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We present an R package developed to quantify coronavirus disease 2019 (COVID-19) importation risk. Quantifying and visualizing the importation risk of COVID-19 from inbound travelers is urgent and imperative to trigger public health responses, especially in the early stages of the COVID-19 pandemic and emergence of new SARS-CoV-2 variants. We provide a general modeling framework to estimate COVID-19 importation risk using estimated pre-symptomatic prevalence of infection and air traffic data from the multi-origin places. We use Hong Kong as a case study to illustrate how our modeling framework can estimate the COVID-19 importation risk into Hong Kong from cities in Mainland China in real time. This R package can be used as a complementary component of the pandemic surveillance system to monitor spread in the next pandemic.

Predictive assessment of possible risks of FMD introduction from neighboring countries to the territory of eight RF Federal Districts was presented. The risk quantitative parameters were determined by experts, specialists in the field of FMD epidemiology. To implement the expert survey method most significant routes of infection introduction to the RF were determined. The experts performed FMD introduction risk assessment for each federal district and determined its score. As a result of statistical analysis the greatest probability was determined for the Far-Eastern Federal District. The North Caucasus and Siberian Federal Okrugs demonstrate lower probability. Basing on the obtained data the major routes of FMD introduction to the territory of the country were determined. Preventive vaccination of susceptible animal population is carried out in order to prevent FMD occurrence and spread in the zones at risk of its introduction. It is aimed at FMD outbreak prevention in the specified RF Subjects by inducing protective immunity in at least 81% of immunized cattle and at least 95% of immunized pigs.

In recent years, several generic risk assessment (RA) tools have been developed that can be applied to assess the incursion risk of multiple infectious animal diseases allowing for a rapid response to a variety of newly emerging or re-emerging diseases. Although these tools were originally developed for different purposes, they can be used to answer similar or even identical risk questions. To explore the opportunities for cross-validation, seven generic RA tools were used to assess the incursion risk of African swine fever (ASF) to the Netherlands and Finland for the 2017 situation and for two hypothetical scenarios in which ASF cases were reported in wild boar and/or domestic pigs in Germany. The generic tools ranged from qualitative risk assessment tools to stochastic spatial risk models but were all parameterized using the same global databases for disease occurrence and trade in live animals and animal products. A comparison of absolute results was not possible, because output parameters represented different endpoints, varied from qualitative probability levels to quantitative numbers, and were expressed in different units. Therefore, relative risks across countries and scenarios were calculated for each tool, for the three pathways most in common (trade in live animals, trade in animal products, and wild boar movements) and compared. For the 2017 situation, all tools evaluated the risk to the Netherlands to be higher than Finland for the live animal trade pathway, the risk to Finland the same or higher as the Netherlands for the wild boar pathway, while the tools were inconclusive on the animal products pathway. All tools agreed that the hypothetical presence of ASF in Germany increased the risk to the Netherlands, but not to Finland. The ultimate aim of generic RA tools is to provide risk-based evidence to support risk managers in making informed decisions to mitigate the incursion risk of infectious animal diseases. The case study illustrated that conclusions on the ASF risk were similar across the generic RA tools, despite differences observed in calculated risks. Hence, it was concluded that the cross-validation contributed to the credibility of their results.

Abstract This Technical Report describes the activities developed in the scope of the EU‐FORA Fellowship, within the work programme of risk assessment (RA) of exotic disease incursion and spread, developed at Wageningen Bioveterinary Research (WBVR). The programme focused on the work carried out in the Generic risk assessment for introduction of animal diseases (G‐RAID) project, which brings together a number of different generic RA tools from multiple European partners. The aim of the fellowship was to gain understanding of veterinary import risk assessment by using different RA tools and to learn how different algorithms can be used to calculate disease incursion risks. G‐RAID's tools cover a wide range of RA methodologies; from purely qualitative, to semi‐quantitative and fully stochastic quantitative methods, which allowed the fellow to understand a variety of algorithms used to produce the final risk estimate. The fellowship programme provided the fellow with the chance to learn in detail about how generic RAs are performed across Europe, understanding how to deal with the uncertainty and variability involved in RAs and the potential problems of data availability and reliability. The fellow made an inventory of publicly available databases on disease occurrence and international trade that could be used for import RA and assessed their quality and usefulness for the different generic RA tools. The programme also provided the fellow the opportunity to perform several import risk assessments using the RA tools of G‐RAID. She completed a RA on African swine fever using the MINTRISK model developed by WBVR. Furthermore, she assessed the risk of foot and mouth disease introduction using the Rapid Risk Assessment Tool (RRAT) model developed by WBVR and the COMPARE model developed by the Animal and Plant Health Agency (APHA). To this end, the fellow completed a short‐term visit to APHA, enabling her to have additional training in quantitative RA and to expand her professional network in this area.

Worldwide, amphibians are threatened by several factors including climate change and pathogens. One emerging fungal pathogen, Batrachochytrium salamandrivorans (Bsal) has caused die-offs of European salamander populations, representing a conservation concern for hotspots of salamander diversity in the United States of America (U.S.A). While Bsal has not been detected in the U.S.A., previous work has suggested high invasion potential. As species susceptibility to Bsal is temperature dependent, we expect climate change to impact Bsal risk, which has not been explored. Here, we used predicted changes in environmental conditions, species-specific susceptibility estimates, and novel approaches assessing introduction risks to estimate current and future Bsal invasion risk. To generate predictions, we used geospatial data representing introduction risks, species susceptibility, and climatic suitability. Across climatic scenarios, our models predicted greatest overall risk of Bsal emergence in the southeastern and northwestern U.S.A. Bsal climatic suitability was greatest in the northwest, whereas the greatest number of susceptible species was predicted in the southeast. Under future scenarios, we predicted that climatically suitable areas for Bsal will be reduced by 3–14 % under the most extreme climate model. • Greatest Bsal risk is predicted in the southeastern and northwestern U.S.A. • The greatest Bsal climatic suitability is predicted in the northwestern U.S.A. • The majority of susceptible salamanders are in the southeastern U.S.A. • Under future climate scenarios, suitable area for Bsal will be reduced by 3–14 %. • Novel approaches include predicting human-mediated introduction and climate change. [ABSTRACT FROM AUTHOR]

In intra-EU trade, the health status of animals is warranted by issuing a health certificate after clinical inspection in the exporting country. This certificate cannot provide guarantee of absence of infection, especially not for diseases with a long incubation period and no overt clinical signs such as bovine tuberculosis (bTB). The Netherlands are officially free from bTB since 1999. However, frequent reintroductions occurred in the past 15 years through importation of infected cattle. Additional testing (AT) of imported cattle could enhance the probability of detecting an imported bTB infection in an early stage. The goal of this study was to evaluate the effectiveness of risk-based AT for bTB in cattle imported into The Netherlands. A generic stochastic import risk model was developed that simulates introduction of infection into an importing country through importation of live animals. Main output parameters are the number of infected animals that is imported ( N inf ), the number of infected animals that is detected by testing ( N det ), and the economic losses incurred by importing infected animals (loss). The model was parameterized for bTB. Model calculations were optimized to either maximize N det or to minimize loss. Model results indicate that the risk of bTB introduction into The Netherlands is very high. For the current situation in which Dutch health checks on imported cattle are limited to a clinical inspection of a random sample of 5–10% of imported animals, the calculated annual N inf = 99 (median value). Random AT of 8% of all imported cattle results in N det = 7 (median value), while the median N det = 75 if the sampling strategy for AT is optimized to maximize N det . However, in the latter scenario, loss is more than twice as large as in the current situation, because only calves are tested for which cost of detection is higher than the expected gain of preventing a possible outbreak. When optimizing the sampling strategy for AT to minimize loss, only breeding and production cattle are selected for AT resulting in N det = 1 (median value). Loss is; however, reduced by 75% if compared to the current situation. We conclude that the effectiveness of AT can greatly be improved by risk-based sampling. The optimal sampling strategy for risk-based AT for bTB is highly dependent on the objective of AT. If economic losses are to be contained, AT should focus on breeding and production cattle originating from high-risk countries. [ABSTRACT FROM AUTHOR]

Aim After J. L. Lockwood, P. Cassey and T. Blackburn (2009, Diversity and Distributions, 15, 904-910) first described a theoretical relationship between propagule pressure and colonization pressure, two empirical studies demonstrated that the transport stage of the invasion process can profoundly influence the strength of the relationship among multiple events, as well as predictions of introduction risk. However, studies exploring dynamics of transported communities are rare, as repeated-measures sampling during transportation by any vector is logistically difficult. We constructed a conceptual model of community dynamics during transportation and supported it by empirical data for propagule pressure and colonization pressure of plankton. Location Global. Methods A conceptual model of community dynamics was developed based on lognormal species abundance distribution and the simulation model of J. L. Lockwood, P. Cassey and T. Blackburn (2009, Diversity and Distributions, 15, 904-910). We considered four cases: case 'A' - no reduction in propagule nor colonization pressure; case 'B' - strong reduction in propagule and mild reduction in colonization pressure; case 'C' - mild reduction in propagule and strong reduction in colonization pressure; and case 'D' - strong reduction in both propagule and colonization pressures. Results The cases 'B', 'C' and 'D' were supported by empirical data for invertebrates, dinoflagellates and diatoms from ships' ballast tanks, respectively. Propagule pressure of invertebrates, dinoflagellates and diatoms decreased 99.95%, 80% and 94% in 25 days, respectively, while colonization pressure decreased 34%, 57% and 64%. Main conclusions Transport affects both propagule pressure and colonization pressure of taxa, with the magnitude of change dependent on length of transport and taxon-specific survival and reproduction. Our model demonstrates that introduction risk varies substantially across and within taxa depending on the occurrence and severity of selection pressures during transportation which serve to change species abundance distributions. [ABSTRACT FROM AUTHOR]

Low pathogenic avian influenza (LPAI) caused by H5 and H7 viruses is considered a threatening disease for poultry production due to the possibility of prolonged undetected virus circulation in a poultry flock and its potential to mutate to highly pathogenic avian influenza (HPAI). The occurrence of HPAI may have devastating impact on the poultry industry and has serious economic consequences. The possibility of LPAI virus (LPAIV) being introduced into Poland via import of live poultry from EU countries was considered. The main aim of the study was to quantitatively assess the probability of LPAIV H5 and H7 introduction into Poland (P LPAI) via this pathway, to evaluate the relative contribution of exporting countries and species of poultry to this probability and to present the spatial distribution of the introduction probability in Poland. To this end, a stochastic multilevel binomial risk model, taking into account uncertainty and variability of input parameter values, was developed. The results of this model indicate that the mean annual probability of LPAIV H5 or H7 introduction into Poland is 0.088 [95 % uncertainty interval: 0.0575, 0.128], which corresponds to, on average, one outbreak every 11 years. The countries contributing most to this probability are Germany, Czech Republic and Denmark. Importations of ducks, chickens and turkeys contribute most to P LPAI , whereas importations of geese and guinea fowl represent a minor risk. The probability of LPAIV introduction is not equally distributed across Poland with the majority of counties having a high probability of LPAIV introduction being located in the Western part of the country. The results of this study can be used to support decision makers on targeted prevention or risk-based surveillance strategies for LPAI. [ABSTRACT FROM AUTHOR]

Summary China's Belt and Road Initiative (BRI) is an unprecedented global development program that involves nearly half of the world's countries [ 1 ]. It not only will have economic and political influences, but also may generate multiple environmental challenges and is a focus of considerable academic and public concerns [ 2–6 ]. The Chinese government expects BRI to be a sustainable development, paying equal attention to economic development and environmental conservation [ 7 ]. However, BRI's high expenditure on infrastructure construction, by accelerating trade and transportation, is likely to promote alien species invasions [ 5 ], one of the primary anthropogenic threats to global biodiversity [ 8 ]. BRI countries may have different susceptibilities to invasive species due to different financial and response capacities [ 9 ]. Moreover, these countries overlap 27 of 35 recognized global biodiversity hotspots [ 10 ]. Identifying those areas with high-invasion risks, and species with high invasive potentials within BRI countries, is therefore of vital importance for the sustainable implementation of the BRI, and the development of early, economical, and effective biosecurity strategies [ 11 ]. In response, we present here a comprehensive study to evaluate invasion risks by alien vertebrates within BRI. We identified a total of 14 invasion hotspots, the majority of which fall along the six proposed BRI economic corridors, with the proportion of grid cells in invasion hotspots 1.6 times higher than other regions. Based on our results, we recommend the initiation of a project targeting early prevention, strict surveillance, rapid response, and effective control of alien species in BRI countries to ensure that this development is sustainable. Graphical Abstract Highlights • China's Belt and Road Initiative (BRI) is an unprecedented global development project • BRI's high expenditure on trade and transportation may promote alien species invasion • We evaluate the invasion risks of 816 alien terrestrial vertebrates within BRI • We identify 14 invasion hotspots to help the sustainable implementation of BRI Liu et al. quantify invasion risks of 816 alien terrestrial vertebrates along 121 China's Belt and Road Initiative countries. There are 14 invasion hotspots facing a high invasion risks with both high introduction risk and habitat suitability overlap, a majority of which falls along the 6 proposed BRI Economic Corridors. [ABSTRACT FROM AUTHOR]

This Technical Report describes the activities developed in the scope of the EU‐FORA Fellowship, within the work programme of risk assessment (RA) of exotic disease incursion and spread, developed at Wageningen Bioveterinary Research (WBVR). The programme focused on the work carried out in the Generic risk assessment for introduction of animal diseases (G‐RAID) project, which brings together a number of different generic RA tools from multiple European partners. The aim of the fellowship was to gain understanding of veterinary import risk assessment by using different RA tools and to learn how different algorithms can be used to calculate disease incursion risks. G‐RAID's tools cover a wide range of RA methodologies; from purely qualitative, to semi‐quantitative and fully stochastic quantitative methods, which allowed the fellow to understand a variety of algorithms used to produce the final risk estimate. The fellowship programme provided the fellow with the chance to learn in detail about how generic RAs are performed across Europe, understanding how to deal with the uncertainty and variability involved in RAs and the potential problems of data availability and reliability. The fellow made an inventory of publicly available databases on disease occurrence and international trade that could be used for import RA and assessed their quality and usefulness for the different generic RA tools. The programme also provided the fellow the opportunity to perform several import risk assessments using the RA tools of G‐RAID. She completed a RA on African swine fever using the MINTRISK model developed by WBVR. Furthermore, she assessed the risk of foot and mouth disease introduction using the Rapid Risk Assessment Tool (RRAT) model developed by WBVR and the COMPARE model developed by the Animal and Plant Health Agency (APHA). To this end, the fellow completed a short‐term visit to APHA, enabling her to have additional training in quantitative RA and to expand her professional network in this area. [ABSTRACT FROM AUTHOR]