively identifying knowledge gaps they may need to fill together) as well as working autonomously.
Applications are sought from those who are eligible at the time of application, or who will have become eligible at the start of Semester/Trimester 1 2021, to enrol for a Master of Science (Science in Society) thesis or a Master of Design at Massey University.
Usually, these courses require the applicant to have completed relevant graduate study such as an Honours degree or postgraduate diploma. However, extensive relevant practical or professional experience may be approved for entry to the programme in exceptional circumstances.
As well as discipline-specific experience, demonstrated interest and experience/qualifications related to climate change mitigation, environmental management, tree ecology and/or mātauranga Māori would be advantageous.
Applicants will be required to enrol full time in a Master of Science (Science in Society) Part 2 (thesis) at Victoria University of Wellington or a Master of Design at Massey University College of Creative Arts at the start of Semester/Trimester 1, 2021. The project will run for one calendar year. Fees are covered by the scholarship, as well as a $17k stipend.
Applicants who are interested in applying for either of these scholarships are required to send an email titled “Using Tree Planting Projects to Communicate about Climate Change Scholarship” to: Dr Rhian Salmon and Jo Bailey by 29 January 2020.
Applicants should also include the following documentation in their email:
- A CV
- A personal statement outlining why they want to apply for this scholarship
- One written academic or professional reference
A shortlist of eligible applicants will be drawn up by an internal panel consisting of nominees from Te Pūnaha Matatini on the basis of the applicants’ study record, CV, academic or professional reference and personal statement. An interview or interviews may be required. The successful recipient will be chosen by the same internal panel.
Regulations and conditions
Applicants should satisfy the requirements for admission as a Master’s candidate at Victoria University of Wellington or Massey University College of Creative Arts. They will also need to sign a Research Scholarship contract.
NEW RESEARCH — LINK TO FULL PDF
9 November 2020
Early intervention is the key to success in COVID-19 control
- Evaluating the effectiveness of New Zealand’s COVID-19 response, relative to counterfactual (alternative ‘what-if’) scenarios, is important for guiding future response strategies. We assess the importance of early implementation of interventions for controlling COVID-19.
- We model counterfactual scenarios in which the timings of three policy interventions are varied: border restrictions requiring 14-day quarantine of all international arrivals, border closure except to returning residents and citizens, and Alert Level 4 restrictions. We compare these to a modelled factual scenario in which intervention timings are the same as occurred in reality.
- Key measures describing the dynamics of a COVID-19 outbreak (notably peak load on the contact tracing system, the total number of reported COVID-19 cases and deaths, and the probability of elimination within a specified time frame), are used to compare outcomes between scenarios.
- Key measures were more sensitive to the timing of Alert Level 4, than to timing of border restrictions and border closure. Of the counterfactual scenarios, an earlier start to Alert Level 4 would have resulted in the greatest reduction in numbers of cases and deaths.
- Delaying the start of Alert Level 4 by 20 days could have led to over 11,500 cases and 200 deaths, and would have substantially reduced the probability of eliminating community transmission of COVID-19, requring a longer period at Alert Level 4 to achieve control.
NEW RESEARCH — LINK TO FULL PDF
21 October 2020
Economic comparison of the use of Alert Levels 3 and 4 in eliminating the Auckland August outbreak: a cost-effectiveness analysis
- We compare the economic costs of containing the Auckland August outbreak of COVID-19 using Alert Level 3 to those that might have been incurred from the use of Alert Level 4.
- We estimate the effectiveness of Alert Level 3 using data from the actual August outbreak. The effectiveness of a putative regional Alert Level 4 is less certain, but we consider an optimistic estimate based on what was achieved in the March-April outbreak, as well as a more pessimistic estimate, which reflects the higher transmission rates observed in August.
- We use a decision-making model for de-escalation of alert levels based on observations of weekly case numbers, which is a simpler decision-making criterion to that used in New Zealand and likely underestimates the duration of Alert Level 4 periods that would be used in practise.
- To achieve the same likelihood of elimination, we find that both the optimistic and pessimistic Alert Level 4 period has a shorter duration than the period needed at Level 3.
- To achieve the same likelihood of elimination, the optimistic Alert Level 4 controls have a lower economic cost than the Alert Level 3 controls.
- To achieve the same likelihood of elimination, the pessimistic Alert Level 4 controls come at a comparable economic cost to the Alert Level 3 controls.
- This analysis does not take into account the longer term economic costs of these measures, nor does it consider social, or health impacts that might differ between strategies.
NEW REPORT — LINK TO FULL PDF
31 October 2020
Impact of the COVID-19 pandemic on research students in Aotearoa New Zealand
Early career researchers (ECRs) provide a valuable contribution to the productivity and connectivity of the research ecosystem in Aotearoa New Zealand, but are particularly vulnerable to the societal fallout from the COVID-19 pandemic.
This report – a letter prepared on behalf of Te Pūnaha Matatini Whānau, a national network of emerging researchers associated with Te Pūnaha Matatini – calls for everyone, at all levels, to find ways to support our new generation of academics at this critical time.
NEW RESEARCH — LINK TO FULL PDF
19 October 2020
Network-based simulations of re-emergence and spread of COVID-19 in Aotearoa New Zealand
- We simulate the late July/early August re-emergence and spread of COVID-19 in Aotearoa New Zealand.
- We use a stochastic, individual-based network model of all ~5 million individuals in Aotearoa, and run simulations for a period of 30 days.
- Based on these simulations, we calculate: the expected time to detection of the first case after initial seed cases; the number of cases at the time of detection; the time until detection of a first case outside of Auckland; and how the overall number of cases increases without intervention.
- Our model includes interaction pathways, referred to as ‘contexts’ in the network, broken down into network ‘layers’ representing home, work, school, and community structure.
- Each simulation starts from initial (seed) cases corresponding to the first detected re-emergence cases in August 2020.
- We run 50 realisations of each simulation for 30 days – each simulation scenario corresponding to one of three different levels of transmission rate.
- To model the behaviour of individuals in the weeks prior to the August 11th re-emergence, we assume a moderate rate of people getting tested if mildly symptomatic.
- No contact tracing or intervention is present in this scenario, other than cases that test positive being isolated to their dwelling.
NEW REPORT — LINK TO FULL PDF
14 October 2020
Summary of Advice to Cabinet on Auckland’s August 2020 COVID-19 Outbreak
This paper summarises the modelling advice provided to Cabinet during the Auckland August outbreak in 2020 as well as detailing the methods used to provide that advice. The actual values in this report, particularly the probability of elimination and the effective R value, varied depending on the date the advice was given. Values given here are representative of those calculated in the later part of the outbreak (October 2020).
- For the Auckland August outbreak, the effective reproduction number Reff was found to be between 2.1 and 2.5 before Auckland moved to Level 3 on August 12 and between 0.6 and 0.8 during Level 3.
- This was a higher value for Reff in August pre-lockdown compared to that seen pre-lockdown in the March/April outbreak. This may be due to a combination of factors, including Level 1 conditions (no gathering size restrictions, etc.), different behaviour of cases associated with international travel in March/April, higher transmission rates in winter, and differences between the communities affected.
- Highly effective contact tracing and case isolation played an important role in keeping below 1 in Alert Level 3 and 2.5/2.
- We estimated that it was highly likely that the Auckland August cluster was eliminated by October 5 before Auckland returned to Alert Level 1 on October 7. However, in scenarios that did not lead to elimination, case numbers grew rapidly in the absence of Alert Level 3 restrictions.
Te Pūnaha Matatini has been successful in its bid to be refunded by the New Zealand Government’s Tertiary Education Commission (TEC) in the recent CoRE round. From 1 July 2021, the Centre’s funding will rise from $2.1 million per annum to $4 million per annum through to the end of 2028. In its announcement, the TEC singled out Te Pūnaha Matatini’s contribution to the COVID-19 response through its modelling of infection spread.
Te Pūnaha Matatini incoming co-directors Priscilla (Cilla) Wehi, a Conservation Biologist with Manaaki Whenua Landcare, and Murray Cox, a Professor of Computational Biology at Massey University, were delighted to hear the news.
“It is amazing to be leading such a strong cohort of researchers who can cross disciplines and address the complexity of systems,” said Cilla. “These ways of thinking will provide real traction in addressing some of the huge problems we are facing globally, and stimulate innovation.”
“We’ve have a lot of impact on New Zealand over the last six years and we’re really looking forward to delivering even more over the next eight,” added Murray.
Director Shaun Hendy, Professor of Physics at the University of Auckland, who has led Te Pūnaha Matatini from its inception in 2013, said the successful rebid was underpinned by a massive team effort.
“[It’s] the culmination of eighteen months of enormously hard work by Kate Hannah, Cilla Wehi, Murray Cox, Kathryn Morgan, and many others,” said Shaun. “It also reflects the commitment of all our investigators, our Whānau, and our friends to Te Pūnaha Matatini’s mission over the last seven years. Congratulations and commiserations to the other applicants, who have also worked hard over the last year or more.”
NEW RESEARCH — LINK TO FULL PDF
15 September 2020
Effective reproduction number and likelihood of cases outside Auckland
- The effective reproduction number 𝑅𝑒𝑓𝑓 measures the potential for COVID-19 to spread. If 𝑅𝑒𝑓𝑓 > 1, new daily cases are likely to increase over time, if 𝑅𝑒𝑓𝑓 < 1 new daily cases will decrease over time.
- For the March-April outbreak, 𝑅𝑒𝑓𝑓 was between 1.2 and 2.2 before moving to Level 4 and between 0.35 and 0.55 during Level 4.
- For the August-September outbreak, 𝑅𝑒𝑓𝑓 was between 2.3 and 2.7 before Auckland moved to Level 3 and between 0.5 and 0.8 during Level 3.
- In both March and August, the Alert Level response was successful in reducing 𝑅𝑒𝑓𝑓 below 1 and hence containing the outbreak.
- The bigger relative reduction in 𝑅𝑒𝑓𝑓 achieved by lockdown in August relative to lockdown in March may be explained by better performance of the testing and contact tracing system.
- The higher value for pre-lockdown 𝑅𝑒𝑓𝑓 in August compared to March may be due to a combination of factors, including Level 1 conditions (no gathering size restrictions, etc.), different behaviour of cases associated with international travel in March/April, higher transmission rates in winter, and potentially higher rates of crowded housing in affected communities.
- It is still too early to produce a reliable estimate for 𝑅𝑒𝑓𝑓 at Alert Level 2.5 in Auckland. The confidence interval for 𝑅𝑒𝑓𝑓 is very wide and it is possible that 𝑅𝑒𝑓𝑓 > 1 under current conditions.
- The likelihood of undetected active cases outside the Auckland region is also uncertain and could be up to 40% for the North Island and up to 20% for the South Island. The possibility of spread to other regions will remain as long as there are active cases in the Auckland cluster combined with near normal rates of inter-regional travel.
NEW RESEARCH — LINK TO FULL PDF
6 September 2020
Assessing the prevalence and nature of COVID-19 unreliable and untrustworthy information in Aotearoa New Zealand’s social media, Jan-Aug 2020
The arrival of the COVID-19 pandemic in Aotearoa New Zealand saw New Zealanders presented with the accompanying infodemic. Aotearoa New Zealand’s experience, which is characterised by mis- and dis-information, as well as the emergence of a number of conspiracy theories, is linked to international patterns within the COVID-19 infodemic overall, but also displays significant situated and differential themes and impacts. We evaluate the prevalence of the COVID-19 infodemic in social and mainstream media February-August 2020, and analyse the narrative intent and social or political discourses of the content collated. In evaluating the nature of COVID-19 narratives over this time period, we find that there are significant changes in the types of discourses these narratives engage with, with an increasing prevalence of conspiracy narratives noted since the re-emergence of community transmission in August. Assessing the impact of these unreliable and/or untrustworthy narratives and their sources, including narrators, we develop preliminary understanding of the ways in which these narratives are at work in Aotearoa New Zealand.
NEW RESEARCH — LINK TO FULL PDF
26 August 2020
Potential reduction in transmission of COVID-19 by digital contact tracing
- To maintain elimination of COVID-19, digital contact tracing systems should be designed to complement manual contact tracing, for example by enhancing coverage or speed of tracing, rather than as a separate or fully automated system.
- To reduce the effective reproduction number to around 1 requires a combination of rapid testing and case isolation, a well-functioning manual contact tracing system, digital contact tracing with an uptake rate of at least 75% and recording 90% of close contacts, and highly effective quarantine of traced contacts.
- Ensuring that individuals with COVID-19 symptoms get tested quickly and are able to isolate effectively is just as important as investment in contact tracing.
- Digital systems based on QR codes with no proximity detection are likely to be less effective as a result of recording fewer contacts.
- Bluetooth apps and card-based proximity detection systems perform comparably at a given level of coverage, but other factors such as usability, reliability and longevity need to be considered.
- In the event of a large ongoing outbreak, scalability and false positive rates are more important, but significant population-wide control measures are also likely be required to prevent a major epidemic.
- Tracing and quarantining second-order contacts of a confirmed case provides a relatively small additional benefit. This could be useful in the very early stages of an outbreak, but for a larger outbreak ensuring fast and effective quarantine of first-order contacts should be a higher priority.
NEW RESEARCH — LINK TO FULL PDF
20 August 2020
Managing the risk of a COVID-19 outbreak from border arrivals
- Weekly testing of all workers who have direct or indirect contact with border arrivals and quarantine residents will greatly reduce the chance of another outbreak.
- These tests should be conducted by a health professional with knowledge of COVID-19 symptoms to reduce false negatives and help diagnose probable cases.
- If the first detected case of COVID-19 is in a frontline worker, there is a high probability that the outbreak is still very small and can be contained by fast case isolation and contact tracing.
- If the first detected case of COVID-19 is in an individual without a direct link to arrivals or quarantine facilities, then an immediate local lockdown may be necessary to contain the outbreak.
- If the first detected case of COVID-19 is in an individual who is a household contact of a frontline worker and does not themselves have direct contact with the quarantine process, this should be treated in the same way as community transmission and strong community-wide social distancing measures, possible a regional return to a high alert level, should be considered.
- This applies even if the first detected community cases is a household contact of a frontline worker because it means there is a high risk the frontline worker has already infected others.
- Well-managed 14 day quarantine, with minimal interactions between travellers beyond family groups, and tests on day 3 and day 12 provides a very good safeguard against infected travellers initiating community outbreaks.
An early version of this paper was leaked after being supplied confidentially to government, and was reported on in this story.
Te Pūnaha Matatini researcher Giorgia Vattiato (above) and colleagues, from the School of Mathematics and Statistics at the University of Canterbury, are modelling the effects of individual animal personalities in New Zealand on conservation efforts. The purpose – to answer questions such as why some invasive mammal pests always manage to avoid traps, and what kind of reintroduction measures for Kiwi might help them settle more efficiently.
Enhancing the efficiency of invasive mammal pest trapping
Invasive mammal pests such as stoats, possums and rats represent a major threat to New Zealand’s native birds such as Kiwi. Trapping pests as part of wider eradication efforts has worked well on small offshore islands and fenced-off areas of the mainland. However, a few individual animals always seem to be uncatchable – an issue that has led to a growing need for more robust eradication approaches.
Giorgia’s research looks beyond what we already know about factors that influence the behaviour of animal populations. It is well known, for example, that differences in habitat, predation, food availability, social environment and physiology can all affect animal behaviours (and personalities). Common personality differences include boldness or shyness, activity level, resource selection, sociability, and home range size. These different personalities can affect a population as a whole, but very few population dynamic modelling studies have taken them into consideration.
The study of animal personalities can therefore be seen as an important step towards developing accurate, non-biased models that can better predict the efficiency of different programmes underway in New Zealand that aim to eradicate pests, reintroduce threatened species and protect biodiversity.
This has been the rationale of Giorgia’s research – modelling the effects of individual animal personalities in New Zealand. Together with her Te Pūnaha Matatini supervisors, Dr Rachelle Binny at Manaaki Whenua Landcare Research, Associate Professor Alex James and Professor Michael Plank at the University of Canterbury, plus Associate Professor Isabel Castro at Massey University, she has conducted two different types of projects as part of her PhD study.
The first project involves modelling different scenarios of heterogeneity in a pest population, where individual animals are assigned a different probability of interacting with a newly-found trap (their ‘trapability’). Running simulations of two different pest populations – homogenous (all individuals had the same trapability) and heterogenous (individuals have varying levels of trapability), revealed that it takes much longer to eradicate the latter population than the former.
“One of the outputs of our model is the time that you need to wait to be sure that your population has been completely eradicated,” explained Giorgia. “Usually what a pest manager would do is wait until a number of consecutive nights when there have been no captures. After a certain number of nights, they would say ‘okay, we’re 95% sure that we’ve eradicated the population.’ So what we’ve done is simulated this number of nights to have 95% probability of eradication in different scenarios, and we’ve looked at how long we have to wait. So this is one way our model can be used.”
“The model can be used to predict when to change eradication approaches. At one point the curves start to flatten and tail off as those last few very trap-shy individuals keep evading capture. So the flattening curve could inform a pest manager when to switch to a more intensive eradication mode – one that may be more expensive than the first part of the eradication.”
Different Kiwi behave and react differently in response to being moved
The second project the team are working on aims to identify possible differences in the behaviour of Kiwi populations on Motuarohia Island in the Bay of Islands and Ponui Island in the Hauraki Gulf. One of Giorgia’s supervisors on this project, Isabel Castro, had acquired data from previous years when capturing and recording information about the Kiwi population on Ponui Island.
“Isabel could see how different the birds were – some were very friendly, some were not,” said Giorgia. “But nobody had actually ever looked at the numbers behind that. And so I went with her this year and we did a few experiments. We filmed the Kiwi right after capture, under different circumstances – holding them upside down, looking at them in the eye, whilst also recording their heart beat and respiratory rate, to look for differences between birds. They were so different. Some of them would just fall asleep in your arms, and others would never stop struggling. Some of them would even growl or snap their beak.”
Their findings, yet to be published, are expected to be useful for guiding relocation efforts. “Just knowing that the birds have different personalities is something that conservation managers will want to know, especially for situations such as translocations of birds,” explained Giorgia.
NEW RESEARCH — LINK TO FULL PDF
7 August 2020
Successful contact tracing systems for COVID-19 rely on effective quarantine and isolation
Background. Test, trace and isolate are the three crucial components of the response to COVID-19 identified by the World Health Organisation. Mathematical models of contact tracing often over-simplify the ability of traced contacts to quarantine or isolate.
Method. We use an age-structured branching process model of individual disease transmission combined with a detailed model of symptom onset, testing, contact quarantine and case isolation to model each aspect of the test, trace, isolate strategy. We estimated the effective reproduction number under a range of scenarios to understand the importance of each aspect of the system.
Findings. People’s ability to quarantine and isolate effectively is a crucial component of a successful contact tracing system. 80% of cases need to be quarantined or isolated within 4 days of quarantine or isolation of index case to be confident the contact tracing system is effective.
Interpretation. Provision of universal support systems to enable people to quarantine and isolate effectively, coupled with investment in trained public health professionals to undertake contact tracing, are crucial to success. We predict that a high-quality, rapid contact tracing system with strong support structures in place, combined with moderate social distancing measures, is required to contain the spread of COVID19.
This paper was written in Dr Verrall’s capacity as Senior Lecturer at the University of Otago, not in her capacity as a candidate for Parliament. The views in this paper are not necessarily the views of the New Zealand Labour Party. All other authors declare no competing interests.
NEW RESEARCH — LINK TO FULL PDF
16 July 2020
The effect of border controls on the risk of COVID-19 reincursion from international arrivals
- A 14-day period of managed isolation or quarantine (MIQ) with day 3 and day 12 testing reduces the risk of an infectious case being released into the community to a very low level.
- A five-day quarantine period is ineffective and would present a much greater risk to the community.
- Any mixing of individuals in MIQ that could allow transmission of COVID-19 increases the risk of an infectious case being released into the community.
- Strict infection control and use of PPE by staff at MIQ is essential and close contact between individuals in MIQ and staff must be avoided.
- Provided the above guidelines are followed, special exemptions restricted to the second week of stay and after an additional negative test result has been returned pose little additional risk.
- The ratio of cases detected in the second week to cases detected in the first week can be used to estimate whether transmission within MIQ is occurring, although this requires a larger sample size than is currently available.