Bayesian analysis for inference of an emerging epidemic: citrus canker in urban landscapes.

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.FMN gratefully acknowledges financial support from BBSRC, USDA-ARS, USDA-Aphis PPQ, Citrus Research and Development Foundation. CAG gratefully acknowledges the support of a BBSRC Professorial Fellowship, with additional support from USDA and Defra. ARC was supported by BBSRC, USDA, the National University of Singapore, and NMRC. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Cost-effective control of plant disease when epidemiological knowledge is incomplete: modelling Bahia bark scaling of citrus.

A spatially-explicit, stochastic model is developed for Bahia bark scaling, a threat to citrus production in north-eastern Brazil, and is used to assess epidemiological principles underlying the cost-effectiveness of disease control strategies. The model is fitted via Markov chain Monte Carlo with data augmentation to snapshots of disease spread derived from a previously-reported multi-year experiment. Goodness-of-fit tests strongly supported the fit of the model, even though the detailed etiology of the disease is unknown and was not explicitly included in the model. Key epidemiological parameters including the infection rate, incubation period and scale of dispersal are estimated from the spread data. This allows us to scale-up the experimental results to predict the effect of the level of initial inoculum on disease progression in a typically-sized citrus grove. The efficacies of two cultural control measures are assessed: altering the spacing of host plants, and roguing symptomatic trees. Reducing planting density can slow disease spread significantly if the distance between hosts is sufficiently large. However, low density groves have fewer plants per hectare. The optimum density of productive plants is therefore recovered at an intermediate host spacing. Roguing, even when detection of symptomatic plants is imperfect, can lead to very effective control. However, scouting for disease symptoms incurs a cost. We use the model to balance the cost of scouting against the number of plants lost to disease, and show how to determine a roguing schedule that optimises profit. The trade-offs underlying the two optima we identify-the optimal host spacing and the optimal roguing schedule-are applicable to many pathosystems. Our work demonstrates how a carefully parameterised mathematical model can be used to find these optima. It also illustrates how mathematical models can be used in even this most challenging of situations in which the underlying epidemiology is ill-understood.FFL was funded via a CNPq Fellowship (Brazil's National Council for Scientific and Technological Development, see http://memoria.cnpq.br/english/cnpq/index.htm). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Statement complementing the EFSA Scientific Opinion on application (EFSA‐GMO‐UK‐2006‐34) for authorisation of food and feed containing, consisting of and produced from genetically modified maize 3272

Following a request from the European Commission, the GMO Panel assessed additional information related to the application for authorisation of food and feed containing, consisting of and produced from genetically modified (GM) maize 3272 (EFSA‐GMO‐UK‐2006‐34). The applicant conducted new agronomic, phenotypic and compositional analysis studies on maize 3272 and assessed the allergenic potential of AMY797E protein, addressing elements that remained inconclusive from previous EFSA opinion issued in 2013. The GMO Panel is of the opinion that the agronomic and phenotypic characteristics as well as forage and grain composition of maize 3272 do not give rise to food and feed safety, and nutritional concerns when compared to non‐GM maize. Considering the scope of this application and the characteristics of the trait introduced in this GM maize, the effect of processing and potential safety implications of specific food or feed products remain to be further investigated. Regarding the allergenic potential of AMY797E protein and considering all possible food and feed uses of maize 3272, the Panel concludes that the information provided does not fully address the concerns previously raised by the Panel in 2013. Owing to the nature and the knowledge available on this protein family, it is still unclear whether under specific circumstances the alpha‐amylase AMY797E has the capacity to sensitise certain individuals and to cause adverse effects. To further support the safety of specific products of maize 3272, the applicant provided thorough information relevant for the allergenicity assessment of dried distiller grains with solubles (DDGS), which is the main product of interest for importation into the EU. Having considered the information provided on this product, the Panel is of the opinion that under the specific conditions of use described by the applicant, DDGS produced from maize 3272 does not raise concerns when compared to DDGS from non‐GM maize

Assessment of genetically modified maize MON 87427 × MON 89034 × MIR162 × MON 87411 and subcombinations, for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA‐GMO‐NL‐2017‐144)

Maize MON 87427 × MON 89034 × MIR162 × MON 87411 (four‐event stack maize) was produced by conventional crossing to combine four single events: MON 87427, MON 89034, MIR162 and MON 87411. The genetically modified organism (GMO) Panel previously assessed the four single maize events and four of the subcombinations and did not identify safety concerns. No new data on the single maize events or the four subcombinations that could lead to modification of the original conclusions on their safety were identified. The molecular characterisation, comparative analysis (agronomic, phenotypic and compositional characteristics) and the outcome of the toxicological, allergenicity and nutritional assessment indicate that the combination of the single maize events and of the newly expressed proteins and dsRNA in the four‐event stack maize does not give rise to food and feed safety and nutritional concerns. The GMO Panel concludes that the four‐event stack maize, as described in this application, is as safe as and nutritionally equivalent to its non‐GM comparator and the non‐GM reference varieties tested. In the case of accidental release of viable grains of the four‐event stack maize into the environment, this would not raise environmental safety concerns. The GMO Panel assessed the likelihood of interactions among the single events in the six maize subcombinations not previously assessed and concludes that these are expected to be as safe as and nutritionally equivalent to the single events, the previously assessed subcombinations and the four‐event stack maize. The post‐market environmental monitoring plan and reporting intervals are in line with the intended uses of the four‐event stack maize. Post‐market monitoring of food/feed is not considered necessary. The GMO Panel concludes that the four‐event stack maize and its subcombinations are as safe as its non‐GM comparator and tested non‐GM reference varieties with respect to potential effects on human and animal health and the environment

Assessment of genetically modified soybean MON 87705 × MON 87708 × MON 89788, for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA‐GMO‐NL‐2015‐126)

Soybean MON 87705 × MON 87708 × MON 89788 (three‐event stack soybean) was produced by conventional crossing to combine three single soybean events: MON 87705, MON 87708 and MON 89788. This combination is intended to alter the fatty acid profile in the seed (in particular increasing the levels of oleic acid) and tolerance to glyphosate‐based and dicamba herbicides. The Genetically Modified Organisms Panel previously assessed the three single soybean events and did not identify safety concerns. No new data on the single soybean events, leading to modification of the original conclusions on their safety have been identified. The molecular characterisation, comparative analysis (agronomic, phenotypic and compositional characteristics) and the outcome of the toxicological, allergenicity and nutritional assessment indicate that the combination of the single soybean events and of the newly expressed proteins in the three‐event stack soybean does not give rise to food and feed safety and nutritional concerns. In the case of accidental release of viable three‐event stack soybean seeds into the environment, this would not raise environmental safety concerns. The post‐market environmental monitoring plan and the reporting intervals are in line with the intended uses of soybean MON 87705 × MON 87708 × MON 89788. Considering the altered fatty acid profile of the three‐event stack soybean, a proposal for post‐market monitoring needs to be provided by the applicant. The GMO Panel notes that in the context of this application EFSA‐GMO‐NL‐2015‐126 the applicant did not provide a 90‐day study on MON 87705 soybean in line with the applicable legal requirements. Therefore, the GMO Panel is not in the position to finalise the risk assessment of soybean MON 87705 × MON 87708 × MON 89788 under the current regulatory frame

Assessment of genetically modified maize MZIR098 for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA‐GMO‐DE‐2017‐142)

Maize MZIR098 was developed to confer tolerance to glufosinate‐ammonium‐containing herbicides and resistance to certain coleopteran pests. The molecular characterisation data and bioinformatic analyses do not identify issues requiring food/feed safety assessment. None of the identified differences in the agronomic/phenotypic and compositional characteristics tested between maize MZIR098 and its conventional counterpart needs further assessment, except for neutral detergent fibre (NDF) in grains, which does not raise nutritional and safety concerns. The GMO Panel does not identify safety concerns regarding the toxicity and allergenicity of the eCry3.1Ab, mCry3A and PAT proteins as expressed in maize MZIR098, and finds no evidence that the genetic modification would change the overall allergenicity of maize MZIR098. In the context of this application, the consumption of food and feed from maize MZIR098 does not represent a nutritional concern in humans and animals. The GMO Panel concludes that maize MZIR098 is as safe as the conventional counterpart and non‐GM maize reference varieties tested, and no post‐market monitoring of food/feed is considered necessary. In the case of accidental release of viable maize MZIR098 grains into the environment, maize MZIR098 would not raise environmental safety concerns. The post‐market environmental monitoring plan and reporting intervals are in line with the intended uses of maize MZIR098. In conclusion, the GMO Panel considers that maize MZIR098, as described in this application, is as safe as its conventional counterpart and the non‐GM maize reference varieties tested with respect to potential effects on human and animal health and the environment

Assessment of genetically modified oilseed rape MS11 for food and feed uses, import and processing, under Regulation (EC) No 1829/2003 (application EFSA‐GMO‐BE‐2016‐138)

Oilseed rape MS11 has been developed to confer male sterility and tolerance to glufosinate‐ammonium‐containing herbicides. Based on the information provided in the application and in line with the scope of application EFSA‐GMO‐BE‐2016‐138, the genetically modified organism (GMO) Panel concludes that the molecular characterisation data and bioinformatic analyses do not identify issues requiring food/feed safety assessment. None of the identified differences in the agronomic/phenotypic characteristics tested between oilseed rape MS11 and its conventional counterpart needs further assessment. No conclusions can be drawn for the compositional analysis due to the lack of an appropriate compositional data set. No toxicological or allergenicity concerns are identified for the Barnase, Barstar and PAT/bar proteins expressed in oilseed rape MS11. Owing to the incompleteness of the compositional analysis, the toxicological, allergenicity and nutritional assessment of oilseed rape MS11 cannot be completed. In the case of accidental release of viable oilseed rape MS11 seeds into the environment, oilseed rape MS11 would not raise environmental safety concerns. The post‐market environmental monitoring plan and reporting intervals are in line with the scope of the application. Since oilseed rape MS11 is designed to be used only for the production of hybrid seed, it is not expected to be commercialised as a stand‐alone product for food/feed uses. Thus, seeds harvested from oilseed rape MS11 are not expected to enter the food/feed chain, except accidentally. In this context, the GMO Panel notes that, oilseed rape MS11 would not pose risk to humans and animals, while the scale of environmental exposure will be substantially reduced compared to a stand‐alone product

Assessment of genetically modified soybean MON 87751 × MON 87701 × MON 87708 × MON 89788 for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA‐GMO‐NL‐2016‐128)

Soybean MON 87751 × MON 87701 × MON 87708 × MON 89788 (four‐event stack soybean) was produced by conventional crossing to combine four single events: MON 87751, MON 87701, MON 87708 and MON 89788. The GMO Panel previously assessed the four single events and did not identify safety concerns. No new data on the single events have been identified that would lead to modification of the original conclusions on their safety. The molecular characterisation, comparative analysis (agronomic, phenotypic and compositional characteristics) and the outcome of the toxicological and allergenicity assessment indicate that the combination of the single soybean events and of the newly expressed proteins in the four‐event stack soybean does not give rise to food and feed safety and nutritional concerns. The GMO Panel concludes that the four‐event stack soybean, as described in this application, is as safe as and nutritionally equivalent to the non‐GM comparator and the non‐GM reference varieties tested. In the case of accidental release of viable seeds of the four‐event stack soybean into the environment, this would not raise environmental safety concerns. The post‐market environmental monitoring plan and reporting intervals are in line with the intended uses of the four‐event stack soybean. Post‐market monitoring of food/feed is not considered necessary. The GMO Panel concludes that the four‐event stack soybean is as safe as the non‐GM comparator and the tested non‐GM reference varieties with respect to potential effects on human and animal health and the environment