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Nowhere in the U.S. is Huanglongbing (HLB) under adequate control due to the lack of effective tools to reduce spread of the vector, Diaphorina citri (Asian citrus psyllid), and transmission of the associated pathogen, Candidatus Liberibacter asiaticus, in the absence of disease resistance in commercial citrus varieties. In Florida, Asian citrus psyllid was well established by the time of HLB discovery and growers did not remove trees to eliminate inoculum, so there was no chance of controlling the epidemic. Based on the Florida experience, Texas proactively controlled the vector by implementing area-wide management and disease spread was slower than in Florida, however, they also did not remove infected trees. California controlled both ACP and tree inoculum and have delayed the development of an epidemic in the Central Valley. This situation is aided by topographic isolation from the Los Angeles basin where ACP and HLB are endemic and a climate distinctly different from other citrus growing regions in the U.S.

Citrus huanglongbing disease (HLB) is an acute bacterial disease that threatens the sustainability of citrus production across the world. In the USA, the Asian citrus psyllid (ACP) is the vector responsible for spreading the disease. Successful suppression of HLB requires action against ACP at large spatial scales, i.e. growers must cooperate. In Florida and California, the citrus production regions have been split into vector-management areas and growers are encouraged to coordinate spraying of insecticide across these (to achieve area-wide control). We surveyed growers from Florida and California, obtaining samples of opportunity at grower meetings, to assess the consensus of opinions concerning issues that influence HLB management. Our results show that a grower's perception of the risk of disease infection and their trust in control options are central to the decision on whether to join an area-wide control program. Growers' perceptions on risk and control efficacy were found to be influenced by information networks and observations about the state of the HLB epidemic and psyllid populations. Within the growers' information networks, researchers and extension agents were reported to have the largest influence on perceptions. Differences in opinion between California and Florida growers as to the efficacy of treatments could be explained as a function of experience: growers from areas with lower densities of ACP were associated with rating insecticide control more positively than those where psyllids population density was higher. Thirty percent of growers identified the expected lack of participation by other growers as a reason why they themselves would not participate in area-wide control.

We describe a series of operational questions posed during the state-wide response in California to the arrival of the invasive citrus disease Huanglongbing. The response is coordinated by an elected committee from the citrus industry and operates in collaboration with the California Department of Food and Agriculture, which gives it regulatory authority to enforce the removal of infected trees. The paper reviews how surveillance for disease and resource allocation between detection and delimitation have been addressed, based on epidemiological principles. In addition, we describe how epidemiological analyses have been used to support rule-making to enact costly but beneficial regulations and we highlight two recurring themes in the programme support work: (i) data are often insufficient for quantitative analyses of questions and (ii) modellers and decision-makers alike may be forced to accept the need to make decisions on the basis of simple or incomplete analyses that are subject to considerable uncertainty.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’.

International travel offers an extensive network for new and recurring human-mediated introductions of exotic infectious pathogens and biota, freeing geographical constraints. We present a predictive census-travel model that integrates international travel with endpoint census data and epidemiological characteristics to predict points of introduction. Population demographics, inbound and outbound travel patterns, and quantification of source strength by country are combined to estimate and rank risk of introduction at user-scalable land parcel areas (e.g. state, county, zip code, census tract, gridded landscapes (1 mi 2 , 5 km 2 , etc.)). This risk ranking by parcel can be used to develop pathogen surveillance programmes, and has been incorporated in multiple US state/federal surveillance protocols. The census-travel model is versatile and independent of pathosystems, and applies a risk algorithm to generate risk maps for plant, human and animal contagions at different spatial scales. An interactive, user-friendly interface is available online (https://epi-models.shinyapps.io/Census_Travel/) to provide ease-of-use for regulatory agencies for early detection of high-risk exotics. The interface allows users to parametrize and run the model without knowledge of background code and underpinning data. 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’.

The Citrus tristeza virus (CTV) is one of the most economically devastating citrus diseases worldwide. The spread of CTV in eastern Spain was studied by Gottwald et al. with the goal of determining the spatio-temporal mechanisms of spread. Since the subjects in this study are individual trees, it is natural to think of infections as Bernoulli trials. This approach is difficult however, due to the spatial and temporal dependence of the observations. Consequently, a system of ordinary differential equations (ODE) was used to model the probabilities of infection as well as the spatial and temporal dependence. Given the parameters in the ODE, the probabilities of infection are treated as conditionally independent. Using the conditional independence we then specify the joint likelihood function as a Poisson binomial distribution. For the purpose of model selection and hypothesis testing we, employed accumulated prediction error (APE) which has connections to both Bayesian and frequentist frameworks. We demonstrated the robustness of our method in accounting for spatio-temporal dependencies in the data by accurately predicting the spatial distribution of the disease through Join Counts.

Citrus greening or huanglonbing (HLB) is thought to be caused by Candidatus Liberibacter asiaticus (CLas) and is devastating the citrus industry worldwide. One symptom of HLB disease is excessive pre-harvest fruit drop. Recently, higher incidence of Lasiodiplodia theobromae (Diplodia) was found in HLB-symptomatic orange calyx abscission zones (AZ-C) than in non-symptomatic fruit, and the infection was positively correlated with the reduction in fruit detachment force (FDF), suggesting that Diplodia infection may be involved in the HLB-related pre-harvest fruit drop. To verify the hypothesis, we conducted two experiments. Experiment 1 was conducted by shaking HLB-affected ‘Hamlin’ and ‘Valencia’ orange trees during the harvest season (twice for ‘Hamlin’ and once for ‘Valencia’). The fruit that dropped from trees upon shaking were collected (D), and the fruit retained on trees after shaking were harvested (R). Fruit ethylene production was measured, and the levels of Diplodia and CLas in AZ-C of D and R fruit were analyzed. The results revealed significantly higher levels of Diplodia in D compared with R fruit; and ethylene was produced from more than half of the D fruit but none of the R fruit. Ethylene production was positively correlated with Diplodia level in D fruit. In experiment 2, a preliminary trial on the effect of fungicide (Quadris Top) application on incidence of Diplodia infection and fruit drop was investigated. The experiment was conducted in a commercial grove with essentially 100% of the trees being HLB-symptomatic, and included five citrus cultivars (‘Early Gold’ orange, ‘Midsweet’ orange, ‘Murcott’ tangor, ‘Navel’ orange and ‘Ray Ruby’ grapefruit). Diplodia levels were lower and FDF significantly higher in fungicide-treated compared to non-treated ‘Early Gold’, ‘Midsweet’ and ‘Murcott’ fruit, and consequently, the fruit drop was reduced by 45%, 30% and 46% that of non-sprayed controls, respectively. For ‘Navel’ or ‘Ray Ruby’ fruit, there was no significant change between sprayed and non-sprayed controls in the level of Diplodia, FDF or fruit-drop. The results consistently showed a positive correlation between Diplodia infection and fruit drop in HLB-affected fruit, indicating the possible involvement of the fungus in HLB-related excessive fruit drop. This suggests that control of Diplodia fungal infection in the field may reduce HLB-associated pre-harvest fruit drop.

The global distribution of citrus black spot (CBS) disease, caused by Phyllosticta citricarpa, is climatically constrained, which is evident from its occurrence in citrus growing areas with warm, summer rainfall and its absence from areas with cooler, Mediterranean-type winter rainfall. Various epidemiological and modelling studies have supported this observation, predominantly estimating unsuitability for P. citricarpa in Mediterranean type climates, with no more than marginal suitability estimated at a few localities within some regions with Mediterranean type climates. The study by Martinez-Minaya et al. (European Journal of Plant Pathology, 143, 69–83, 2015), describes an historic sequence of recorded CBS occurrence in parts of South Africa, conducts an autocorrelation analysis and a correlative analysis with Koppen-Geiger climate zones and makes observations about the occurrence of certain Koppen-Geiger climate zones in the European Union. The study suggests that significant portions of the European Union and the broader Mediterranean basin are climatically similar to warm, summer rainfall areas in South Africa where P. citricarpa persists and causes CBS disease and concludes that the potential distribution of P. citricarpa is less constrained by climatic factors than spatial contagion. However, in this critique we expose methodological shortcomings in the Martinez-Minaya et al. (European Journal of Plant Pathology, 143, 69–83, 2015) study and conclude that the study grossly overestimated the extent of the geographical area that could support P. citricarpa, thereby rendering the findings scientifically unreliable.

Huanglongbing (HLB) disease is the most serious threat to citrus production worldwide and, in the last decade, has devastated the Florida citrus industry. In the United States, HLB is associated with the phloem-limited α-proteobacterium ‘Candidatus Liberibacter asiaticus’ and its insect vector, the Asian citrus psyllid (ACP; Diaphorina citri). Significant effort is being put forth to develop novel citrus germplasm that has a lower propensity to succumb to HLB than do currently available varieties. Effective methods of screening citrus germplasm for susceptibility to HLB are essential. In this study, we exposed small, grafted trees of 16 citrus types to free-ranging ACP vectors and ‘Ca. L. asiaticus’ inoculum in the greenhouse. During 45 weeks of exposure to ACP, the cumulative incidence of ‘Ca. L. asiaticus’ infection was 70%. Trees of Citrus macrophylla and C. medica were most susceptible to ‘Ca. L. asiaticus’, with 100% infection by the end of the test period in three trials, while the complex genetic hybrids ‘US 1-4-59’ and ‘Fallglo’ consistently were least susceptible, with approximately 30% infection. Results obtained in this greenhouse experiment showed good agreement with trends observed in the orchard, supporting the validity of our approach for screening citrus germplasm for susceptibility to HLB.

Asiatic citrus canker (ACC, caused by Xanthomonas citri subsp. citri, [Xcc]) is a serious disease of citrus, reducing yield and impacting marketability of fresh fruit. ACC has phytosanitary implications for fresh fruit trade. Lesions on fruit, leaves, and shoots in an orchard of ACC-susceptible grapefruit were monitored for production of Xcc from June to the following January in 2009 and 2010. Lesions on fruit post-harvest either packingline-treated or not treated were also monitored for production of Xcc on fruit harvested in November 2013 and January 2014. Shoot lesions generally produced fewer bacteria and had a smaller proportion of active lesions compared to leaf and fruit lesions. As the season progressed the proportion of active lesions on fruit and shoots gradually declined. Bacterial flux density (BFD) in surviving lesions was >103 on all organs at all sample times. A window-pane analysis revealed weather variables associated with bacterial survival within the lesion. The packingline treatment had no effect in reducing the proportion of active lesions, and had only a small, transient effect reducing BFD (~1.5 log units). Lesion size affected survival – small lesions (

Biggs, A. R., Turechek, W. W., and Gottwald, T. R. 2008. Analysis of fire blight shoot infection epidemics on apple. Plant Dis. 92:1349-1356. Fire blight incidence and spread of the shoot blight phase of the disease was studied in four apple cultivars in replicated blocks over 4 years (1994 to 1997). Cv. York was highly susceptible, followed by ‘Fuji’ and ‘Golden Delicious,’ which were moderately susceptible, and ‘Liberty,’ which was least susceptible. On York, the first appearance of shoot blight was within 48 h of its predicted appearance according to the Maryblyt model in 3 of the 4 years studied. Shoot blight epidemics in York in 1995 and 1996, and Fuji in 1995, were best described with a logistic model that showed apparent infection rates ranging from 0.05 to 0.20, indicating a low to moderately high rate of disease increase. The spatial positions (row and column) of all infected plants in each subplot were recorded on plot maps on each sampling date. The binomial and β-binomial distributions were fit to the data to test for spatial aggregation of disease incidence for each cultivar plot. Maximum likelihood estimation was possible for 92 (43.6%) of the 211 data sets subjected to this analysis. Of these, 35 data sets were better fit by the β-binomial distribution than the binomial distribution. The binary power law was used to characterize the relationship between the variance among quadrats within each plot to the variance expected for that plot given the observed level of disease incidence. The binary power law provided an excellent fit to the full data set and to nearly all of the subsets and, with b > 1, indicated that heterogeneity changed systematically with disease incidence. A covariance analysis was conducted to determine the effect of the factors ‘year,’ ‘cultivar,’ ‘orchard plot,’ and ‘observation date’ on the intercept and slope parameters of the binary power law. In general, plot followed by year had the greatest impact on parameter estimates and is an indication that location and seasonal factors impact heterogeneity of disease, although the specifics could not be ascertained from this study. Ordinary runs analysis was used to analyze the pattern of diseased trees within rows and detected significant nonrandom patterns of disease incidence in 63.5% of the orchard plots over the 4year study. From these data sets, 68.7% had significantly fewer runs, particularly at disease incidences greater than 0.1. The fewer-than-expected runs at incidences greater than 0.10 provides strong evidence of localized spread. Additional keywords: Erwinia amylovora

A new bacterial disease of citrus was recently identified in Florida and is here named bacterial brown leaf spot (BBLS) of citrus. BBLS-infected citrus leaves from the field displayed circular, brownish, flat lesions with slightly raised and water-soaked margins surrounded by a chlorotic halo. Based on Biolog carbon source metabolic “fingerprinting”, fatty acid analysis, and sequence analysis of partial 16S rDNA, gyrB, and rpoD genes, the causal agent of the disease was identified as Burkholderia andropogonis. Pathogenicity of these B. andropogonis isolates taken from multiple citrus leaves with BBLS was tested by various inoculation methods on three species of citrus as well as on carnation, corn, and sorghum. All isolates infected carnation, corn, and sorghum with varying degrees of pathogenicity. Variation among citrus isolates in pathogenicity was also observed in high titer (108 CFU/ml) inoculations of citrus leaves, ranging from a hypersensitive-like response to canker-like lesions. When the inoculum concentration was low (106 CFU/ml), only necrotic spots or small lesions slowly developed with all strains. Growth of B. andropogonis in citrus was relatively slow, tissue wounding appeared necessary for symptom appearance with many isolates, and field samples were recovered only after severe storms, indicating that this wide-host-range bacterium is a weak, opportunistic pathogen of citrus.

Pecan scab is caused by the fungus Fusicladium effusum, and is the most destructive disease of pecan in the United States. Accurate and reliable disease assessments are needed to ensure that data provide a measure of actual disease intensity. The Horsfall-Barratt (H-B) category scale and its derivatives are commonly used to assess disease. Estimates using the H-B scale were compared with nearest percent estimate (NPEs) for rating disease severity of pecan scab on valves of fruit. Both inexperienced and experienced raters were included in the experiment. Lin's concordance correlation showed that agreement using NPEs was variable (ρc = 0.57 to 0.96), whereas estimates of disease severity using the H-B scale had similar agreement among most raters (ρc = 0.59 to 0.98). Converted values of NPEs to the H-B midpoints (NPEH-B) also provided a similar range (ρc = 0.61 to 0.96). Neither experienced nor inexperienced raters were consistently better using any of the three methods. Bootstrap analysis indicated that, among experienced raters, precision (r) and agreement (ρc) were often reduced when using the H-B scale compared with NPEs. There was no consistent effect of converting NPEs to NPEH-B midpoint values compared with actual H-B values. Inter-rater reliability using the H-B scale was never better than NPEs. Bootstrap analysis indicated no difference in the length of time needed to assess disease but regression analysis suggested that raters who were inherently fast in assessing disease with NPEs were often slower when using the H-B scale; conversely, raters who were slow assessing with NPEs were often faster when using the H-B scale. Thus, there appears to be no advantage in accuracy or reliability or reduction in time when inexperienced or experienced raters used a category rating scale to assess pecan scab.

Bassanezi, R. B., Montesino, L. H., Gimenes-Fernandes, N., Yamamoto, P. T., Gottwald, T. R., Amorim, L., and Bergamin Filho, A. 2013. Efficacy of area-wide inoculum reduction and vector control on temporal progress of huanglongbing in young sweet orange plantings. Plant Dis. 97:789796. Huanglongbing (HLB), caused by ‘Candidatus Liberibacter’ spp. and transmitted by the Asian citrus psyllid Diaphorina citri (ACP), is an important threat to citrus industries worldwide, causing significant yield loss. The current recommended strategies to manage HLB are to eliminate HLB-symptomatic trees to reduce sources of bacterial inoculum and to apply insecticides to reduce psyllid vector populations. The objective of this study was to assess the effectiveness and the importance of both strategies applied within young citrus plots (local management), in different frequencies and combinations, on HLB temporal progress. Two factorial field experiments, E1 and E2, were initiated in a new plantation of sweet orange in an HLB epidemic region of Sao Paulo, Brazil, in October 2005 and May 2006, respectively. Local inoculum reduction (tree removal) intervals for E1 were every 4, 8, and 16 weeks and, for E2, every 2, 4, 12, and 26 weeks. Local vector control strategies for E1 were no control, program A (PA), and program B (PB); and, for E2, no control and program C (PC), as follows. Psyllids were controlled with two 56-day-interval soil or drench applications of systemic insecticides concurrently with the rainy season each year and, during the rest of the year, with insecticide sprays every 28 days for PA and every 14 days for PB and PC. Regional HLB management was present for E1 and absent for E2. The beginning of the HLB epidemic was delayed for 10 months in E1 compared with appearance of the first diseased tree in E2 but wasn’t affected by different local strategies in either experiment. After 60 (E1) and 53 (E2) months, the HLB incidence and progress rates were not affected by different frequencies of local inoculum reduction in either experiment, and were different only in plots with and without local vector control in E2. In E1, the disease incidence was reduced by 90% and the disease progress rate by 50% in plots both with and without vector control. These reductions were explained by smaller psyllid populations and lower frequency of bacterialiferous psyllids in E1 compared with E2. Annual productivity increased over time in E1, as expected for young plantings, but remained stable or decreased in E2. These results confirm that immigration of bacterialiferous ACP vectors plays a critical role in HLB epidemics and suggest that area-wide inoculum reduction and ACP management strongly affect HLB control.

Monitoring a population for a disease requires the hosts to be sampled and tested for the pathogen. This results in sampling series from which we may estimate the disease incidence, i.e. the proportion of hosts infected. Existing estimation methods assume that disease incidence does not change between monitoring rounds, resulting in an underestimation of the disease incidence. In this paper, we develop an incidence estimation model accounting for epidemic growth with monitoring rounds that sample varying incidence. We also show how to accommodate the asymptomatic period that is the characteristic of most diseases. For practical use, we produce an approximation of the model, which is subsequently shown to be accurate for relevant epidemic and sampling parameters. Both the approximation and the full model are applied to stochastic spatial simulations of epidemics. The results prove their consistency for a very wide range of situations. The estimation model is made available as an online application. 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’.

The control of highly infectious diseases of agricultural and plantation crops and livestock represents a key challenge in epidemiological and ecological modelling, with implemented control strategies often being controversial. Mathematical models, including the spatio-temporal stochastic models considered here, are playing an increasing role in the design of control as agencies seek to strengthen the evidence on which selected strategies are based. Here, we investigate a general approach to informing the choice of control strategies using spatio-temporal models within the Bayesian framework. We illustrate the approach for the case of strategies based on pre-emptive removal of individual hosts. For an exemplar model, using simulated data and historic data on an epidemic of Asiatic citrus canker in Florida, we assess a range of measures for prioritizing individuals for removal that take account of observations of an emerging epidemic. These measures are based on the potential infection hazard a host poses to susceptible individuals (hazard), the likelihood of infection of a host (risk) and a measure that combines both the hazard and risk (threat). We find that the threat measure typically leads to the most effective control strategies particularly for clustered epidemics when resources are scarce. The extension of the methods to a range of other settings is discussed. A key feature of the approach is the use of functional-model representations of the epidemic model to couple epidemic trajectories under different control strategies. This induces strong positive correlations between the epidemic outcomes under the respective controls, serving to reduce both the variance of the difference in outcomes and, consequently, the need for extensive simulation., Hola Adrakey was supported during the course of this research by a James Watt Postgraduate Research Scholarship from Heriot–Watt University.

Effective control of plant disease remains a key challenge. Eradication attempts often involve removal of host plants within a certain radius of detection, targeting asymptomatic infection. Here we develop and test potentially more effective, epidemiologically motivated, control strategies, using a mathematical model previously fitted to the spread of citrus canker in Florida.\ud We test risk-based control, which preferentially removes hosts expected to cause a high number of infections in the remaining host population. Removals then depend on past patterns of pathogen spread and host removal, which might be nontransparent to affected stakeholders. This motivates a variable radius strategy, which approximates risk-based control via removal radii that vary by location, but which are fixed in advance of any epidemic.\ud Risk-based control outperforms variable radius control, which in turn outperforms constant radius removal. This result is robust to changes in disease spread parameters and initial patterns of susceptible host plants. However, efficiency degrades if epidemiological parameters are incorrectly characterised.\ud Risk-based control including additional epidemiology can be used to improve disease management, but it requires good prior knowledge for optimal performance. This focuses attention on gaining maximal information from past epidemics, on understanding model transferability between locations and on adaptive management strategies that change over time.

The Asian citrus psyllid (ACP), Diaphorina citri Kuwayama (Hemiptera: Liviidae), is an important pest of citrus in the United States of America primarily because it vectors ‘Candidatus Liberibacter asiaticus’, the bacterium putatively responsible for Asiatic huanglongbing (HLB). Asiatic HLB is considered one of the most serious diseases of citrus. In the United States where Asiatic HLB was first found in the state of Florida, vector control is considered an essential component to mitigate pathogen infection and spread of the disease. Therefore commercial citrus growers in Florida have adopted intensive insecticide programs to manage psyllid populations. However, the repetitive use of insecticides for ACP control is expensive and interferes with biological control of ACP and other citrus pests. As an alternative to insecticides, reports from Vietnam indicated that infestations of ACP in citrus (and consequently incidence of HLB) were reduced when citrus was interplanted with white guava, Psidium guajava L. Speculations were that guava volatiles reduced ACP infestations in citrus by either repelling ACP or interfering with ACP ability to locate and infest citrus grown next to guava. We present the results of two studies conducted in Florida (where both ACP and HLB occur) to assess ACP infestations and HLB incidence in citrus interplanted with either white or pink guava compared to infestations and disease incidence in citrus grown as a monoculture, both in orchards and nurseries. In the field study, the effect of guava on ACP infestations was assessed alone and in combination with insecticide or oil applications. Significant reductions in ACP infestations in citrus interplanted with pink guava were identified, but there was no reduction in citrus interplanted with white guava. The effect of pink guava on ACP infestations could be investigated further. However, intercropping citrus with either white or pink guava did not prevent the introduction and spread of HLB. Conclusions from field studies regarding guava as a management tactic against ACP were difficult to make due to persistent nematode problems and freeze damage to guava, which could have interfered with the production of guava volatiles responsible for deterring ACP infestations. Conversely, citrus nursery trees interspersed with guava did show reduced HLB incidence and disease progression over time. However, vector and disease reduction resulting from guava intercropping in citrus nurseries was not adequate to recommend it as a management strategy.

The incidence and severity of citrus variegated chlorosis (CVC) caused by Xylella fastidiosa are higher in the northern region of Sao Paulo, Brazil than in the southern region. This phenomenon is partly due to differences in the climate, especially rainfall, as the northern region tends to be drier than the southern region. The progress of CVC under three levels of irrigation was assessed in a grove located in the northern region of Sao Paulo. Trees (10-year-old Natal sweet orange) were arranged in a randomized complete block in a 3 × 2 factorial scheme with three levels of irrigation and two methods of infection with X. fastidiosa . The disease incidence in branches and the number of symptomatic fruits per tree were evaluated for three years. A monomolecular model was used to describe the progress of CVC incidence for all treatments. Irrigation reduced CVC symptoms in trees, especially the number of symptomatic fruits per tree. Based on this significant reduction, citrus irrigation can be used to reduce the main negative effect of CVC: reduced fruit size. Our results also explain the higher incidence of CVC in the northern region of Sao Paulo, where a dry season occurs.

Citrus canker (Xanthomonas citri subsp. citri, Xcc) is one of the most serious diseases citrus in Florida, and elsewhere in the world. The disease causes yield loss and some fresh fruit trade restrictions may apply. Cultural management techniques such as windbreaks may work by not only reducing wind speed, but also reducing the period of exposure of susceptible foliage or fruit to those wind speeds that support infection from incoming inoculum. To investigate the effect of exposure period to inoculum of Xcc, seedlings of canker-susceptible Swingle citrumelo were exposed to sprayed inoculum for increasing periods at different wind speeds. The incidence and severity of citrus canker was assessed. In three experiments the incidence and severity of citrus canker most often increased with longer periods of exposure to inoculum, especially so at wind speeds of ≥16 m/s compared to wind speeds of ≤5 m/s (wind speed also increased disease incidence and severity). Regression analysis demonstrated relationships between period of exposure to inoculum and the percent infected leaves per plant, the number of lesions per plant, the number of lesions per infected leaf, and for the percent of infected leaves with lesions on the petioles at wind speeds of ≥16 m/s (R2 = 0.16–0.72). Due to the effect of inoculum exposure period and wind speed, attempts should be made to minimize exposure of canker-susceptible citrus when wind speed is highest and inoculum is available. Windbreaks should help minimize periods of exposure to splashed inoculum in high winds.

Citrus canker [caused by Xanthomonas citri subsp. citri (Xcc)] can cause yield loss of susceptible citrus and result in trade restrictions of fresh fruit. For both regulatory purposes and epidemiological studies, accurate detection and quantification of viable inoculum are critical. Two accepted methods used to detect and quantify Xcc are injection–infiltration bioassay and culture, but these two methods have not been directly compared using field-obtained samples. The two methods were compared using washates of lesions taken from fruit, leaves and shoots in a commercial orchard in Florida in 2009–2010 and 2010–2011, with bioassay being the assumed standard. Despite some misclassifications, true positives (sensitivity) and true negatives (specificity) were the dominant classes using culture. False positives for lesions from shoots ranged from 13.1 to 21.4% in 2009–2010 and 2010–2011, respectively, and false positives for lesions from fruit and leaves ranged from 4.3 to 15.7%, in the two seasons, respectively. The false positive rate for culture compared with injection–infiltration bioassay was highest (0.16–0.55), due to more frequent recovery of Xcc by culture at ≤103 colony-forming units (CFU) Xcc per ml. The false negative rate was consistently lower (0.02–0.21), confirming that in only a few cases did culture fail to detect Xcc when it was present. The area under the curve for receiver operator characteristic analysis ranged from 0.80 to 0.97, confirming that culture provided an accurate diagnosis in most cases. There was a higher frequency of lesions from shoots with a CFU ≤103 Xcc compared with lesions from fruit or leaves, making culture more effective at detecting these. The data demonstrate that culture is a reliable way to detect and quantify Xcc compared with injection–infiltration bioassay, particularly when the CFU is ≤103 Xcc per ml.

Asiatic huanglongbing (HLB) is a devastating disease of citrus associated in North America with the bacterium ‘Candidatus Liberibacter asiaticus’ (LAS) vectored by the Asian citrus psyllid (ACP), Diaphorina citri Kuwayama. ACP management is considered a vital component of a program aimed at reducing the incidence and spread of HLB. Considerable research has been published comparing the efficacy of different insecticides for ACP control as well as on seasonal strategies for applying ACP insecticides. However, published information was largely lacking for even the most intense insecticide programs on their effectiveness for keeping HLB out of a new citrus planting in Florida citrus. We therefore conducted two replicated (individual plots 0.2 to 0.4 ha in size) experiments on protecting young citrus from HLB using different ACP management programs. An intensive insecticide program was evaluated in each experiment: eight annual calendar applications of traditional insecticides (hereafter referred to as the “complete” program). In one experiment, citrus was either planted alone and subjected to the complete program or citrus was interplanted with orange jasmine, Murraya exotica L. (a favored ACP host plant) and subjected to a reduced insecticide program (four calendar sprays of traditional insecticides). There was one set of plots in which both jasmine and citrus were treated with insecticides and one set in which jasmine was not treated at all. In the second experiment, citrus was either subjected to the complete program or to one of two other programs: a reduced insecticide program consisting of five calendar applications of traditional insecticides or a mineral oil program (oil applications every 3 weeks plus one dormant insecticide spray). The results of the two experiments were similar. Relatively good ACP control was achieved under each ACP management program during the first year but, as the experiments progressed and trees increased in size, ACP outbreaks occurred regardless of the psyllid management program. Little HLB developed under any ACP management program during the first year, but thereafter HLB increased and large percentages of the trees in each experiment became LAS-infected in less than two to three years. The combined results of the experiments indicated that up to eight monthly pesticide treatments per year applied on a calendar schedule were ineffective for preventing young citrus from becoming diseased. Of important significance is that the orchard within which the two experiments were conducted was subjected to a minimal psyllid management program and contained many older trees known to be infected by the HLB pathogen, a challenging situation for getting young trees into production without contracting the disease. Thus, the ACP management programs we evaluated might have been more effective if ACP in the surrounding areas had been more aggressively controlled and diseased trees in the surrounding areas removed to reduce inoculum loads. Also, the programs might have been more effective for slowing the spread of HLB if our research plots had been larger.

Author(s): Gottwald, Tim R.; McCollum, Thomas G. | Abstract: Citrus huanglongbing (HLB) has been recognized for a century yet control and management remain elusive despite over 90 years of intensive research. The bacterial pathogen is an insect endosymbiont that was most likely inadvertently introduced into citrus where it found a compatible environment for growth in citrus phloem cells and therefore jumped from the animal to plant kingdom. Because the genus citrus did not coevolve with the bacteria it has no resistance and little tolerance to it and the resulting vascular disease is severe. The winged insect vector of the bacteria, the Asian citrus psyllid (ACP), is an exotic introduced species in its own right, prolific, and difficult to control even on a regional spatial scale. The resulting disease has a long latent period prior to symptom expression and a challenging cryptic period during which detection by convention PCR and other methods can be elusive. The result is an unusually rapid increase and spread of the resulting disease. This article offers some nonconventional perspectives to examine this unusual and devastating pathosystem to stimulate though toward improved control/mitigation.

A two-year field study was conducted in an orange grove in the United States (Florida) to characterize the phenology of the entomopathogen Hirsutella citriformis Speare infecting adults of the Asian citrus psyllid, Diaphorina citri Kuwayama. On the average, 23% of adults observed on mature leaves were killed by H. citriformis. These dead psyllids were characterized as being mummified and covered to various extents by synnemata produced by the fungus. Mummified cadavers were most abundant on citrus leaves during the fall and winter months, with the maximal percentage of mummified psyllids sometimes exceeding 75% of the total number of adults observed. Mummified cadavers were nearly absent each spring, presumably because relative humidity levels were suboptimal for the fungus at this time. Based on dispersion analyses, a monitoring plan for mummified cadavers would best include multiple samples in individual trees as well as multiple tree samples throughout a grove. Mummified cadavers with synnemata, which serve as point sources for new infections of the fungus in psyllids, were observed to remain on leaves for a mean of 68 days (one cadaver remained on a leaf for 168 days). Rainfall was positively correlated with the number of days mummies remained on leaves while mean daily air temperature was negatively correlated. Mummified cadavers were abundant in the summer during 2006 but not during 2007. This may have been a density-dependent consequence of low psyllid host populations in the grove in 2007. Alternatively, combination sprays of oil and copper applied during 2007 may have suppressed the fungus. This latter possibility prompted a laboratory investigation into the toxicity to H. citriformis of six chemicals commonly used in citrus. Copper hydroxide, petroleum oil, and elemental sulfur at maximum label rates each significantly reduced the infectivity of a laboratory culture of H. citriformis while copper sulfate pentahydrate, aluminum tris and alpha-keto/humic acids did not. This finding indicates that citrus growers interested in capitalizing on H. citriformis as a biological control agent of D. citri should avoid applying high rates of copper hydroxide, oil or sulfur.

Huanglongbing (HLB) is the most destructive citrus pathosystem worldwide. Previously known primarily from Asia and Africa, it was introduced into the Western Hemisphere in 2004. All infected commercial citrus industries continue to decline owing to inadequate current control methods. HLB increase and regional spatial spread, related to vector populations, are rapid compared with other arboreal pathosystems. Disease dynamics result from multiple simultaneous spatial processes, suggesting that psyllid vector transmission is a continuum from local area to very long distance. Evolutionarily, HLB appears to have originated as an insect endosymbiont that has moved into plants. Lack of exposure of citrus to the pathogen prior to approximately 100 years ago did not provide sufficient time for development of resistance. A prolonged incubation period and regional dispersal make eradication nonviable. Multiple asymptomatic infections per symptomatic tree, incomplete systemic distribution within trees, and prolonged incubation period make detection difficult and greatly complicate disease control.

Citrus canker (caused by the bacterial pathogen Xanthomonas citri subsp. citri, Xcc) can cause severe damage to citrus. It is endemic in Florida, and occurs in other citrus growing regions. The bacterium is dispersed predominantly in rain splash. To simulate dispersal in splash, and to investigate the effect of wind speed on infection, young plants of Swingle citrumelo were exposed to sprayed inoculum at different wind speeds. Wind was generated using an axial fan, and a pressurized sprayer delivered the inoculum spray. In the five experiments, higher wind speeds (>10 m s−1) consistently resulted in higher incidence and severity of citrus canker developing. By 15 ms−1, there was a dramatic increase in disease. Visible injury to leaves of Swingle citrumelo due to wind was evident at wind speeds ≥ 13 m s−1. The relationship between wind speed and disease, and wind speed and injury was described by a logistic model. More disease was associated with visible injury as the wind speed increased, and disease not associated with visible injury also increased with wind speed. The petiole-leaflet junction was more often infected at higher wind speeds (≥17 m s−1). The concentration of the Xcc inoculum increased the incidence and severity of citrus canker in all experiments. Reducing wind speed in citrus groves with the aid of wind breaks may contribute to a reduction in the severity of an epidemic by reducing dispersal and infection events.

Fourier transform infrared (FTIR) spectroscopy has the ability to quickly identify the presence of specific carbohydrates in plant materials. The presence of the disease huanglongbing (HLB) in the leaves of infected citrus plants has a distinctive spectrum that can be used to distinguish an infected plant from a healthy plant. However, many citrus diseases display similar visible symptoms and are of concern to citrus growers. In this study several citrus diseases (citrus leaf rugose virus, citrus tristeza virus, citrus psorosis virus, and Xanthomonas axonopodis ) and nutrient deficiencies (iron, copper, zinc, manganese, and magnesium) were compared with HLB using FTIR spectroscopy to determine if the spectra alone can be used to identify plants that are infected with HLB instead of another disease. The results indicate that the spectra of some diseases and deficiencies more closely resemble those of apparently healthy plants and some share the carbohydrate transformation that has been seen in the spectra of HLB-infected plants.

Citrus huanglongbing is the most destructive disease of citrus worldwide. It is spread by citrus psyllids and is associated with a low-titer, phloem-limited infection by any of three uncultured species of α-Proteobacteria, ‘Candidatus Liberibacter asiaticus’, ‘Ca. L. americanus’, and ‘Ca. L. africanus’. A complete circular ‘Ca. L. asiaticus’ genome has been obtained by metagenomics, using the DNA extracted from a single ‘Ca. L. asiaticus’–infected psyllid. The 1.23-Mb genome has an average 36.5% GC content. Annotation revealed a high percentage of genes involved in both cell motility (4.5%) and active transport in general (8.0%), which may contribute to its virulence. ‘Ca. L. asiaticus’ appears to have a limited ability for aerobic respiration and is likely auxotrophic for at least five amino acids. Consistent with its intracellular nature, ‘Ca. L. asiaticus’ lacks type III and type IV secretion systems as well as typical free-living or plant-colonizing extracellular degradative enzymes. ‘Ca. L. asiaticus’ appears to have all type I secretion system genes needed for both multidrug efflux and toxin effector secretion. Multi-protein phylogenetic analysis confirmed ‘Ca. L. asiaticus’ as an early-branching and highly divergent member of the family Rhizobiaceae. This is the first genome sequence of an uncultured α-proteobacteria that is both an intracellular plant pathogen and insect symbiont.

Brevipalpus phoenicis (Geijskes) (Acari: Tenuipalpidae) is a polyphagous mite with worldwide distribution and it is also a vector of several plant viruses. In citrus, B. phoenicis transmits Citrus leprosis virus (CiLV), the causal agent of leprosis, a disease that costs millions of dollars per year for its prevention and control. Brevipalpus phoenicis mites reproduce through thelytokous parthenogenesis, producing haploid females. This characteristic is attributable to the presence of an endosymbiont bacterium of the genus Cardinium; however, very little is known about the biological and ecological implications of the presence of this endosymbiont in Brevipalpus mites. In order to investigate the role of Cardinium in the transmission of CiLV to citrus plants, our goal was to eliminate the bacterium from the mite. We assessed the effectiveness of different doses of radiation from a Cobalt-60 source to cure B. phoenicis populations from Cardinium sp. The efficiency of irradiation on the elimination of the endosymbiont was determined by counting the number of females and males obtained in the F(1) generation after irradiation and confirming the presence of the endosymbiont by PCR. Both radiation treatments influenced the oviposition period and the number of eggs laid by irradiated females. Also, irradiation eliminated the Cardinium endosymbiont and increased the number of males in progeny of the exposed populations. Although macroscopic morphological abnormalities were not observed among the treated mites, the mortality was higher compared to the non-irradiated control group.

plaguing citrus industries in the Western Hemisphere. The two largest citrus producing areas in the Americas, located in Florida and the states of Sao Paulo, Parana and Minas Geris, Brazil, are presently battling these devastating diseases. The presence of these diseases in the Florida and Brazilian citrus industries also poses an imminent threat to other major citrus producing areas within the US, such as California, Texas, and Arizona and the important northern citrus producing areas in Argentina.

A Clorose Variegada dos Citros (CVC) tem sido considerada a mais importante doença citrícola no Brasil, mas diversos aspectos de sua epidemiologia ainda não são bem conhecidos. O presente trabalho objetivou estudar o arranjo espacial das plantas afetadas, visando caracterizar a dinâmica da doença em três regiões do Estado de São Paulo (Noroeste, Centro e Sul). Por meio de avaliação de sintomas visuais, foram mapeados, quinzenalmente, três talhões de laranja-doce (Citrus sinensis) Pêra enxertada em limão Cravo (Citrus limonia), em três regiões do Estado de São Paulo, desde julho de 1998 até dezembro de 2000. Para o estudo da dinâmica espacial, foram aplicadas as seguintes análises: seqüências ordinárias; áreas isópatas; lei de Taylor modificada; índice de dispersão e análise de dinâmica e estrutura de focos. As seqüências ordinárias indicaram uma tendência à aleatoriedade na maioria das avaliações, indicando baixa transmissão a plantas imediatamente vizinhas. A análise de áreas isópatas mostrou pouca formação de focos compactos, numa tendência à uniformidade da incidência da CVC. As demais análises demonstraram pouca diferença no padrão espacial da doença entre as regiões, que pode ser considerado levemente agregado.

BGPI - Equipe 6 Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; International audience; The spatial pattern of Sharka disease, caused by Plum pox virus (PPV) strain M, was investigated in 18 peach plots located in two areas of southern France. PPV infections were monitored visually for each individual tree during one to three consecutive years. Point pattern and correlation-type approaches were undertaken using the binary data directly or after parsing them in contiguous quadrats of 4, 9, and 16 trees. Ordinary runs generally revealed a low but variable proportion of rows with adjacent symptomatic trees. Aggregation of disease incidence was indicated by the θ parameter of the beta-binomial distribution and related indices in 15 of the 18 plots tested for at least one assessment date of each. When aggregation was detected, it was indicated at all quadrat sizes and tended to be a function of disease incidence, as shown by the binary form of Taylor's power law. Spatial analysis by distance indices (SADIE) showed a nonrandom arrangement of quadrats with infected trees in 14 plots. The detection of patch clusters enclosing quadrats with above-average density of symptomatic trees, ellipsoidal in shape and generally extending from 4 to 14 trees within rows and from 4 to 10 trees perpendicular to the rows, could be interpreted as local areas of influence of PPV spread. Spatial patterns at the plot scale were often characterized by the occurrence of several clusters of infected trees located up to 90 m apart in the direction of the rows. When several time assessments were available, increasing clustering over time was generally evidenced by stronger values of the clustering index and by increasing patch cluster size. The combination of the different approaches revealed a wide range of spatial patterns of PPV-M, from no aggregation to high aggregation of symptomatic trees at all spatial scales investigated. Such patterns suggested that aphid transmission to neighboring trees occurred frequently but was not systematic. The mechanism of primary virus introduction, the age and structure of the orchards when infected, and the diversity of vector species probably had a strong influence on the secondary spread of the disease. This study provides a more complete understanding of PPV-M patterns which could help to improve targeting of removal of PPV-infected trees for more effective disease control.

Este trabalho objetivou esclarecer se o progresso da Clorose Variegada dos Citros (CVC) diferia entre três regiões de São Paulo, distintas quanto à incidência da CVC em citrus (Citrus spp.). Foram avaliadas três áreas, Noroeste, Centro e Sul de São Paulo, durante dois anos, em avaliações quinzenais, quando eram mapeadas as plantas sintomáticas. Tentou-se o ajuste de nove modelos ao progresso da doença, além do ajuste de três modelos a segmentos das curvas originais. Foram estimadas também as diferenciais e as diferenciais secundárias de cada curva de progresso. Apenas quando as curvas foram divididas é que foram obtidos bons ajustes aos modelos de progresso. A diferencial (velocidade da doença) e diferencial secundária (aceleração do aparecimento de novas plantas doentes) apresentaram diversos picos ao longo do tempo. Esses picos ocorreram em meses de Primavera e Verão. Levanta-se aqui a hipótese de que os picos de diferencial - incomuns na quantidade encontrada - estejam relacionados a determinados picos de emissão de brotações, já que as novas brotações são o local preferido de alimentação dos vetores de Xylella fastidiosa. This study aimed to discover if the incidence differences between three regions in the State of São Paulo, Brazil could be related to different dynamics of Citrus Variegated Chlorosis (CVC) progress. Three areas of the State (Northwest, Center and South) were evaluated by visual assessments performed two times a month for two years. For each evaluation all plants were inspected and designated as diseased or healthy. Nine models were fit to each CVC progress curve, and three were fit to segments of original curves. Also, first and second derivatives were estimated for each curve. A good fit was obtained for segments of original curves. First and second derivatives showed many peaks over time. Most of those peaks occurred during the spring and summer months. Our hypothesis is that derivative peaks are related to flush emission peaks, considering that new sprouts are the preferred feed sites of Xylella fastidiosa vectors.

Experimental inoculations of Xanthomonas axonopodis pv. citri in different tissues of Tahiti lime and Pineapple sweet orange were conducted monthly under natural conditions on Réunion Island. The interactions between a set of environmental and epidemic variables associated with disease expression and 184 different factor combinations were investigated to determine the parameters needed to explain Asiatic citrus canker (ACC) disease expression. Area under the disease progress curve (AUDPC), inoculation date (Id), fruit and leaf age ratings (FAR and LAR), and number of days during the first 2 weeks postinoculation for which the temperature was less than 14°C (Tmin) or more than 28°C (Tmax) were retained by principal component analysis and canonical correlation analysis as the most meaningful epidemic and environmental variables, respectively. AUDPC as the strongest dependent variable and combinations of the environmental variables as independent variables were used in multiple regression analyses. Tissue age rating at the time of infection was a good predictor for disease resulting from spray inoculation on fruits and leaves and also on fruits following a wound inoculation. Temperature, as expressed by Tmin or Tmax, was also a significant factor in determining disease development described by AUDPC. Mature green stems were highly susceptible after wounding, similarly to leaves, but buds and leaf scars expressed the lowest susceptibility. These variations in disease expression according to the tissues will have different impacts on ACC epidemiology.

Citrus sudden death (CSD), a new disease of unknown etiology that affects sweet orange grafted on Rangpur lime, was visually monitored for 14 months in 41 groves in Brazil. Ordinary runs analysis of CSD-symptomatic trees indicated a departure from randomness of symptomatic trees status among immediately adjacent trees mainly within rows. The binomial index of dispersion (D) and the intraclass correlation (k) for various quadrat sizes suggested aggregation of CSD-symptomatic trees for almost all plots within the quadrat sizes tested. Estimated parameters of the binary form of Taylor's power law provided an overall measure of aggregation of CSD-symptomatic trees for all quadrat sizes tested. Aggregation in each plot was dependent on disease incidence. Spatial autocorrelation analysis of proximity patterns suggested that aggregation often existed among quadrats of various sizes up to three lag distances; however, significant lag positions discontinuous from main proximity patterns were rare, indicating a lack of spatial association among discrete foci. Some asymmetry was also detected for some spatial autocorrelation proximity patterns, indicating that within-row versus across-row distributions are not necessarily equivalent. These results were interpreted to mean that the cause of the disease was most likely biotic and its dissemination was common within a local area of influence that extended to approximately six trees in all directions, including adjacent trees. Where asymmetry was indicated, this area of influence was somewhat elliptical. Longer-distance patterns were not detected within the confines of the plot sizes tested. Annual rates of CSD progress based on the Gompertz model ranged from 0.37 to 2.02. Numerous similarities were found between the spatial patterns of CSD and Citrus tristeza virus (CTV) described in the literature, both in the presence of the aphid vector, Toxoptera citricida. CSD differs from CTV in that symptoms occur in sweet orange grafted on Rangpur lime. Based on the symptoms of CSD and on its spatial and temporal patterns, our hypothesis is that CSD may be caused by a similar but undescribed pathogen such as a virus and probably vectored by insects such as aphids by similar spatial processes to those affecting CTV.

BGPI : équipe 6; Many plant epidemics that cause major economic losses cannot be controlled with pesticides. Among them, sharka epidemics severely affect prunus trees worldwide. Its causal agent, Plum pox virus (PPV; genus Potyvirus), has been classified as a quarantine pathogen in numerous countries. As a result, various management strategies have been implemented in different regions of the world, depending on the epidemiological context and on the objective (i.e., eradication, suppression, containment, or resilience). These strategies have exploited virus-free planting material, varietal improvement, surveillance and removal of trees in orchards, and statistical models. Variations on these management options lead to contrasted outcomes, from successful eradication to widespread presence of PPV in orchards. Here, we present management strategies in the light of sharka epidemiology to gain insights from this worldwide experience. Although focused on sharka, this review highlights more general levers and promising approaches to optimize disease control in perennial plants. Expected final online publication date for the Annual Review of Phytopathology Volume 53 is August 04, 2015. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.

Huanglongbing (HLB), a systemic and destructive disease of citrus, is associated with 'Candidatus Liberibacter asiaticus' (Las) in the United States. Our earlier work has shown that Las bacteria were significantly reduced or eliminated when potted HLB-affected citrus were continuously exposed to high temperatures of 40 to 42 °C for a minimum of 48 h. To determine the feasibility and effectiveness of solar thermotherapy in the field, portable plastic enclosures were placed over commercial and residential citrus, exposing trees to high temperatures through solarization. Within 3-6 weeks after treatment, most trees responded with vigorous new growth. Las titer in new growth was greatly reduced for 18-36 months after treatment. Unlike with potted trees, exposure to high heat did not eradicate the Las population under field conditions. This may be attributed to reduced temperatures at night in the field compared to continuous high temperature exposure that can be maintained in growth chambers, and the failure to achieve therapeutic temperatures in the root zone. Despite the presence of Las in heat-treated commercial citrus, many trees produced abundant flush and grew vigorously for 2 to 3 years after treatment. Transcriptome analysis comparing healthy trees to HLB-affected citrus both before and after heat treatment demonstrated that post-treatment transcriptional expression patterns more closely resembled the expression patterns of healthy controls for most differentially expressed genes and that genes involved with plant-bacterium interactions are upregulated after heat treatment. Overall, these results indicate that solar thermotherapy can be an effective component of an integrated control strategy for citrus HLB.

Field data on intensity of plant diseases is very often irregularly spaced (i.e., there are varying amounts of distance between rows, ponds, voids, roads, houses, or other land areas). Typically, this type of data is gridded and the average disease intensity of the plants within the grid is used instead of the original data on each separate plant. This is done because the underlying statistical assumptions in the analysis of spatial data usually require that data be equally spaced. However, a new method of analysis, sometimes called second-generation wavelet analysis, can be used on irregularly spaced spatial data. Wavelet analysis is a method used to analyze variations in scale and position of non-stationary spatial signals (non-stationary for our data means the statistical properties can vary based on location within the orchard), and the second-generation refers to an iterative process, called a lifting scheme (1), which allows for the irregular spacing. Irregular spacing is often found in citrus groves as spacing within and between rows is often not uniform, and on a larger spatial scale, distance between blocks and plantings are not necessarily simple multiples of distances between rows and trees. In addition, there are a number of other issues such as missing trees, the presence of irregular roads, ponds, staging areas, etc., that cause citrus groves to have irregular distances between trees when viewed at the plantation or regional scale. Therefore, to test this new method, we conducted a second-generation spatial wavelet analysis on a large irregularly spaced citrus planting (Southern Gardens) in Florida where over 260,000 trees were assessed for incidence of huanglongbing (HLB) over five sampling times.

Candidatus Liberibacter americanus and Candidatus Liberibacter asiaticus are two bacterial species that cause huanglongbing (HLB) disease in citrus-growing regions of Brazil. A concentrated sampling plan of a grove in Matao, Brazil was initiated to evaluate the spatial and temporal spread of these bacteria. The exact location of each of 8697 trees was recorded, and each symptomatic tree was assessed by PCR for the presence of Ca. L. americanus and Ca. L. asiaticus during 17 different months from April 2006 to May 2008 (Fig. 1). In the first month, only five trees were confirmed to have Ca. L. asiaticus. The first trees with confirmed cases of Ca. L. americanus were not found until February 2007. By the end of the study, 43 trees were confirmed to have Ca. L. americanus, 1164 trees were confirmed to have Ca. L. asiaticus, and three trees were coinfected.

This chapter provides insights into the types of biotic threats to plants, the nature of the U.S. plant health infrastructure, the resources available to address and mitigate losses due to emerging plant diseases, and whether they arise as a result of the arrival of exotic pathogens, the mutation of endemic pathogens, or the intentional dissemination of pathogens by perpetrators wishing to cause harm. Pathogens of plants, like those of animal and human hosts, belong to a number of different taxa including fungi, oomycetes, bacteria, viruses, nematodes, protozoa, and even parasitic plants. Technologies relying on more complex chemistry and instrumentation, such as PCR, microarrays, or sequence-based assays, may provide definitive identification of a pathogen but lack portability and thus are more often deployed in clinical laboratories. Natural means of spread include weather, biological features such as aerodynamic spore morphology, the involvement of biological vectors, moving water, and even being borne on seeds or pollen, which are adapted for their own dissemination. These mechanisms, and their implications for disease epidemiology, are discussed in the chapter. Emerging, infectious plant diseases have long been of concern not only to growers and plant pathologists but also to legislators and policy makers. Although plant diseases generally do not cause immediate, acute, or lethal consequences for humans, they can and do result in significant economic harm, as trade is affected, and rural communities and downstream industries experience the impacts of crop quarantines, trade embargoes, and loss of income.

Outbreaks of infectious diseases require a rapid response from policy makers. The choice of an adequate level of response relies upon available knowledge of the spatial and temporal parameters governing pathogen spread, affecting, amongst others, the predicted severity of the epidemic. Yet, when a new pathogen is introduced into an alien environment, such information is often lacking or of no use, and epidemiological parameters must be estimated from the first observations of the epidemic. This poses a challenge to epidemiologists: how quickly can the parameters of an emerging disease be estimated? How soon can the future progress of the epidemic be reliably predicted? We investigate these issues using a unique, spatially and temporally resolved dataset for the invasion of a plant disease, Asiatic citrus canker in urban Miami. We use epidemiological models, Bayesian Markov-chain Monte Carlo, and advanced spatial statistical methods to analyse rates and extent of spread of the disease. A rich and complex epidemic behaviour is revealed. The spatial scale of spread is approximately constant over time and can be estimated rapidly with great precision (although the evidence for long-range transmission is inconclusive). In contrast, the rate of infection is characterised by strong monthly fluctuations that we associate with extreme weather events. Uninformed predictions from the early stages of the epidemic, assuming complete ignorance of the future environmental drivers, fail because of the unpredictable variability of the infection rate. Conversely, predictions improve dramatically if we assume prior knowledge of either the main environmental trend, or the main environmental events. A contrast emerges between the high detail attained by modelling in the spatiotemporal description of the epidemic and the bottleneck imposed on epidemic prediction by the limits of meteorological predictability. We argue that identifying such bottlenecks will be a fundamental step in future modelling of weather-driven epidemics., Author Summary We consider emerging epidemics, arising, e.g., when a new pathogen is introduced in a host population. In face of the new threat, crucial control measures have to be implemented quickly, yet prior knowledge of the parameters underlying pathogen spread and transmission is often missing. Predictive modelling can greatly help in informing decision making by estimating those parameters from early observations of the outbreak. The important questions are then: can a modeller characterise the disease “soon enough,” i.e., within a useful time frame, in order to enact the proper control measures? At what stage of the outbreak can the future epidemic progress be reliably predicted? We analyse an outbreak of citrus canker, a wind-spread bacterial disease of citrus, in urban Miami. The model succeeds in capturing the main epidemiological features of the disease, but we find contrasting answers. The spatial scale of disease spread can be identified quickly and accurately from early observations. However, the rate of spread is rapidly changing in time, driven mainly by rare thunderstorms with very short-time predictability, which frustrates epidemic prediction.

Aphid vector species population composition is known to affect the spatial patterns of citrus tristeza virus (CTV) and the changes in these patterns over time. However, the biological processes that are associated with virus spread have not been well defined. The spatiotemporal dynamics of CTV were examined using data collected from research plots in the Dominican Republic and Costa Rica, where the brown citrus aphid (BCA), Toxoptera citricida, was the predominant species, and in Florida, where the BCA was absent and the melon aphid, Aphis gossypii, was the predominant vector. Data were analyzed using a spatiotemporal stochastic model for disease spread, and parameter values were evaluated using Markov chain Monte Carlo stochastic integration methods. Where the melon aphid was the dominant species, the model parameter likelihood values supported the hypothesis that the disease was spread through a combination of random background transmission (transmission originating from inoculum sources outside the plot) and a local interaction (transmission from inoculum sources within the plot) operating over short distances. Conversely, when BCA was present, results often suggested a local short-range transmission interaction that was not restricted to nearest-neighbor interactions and that the presence of background infection was not necessary to explain the observations.

Plant pathologists most often obtain quantitative information on disease severity using visual assessments. Category scales have been used for assessing plant disease severity in field experiments, epidemiological studies, and for screening germplasm. The most widely used category scale is the Horsfall-Barratt (H-B) scale, but reports show that estimates of disease severity using the H-B scale are less precise compared with nearest percent estimates (NPEs) using the 0 to 100% ratio scale. Few studies have compared different category scales. The objective of this study was to compare NPEs, the H-B midpoint converted data, and four different linear category scales (5 and 10% increments, with and without additional grades at low severity [0.1, 0.5, 1.0, 2.0, 5.0, 10.0, 15.0, 20.0…100%, and 0.1, 0.5, 1.0, 2.0, 5.0, 10.0, 20.0, 30.0…100%, respectively]). Results of simulations based on known distributions of disease estimation using the type II error rate (the risk of failing to reject H0 when H0 is false) showed that at disease severity ≤5%, a 10% category scale had a greater probability of failing to reject H0 when H0 is false compared with all other methods, while the H-B scale performed least well at 20 to 50% severity. The 5% category scale performed as well as NPEs except when disease severity was ≤1%. Both the 5 and 10% category scales with the additional grades included performed as well as NPEs. These results were confirmed with a mixed model analysis and bootstrap analysis of the original rater assessment data. A better knowledge of the advantages and disadvantages of category scale types will provide a basis for plant pathologists and plant breeders seeking to maximize accuracy and reliability of assessments to make an informed decision when choosing a disease assessment method.

The spread of Huanglongbing through citrus groves is used as a case study for modeling an emerging epidemic in the presence of a control. Specifically, the spread of the disease is modeled as a susceptible-exposed-infectious-detected-removed epidemic, where the exposure and infectious times are not observed, detection times are censored, removal times are known, and the disease is spreading through a heterogeneous host population with trees of different age and susceptibility. We show that it is possible to characterize the disease transmission process under these conditions. Two innovations in our work are (i) accounting for control measures via time dependence of the infectious process and (ii) including seasonal and host age effects in the model of the latent period. By estimating parameters in different subregions of a large commercially cultivated orchard, we establish a temporal pattern of invasion, host age dependence of the dispersal parameters, and a close to linear relationship between primary and secondary infectious rates. The model can be used to simulate Huanglongbing epidemics to assess economic costs and potential benefits of putative control scenarios.