School of BioSciences - Research Publications

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    COVID-19 vaccine coverage targets to inform reopening plans in a low incidence setting
    Conway, E ; Walker, CR ; Baker, C ; Lydeamore, MJ ; Ryan, GE ; Campbell, T ; Miller, JC ; Rebuli, N ; Yeung, M ; Kabashima, G ; Geard, N ; Wood, J ; McCaw, JM ; McVernon, J ; Golding, N ; Price, DJ ; Shearer, FM (ROYAL SOC, 2023-08-30)
    Since the emergence of SARS-CoV-2 in 2019 through to mid-2021, much of the Australian population lived in a COVID-19-free environment. This followed the broadly successful implementation of a strong suppression strategy, including international border closures. With the availability of COVID-19 vaccines in early 2021, the national government sought to transition from a state of minimal incidence and strong suppression activities to one of high vaccine coverage and reduced restrictions but with still-manageable transmission. This transition is articulated in the national 're-opening' plan released in July 2021. Here, we report on the dynamic modelling study that directly informed policies within the national re-opening plan including the identification of priority age groups for vaccination, target vaccine coverage thresholds and the anticipated requirements for continued public health measures-assuming circulation of the Delta SARS-CoV-2 variant. Our findings demonstrated that adult vaccine coverage needed to be at least 60% to minimize public health and clinical impacts following the establishment of community transmission. They also supported the need for continued application of test-trace-isolate-quarantine and social measures during the vaccine roll-out phase and beyond.
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    Defining and evaluating predictions of joint species distribution models
    Wilkinson, DP ; Golding, N ; Guillera-Arroita, G ; Tingley, R ; McCarthy, MA ; Freckleton, R (WILEY, 2021-03)
    Abstract Joint species distribution models (JSDMs) simultaneously model the distributions of multiple species, while accounting for residual co‐occurrence patterns. Despite increasing adoption of JSDMs in the literature, the question of how to define and evaluate JSDM predictions has only begun to be explored. We define four different JSDM prediction types that correspond to different aspects of species distribution and community assemblage processes. Marginal predictions are environment‐only predictions akin to predictions from single‐species models; joint predictions simultaneously predict entire community assemblages; and conditional marginal and conditional joint predictions are made at the species or assemblage level, conditional on the known occurrence state of one or more species at a site. We define five different classes of metrics that can be used to evaluate these types of predictions: threshold‐dependent, threshold‐independent, community dissimilarity, species richness and likelihood metrics. We illustrate different prediction types and evaluation metrics using a case study in which we fit a JSDM to a frog occurrence dataset collected in Melbourne, Australia. Joint species distribution models present opportunities to investigate the facets of species distribution and community assemblage processes that are not possible to explore with single‐species models. We show that there are a variety of different metrics available to evaluate JSDM predictions, and that choice of prediction type and evaluation metric should closely match the questions being investigated.
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    Modelling temperature-driven changes in species associations across freshwater communities
    Perrin, SW ; van der Veen, B ; Golding, N ; Finstad, AG (WILEY, 2022-01)
    Due to global climate change-induced shifts in species distributions, estimating changes in community composition through the use of Species Distribution Models has become a key management tool. Being able to determine how species associations change along environmental gradients is likely to be pivotal in exploring the magnitude of future changes in species' distributions. This is particularly important in connectivity-limited ecosystems, such as freshwater ecosystems, where increased human translocation is creating species associations over previously unseen environmental gradients. Here, we use a large-scale presence-absence dataset of freshwater fish from lakes across the Fennoscandian region in a Joint Species Distribution Model, to measure the effect of temperature on species associations. We identified a trend of negative associations between species tolerant of cold waters and those tolerant of warmer waters, as well as positive associations between several more warm-tolerant species, with these associations often shifting depending on local temperatures. Our results confirm that freshwater ecosystems can expect to see a large-scale shift towards communities dominated by more warm-tolerant species. While there remains much work to be done to predict exactly where and when local extinctions may take place, the model implemented provides a starting-point for the exploration of climate-driven community trends. This approach is especially informative in regards to determining which species associations are most central in shaping future community composition, and which areas are most vulnerable to local extinctions.
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    Establishment of Wolbachia Strain wAlbB in Malaysian Populations of Aedes aegypti for Dengue Control
    Nazni, WA ; Hoffmann, AA ; NoorAfizah, A ; Cheong, YL ; Mancini, MV ; Golding, N ; Kamarul, GMR ; Arif, MAK ; Thohir, H ; NurSyamimi, H ; ZatilAqmar, MZ ; NurRuqqayah, M ; NorSyazwani, A ; Faiz, A ; Irfan, F-RMN ; Rubaaini, S ; Nuradila, N ; Nizam, NMN ; Irwan, SM ; Endersby-Harshman, NM ; White, VL ; Ant, TH ; Herd, CS ; Hasnor, AH ; AbuBakar, R ; Hapsah, DM ; Khadijah, K ; Kamilan, D ; Lee, SC ; Paid, YM ; Fadzilah, K ; Topek, O ; Gill, BS ; Lee, HL ; Sinkins, SP (CELL PRESS, 2019-12-16)
    Dengue has enormous health impacts globally. A novel approach to decrease dengue incidence involves the introduction of Wolbachia endosymbionts that block dengue virus transmission into populations of the primary vector mosquito, Aedes aegypti. The wMel Wolbachia strain has previously been trialed in open releases of Ae. aegypti; however, the wAlbB strain has been shown to maintain higher density than wMel at high larval rearing temperatures. Releases of Ae. aegypti mosquitoes carrying wAlbB were carried out in 6 diverse sites in greater Kuala Lumpur, Malaysia, with high endemic dengue transmission. The strain was successfully established and maintained at very high population frequency at some sites or persisted with additional releases following fluctuations at other sites. Based on passive case monitoring, reduced human dengue incidence was observed in the release sites when compared to control sites. The wAlbB strain of Wolbachia provides a promising option as a tool for dengue control, particularly in very hot climates.
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    Data Integration for Large-Scale Models of Species Distributions
    Isaac, NJB ; Jarzyna, MA ; Keil, P ; Dambly, LI ; Boersch-Supan, PH ; Browning, E ; Freeman, SN ; Golding, N ; Guillera-Arroita, G ; Henrys, PA ; Jarvis, S ; Lahoz-Monfort, J ; Pagel, J ; Pescott, OL ; Schmucki, R ; Simmonds, EG ; O'Hara, RB (ELSEVIER SCIENCE LONDON, 2020-01)
    With the expansion in the quantity and types of biodiversity data being collected, there is a need to find ways to combine these different sources to provide cohesive summaries of species' potential and realized distributions in space and time. Recently, model-based data integration has emerged as a means to achieve this by combining datasets in ways that retain the strengths of each. We describe a flexible approach to data integration using point process models, which provide a convenient way to translate across ecological currencies. We highlight recent examples of large-scale ecological models based on data integration and outline the conceptual and technical challenges and opportunities that arise.
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    steps: Software for spatially and temporally explicit population simulations
    Visintin, C ; Briscoe, NJ ; Woolley, SNC ; Lentini, PE ; Tingley, R ; Wintle, BA ; Golding, N ; Graham, L (WILEY, 2020-04)
    Abstract Species population dynamics are driven by spatial and temporal changes in the environment, anthropogenic activities and conservation management actions. Understanding how populations will change in response to these drivers is fundamental to a wide range of ecological applications, but there are few open‐source software options accessible to researchers and managers that allow them to predict these changes in a flexible and transparent way. We introduce an open‐source, multi‐platform r package, steps, that models spatial changes in species populations as a function of drivers of distribution and abundance, such as climate, disturbance, landscape dynamics and species ecological and physiological requirements. To illustrate the functionality of steps, we model the population dynamics of the greater glider Petauroides volans, an arboreal Australian mammal. We demonstrate how steps can be used to simulate population responses of the glider to forest dynamics and management with the types of data commonly used in ecological analyses. steps expands on the features found in existing software packages, can easily incorporate a range of spatial layers (e.g. habitat suitability, vegetation dynamics and disturbances), facilitates integrated and transparent analyses within a single platform and produces interpretable outputs of changes in species' populations through space and time. Further, steps offers both ready‐to‐use, built‐in functionality, as well as the ability for advanced users to define their own modules for custom analyses. Thus, we anticipate that steps will be of significant value to environment and wildlife managers and researchers from a broad range of disciplines.
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    Reconstructing the early global dynamics of under-ascertained COVID-19 cases and infections
    Russell, T ; Russell, T ; Golding, N ; Hellewell, J ; Abbott, S ; Wright, L ; Pearson, C ; Pearson, C ; Zandvoort, KV ; Jarvis, C ; Gibbs, H ; Liu, Y ; Eggo, R ; Edmunds, J ; Kucharski, A ( 2020)

    Background

    Asymptomatic or subclinical SARS-CoV-2 infections are often unreported, which means that confirmed case counts may not accurately reflect underlying epidemic dynamics. Understanding the level of ascertainment (the ratio of confirmed symptomatic cases to the true number of symptomatic individuals) and undetected epidemic progression is crucial to informing COVID-19 response planning, including the introduction and relaxation of control measures. Estimating case ascertainment over time allows for accurate estimates of specific outcomes such as seroprevalence, which is essential for planning control measures.

    Methods

    Using reported data on COVID-19 cases and fatalities globally, we estimated the proportion of symptomatic cases (i.e. any person with any of fever >= 37.5°C, cough, shortness of breath, sudden onset of anosmia, ageusia or dysgeusia illness) that were reported in 210 countries and territories, given those countries had experienced more than ten deaths. We used published estimates of the baseline case fatality ratio (CFR), which was adjusted for delays and under-ascertainment, then calculated the ratio of this baseline CFR to an estimated local delay-adjusted CFR to estimate the level of under-ascertainment in a particular location. We then fit a Bayesian Gaussian process model to estimate the temporal pattern of under-ascertainment.

    Results

    Based on reported cases and deaths, we estimated that, during March 2020, the median percentage of symptomatic cases detected across the 84 countries which experienced more than ten deaths ranged from 2.4% (Bangladesh) to 100% (Chile). Across the ten countries with the highest number of total confirmed cases as of 6th July 2020, we estimated that the peak number of symptomatic cases ranged from 1.4 times (Chile) to 18 times (France) larger than reported. Comparing our model with national and regional seroprevalence data where available, we find that our estimates are consistent with observed values. Finally, we estimated seroprevalence for each country. As of the 7th June, our seroprevalence estimates range from 0% (many countries) to 13% (95% CrI: 5.6% – 24%) (Belgium).

    Conclusions

    We found substantial under-ascertainment of symptomatic cases, particularly at the peak of the first wave of the SARS-CoV-2 pandemic, in many countries. Reported case counts will therefore likely underestimate the rate of outbreak growth initially and underestimate the decline in the later stages of an epidemic. Although there was considerable under-reporting in many locations, our estimates were consistent with emerging serological data, suggesting that the proportion of each country’s population infected with SARS-CoV-2 worldwide is generally low.

    Funding

    Wellcome Trust, Bill & Melinda Gates Foundation, DFID, NIHR, GCRF, ARC.
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    Factors influencing the residency of bettongs using one-way gates to exit a fenced reserve
    Moyses, J ; Hradsky, B ; Tuft, K ; Moseby, K ; Golding, N ; Wintle, B (Wiley, 2020-11)
    Understanding the conditions under which small native Australian mammals can persist in the presence of introduced predators remains a key challenge to conservation ecologists. Bettong‐specific one‐way gates were used at a predator‐free reserve in South Australia to allow the burrowing bettong (Bettongia lesueur) – a small potoroid, listed as ‘vulnerable’ nationally – to disperse out of the reserve. We conducted a field experiment to explore the conditions affecting residence time of bettongs that left the reserve. We monitored bettong and mammalian predator activity outside the fence using track surveys across 18 sites over two seasons. We examined the effect of supplementary feeding as a strategy for increasing residence time, as well as the influence of predator presence and habitat quality, using linear mixed models. Bettong activity was positively associated with supplementary feeding, midstorey vegetation cover and shelter availability. After gates were closed, bettong activity near gates declined to almost zero the following weeks, likely either due to death from predation or due to movement away from the sites. To a small extent, mammalian predators were more likely to be present at sites with high bettong activity. Further research on conditions to support persistence of burrowing bettongs and other small mammals, including understanding minimum necessary predator control effort, is required before successful establishment of populations outside of fences can occur.
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    Assessing biophysical and socio-economic impacts of climate change on regional avian biodiversity
    Kapitza, S ; Van Ha, P ; Kompas, T ; Golding, N ; Cadenhead, NCR ; Bal, P ; Wintle, BA (NATURE PORTFOLIO, 2021-02-08)
    Climate change threatens biodiversity directly by influencing biophysical variables that drive species' geographic distributions and indirectly through socio-economic changes that influence land use patterns, driven by global consumption, production and climate. To date, no detailed analyses have been produced that assess the relative importance of, or interaction between, these direct and indirect climate change impacts on biodiversity at large scales. Here, we apply a new integrated modelling framework to quantify the relative influence of biophysical and socio-economically mediated impacts on avian species in Vietnam and Australia and we find that socio-economically mediated impacts on suitable ranges are largely outweighed by biophysical impacts. However, by translating economic futures and shocks into spatially explicit predictions of biodiversity change, we now have the power to analyse in a consistent way outcomes for nature and people of any change to policy, regulation, trading conditions or consumption trend at any scale from sub-national to global.
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    Past and future spread of the arbovirus vectors Aedes aegypti and Aedes albopictus (vol 4, pg 854, 2019)
    Kraemer, MUG ; Reiner, RC ; Brady, OJ ; Messina, JP ; Gilbert, M ; Pigott, DM ; Yi, D ; Johnson, K ; Earl, L ; Marczak, LB ; Shirude, S ; Weaver, ND ; Bisanzio, D ; Perkins, TA ; Lai, S ; Lu, X ; Jones, P ; Coelho, GE ; Carvalho, RG ; Van Bortel, W ; Marsboom, C ; Hendrickx, G ; Schaffner, F ; Moore, CG ; Nax, HH ; Bengtsson, L ; Wetter, E ; Tatem, AJ ; Brownstein, JS ; Smith, DL ; Lambrechts, L ; Cauchemez, S ; Linard, C ; Faria, NR ; Pybus, OG ; Scott, TW ; Liu, Q ; Yu, H ; Wint, GRW ; Hay, SI ; Golding, N (NATURE PUBLISHING GROUP, 2019-05)
    This Article was mistakenly not made Open Access when originally published; this has now been amended, and information about the Creative Commons Attribution 4.0 International License has been added into the 'Additional information' section.