Predicting the economic costs and property value losses attributed to sudden oak death damage in California (2010-2020)

Optimal strategies to protect a sub-population at risk due to an established epidemic

Epidemics can particularly threaten certain sub-populations. For example, for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the elderly are often preferentially protected. For diseases of plants and animals, certain sub-populations can drive mitigation because they are intrinsically more valuable for ecological, economic, socio-cultural or political reasons. Here, we use optimal control theory to identify strategies to optimally protect a ‘high-value’ sub-population when there is a limited budget and epidemiological uncertainty. We use protection of the Redwood National Park in California in the face of the large ongoing state-wide epidemic of sudden oak death (caused by Phytophthora ramorum) as a case study. We concentrate on whether control should be focused entirely within the National Park itself, or whether treatment of the growing epidemic in the surrounding ‘buffer region’ can instead be more profitable. We find that, depending on rates of infection and the size of the ongoing epidemic, focusing control on the high-value region is often optimal. However, priority should sometimes switch from the buffer region to the high-value region only as the local outbreak grows. We characterize how the timing of any switch depends on epidemiological and logistic parameters, and test robustness to systematic misspecification of these factors due to imperfect prior knowledge.

Economic Loss of Pine Wood Nematode Disease in Mainland China from 1998 to 2017

The occurrence and prevalence of pine wood nematode disease has had a great impact on China’s forestry production and ecological environment, but the quantitative evaluation of the economic losses of this biological disease is lacking from a macro-geographic scale and long-term series perspective. This study establishes a pine wood nematode disease economic loss evaluation index system, covering the loss of natural ecology, landscape aesthetics and economic production, and quantitatively evaluates the economic losses of pine wood nematode disease in mainland China at a provincial level from 1998 to 2017. The results show that the economic losses of the pine wood nematode disease in China showed a fluctuant rising trend from 1998, since 2013, it has entered a full-scale outbreak phase, and since 2015, the economic loss has increased significantly, with a growth rate higher than 40%. The average annual total economic loss is CNY 7.17 billion, of which the direct economic losses is CNY 1.53 billion, and the indirect economic losses is CNY 5.64 billion. The loss of forest material resources, the expenditure of ineffective forest management expenditure and prevention and control expenditure were CNY 817 million, CNY 649 million, and CNY 67 million, respectively. Regulate service value loss, support service value loss and cultural service loss are CNY 3.95 billion, CNY 1.41 billion, CNY 276 million, respectively. East China and South China suffered the most due to pine wood nematode disease, and the economic loss of these regions accounted for 79.9% of the total national economic losses. Among them, Zhejiang Province, Guangdong Province and Jiangsu Province lost CNY 2.14 billion, CNY 1.81 billion, and CNY 1.22 billion, respectively, accounting for 26.8%, 22.7% and 15.3% of the total national economic loss.

Spread externalities and the implications of heterogeneous ecological capacity constraints

We develop a spatial-dynamic model of resource management in the presence of externalities, such as the spread of harmful invasive species, and show that ecological capacity constraints influence optimal management strategies across space. We use integer-programming methods to solve for optimal control strategies in both homogeneous and heterogeneous landscapes. Using the spread of gypsy moths as an application, our results show that optimal levels of control vary over space in landscapes with heterogeneous capacity constraints. Optimal outcomes depend on the marginal costs and damages associated with the externality and the emergence of spread externalities from relative differences in population levels between adjacent patches. In models with high degrees of heterogeneity, we show that a naïve policy assuming homogeneous carrying capacity results in a significantly higher welfare losses from the externality.

Draft Genome Resource for the Ex-types of Phytophthora ramorum, P. kernoviae, and P. melonis, Species of Regulatory Concern, Using Ultra-Long Read MinION Nanopore Sequencing

Phytophthora ramorum, P. kernoviae, and P. melonis are each species of current regulatory concern in the United States, the United Kingdom, and other areas of the world. Ex-type material are cultures and duplicates of the type that was used to describe each species and that are deposited in additional culture collections. Using these type specimens as references is essential to designing correct molecular identification and diagnostic systems. Here, we report a whole genome sequence for the Ex-type material of P. ramorum, P. kernoviae, and P. melonis generated using high-throughput sequencing via the MinION third generation platform from Oxford Nanopore Technology. We assembled the quality filtered reads into contigs for each species. We assembled the continuous contigs of P. ramorum, P. kernoviae, and P. melonis (1,322, 545, and 2,091 contigs, respectively). The ab initio prediction of genes from these species reveals that there are 16,838, 12,793, and 34,580 genes in P. ramorum, P. kernoviae, and P. melonis, respectively. Of the 34,580 P. melonis genes, 10,164 genes were conserved among all three of these Phytophthora species which may include pathogenicity genes. We compared the ex-type of P. ramorum EU1 lineage assembly with another selected isolate of EU1 available at the National Center for Biotechnology Information and found 251,859 single nucleotide polymorphisms (SNPs) genome-wide; the comparison with the EU2 lineage genome isolate revealed 441,859 SNPs genome-wide. This genome resource of the ex-types of P. ramorum, and P. kernoviae is a significant contribution as these species are among the most important pathogens of regulatory concern in different regions of the world.

Forecasting and control of emerging infectious forest disease through participatory modelling

Epidemiological models are powerful tools for evaluating scenarios and visualizing patterns of disease spread, especially when comparing intervention strategies. However, the technical skill required to synthesize and operate computational models frequently renders them beyond the command of the stakeholders who are most impacted by the results. Participatory modelling (PM) strives to restructure the power relationship between modellers and the stakeholders who rely on model insights by involving these stakeholders directly in model development and application; yet, a systematic literature review indicates little adoption of these techniques in epidemiology, especially plant epidemiology. We investigate the potential for PM to integrate stakeholder and researcher knowledge, using Phytophthora ramorum and the resulting sudden oak death disease as a case study. Recent introduction of a novel strain (European 1 or EU1) in southwestern Oregon has prompted significant concern and presents an opportunity for coordinated management to minimize regional pathogen impacts. Using a PM framework, we worked with local stakeholders to develop an interactive forecasting tool for evaluating landscape-scale control strategies. We find that model co-development has great potential to empower stakeholders in the design, development and application of epidemiological models for disease control.

This article is part of the theme issue ‘Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control’. This theme issue is linked with the earlier issue ‘Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes’.

Applying optimal control theory to a spatial simulation model of sudden oak death: ongoing surveillance protects tanoak while conserving biodiversity

Sudden oak death has devastated tree populations across California. However, management might still slow disease spread at local scales. We demonstrate how to unambiguously characterize effective, local management strategies using a detailed, spatially explicit simulation model of spread in a single forest stand. This pre-existing, parameterized simulation is approximated here by a carefully calibrated, non-spatial model, explicitly constructed to be sufficiently simple to allow optimal control theory (OCT) to be applied. By lifting management strategies from the approximate model to the detailed simulation, effective time-dependent controls can be identified. These protect tanoak-a culturally and ecologically important species-while conserving forest biodiversity within a limited budget. We also consider model predictive control, in which both the approximating model and optimal control are repeatedly updated as the epidemic progresses. This allows management which is robust to both parameter uncertainty and systematic differences between simulation and approximate models. Including the costs of disease surveillance then introduces an optimal intensity of surveillance. Our study demonstrates that successful control of sudden oak death is likely to rely on adaptive strategies updated via ongoing surveillance. More broadly, it illustrates how OCT can inform effective real-world management, even when underpinning disease spread models are highly complex.

Ecology and Evolution of the Sudden Oak Death Pathogen Phytophthora ramorum

The sudden oak and sudden larch death pathogen Phytophthora ramorum emerged simultaneously in the United States on oak and in Europe on Rhododendron in the 1990s. This pathogen has had a devastating impact on larch plantations in the United Kingdom as well as mixed conifer and oak forests in the Western United States. Since the discovery of this pathogen, a large body of research has provided novel insights into the emergence, epidemiology, and genetics of this pandemic. Genetic and genomic resources developed for P. ramorum have been instrumental in improving our understanding of the epidemiology, evolution, and ecology of this disease. The recent reemergence of EU1 in the United States and EU2 in Europe and the discovery of P. ramorum in Asia provide renewed impetus for research on the sudden oak death pathogen.

Optimal Inspection of Imports to Prevent Invasive Pest Introduction

The United States imports more than 1 billion live plants annually-an important and growing pathway for introduction of damaging nonnative invertebrates and pathogens. Inspection of imports is one safeguard for reducing pest introductions, but capacity constraints limit inspection effort. We develop an optimal sampling strategy to minimize the costs of pest introductions from trade by posing inspection as an acceptance sampling problem that incorporates key features of the decision context, including (i) simultaneous inspection of many heterogeneous lots, (ii) a lot-specific sampling effort, (iii) a budget constraint that limits total inspection effort, (iv) inspection error, and (v) an objective of minimizing cost from accepted defective units. We derive a formula for expected number of accepted infested units (expected slippage) given lot size, sample size, infestation rate, and detection rate, and we formulate and analyze the inspector's optimization problem of allocating a sampling budget among incoming lots to minimize the cost of slippage. We conduct an empirical analysis of live plant inspection, including estimation of plant infestation rates from historical data, and find that inspections optimally target the largest lots with the highest plant infestation rates, leaving some lots unsampled. We also consider that USDA-APHIS, which administers inspections, may want to continue inspecting all lots at a baseline level; we find that allocating any additional capacity, beyond a comprehensive baseline inspection, to the largest lots with the highest infestation rates allows inspectors to meet the dual goals of minimizing the costs of slippage and maintaining baseline sampling without substantial compromise.

Nonnative forest insects and pathogens in the United States: Impacts and policy options

We review and synthesize information on invasions of nonnative forest insects and diseases in the United States, including their ecological and economic impacts, pathways of arrival, distribution within the United States, and policy options for reducing future invasions. Nonnative insects have accumulated in United States forests at a rate of ~2.5 per yr over the last 150 yr. Currently the two major pathways of introduction are importation of live plants and wood packing material such as pallets and crates. Introduced insects and diseases occur in forests and cities throughout the United States, and the problem is particularly severe in the Northeast and Upper Midwest. Nonnative forest pests are the only disturbance agent that has effectively eliminated entire tree species or genera from United States forests within decades. The resulting shift in forest structure and species composition alters ecosystem functions such as productivity, nutrient cycling, and wildlife habitat. In urban and suburban areas, loss of trees from streets, yards, and parks affects aesthetics, property values, shading, stormwater runoff, and human health. The economic damage from nonnative pests is not yet fully known, but is likely in the billions of dollars per year, with the majority of this economic burden borne by municipalities and residential property owners. Current policies for preventing introductions are having positive effects but are insufficient to reduce the influx of pests in the face of burgeoning global trade. Options are available to strengthen the defenses against pest arrival and establishment, including measures taken in the exporting country prior to shipment, measures to ensure clean shipments of plants and wood products, inspections at ports of entry, and post-entry measures such as quarantines, surveillance, and eradication programs. Improved data collection procedures for inspections, greater data accessibility, and better reporting would support better evaluation of policy effectiveness. Lack of additional action places the nation, local municipalities, and property owners at high risk of further damaging and costly invasions. Adopting stronger policies to reduce establishments of new forest insects and diseases would shift the major costs of control to the source and alleviate the economic burden now borne by homeowners and municipalities.

Management of invading pathogens should be informed by epidemiology rather than administrative boundaries

Plant and animal disease outbreaks have significant ecological and economic impacts. The spatial extent of control is often informed solely by administrative geography - for example, quarantine of an entire county or state once an invading disease is detected - with little regard for pathogen epidemiology. We present a stochastic model for the spread of a plant pathogen that couples spread in the natural environment and transmission via the nursery trade, and use it to illustrate that control deployed according to administrative boundaries is almost always sub-optimal. We use sudden oak death (caused by Phytophthora ramorum) in mixed forests in California as motivation for our study, since the decision as to whether or not to deploy plant trade quarantine is currently undertaken on a county-by-county basis for that system. However, our key conclusion is applicable more generally: basing management of any disease entirely upon administrative borders does not balance the cost of control with the possible economic and ecological costs of further spread in the optimal fashion.

Host Phenology and Leaf Effects on Susceptibility of California Bay Laurel to Phytophthora ramorum

Spread of the plant pathogen Phytophthora ramorum, causal agent of the forest disease sudden oak death, is driven by a few competent hosts that support spore production from foliar lesions. The relationship between traits of a principal foliar host, California bay laurel (Umbellularia californica), and susceptibility to P. ramorum infection were investigated with multiple P. ramorum isolates and leaves collected from multiple trees in leaf-droplet assays. We examined whether susceptibility varies with season, leaf age, or inoculum position. Bay laurel susceptibility was highest during spring and summer and lowest in winter. Older leaves (>1 year) were more susceptible than younger ones (8 to 11 months). Susceptibility was greater at leaf tips and edges than the middle of the leaf. Leaf surfaces wiped with 70% ethanol were more susceptible to P. ramorum infection than untreated leaf surfaces. Our results indicate that seasonal changes in susceptibility of U. californica significantly influence P. ramorum infection levels. Thus, in addition to environmental variables such as temperature and moisture, variability in host plant susceptibility contributes to disease establishment of P. ramorum.

RNA-Seq Analysis of the Expression of Genes Encoding Cell Wall Degrading Enzymes during Infection of Lupin (Lupinus angustifolius) by Phytophthora parasitica

RNA-Seq analysis has shown that over 60% (12,962) of the predicted transcripts in the Phytophthora parasitica genome are expressed during the first 60 h of lupin root infection. The infection transcriptomes included 278 of the 431 genes encoding P. parasitica cell wall degrading enzymes. The transcriptome data provide strong evidence of global transcriptional cascades of genes whose encoded proteins target the main categories of plant cell wall components. A major cohort of pectinases is predominantly expressed early but as infection progresses, the transcriptome becomes increasingly dominated by transcripts encoding cellulases, hemicellulases, β-1,3-glucanases and glycoproteins. The most highly expressed P. parasitica carbohydrate active enzyme gene contains two CBM1 cellulose binding modules and no catalytic domains. The top 200 differentially expressed genes include β-1,4-glucosidases, β-1,4-glucanases, β-1,4-galactanases, a β-1,3-glucanase, an α-1,4-polygalacturonase, a pectin deacetylase and a pectin methylesterase. Detailed analysis of gene expression profiles provides clues as to the order in which linkages within the complex carbohydrates may come under attack. The gene expression profiles suggest that (i) demethylation of pectic homogalacturonan occurs before its deacetylation; (ii) cleavage of the backbone of pectic rhamnogalacturonan I precedes digestion of its side chains; (iii) early attack on cellulose microfibrils by non-catalytic cellulose-binding proteins and enzymes with auxiliary activities may facilitate subsequent attack by glycosyl hydrolases and enzymes containing CBM1 cellulose-binding modules; (iv) terminal hemicellulose backbone residues are targeted after extensive internal backbone cleavage has occurred; and (v) the carbohydrate chains on glycoproteins are degraded late in infection. A notable feature of the P. parasitica infection transcriptome is the high level of transcription of genes encoding enzymes that degrade β-1,3-glucanases during middle and late stages of infection. The results suggest that high levels of β-1,3-glucanases may effectively degrade callose as it is produced by the plant during the defence response.

Optimising and communicating options for the control of invasive plant disease when there is epidemiological uncertainty

Although local eradication is routinely attempted following introduction of disease into a new region, failure is commonplace. Epidemiological principles governing the design of successful control are not well-understood. We analyse factors underlying the effectiveness of reactive eradication of localised outbreaks of invading plant disease, using citrus canker in Florida as a case study, although our results are largely generic, and apply to other plant pathogens (as we show via our second case study, citrus greening). We demonstrate how to optimise control via removal of hosts surrounding detected infection (i.e. localised culling) using a spatially-explicit, stochastic epidemiological model. We show how to define optimal culling strategies that take account of stochasticity in disease spread, and how the effectiveness of disease control depends on epidemiological parameters determining pathogen infectivity, symptom emergence and spread, the initial level of infection, and the logistics and implementation of detection and control. We also consider how optimal culling strategies are conditioned on the levels of risk acceptance/aversion of decision makers, and show how to extend the analyses to account for potential larger-scale impacts of a small-scale outbreak. Control of local outbreaks by culling can be very effective, particularly when started quickly, but the optimum strategy and its performance are strongly dependent on epidemiological parameters (particularly those controlling dispersal and the extent of any cryptic infection, i.e. infectious hosts prior to symptoms), the logistics of detection and control, and the level of local and global risk that is deemed to be acceptable. A version of the model we developed to illustrate our methodology and results to an audience of stakeholders, including policy makers, regulators and growers, is available online as an interactive, user-friendly interface at http://www.webidemics.com/. This version of our model allows the complex epidemiological principles that underlie our results to be communicated to a non-specialist audience.

Estimating the economic value of cultural ecosystem services in an urbanizing area using hedonic pricing

A need exists to increase both knowledge and recognition of the values associated with ecosystem services and amenities. This article explores the use of hedonic pricing as a tool for eliciting these values. We take a case study approach, valuing several services provided by ecosystems, namely aesthetic quality (views), access to outdoor recreation, and the benefits provided by tree cover in Dakota County, Minnesota, USA. Our results indicate that these services are valued by local residents and that hedonic pricing can be used to elicit at least a portion of this value. We find that many aspects of the aesthetic environment significantly impact home sale prices. Total view area as well as the areas of some land-cover types (water and lawn) in views positively influenced home sale prices while views of impervious surfaces generally negatively influenced home sale price. Access to outdoor recreation areas significantly and positively influenced home sale prices as did tree cover in the neighborhood surrounding a home. These results illustrate the ability of hedonic pricing to identify partial values for ecosystem services and amenities in a manner that is highly relevant to local and regional planning. These values could be used to increase policy-maker and public awareness of ecosystem services and could improve their consideration in planning and policy decisions.

Landscape epidemiology and control of pathogens with cryptic and long-distance dispersal: sudden oak death in northern Californian forests

Exotic pathogens and pests threaten ecosystem service, biodiversity, and crop security globally. If an invasive agent can disperse asymptomatically over long distances, multiple spatial and temporal scales interplay, making identification of effective strategies to regulate, monitor, and control disease extremely difficult. The management of outbreaks is also challenged by limited data on the actual area infested and the dynamics of spatial spread, due to financial, technological, or social constraints. We examine principles of landscape epidemiology important in designing policy to prevent or slow invasion by such organisms, and use Phytophthora ramorum, the cause of sudden oak death, to illustrate how shortfalls in their understanding can render management applications inappropriate. This pathogen has invaded forests in coastal California, USA, and an isolated but fast-growing epidemic focus in northern California (Humboldt County) has the potential for extensive spread. The risk of spread is enhanced by the pathogen's generalist nature and survival. Additionally, the extent of cryptic infection is unknown due to limited surveying resources and access to private land. Here, we use an epidemiological model for transmission in heterogeneous landscapes and Bayesian Markov-chain-Monte-Carlo inference to estimate dispersal and life-cycle parameters of P. ramorum and forecast the distribution of infection and speed of the epidemic front in Humboldt County. We assess the viability of management options for containing the pathogen's northern spread and local impacts. Implementing a stand-alone host-free "barrier" had limited efficacy due to long-distance dispersal, but combining curative with preventive treatments ahead of the front reduced local damage and contained spread. While the large size of this focus makes effective control expensive, early synchronous treatment in newly-identified disease foci should be more cost-effective. We show how the successful management of forest ecosystems depends on estimating the spatial scales of invasion and treatment of pathogens and pests with cryptic long-distance dispersal.