Estimating the risk of SARS-CoV-2 infection in New Zealand border arrivals.

Background: Travel restrictions and border controls were used extensively during the COVID-19 pandemic. However, the processes for making robust evidence-based risk assessments of source countries to inform border control policies was in many cases very limited.

Methods: Between April 2020 and February 2022, all international arrivals to New Zealand were required to spend 14 days in government-managed quarantine facilities and were tested at least twice.

Optimising Control Device Luring Strategies for Invasive Predator Control: A Modelling Approach.

Invasive predators pose a serious threat to native biodiversity, with trapping being one of several methods developed to manage and monitor their populations. Many individuals in these predator populations have been found to display trap-shyness, which hinders eradication and results in inaccurate estimates of population size. Lures are used to help overcome trap-shyness by increasing the probability of interaction with the device, but the extent of trap-shyness in wild populations, and the best timing for the introduction of a new lure or combination of lures, are uncertain.

Emerging advances in biosecurity to underpin human, animal, plant, and ecosystem health.

One Biosecurity is an interdisciplinary approach to policy and research that builds on the interconnections between human, animal, plant, and ecosystem health to effectively prevent and mitigate the impacts of invasive alien species. To support this approach requires that key cross-sectoral research innovations be identified and prioritized. Following an interdisciplinary horizon scan for emerging research that underpins One Biosecurity, four major interlinked advances were identified: implementation of new surveillance technologies adopting state-of-the-art sensors connected to the Internet of Things, deployable handheld molecular and genomic tracing tools, the incorporation of wellbeing and diverse human values into biosecurity decision-making, and sophisticated socio-environmental models and data capture.

Modelling Aotearoa New Zealand's COVID-19 protection framework and the transition away from the elimination strategy.

For the first 18 months of the COVID-19 pandemic, New Zealand used an elimination strategy to suppress community transmission of SARS-CoV-2 to zero or very low levels. In late 2021, high vaccine coverage enabled the country to transition away from the elimination strategy to a mitigation strategy. However, given negligible levels of immunity from prior infection, this required careful planning and an effective public health response to avoid uncontrolled outbreaks and unmanageable health impacts.

Using mechanistic model-based inference to understand and project epidemic dynamics with time-varying contact and vaccination rates.

Epidemiological models range in complexity from relatively simple statistical models that make minimal assumptions about the variables driving epidemic dynamics to more mechanistic models that include effects such as vaccine-derived and infection-derived immunity, population structure and heterogeneity. The former are often fitted to data in real-time and used for short-term forecasting, while the latter are more suitable for comparing longer-term scenarios under differing assumptions about control measures or other factors. Here, we present a mechanistic model of intermediate complexity that can be fitted to data in real-time but is also suitable for investigating longer-term dynamics.

Real-time estimation of the effective reproduction number of SARS-CoV-2 in Aotearoa New Zealand.

During an epidemic, real-time estimation of the effective reproduction number supports decision makers to introduce timely and effective public health measures. We estimate the time-varying effective reproduction number, , during Aotearoa New Zealand's August 2021 outbreak of the Delta variant of SARS-CoV-2, by fitting the publicly available EpiNow2 model to New Zealand case data. While we do not explicitly model non-pharmaceutical interventions or vaccination coverage, these two factors were the leading drivers of variation in transmission in this period and we describe how changes in these factors coincided with changes in .

Predicting elimination of evolving virus variants.

As the SARS-CoV-2 virus spreads around the world new variants are appearing regularly. Although some countries have achieved very swift and successful vaccination campaigns, on a global scale the vast majority of the population is unvaccinated and new variants are proving more resistant to the current set of vaccines. We present a simple model of disease spread, which includes the evolution of new variants of a novel virus and varying vaccine effectiveness to these new strains.

Sensitivity of Reverse Transcription Polymerase Chain Reaction Tests for Severe Acute Respiratory Syndrome Coronavirus 2 Through Time.

Background: Reverse transcription polymerase chain reaction (RT-PCR) tests are the gold standard for detecting recent infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Reverse transcription PCR sensitivity varies over the course of an individual's infection, related to changes in viral load. Differences in testing methods, and individual-level variables such as age, may also affect sensitivity.

An assessment of the potential impact of the Omicron variant of SARS-CoV-2 in Aotearoa New Zealand.

New Zealand delayed the introduction of the Omicron variant of SARS-CoV-2 into the community by the continued use of strict border controls through to January 2022. This allowed time for vaccination rates to increase and the roll out of third doses of the vaccine (boosters) to begin. It also meant more data on the characteristics of Omicron became available prior to the first cases of community transmission.

Potential reduction in transmission of COVID-19 by digital contact tracing systems: a modelling study.

Background: Digital tools are being developed to support contact tracing as part of the global effort to control the spread of COVID-19. These include smartphone apps, Bluetooth-based proximity detection, location tracking and automatic exposure notification features. Evidence on the effectiveness of alternative approaches to digital contact tracing is so far limited.

A COVID-19 vaccination model for Aotearoa New Zealand.

We develop a mathematical model to estimate the effect of New Zealand's vaccine rollout on the potential spread and health impacts of COVID-19. The main purpose of this study is to provide a basis for policy advice on border restrictions and control measures in response to outbreaks that may occur during the vaccination roll-out. The model can be used to estimate the theoretical population immunity threshold, which represents a point in the vaccine rollout at which border restrictions and other controls could be removed and only small, occasional outbreaks would take place.

Effect of vaccination, border testing, and quarantine requirements on the risk of COVID-19 in New Zealand: A modelling study.

We couple a simple model of quarantine and testing strategies for international travellers with a model for transmission of SARS-CoV-2 in a partly vaccinated population. We use this model to estimate the risk of an infectious traveller causing a community outbreak under various border control strategies and different levels of vaccine coverage in the population. Results are calculated from N = 100,000 independent realisations of the stochastic model.

Early intervention is the key to success in COVID-19 control.

New Zealand responded to the COVID-19 pandemic with a combination of border restrictions and an Alert Level (AL) system that included strict stay-at-home orders. These interventions were successful in containing an outbreak and ultimately eliminating community transmission of COVID-19 in June 2020. The timing of interventions is crucial to their success.

Vaccination and testing of the border workforce for COVID-19 and risk of community outbreaks: a modelling study.

Throughout 2020 and the first part of 2021, Australia and New Zealand have followed a COVID-19 elimination strategy. Both countries require overseas arrivals to quarantine in government-managed facilities at the border. In both countries, community outbreaks of COVID-19 have been started via infection of a border worker.

Māori and Pacific people in New Zealand have a higher risk of hospitalisation for COVID-19.

Aims: We aim to quantify differences in clinical outcomes from COVID-19 infection in Aotearoa New Zealand by ethnicity and with a focus on risk of hospitalisation.

Methods: We used data on age, ethnicity, deprivation index, pre-existing health conditions and clinical outcomes on 1,829 COVID-19 cases reported in New Zealand. We used a logistic regression model to calculate odds ratios for the risk of hospitalisation by ethnicity.

Managing the risk of a COVID-19 outbreak from border arrivals.

In an attempt to maintain the elimination of COVID-19 in New Zealand, all international arrivals are required to spend 14 days in government-managed quarantine and to return a negative test result before being released. We model the testing, isolation and transmission of COVID-19 within quarantine facilities to estimate the risk of community outbreaks being seeded at the border. We use a simple branching process model for COVID-19 transmission that includes a time-dependent probability of a false-negative test result.

Model-free estimation of COVID-19 transmission dynamics from a complete outbreak.

New Zealand had 1499 cases of COVID-19 before eliminating transmission of the virus. Extensive contract tracing during the outbreak has resulted in a dataset of epidemiologically linked cases. This data contains useful information about the transmission dynamics of the virus, its dependence on factors such as age, and its response to different control measures.

How important is individual foraging specialisation in invasive predators for native-prey population viability?

Predation by invasive species is a major threat to the persistence of naïve prey. Typically, this negative effect is addressed by suppressing the population size of the invasive predator to a point where the predation pressure does not hinder the viability of the prey. However, this type of intervention may not be effective whenever a few specialised predators are the cause of the decline.

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

Aims: 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.

Methods: We combine existing demographic and health data for ethnic groups in New Zealand with international data on COVID-19 IFR for different age groups.

A concise guide to developing and using quantitative models in conservation management.

Quantitative models are powerful tools for informing conservation management and decision-making. As applied modeling is increasingly used to address conservation problems, guidelines are required to clarify the scope of modeling applications and to facilitate the impact and acceptance of models by practitioners. We identify three key roles for quantitative models in conservation management: (a) to assess the extent of a conservation problem; (b) to provide insights into the dynamics of complex social and ecological systems; and, (c) to evaluate the efficacy of proposed conservation interventions.

Optimal control of irrupting pest populations in a climate-driven ecosystem.

Irruptions of small consumer populations, driven by pulsed resources, can lead to adverse effects including the decline of indigenous species or increased disease spread. Broad-scale pest management to combat such effects benefits from forecasting of irruptions and an assessment of the optimal control conditions for minimising consumer abundance. We use a climate-based consumer-resource model to predict irruptions of a pest species () population in response to masting (episodic synchronous seed production) and extend this model to account for broad-scale pest control of mice using toxic bait.

Inferring parameters for a lattice-free model of cell migration and proliferation using experimental data.

Collective cell spreading takes place in spatially continuous environments, yet it is often modelled using discrete lattice-based approaches. Here, we use data from a series of cell proliferation assays, with a prostate cancer cell line, to calibrate a spatially continuous individual based model (IBM) of collective cell migration and proliferation. The IBM explicitly accounts for crowding effects by modifying the rate of movement, direction of movement, and the rate of proliferation by accounting for pair-wise interactions.

How Herbivore Browsing Strategy Affects Whole-Plant Photosynthetic Capacity.

If a browse damage index indicates that a tree has been 50% browsed by herbivores, does this mean half the leaves are entirely eaten or are all the leaves half eaten? Were the affected leaves old or young? Large or small? In sunshine or shade? Understanding what effect browsing will have on the photosynthetic capacity and the plant's survival ability clearly requires a greater understanding of browsing strategy across the canopy than can be given by a single index value. We developed stochastic models of leaf production, growth and consumption using data from kamahi (Weinmannia racemosa) trees in New Zealand which have been browsed by possums (Trichosurus vulpecula), to ascertain which of six feasible browsing strategies possums are most likely to be employing. We compared the area distribution of real fallen leaves to model output in order to select the best model, and used the model to predict the age distribution of leaves on the tree and thus infer its photosynthetic capability.

Collective Cell Behaviour with Neighbour-Dependent Proliferation, Death and Directional Bias.

Collective cell migration and proliferation are integral to tissue repair, embryonic development, the immune response and cancer. Central to collective cell migration and proliferation are interactions among neighbouring cells, such as volume exclusion, contact inhibition and adhesion. These individual-level processes can have important effects on population-level outcomes, such as growth rate and equilibrium density.

Spatial structure arising from neighbour-dependent bias in collective cell movement.

Mathematical models of collective cell movement often neglect the effects of spatial structure, such as clustering, on the population dynamics. Typically, they assume that individuals interact with one another in proportion to their average density (the mean-field assumption) which means that cell-cell interactions occurring over short spatial ranges are not accounted for. However, in vitro cell culture studies have shown that spatial correlations can play an important role in determining collective behaviour.