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.
A hui held at the University of Auckland on 2 July 2019 marked a special moment in the history of Te Pūnaha Matatini – the inauguration of our first ever kaumatua Dr Tom Roa (Ngāti Maniapoto, Waikato).
Dr Tom Roa, a Tainui leader and Manukura / Associate Professor in the University of Waikato’s Faculty of Māori and Indigenous Studies, is a familiar figure on marae throughout Tainui and the country. Over the years, Tom has also been a leading figure helping to bring the Māori language into the mainstream, and he is one of the founders of Te Wiki o Te Reo Māori movement in the 1970s.
Tom’s appointment as Te Pūnaha Matatini kaumatua enables us to continue to grow a safe and inclusive CoRE for our multicultural team of investigators and students, and maintains our leadership in this particular area within the Aotearoa New Zealand science and research system.
The July hui at the University of Auckland comprised a large gathering of Te Pūnaha Matatini investigators, friends and Whānau from all over New Zealand.
Following a warm mihi whakatau, Te Pūnaha Matatini Incoming Co-Director Cilla Wehi shared stories about her work with Tom over the years and provided some personal insights.
“Matua Tom has a very long research career in linguistics and translation,” said Cilla. “More than that even, he is valued for his immense skills in the Māori world as somebody who has incredible expertise in whaikōrero, in the art of oratory, but who can also cut to the point in a very pithy way.”
Cilla then welcomed Tom to the stage for his keynote speech – ‘He Puna Pūnaha’ – a springboard for ideas in the myriad of theories and systems to be explored.
Tom’s talk was inspiring and it was a privilege to hear him speak. He talked about key concepts and traditions central to mātauranga in a way that his audience, many of whom are relative newcomers to Aotearoa, appreciated immensely. Tom also shared a karakia, a prayer invoking spiritual guidance.
“I have a fascination with how mātauranga Māori and science can be woven together. So TPM fascinates me even more because of the interdisciplinary nature of so many of the projects that I’ve had a glance through,” said Tom.
“When Potatau, the first Māori King was anointed, he said ‘there is but one eye of the needle through which must pass the red, the black and the white threads’. Many people have taken that to mean that it’s about bringing people together,” said Tom. “But for TPM, I suggest that you might have a mathematical thread, somebody else might have an ecological thread, somebody might have an economic thread.
“Somebody might have all of these different kinds of threads, along with my Māori thread,” said Tom. “And if we thread those through the eye of the needle, they become something else. They become interweaved, and my suggestion is that if we thread that eye of the needle and if we bring all of that together properly, then we have a new creation – new data, new knowledges, new insights. Through that weaving.”