Integrated models, frameworks and decision support tools to guide management and planning in Northern Australia. Final report

[Extract] There is a lot of interest in developing northern Australia while also caring for the unique Australian landscape (Commonwealth of Australia 2015). However, trying to decide how to develop and protect at the same time can be a challenge. There are many modelling tools available to inform these decisions, including integrated models, frameworks, and decision support tools, but there are so many different kinds that it’s difficult to determine which might be best suited to inform different decisions. To support planning and development decisions across northern Australia, this project aimed to create resources to help end-users (practitioners) to assess: 1. the availability and suitability of particular modelling tools; and 2. the feasibility of using, developing, and maintaining different types of modelling tools

Key epidemiological drivers and impact of interventions in the 2020 SARS-CoV-2 epidemic in England.

We fitted a model of SARS-CoV-2 transmission in care homes and the community to regional surveillance data for England. Compared with other approaches, our model provides a synthesis of multiple surveillance data streams into a single coherent modeling framework, allowing transmission and severity to be disentangled from features of the surveillance system. Of the control measures implemented, only national lockdown brought the reproduction number (Rt eff) below 1 consistently; if introduced 1 week earlier, it could have reduced deaths in the first wave from an estimated 48,600 to 25,600 [95% credible interval (CrI): 15,900 to 38,400]. The infection fatality ratio decreased from 1.00% (95% CrI: 0.85 to 1.21%) to 0.79% (95% CrI: 0.63 to 0.99%), suggesting improved clinical care. The infection fatality ratio was higher in the elderly residing in care homes (23.3%, 95% CrI: 14.7 to 35.2%) than those residing in the community (7.9%, 95% CrI: 5.9 to 10.3%). On 2 December 2020, England was still far from herd immunity, with regional cumulative infection incidence between 7.6% (95% CrI: 5.4 to 10.2%) and 22.3% (95% CrI: 19.4 to 25.4%) of the population. Therefore, any vaccination campaign will need to achieve high coverage and a high degree of protection in vaccinated individuals to allow nonpharmaceutical interventions to be lifted without a resurgence of transmission

Evidence of initial success for China exiting COVID-19 social distancing policy after achieving containment.

Background: The COVID-19 epidemic was declared a Global Pandemic by WHO on 11 March 2020. By 24 March 2020, over 440,000 cases and almost 20,000 deaths had been reported worldwide. In response to the fast-growing epidemic, which began in the Chinese city of Wuhan, Hubei, China imposed strict social distancing in Wuhan on 23 January 2020 followed closely by similar measures in other provinces. These interventions have impacted economic productivity in China, and the ability of the Chinese economy to resume without restarting the epidemic was not clear. Methods: Using daily reported cases from mainland China and Hong Kong SAR, we estimated transmissibility over time and compared it to daily within-city movement, as a proxy for economic activity. Results: Initially, within-city movement and transmission were very strongly correlated in the five mainland provinces most affected by the epidemic and Beijing. However, that correlation decreased rapidly after the initial sharp fall in transmissibility. In general, towards the end of the study period, the correlation was no longer apparent, despite substantial increases in within-city movement. A similar analysis for Hong Kong shows that intermediate levels of local activity were maintained while avoiding a large outbreak. At the very end of the study period, when China began to experience the re-introduction of a small number of cases from Europe and the United States, there is an apparent up-tick in transmission. Conclusions: Although these results do not preclude future substantial increases in incidence, they suggest that after very intense social distancing (which resulted in containment), China successfully exited its lockdown to some degree. Elsewhere, movement data are being used as proxies for economic activity to assess the impact of interventions. The results presented here illustrate how the eventual decorrelation between transmission and movement is likely a key feature of successful COVID-19 exit strategies

Database of epidemic trends and control measures during the first wave of COVID-19 in mainland China.

OBJECTIVES: In this data collation study, we aimed to provide a comprehensive database describing the epidemic trends and responses during the first wave of coronavirus disease 2019 (COVID-19) throughout the main provinces in China. METHODS: From mid-January to March 2020, we extracted publicly available data regarding the spread and control of COVID-19 from 31 provincial health authorities and major media outlets in mainland China. Based on these data, we conducted descriptive analyses of the epidemic in the six most-affected provinces. RESULTS: School closures, travel restrictions, community-level lockdown, and contact tracing were introduced concurrently around late January but subsequent epidemic trends differed among provinces. Compared with Hubei, the other five most-affected provinces reported a lower crude case fatality ratio and proportion of critical and severe hospitalised cases. From March 2020, as the local transmission of COVID-19 declined, switching the focus of measures to the testing and quarantine of inbound travellers may have helped to sustain the control of the epidemic. CONCLUSIONS: Aggregated indicators of case notifications and severity distributions are essential for monitoring an epidemic. A publicly available database containing these indicators and information regarding control measures is a useful resource for further research and policy planning in response to the COVID-19 epidemic

Spatial scale and movement behaviour traits control the impacts of habitat fragmentation on individual fitness

1. Habitat fragmentation, that is the breaking apart of habitat, can occur at multiple spatial scales at the same time, as a result of different land uses. Individuals of most species spend different amounts of times moving in different modes, during which they cover different distances and experience different fitness impacts. The scale at which fragmentation occurs interacts with the distance that individuals move in a particular mode to affect an individual's ability to find habitat. However, there is little knowledge of the fitness consequences of different scales of fragmentation for individuals with different traits of movement behaviour. This is critical to understand the mechanisms of persistence of different species in fragmented landscapes

Incidental catch of marine turtles by Italian trawlers and longliners in the central Mediterranean

1. The fishing effort and turtle catch of vessels harbouring at Lampedusa island and fishing in the wider central Mediterranean area was monitored using a voluntary logbook programme. Two large trawlers were monitored between 2003 and 2005 and six small vessels using trawl nets, pelagic longline or bottom longline were monitored in the summer 2005. 2. The observed turtle catch rates of pelagic longline and bottom trawl were among the highest recorded in the basin, and high catch rates by bottom longline were observed too. This suggests that the area contains major oceanic and neritic habitats for the loggerhead turtle Caretta caretta in the Mediterranean Sea. 3. When fishing effort is considered, these results suggest a very high number of captures by Italian trawlers and longliners in the area, as well as by fleets from other countries. This is reason of concern for the conservation of the loggerhead turtle within the Mediterranean Sea. 4. Different fishing gear have different technical/operational characteristics affecting turtle catch and mortality and the present knowledge about associated parameters of these gear varies too. 5. All this considered, specific actions are recommended: (i) an awareness campaign to fishermen to reduce post-release mortality, (ii) technical modifications to pelagic longline gear to reduce turtle catch, (iii) further investigation into turtle bycatch in all fishing gear, with priority given to bottom longline fishing and quantification of mortality caused by trawlers, (iv) assessment of the turtle populations affected by fishing activity in the area, and (v) international cooperation in undertaking threat assessments, and implementing regulations, management measures and monitoring. Copyright © 2007 John Wiley & Sons, Ltd

Data from: Catchment zoning for freshwater conservation: refining plans to enhance action on the ground

1. Recent advances in freshwater conservation planning allow addressing some of the specific needs of these systems. These include spatial connectivity or propagation of threats along stream networks, essential to ensure the maintenance of ecosystem processes and the biodiversity they sustain. However, these peculiarities make conservation recommendations difficult to implement as they often require considering large areas that cannot be managed under conventional conservation schemes (e.g. strict protection). 2. To facilitate the implementation of conservation in freshwater systems, a multizoning approach with different management zones subject to different management regimes was proposed. So far, this approach has only been used in post hoc exercises where zones were allocated using expert criteria. This might undermine the cost-effectiveness of conservation recommendations, because both the allocation and extent of these zones have never been optimized using the principles of systematic planning. 3. Here, we demonstrate how to create a catchment multizone plan by using a commonly applied tool in marine and terrestrial realms. We first test the capability of Marxan with Zones to address problems in rivers by using a simulated example and then apply the findings to a real case in the Daly River catchment, northern Australia. We also demonstrate how to address common conservation planning issues, such as accounting for threats or species-specific connectivity needs in this multizone framework, and evaluate their effects on the spatial distribution and extent of different zones. 4. We found that by prioritizing the allocation of zones subject to different management regimes, we could minimize the total area in need of strict conservation by a twofold factor. This reduction can be further reduced (threefold) when considering species’ connectivity needs. The integration of threats helped reduce the average threats of areas selected by a twofold factor. 5. Synthesis and applications. Catchment zoning can help refine conservation recommendations and enhance cost-effectiveness by prescribing different management regimes informed by ecological needs or distribution of threats. Reliable information on these factors is a key to ensure soundness of planning. Freely available software can be used to implement the approach we demonstrate here

Catchment zoning for freshwater conservation: refining plans to enhance action on the ground

Summary: Recent advances in freshwater conservation planning allow addressing some of the specific needs of these systems. These include spatial connectivity or propagation of threats along stream networks, essential to ensure the maintenance of ecosystem processes and the biodiversity they sustain. However, these peculiarities make conservation recommendations difficult to implement as they often require considering large areas that cannot be managed under conventional conservation schemes (e.g. strict protection). To facilitate the implementation of conservation in freshwater systems, a multizoning approach with different management zones subject to different management regimes was proposed. So far, this approach has only been used in post hoc exercises where zones were allocated using expert criteria. This might undermine the cost-effectiveness of conservation recommendations, because both the allocation and extent of these zones have never been optimized using the principles of systematic planning. Here, we demonstrate how to create a catchment multizone plan by using a commonly applied tool in marine and terrestrial realms. We first test the capability of Marxan with Zones to address problems in rivers by using a simulated example and then apply the findings to a real case in the Daly River catchment, northern Australia. We also demonstrate how to address common conservation planning issues, such as accounting for threats or species-specific connectivity needs in this multizone framework, and evaluate their effects on the spatial distribution and extent of different zones. We found that by prioritizing the allocation of zones subject to different management regimes, we could minimize the total area in need of strict conservation by a twofold factor. This reduction can be further reduced (threefold) when considering species' connectivity needs. The integration of threats helped reduce the average threats of areas selected by a twofold factor. Synthesis and applications. Catchment zoning can help refine conservation recommendations and enhance cost-effectiveness by prescribing different management regimes informed by ecological needs or distribution of threats. Reliable information on these factors is a key to ensure soundness of planning. Freely available software can be used to implement the approach we demonstrate here. Catchment zoning can help refine conservation recommendations and enhance cost-effectiveness by prescribing different management regimes informed by ecological needs or distribution of threats. Reliable information on these factors is a key to ensure soundness of planning. Freely available software can be used to implement the approach we demonstrate here