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.”
Te Pūnaha Matatini incoming co-directors Priscilla (Cilla) Wehi and Murray Cox have collaborated with Hēmi Whaanga and Te Pūnaha Matatini Kaumatua Tom Roa, from the Faculty of Māori and Indigenous Studies at the University of Waikato, on an analysis of Māori ancestral sayings (whakataukī), and their recognition of extinctions and their impact.
Cilla, a conservation biologist with Manaaki Whenua Landcare, and Murray, a Professor of Computational Biology at Massey University, co-authored a paper published in the journal Human Ecology, reporting the linguistic analysis of indigenous Māori whakataukī that focus on fauna and environment, particularly with regard to extinctions of important food sources such as Moa. The findings provide evidence that such extinctions were important as they influenced both ecological and social thought in Māori society. The authors also suggest that oral traditions could have played a similar role in other early societies living through major faunal extinction events.
Examples of whakataukī referring to Moa extinction:
Kua ngaro i te ngaro o te moa
Lost as the moa was lost
Huna i te huna a te moa
Hidden as the moa hid
Ka ngaro ā-moa te iwi nei
The people will disappear like the moa
“Oral tradition, such as these whakataukī passed down by Māori, provide our only real glimpses into the ecological relationships and concerns of early settler populations, and provide early human context to an otherwise relatively dry scientific record of extinction events,” the researchers wrote.
“The whakataukī emphasise that indigenous peoples are not simply passive actors against an environmental backdrop but rather interact with the environment in myriad ways that affect not only the species assemblages present but also the development of cultural values, ideas, and practices.”
Cilla and Murray’s work was picked up by The Conversation in an article entitled ‘Dead as a moa: oral traditions show that early Māori recognised extinction’, and in interviews on Radio NZ, Radio Waatea and TVNZ’s Te Karere.
Several New Zealand university students took up the opportunity to join Te Pūnaha Matatini’s 2019-20 summer internship programme, with paid 10-week placements working on research projects with a variety of our partner organisations.
Once again, our student interns had a range of backgrounds and came from all parts of the country, but they all shared a common desire to make the world a better place through the application and analysis of data, while gaining on-the-job experience.
“This programme is now its fifth year of operation and each year we have had an amazing group of students take up some fantastic opportunities with our partners,” said Kathryn Morgan, Research Operations Coordinator at Te Pūnaha Matatini. “The core objectives remain the same as previous years – providing students with invaluable data analytics experience and insights into working for organisations in the real world.”
The 2019-20 programme featured some very interesting projects involving a mix of both public and private sector work. Here we profile a few of the projects our interns worked on:
Developing complex systems models – Ministry for the Environment
A team of three interns in our programme were placed with the Ministry for the Environment (MfE) where they piloted a complex systems approach to modelling policy problems.
Shnece Duncan, a University of Canterbury Master of Commerce in Economics student, Ellena Black, a University of Auckland Honours degree graduate in Applied Mathematics, and Quyen Nguyen, a University of Otago Finance PhD student, looked at how various aspects of New Zealand’s economy, financial system and environment could be more effectively modelled to improve MfE policy.
“Using a complex systems approach, the models we developed aimed to better understand the cumulative impacts of multiple policies and stressors on the environment and people. As an example, we developed a simulation model that explored the on-farm adoption of new practices in New Zealand. Each farmer was modelled as a separate agent within neighbourhood and social networks. Each farm was modelled to be at a different life-cycle stage, producing either sheep, beef, dairy, or forestry products, with different decision-making strategies. We would like to extend a huge thank you to the MfE, especially senior analyst Jack Bisset, for their support and guidance throughout our internship.”
Analysis of a complex organisation’s carbon footprint – Te Pūnaha Matatini
Two of our interns analysed data on Te Pūnaha Matatini’s carbon emissions over the past few years to better understand our past and current performance in this area.
Ebba Olsen, a University of Auckland Bachelor of Science student majoring in Mathematics and Logic and Computation, and Kahu Te Kani, a University of Canterbury Bachelor of Science graduate with a major in Mathematics and Economics, produced a detailed report that will be used to guide future Te Pūnaha Matatini decisions regarding the need for staff to fly in particular.
“As with any organisation we could lower our CO2 emissions if we simply flew less,” wrote Ebba and Kahu. “We could hold more meetings remotely, for example over Skype, or use other more environmentally-friendly modes of transportation – if travelling is absolutely necessary. However, an obvious hurdle in using these other modes of transportation is the lack of efficient inter-city transport options across New Zealand.”
Ebba’s and Kahu’s internship supervisor, Te Pūnaha Matatini Director Shaun Hendy, is a well-known advocate for flying less to reduce our impact on the climate, and has written extensively on the subject.
“We would encourage other organisations to conduct a similar analysis of their CO2 emissions and to reduce them where possible,” said Shaun.
Creating an app to enrich the network visualisation experience – Nebula Data
Shih-Hao (Samuel) Chen, a University of Auckland Bachelor of Engineering study majoring in software engineering, worked with Te Pūnaha Matatini start-up Nebula Data during his summer internship.
The main objective of this project was to develop an application that would provide analysts with an enhanced way to see (visualise) networks.
“Networks arise in all shapes and forms in our everyday lives,” said Samuel. “However, [their features] are challenging to interpret, and transforming the dataset into a useful visualisation relies on inflexible third-party applications. We wanted to build a supportive, customisable tool that would enable data analysts to uncover new observations.”
Further details about individual and team projects
Following the completion of their placements, some of our interns wrote about their experiences and their detailed reports are available on Te Pūnaha Matatini’s website. Read more about the work of Shnece, Ellena and Quyen with MfE, Kahu and Ebba with Te Pūnaha Matatini, and Samuel with Nebula Data.
NEW RESEARCH — LINK TO FULL PDF HERE
5 June 2020
Probability of elimination for COVID-19 in Aotearoa New Zealand
- Our model of COVID-19 spread estimates that after 2-3 weeks of no new reported cases, there is a 95% probability that COVID-19 has been eliminated in New Zealand.
- A 95% probability of elimination is achieved after 10 consecutive days with no new reported cases under an optimistic scenario with high detection of clinical cases, and after 22 days under a more pessimistic scenario with low case detection.
New research published in the journal Education Sciences suggests that women remain disproportionately under-represented in senior academic positions within New Zealand universities.
The study has shown that from 2012 to 2017 there was little if any improvement in gender parity in senior roles at all eight or our universities – the University of Auckland, Auckland University of Technology, University of Waikato, Massey University, Victoria University of Wellington, University of Canterbury, Lincoln University and University of Otago.
Existing gender diversity programmes appear to have had limited impact
“We’re still seeing an absence of women at the higher levels of academic employment across New Zealand universities,” says the study’s lead author Dr Leilani Walker, Te Pūnaha Matatini Associate Investigator.
“There are disproportionately fewer women in senior lecturer, professor positions and so forth, and this is in spite of various programmes that have been developed to try to improve the situation. Based on the data we have, it looks like women are proceeding up the academic promotion ladder at a slower rate than their male colleagues.”
Most of our universities, except for the University of Canterbury and Lincoln University, had equitable proportions of women in their academic work forces in 2017. However, the study found that men dominated the more senior employment roles, making up 64-69% of Associate Professors/Heads of Department and 74%-81% of Professors/Deans – from 2012 to 2017.
Consistent with previous research, gender disparities in senior university roles within New Zealand could not be explained by male and female age difference distributions.
Potential need for institutions to review their promotion processes
These findings may provide a timely opportunity for New Zealand’s academic institutions to review and update their processes around hiring and promotion, says Dr Walker.
“We have a variety of programmes at New Zealand universities that try and help promote the careers of women into more senior positions, but it’s not really apparent in our minds whether they work,” Dr Walker says.
“We also question the extent to which just increasing the number of people present can create a culture change. Should we instead be starting to look at ways of engendering a culture tilt, rather than just getting more bodies in the room?”
“Perhaps we should be looking at existing models being used to judge success,” says Dr Walker. “The careers of female academics are often disrupted by life’s other priorities – for example, parental leave or to care for parents – and such interruptions can impact their research performance. If New Zealand universities continue to measure academic success based on the assumption of a linear, straight-forward career path, then any deviations will continue to disadvantage women.”
About the study authors
Dr Walker’s co-authors on this paper are all investigators at Te Pūnaha Matatini. They include Dr Tara McAllister (Te Aitanga ā Māhaki, Ngāti Porou), Research Fellow, School of Biological Sciences at the University of Auckland, Dr Isabelle Sin, Research Fellow, Motu Economic and Public Policy Research in Wellington, Associate Professor Cate Macinnis-Ng, School of Biological Sciences at the University of Auckland, and Kate Hannah, Deputy Director, Equity & Diversity Te Pūnaha Matatini.
Feature photo by Clay Banks on Unsplash.
NEW RESEARCH — LINK TO FULL PDF HERE
22 May 2020
Effective reproduction number for COVID-19 in Aotearoa New Zealand
- The effective reproduction number, Reff, is the average number of secondary cases infected by a primary case, a key measure of the transmission potential for a disease.
- Compared to many countries, New Zealand has had relatively few COVID-19 cases, many of which were caused by infections acquired overseas. This makes it difficult to use standard methods to estimate Reff.
- We use a stochastic model to simulate COVID-19 spread in New Zealand, and report the values of Reff from simulations that gave best fit to case data.
- We estimate that New Zealand had an effective reproduction number Reff = 1.8 for COVID-19 transmission prior to moving into Alert Level 4 on March 25 and that after moving into Alert level 4 this was reduced to Reff = 0.35.
- Our estimate Reff = 1.8 for reproduction number before Alert Level 4, is relatively low compared to other countries. This could be due, in part, to measures put in place in early- to mid-March, including: the cancellation of mass gatherings, the isolation of international arrivals, and employees being encouraged to work from home.
Most high achieving female students studying physics at university choose to discontinue physics as a core subject, not because they aren’t good at physics, but because they pursue further study in the life sciences.
This is one of the key findings of a paper published in PLoS One co-authored by Te Pūnaha Matatini researchers Steven Turnbull, Dr Dion O’Neale and Dr Kirsten Locke, and colleague Dr Frédérique Vanholsbeeck, all from the University of Auckland.
“We found that the majority of high achieving female physics students were actually studying physics for life sciences, which is needed for medicine and bioscience, and not actually for core physics,” says lead author Steven Turnbull, Te Pūnaha Matatini PhD student in the University of Auckland’s Faculty of Education and Social Work.
“More importantly, of those students who do pursue further study in physics, we see higher attrition rates for female students after controlling for achievement level, with the exception of higher achievers.”
“The implications of this are potentially career-limiting for women,” says Dr Kirsten Locke, Te Pūnaha Matatini investigator at the University of Auckland’s Faculty of Education and Social Work.
“Higher achieving women are tending to opt for physics engagement strongly associated with specific career pathways, in ways that differ from their male counterparts”.
Sociological methods uncover reasons behind gender difference
It is well known that female students are under-represented in university physics. However, the reasons for this are not so well understood.
“Importantly, our findings debunk any kind of idea that there’s a lack of high achieving female physics students out there. It’s not that they aren’t doing well in physics or aren’t interested in physics, because they are,” says Dr Dion O’Neale, Te Pūnaha Matatini Principal Investigator in the University of Auckland’s Department of Physics.
One of the unique aspects of this study was the combination of sociological methods (Pierre Bourdieu theory) and quantitative network analysis to understand the contexts in which students were making enrolment decisions.
Out now! @turdbull & I asked the ghost of Pierre Bourdieu why there are so few women in physics & where they go when they leave. Then we wrote about it with @FredVanH & Kirsten Locke. Read it here: https://t.co/p5VPNkHO0v
— Dion O’Neale (@droneale) September 13, 2019
“Using these tools to frame the results gives one the chance to come up with hypotheses [explanations] as to why things are a particular way or mechanisms for taking the next step,” says O’Neale. “[From a scientist’s perspective], you’ve got something that you can start to test, as opposed to just saying yeah sure there aren’t many women in physics.”
In terms of their data set, the researchers analysed administrative data from 8,905 students enrolled in University of Auckland undergraduate physics courses from 2009 to 2014.
Implications for New Zealand’s education system
Turnbull says the study’s findings have implications for the New Zealand education system, particularly with respect to the way in which physics is presented to students at school.
“We would suggest that work to address gender disparities in physics also needs to be conducted before university level, even as far down as when students start forming their academic identity around 10 or 11 years old. Most importantly, we need to shift attitudes, both inside physics and in society as a whole, so that all students feel like physics is a field where they belong and can contribute.”
The Head of Physics at the University of Auckland, Prof Richard Easther, said he was excited that his Department had hosted this work.
Easther said it had an immediate impact locally as, “It helps us to make evidence-based changes to our own practice, and the ways we present our subject to students.”
Of note, the Physics Department at the University of Auckland was recently recognised by the Astronomical Society of Australia with a Silver Pleiades accreditation for its progress toward building a culture of equity, diversity, and inclusion.
NEW RESEARCH — LINK TO FULL PDF HERE
15 May 2020
A structured model for COVID-19 spread: Modelling age and healthcare inequities
- We develop a structured model to look at the spread of COVID-19 in different groups within the population. We examine two case studies: the effect of control scenarios aimed at particular age groups (e.g. school closures) and the effect of inequitable access to healthcare and testing. These scenarios illustrate how such evidence could be used to inform specific policy interventions.
- An increase in contact rates among children, which might result from reopening schools, is on its own unlikely to significantly increase the number of cases. However, if this change in turn causes a change in adult behaviour, for example increased contacts among parents, it could have a much bigger effect.
- We also consider scenarios where outbreaks occur undetected in sectors of the community with less access to healthcare. We find that the lower the contact rate between groups with differing access to healthcare, the longer it will take before any outbreaks are detected in any groups who experience unequitable access to healthcare, which in Aotearoa New Zealand includes Māori and Pacific peoples.
- Well-established evidence for health inequities, particularly in accessing primary healthcare and testing, indicates that Māori and Pacific communities in Aotearoa New Zealand are at higher risk of undetected outbreaks. The government should ensure that the healthcare needs of Māori and Pacific communities with respect to COVID-19 are being met equitably.
A New Zealand-specific interactive epidemic simulation app developed by Dr Audrey Lustig, Associate Investigator at Te Pūnaha Matatini, and hosted by the University of Auckland’s Centre for eResearch, has just been released.
Called the COVID-19 Take Control simulator, the app illustrates the effects of hygiene and physical distancing measures that all Kiwis are undertaking to control the spread of COVID-19. One of the app’s key features is that it allows the user to see the effects higher and lower collective cooperation with policies aimed at breaking the chain of transmission.
Try it out now! Check out the app here.