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This review addresses ways to prepare for and to mitigate effects of biohazards on primary production of crops and livestock. These biohazards can be natural or intentional introductions of pathogens, and they can cause major economic damage to farmers, the agricultural industry, society, and international trade. Agroterrorism is the intentional introduction of animal or plant pathogens into agricultural production systems with the intention to cause socioeconomic harm and generate public fear. Although few acts of agroterrorism are reported, the threat of agroterrorism in Europe is real. New concerns about threats arise from the rapid advancements in biotechnology and emerging technologies. FORSA, an analytical framework for risk and vulnerability analysis, was used to review how to prepare for and mitigate the possible effects of natural or intentional biohazards in agricultural production. Analyzing the effects of a biohazard event involves multiple scientific disciplines. A comprehensive analysis of biohazards therefore requires a systems approach. The preparedness and ability to manage events are strengthened by bolstered farm biosecurity, increased monitoring and laboratory capacity, improved inter-agency communication and resource allocation. The focus of this review is on Europe, but the insights gained have worldwide applications. The analytical framework used here is compared to other frameworks. With climate change, Covid-19 and the war in Ukraine, the supply chains are challenged, and we foresee increasing food prices associated with social tensions. Our food supply chain becomes more fragile with more unknowns, thereby increasing the needs for risk and vulnerability analyses, of which FORSA is one example.

Climate change has increased the risk for infection of crops with insect-transmitted viruses. Mild autumns provide prolonged active periods to insects, which may spread viruses to winter crops. In autumn 2018, green peach aphids (Myzus persicae) were found in suction traps in southern Sweden that presented infection risk for winter oilseed rape (OSR; Brassica napus) with turnip yellows virus (TuYV). A survey was carried out in spring 2019 with random leaf samples from 46 OSR fields in southern and central Sweden using DAS-ELISA resulting in TuYV being detected in all fields except one. In the counties of Skåne, Kalmar and Östergötland, the average incidence of TuYV-infected plants was 75% and the incidence reached 100% for nine fields. Sequence analyses of the coat protein gene revealed a close relationship between TuYV isolates from Sweden and other parts of the world. High-throughput sequencing for one of the OSR samples confirmed the presence of TuYV and revealed co-infection with TuYV-associated RNAs. Molecular analyses of seven sugar beet (Beta vulgaris) plants with yellowing, collected in 2019, revealed that two of them were infected by TuYV together with two other poleroviruses: beet mild yellowing virus and beet chlorosis virus. The presence of TuYV in sugar beet suggests a spillover from other hosts. Poleroviruses are prone to recombination, and mixed infection with three poleroviruses in the same plant poses a risk for the emergence of new polerovirus genotypes.

Two begomovirus-associated alphasatellites were isolated from okra and a malvastrum plant (Malvaceae) in Cameroon. The complete nucleotide sequences of the okra- and malvastrum-infecting alphasatellites were 1375 and 1416-1418 nucleotides, respectively, and both exhibited features characteristic of other alphasatellites. Based on pairwise sequence comparisons, these previously undescribed alphasatellites are members of distinct species in the genera Colecusatellite and Gosmusatellite and have been tentatively named "pepper yellow vein Mali alphasatellite" and "cotton leaf curl Gezira alphasatellite3", respectively. Taken together with previous studies, alphasatellites endemic to Cameroon appear to be more diverse and infect plants of many more species and families than currently recognized.

High-throughput sequencing technologies were used to identify plant viruses in cereal samples surveyed from 2012 to 2017. Fifteen genome sequences of a tenuivirus infecting wheat, oats, and spelt in Estonia, Norway, and Sweden were identified and characterized by their distances to other tenuivirus sequences. Like most tenuiviruses, the genome of this tenuivirus contains four genomic segments. The isolates found from different countries shared at least 92% nucleotide sequence identity at the genome level. The planthopper Javesella pellucida was identified as a vector of the virus. Laboratory transmission tests using this vector indicated that wheat, oats, barley, rye, and triticale, but none of the tested pasture grass species (Alopecurus pratensis, Dactylis glomerata, Festuca rubra, Lolium multiflorum, Phleum pratense, and Poa pratensis), are susceptible. Taking into account the vector and host range data, the tenuivirus we have found most probably represents European wheat striate mosaic virus first identified about 60 years ago. Interestingly, whereas we were not able to infect any of the tested cereal species mechanically, Nicotiana benthamiana was infected via mechanical inoculation in laboratory conditions, displaying symptoms of yellow spots and vein clearing evolving into necrosis, eventually leading to plant death. Surprisingly, one of the virus genome segments (RNA2) encoding both a putative host systemic movement enhancer protein and a putative vector transmission factor was not detected in N. benthamiana after several passages even though systemic infection was observed, raising fundamental questions about the role of this segment in the systemic spread in several hosts.

Worldwide, barley/cereal yellow dwarf viruses (YDVs) are the most widespread and damaging group of cereal viruses. In this study, we applied high-throughput sequencing technologies (HTS) to perform a virus survey on symptomatic plants from 47 cereal fields in Estonia. HTS allowed the assembly of complete genome sequences for 22 isolates of cereal yellow dwarf virus RPS, barley yellow dwarf virus GAV, barley yellow dwarf virus PAS (BYDV-PAS), barley yellow dwarf virus PAV (BYDV-PAV), and barley yellow dwarf virus OYV (BYDV-OYV). We also assembled a near-complete genome of the putative novel species BYDV-OYV from Swedish samples of meadow fescue. Previously, partial sequencing of the central part of the coat protein gene indicated that BYDV-OYV represented a putative new species closely related to BYDV-PAV-CN, which currently is recognized as a subtype of BYDV-PAV. The present study found that whereas the 3′gene block of BYDV-OYV shares the closest relationship with BYDV-PAV-CN, the 5′gene block of BYDV-OYV shows the closest relationships to that of BYDV-PAS. Recombination detection analysis revealed that BYDV-OYV is a parental virus for both. Analysis of complete genome sequence data indicates that both BYDV-OYV and BYDV-PAV-CN meet the species criteria of genus Luteovirus. The study discusses BYDV phylogeny, and through a systematic in silico analysis of published primers for YDV detection, the existing gaps in current diagnostic practices for detection of YDVs, proposing primer pairs based on the most recent genomic information for the detection of different BYDV species. Thanks to the rising number of sequences available in databases, continuous updating of diagnostic primers can improve test specificity, e.g., inclusivity and exclusivity at species levels. This is needed to properly survey the geographical and host distribution of the different species of the YDV complex and their prevalence in cereal/barley yellow dwarf disease epidemics.

Antiviral compounds targeting viral replicative processes have been studied as an alternative for the control of begomoviruses. Previously, we have reported that the peptide AmPep1 has strong affinity binding to the replication origin sequence of tomato yellow leaf curl virus (TYLCV). In this study, we describe the mechanism of action of this peptide as a novel alternative for control of plant-infecting DNA viruses. When AmPep1 was applied exogenously to tomato and Nicotiana benthamiana plants infected with TYLCV, a decrease in the synthesis of the two viral DNA strands (CS and VS) was observed, with a consequent delay in the development of disease progress in treated plants. The chemical mechanism of action of AmPep1 was deduced using Raman spectroscopy and molecular modeling showing the formation of chemical interactions such as H bonds and electrostatic interactions and the formation of π-π interactions between both biomolecules contributing to tampering with the viral replication.

A complex of begomoviruses and their associated DNA-satellites is causing leaf curl diseases in Asia, Africa and the Mediterranean Region. Begomoviruses and DNA-satellites native to Asia and Africa are distinct from each other. Different combinations of geographically distinct monopartite begomoviruses, betasatellites and an alphasatellite were analyzed in infection experiments: cotton leaf curl Kokhran virus (CLCuKoV) and cotton leaf curl Multan virus (CLCuMuV) from Pakistan along with their associated cotton leaf curl Multan betasatellite (CLCuMuB); okra yellow crinkle virus (OYCrV), cotton leaf curl Gezira betasatellite (CLCuGeB), ageratum leaf curl Cameroon betasatellite (ALCCMB) and ageratum leaf curl Cameroon alphasatellite (ALCCMA) from Cameroon; tomato yellow leaf curl virus (TYLCV) from the Mediterranean Region. The infectivity assays were carried out in the model host species Nicotiana benthamiana and agro-infectious clones containing partial tandem repeats of the begomovirus and satellite genomes. The tested begomoviruses from different regions could functionally interact with non-cognate betasatellites and alphasatellite. Plants co-inoculated with CLCuKoV/CLCuGeB or CLCuMuV/CLCuGeB developed, for both combinations, more severe symptoms than with the begomovirus alone and the infection was verified by Southern blot hybridization. Nonetheless, CLCuKoV and CLCuMuV were shown also to support infection by ALCCMB, whereas OYCrV and TYLCV were able to support infection with CLCuMuB, ALCCMB and CLCuGeB. Moreover, all begomoviruses from different geographical origins supported ALCCMA from Africa. The results confirm that geographically diverse begomoviruses can functionally interact with non-cognate DNA-satellites, which may cause the emergence of new begomovirus-satellite complexes. Possibly, exchange of DNA-satellites may occur across continents leading to the emergence of new viral diseases.

Non-crop plants such as grasses and volunteer plants are an inseparable part of the flora of crop fields and can influence virus incidence in crop plants. The presence of grasses as virus reservoirs can lead to a higher probability of virus incidence in crop plants. However, the role of reservoirs as an inoculum source in agricultural fields has not been well studied for many viral diseases of crops. Grasses have been found to constitute potential reservoirs for cereal-infecting viruses in different parts of the world. This study revealed that cereal-infecting viruses such as wheat dwarf virus (WDV), barley yellow dwarf viruses (BYDVs), and cereal yellow dwarf virus-RPV (CYDV-RPV) can be found among ryegrass growing in or around winter wheat fields. Phylogenetic analysis showed that a WDV isolate from ryegrass was a typical WDV-E isolate that infects wheat. Similarly, a ryegrass isolate of barley yellow dwarf virus-PAV (BYDV-PAV) grouped in a clade together with other BYDV-PAV isolates. Inoculation experiments under greenhouse conditions confirmed that annual ryegrass of various genotypes can be infected with WDV to a very low titre. Moreover, leafhoppers were able to acquire WDV from infected ryegrass plants, despite the low titre, and transmit the virus to wheat, resulting in symptoms. Information from the grass reservoir may contribute to improving strategies for controlling plant virus outbreaks in the field. Knowledge of the likely levels of virus in potential reservoir plants can be used to inform decisions on insect vector control strategies and may help to prevent virus disease outbreaks in the future.