Rachelle N Binny

• BSc (Hons), PhD in Mathematics
• PostDoc Position at Manaaki Whenua - Landcare Research

Toxoplasma gondii is one of the world’s most prevalent parasites and has significant impacts on the health of humans, domestic animals and wildlife. In New Zealand’s rural environments, T. gondii creates economic losses for the farming industry and threatens vulnerable native avifauna and marine mammals. Predator control of rodents and feral cats h...

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 hel...

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...

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 p...

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-t...

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, R t , during Aotearoa New Zealand’s August 2021 outbreak of the Delta variant of SARS-CoV-2, by fitting the publicly available Ep...

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 d...

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,...

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...

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 traci...

In ‘Government mandated lockdowns do not reduce COVID-19 deaths: implications for evaluating the stringent New Zealand response’ (New Zealand Economic Papers, 2020), Gibson claims that ‘Lockdowns do not reduce COVID-19 deaths’ on the basis of an instrument variable linear regression on county-level cross-sectional data in the United States. Here we...

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 u...

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 t...

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 su...

Invasive mammalian herbivores can have significant unwanted impacts on indigenous ecosystems and production landscapes. Their impacts are often mitigated using sustained lethal control or eradication. If eradication is the chosen option, it is critical to confirm where the pest population is distributed and prove that eradication has been achieved...

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. This workforce is rightly b...

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 re...

Kererū declined rapidly following European settlement in New Zealand, and they remain at a reduced density. We assessed three sources of information to test the hypothesis that predation by introduced mammals and abundance of food resources are the two major factors determining kererū abundance across New Zealand. First, we reviewed the literature...

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 d...

Models of contact tracing often over-simplify the effects of quarantine and isolation on disease transmission. We develop a model that allows us to investigate the importance of these factors in reducing the effective reproduction number. We show that the reduction in onward transmission during quarantine and isolation has a bigger effect than trac...

1. The eradication of invasive small mammal pests is a challenging undertaking, but is needed in many areas of the world to preserve biodiversity. Trapping and poisonous baits are some of the most widespread tools for pest control. Most of the models used to make predictions and to design effective trapping protocols assume that pest populations ar...

We use a stochastic branching process model, structured by age and level of healthcare access, to look at the heterogeneous spread of COVID-19 within a population. We examine the effect of control scenarios targeted at particular groups, such as school closures or social distancing by older people. Although we currently lack detailed empirical data...

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 outbre...

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 cont...

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. Math...

Invasions by alien pest species contribute heavily to global biodiversity decline, with invasive mammals having some of the greatest impacts on endemic biota. Pest management within ecological restorations is therefore critical for conserving threatened biota. Coordinating restoration efforts at global scale requires evidence of the relative effica...

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 specialis...

Aims We aim to quantify differences in clinical outcomes from COVID-19 infection by ethnicity 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 odd...

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

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...

Local interactions among individual members of a population can generate intricate small-scale spatial structure, which can strongly influence population dynamics. The two-way interplay between local interactions and population dynamics is well understood in the relatively simple case where the population occupies a fixed domain with a uniform aver...

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 tracin...

On 25th March 2020, New Zealand implemented stringent lockdown measures (Alert Level 4, in a four-level alert system) with the goal of eliminating community transmission of COVID-19. Once new cases are no longer detected over consecutive days, the probability of elimination is an important measure for informing decisions on when certain COVID-19 re...

The effective reproduction number, R eff , 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 m...

Background 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 dif...

In an attempt to maintain elimination of COVID-19, the New Zealand government has closed the border to everyone except citizens and residents. All arrivals are required to spend 14 days in government-managed isolation/quarantine and to be tested for COVID-19 on day 3 and on day 12 of their stay. We model the testing, isolation and potential transmi...

Contact tracing is a key tool in the fight against COVID-19. Its effectiveness depends on the ability of traced contacts to quarantine and then isolate on symptom onset. We show that these factors crucially affect the reduction in the effective transmission number, but make it difficult to measure the effectiveness of the system using routinely col...

Resource pulses are widespread phenomena in diverse ecosystems. Irruptions of generalist consumers and corresponding generalist predators often follow such resource pulses. This can have severe implications on the ecosystem and also on the spread of diseases or on regional famines. Suitable management strategies are necessary to deal with these sys...

We use stochastic branching process model, structured by age and level of healthcare access, to look at the heterogeneous spread of COVID-19 within a population. We examine the effect of control scenarios targeted at particular groups, such as school closures or social distancing by older people. Although we currently lack detailed empirical data a...

The effective reproduction number, R eff , is an important measure of transmission potential in the modelling of epidemics. It measures the average number of people that will be infected by a single contagious individual. A value of R eff > 1 suggests that an outbreak will occur, while R eff < 1 suggests the virus will die out. In response to the C...

There is limited evidence as to how COVID-19 infection fatality rates (IFR) may vary by ethnicity. We combine demographic and health data for ethnic groupings in Aotearoa New Zealand with international data on IFR for different age groups to estimate inequities in IFR by ethnicity. We find that, if age is the dominant factor determining IFR, estima...

While case numbers remain low, population-wide control methods combined with efficient tracing, testing, and case isolation, offer the opportunity for New Zealand to contain and eliminate COVID-19. We use a stochastic model to investigate containment and elimination scenarios for COVID-19 in New Zealand, as the country considers the exit from its f...

Ephemeral wetlands or kettle holes contain an often unique biodiversity of flora and fauna. In New Zealand, they can be an important breeding ground for iconic taonga species such as kakī/black stilt. Understanding the possible effects of climate change on the holes is a challenge as there is often limited information on the local hydrology, restri...

Local interactions among individual members of a population can generate intricate spatial structure, which can strongly influence population dynamics. The two-way interplay between local interactions and population dynamics is well understood in the relatively simple case where the population occupies a fixed domain with a uniform average density....

Herd formation in animal populations, for example to escape a predator or coordinate feeding, is a widespread phenomenon. Understanding which interactions between individual animals are important for generating such emergent self-organisation has been a key focus of ecological and mathematical research. Here we show the relationship between the alg...

We define an ecosanctuary in a New Zealand context as ‘a project larger than 25 ha implementing multi-species, pest mammal control for ecosystem recovery objectives, and with substantial community involvement’. We present attributes of 84 projects meeting this definition, including three lacustrine islands, 16 marine islands, seven ring-fenced ecos...

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 qua...

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 qua...

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. W...

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....

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....

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 abili...

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...

Worldwide, introduced vertebrate pests impact primary production, native biodiversity, and human health. In New Zealand, extensive pest control (~10 million ha) is undertaken to protect native biota and to prevent losses to the primary sector from wildlife vectors of bovine tuberculosis (TB), primarily possums (Trichosurus vulpecula). Control is co...

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 rang...

The ability of cells to undergo collective movement plays a fundamental role in tissue repair, development and cancer. Interactions occurring at the level of individual cells may lead to the development of spatial structure which will affect the dynamics of migrating cells at a population level. Models that try to predict population-level behaviour...

In general, prokaryotes are considered to be single-celled organisms that lack internal membrane-bound organelles. However, many bacteria produce proteinaceous microcompartments that serve a similar purpose; that is to concentrate specific enzymatic reactions together or to shield the wider cytoplasm from toxic metabolic intermediates. In this work...