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This Guidance describes a two-phase approach for a fit-for-purpose method for the assessment of plant pest risk in the territory of the EU. Phase one consists of pest categorisation to determine whether the pest has the characteristics of a quarantine pest or those of a regulated non-quarantine pest for the area of the EU. Phase two consists of pest risk assessment, which may be requested by the risk managers following the pest categorisation results. This Guidance provides a template for pest categorisation and describes in detail the use of modelling and expert knowledge elicitation to conduct a pest risk assessment. The Guidance provides support and a framework for assessors to provide quantitative estimates, together with associated uncertainties, regarding the entry, establishment, spread and impact of plant pests in the EU. The Guidance allows the effectiveness of risk reducing options (RROs) to be quantitatively assessed as an integral part of the assessment framework. A list of RROs is provided. A two-tiered approach is proposed for the use of expert knowledge elicitation and modelling. Depending on data and resources available and the needs of risk managers, pest entry, establishment, spread and impact steps may be assessed directly, using weight of evidence and quantitative expert judgement (first tier), or they may be elaborated in substeps using quantitative models (second tier). An example of an application of the first tier approach is provided. Guidance is provided on how to derive models of appropriate complexity to conduct a second tier assessment. Each assessment is operationalised using Monte Carlo simulations that can compare scenarios for relevant factors, e.g. with or without RROs. This document provides guidance on how to compare scenarios to draw conclusions on the magnitude of pest risks and the effectiveness of RROs and on how to communicate assessment results.

Cassava brown streak virus (CBSV) isolates were analysed from symptomatic cassava collected between 1997 and 2008 in the major cultivation regions of East Africa. An analysis of complete RNA genomes of seven isolates from Kenya, Tanzania, Mozambique, Uganda and Malawi revealed a common genome structure, but the isolates clearly clustered in two distinct clades. The first comprised isolates from Kenya, Uganda, Malawi, north-western Tanzania and the CBSV described previously, and shared between 87 and 95 % nucleotide sequence identity, whilst the second included isolates from coastal regions of Mozambique and Tanzania, which shared only 70 % nucleotide sequence identities with isolates of the first clade. When the amino acid sequences of viral proteins were compared, identities as low as 47 % (Ham1) and 59 % (P1) between the two clades were found. An antiserum obtained against the capsid protein of a clade 1 isolate identified a 43 kDa protein in clade 1 isolates and a 45 kDa protein in clade 2 isolates. Several cassava cultivars were susceptible to isolates of clade 2 but resistant to those of clade 1. The differences observed both in biological behaviour and in genomic and protein sequences indicate that cassava brown streak disease in East Africa is caused by at least two distinct virus species. It is suggested that those of clade 1 retain the species name Cassava brown streak virus, whilst those of clade 2 be classified as Cassava brown streak Mozambique virus.

The whitefly Bemisia tabaci (Gennadius) is a major cosmopolitan pest capable of feeding on hundreds of plant species and transmits several major plant viruses. The most important and widespread viruses vectored by B. tabaci are in the genus Begomovirus, an unusual group of plant viruses owing to their small, single-stranded DNA genome and geminate particle morphology. B. tabaci transmits begomoviruses in a persistent circulative nonpropagative manner. Evidence suggests that the whitefly vector encounters deleterious effects following Tomato yellow leaf curl virus (TYLCV) ingestion and retention. However, little is known about the molecular and cellular basis underlying these coevolved begomovirus-whitefly interactions. To elucidate these interactions, we undertook a study using B. tabaci microarrays to specifically describe the responses of the transcriptomes of whole insects and dissected midguts following TYLCV acquisition and retention. Microarray, real-time PCR, and Western blot analyses indicated that B. tabaci heat shock protein 70 (HSP70) specifically responded to the presence of the monopartite TYLCV and the bipartite Squash leaf curl virus. Immunocapture PCR, protein coimmunoprecipitation, and virus overlay protein binding assays showed in vitro interaction between TYLCV and HSP70. Fluorescence in situ hybridization and immunolocalization showed colocalization of TYLCV and the bipartite Watermelon chlorotic stunt virus virions and HSP70 within midgut epithelial cells. Finally, membrane feeding of whiteflies with anti-HSP70 antibodies and TYLCV virions showed an increase in TYLCV transmission, suggesting an inhibitory role for HSP70 in virus transmission, a role that might be related to protection against begomoviruses while translocating in the whitefly.T omato yellow leaf curl virus (TYLCV) is a complex of singlestranded-DNA plant viruses of the genus Begomovirus in the family Geminiviridae that causes severe damage in tomatoes by stopping or interfering with normal plant growth, thus significantly affecting crop yields. Begomoviruses exhibit tissue tropism in the plant phloem, and some are effectively transmitted by phloem feeders, such as the whitefly Bemisia tabaci (17,18). TYLCV is transmitted exclusively by B. tabaci, and many of the parameters for acquisition, transmission, and retention of the virus by B. tabaci have been studied in depth (10,11,55,68); however, the molecular interactions that underlie the persistence of the virus in its vector are unknown for the most part. TYLCV is transmitted by B. tabaci in a persistent circulative nonpropagative manner (31); however, it has been shown that virus genes may be transcribed in the whitefly vector (70). TYLCV is ingested by B. tabaci with the phloem sap, passes through the food canal in the stylet, reaches the chitin-lined esophagus in the thorax, and enters the filter chamber which connects the midgut with the hindgut (28, 29). The majority of TYLCV particles are absorbed into the hemolymph in the filter chamber (16,25,71), while some move alon...

The importance of cassava as a food security crop in Africa and the world Cassava, originally from South America, is the fourth most important source of calories in the developing world after the cereal crops wheat, maize, and rice. Worldwide, it feeds an estimated 700 million people directly or indirectly. Cassava production has increased steadily for the last 50 years, with 242 MT harvested in 2012. The increase is likely to continue as farmers in more than 105 countries come to recognize the crop's advantages. A semi-perennial root crop, cassava can stay in the ground for up to 3 years. This makes it an excellent food security crop: when all other crops have been exhausted, cassava roots can still be harvested. It is naturally drought resistant and resilient to climatic changes, high temperatures, and poor soils, and in addition, cassava responds extremely well to high CO 2 concentrations, making it a very important crop for the 21st century. Africa alone accounts for more than 55 % of the world's production, and cassava is the first food crop in fresh tonnage before maize and plantain in sub-Saharan Africa. Cassava is also an important source of income, especially for women in sub-Saharan Africa (SSA). Furthermore, cassava is the second most important source of starch in the world. Cassava is thus a highly valuable crop for the world today and in the future. It is critical that it should not be compromised by viral diseases.

Four forms of Colletotrichum representing three distinct virulence phenotypes were found associated with foliar anthracnose of yam in Nigeria: the highly virulent (= severity of disease) slow-growing grey (SGG); the moderately virulent fastgrowing salmon (FGS); the weakly virulent fast-growing grey (FGG); and the moderately virulent fast-growing olive (FGO) morphotype. Isolates of the four forms were identified as C. gloeosporioides , based on morphology. The reaction of monoconidial cultures on casein hydrolysis medium (CHM), PCR-RFLP and sequence analysis of the internal transcribed spacer region of the ribosomal DNA (ITS1-5·8S-ITS2) were used to establish the identity of the yam anthracnose pathogen(s). All yam isolates were distinguished from C. acutatum by the absence of protease activity on CHM. On ITS PCR and enzymatic digestion of PCR products, all FGS, FGO and SGG isolates produced RFLP patterns identical to those of C. gloeosporioides reference isolates, while FGG isolates revealed unique ITS RFLP banding patterns. Sequence analysis of the ITS1 region and of the entire ITS region revealed that SGG, FGS and FGO isolates were highly similar (98-99% nucleotide identity) and showed 97-100% identity to C. gloeosporioides . Less than 93% similarity of these fungal isolates to reference C. acutatum and C. lindemuthianum isolates was observed. The molecular study confirmed that foliar anthracnose of yam is caused by C. gloeosporioides . While a high similarity was found among most C. gloeosporioides fungi from yam, isolates of the FGG form did not cluster with any previously described Colletotrichum species, and probably represent a distinct species.

Following a request from the European Commission, the EFSA Plant Health Panel updated its pest categorisation of Xylella fastidiosa, previously delivered as part of the pest risk assessment published in 2015. X. fastidiosa is a Gram‐negative bacterium, responsible for various plant diseases, including Pierce's disease, phony peach disease, citrus variegated chlorosis, olive quick decline syndrome, almond leaf scorch and various other leaf scorch diseases. The pathogen is endemic in the Americas and is present in Iran. In the EU, it is reported in southern Apulia in Italy, on the island of Corsica and in the Provence‐Alpes‐Côte d'Azur region in France, as well as in the Autonomous region of Madrid, the province of Alicante and the Balearic Islands in Spain. The reported status is ‘transient, under eradication’, except for the Balearic Islands, Corsica and southern of Apulia, where the status is ‘present with a restricted distribution, under containment’. The pathogen is regulated under Council Directive 2000/29/EC and through emergency measures under http://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX:32015D0789 (as amended http://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX:32017D2352). The pest could enter the EU via host plants for planting and via infectious insect vectors. The host range includes hundreds of host species listed in the EFSA host plant database. In the EU, host plants are widely distributed and climatic conditions are favourable for its establishment. X. fastidiosa can spread by movement of host plants for planting and infectious insect vectors. X. fastidiosa is known to cause severe direct damage to major crops including almonds, citrus, grapevines, olives, stone fruits and also forest trees, landscape and ornamental trees, with high impacts. The criteria assessed by the Panel for consideration as a potential Union quarantine pest are met (the pathogen is present in the EU, but it has a restricted distribution and is under official control). X. fastidiosa is not considered as a regulated non‐quarantine pest (RNQP) as the pathogen may spread also via insect vector transmission.

Bemisia tabaci (Gennadius) populations, collected from cassava and other plants in major cassava-cultivation areas of Sub-saharan Africa and from elsewhere around the world, were studied to determine their biotype status and genetic variation. Random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) markers were used to examine the genetic structure of the populations. The dendogram obtained using the neighbour joining method (NJ) split the cassava-associated populations from the non-cassava types with a 100% bootstrap probability. Analysis of molecular variance (AMOVA) of the RAPD fragments revealed that 63.2% of the total variation was attributable to differences among populations, while the differences among groups (host) and within populations accounted for 27.1 and 9.8% respectively. Analysis of the internally transcribed spacer region I (ITS 1) of the ribosomal DNA confirmed that the cassava populations of B. tabaci populations were distinct from non-cassava populations. Experiments to establish whitefly populations on various host plants revealed that cassava-associated populations were restricted to cassava only, whereas B. tabaci from other hosts were polyphagous but did not colonize cassava. Hence, populations of B. tabaci from cassava in Africa represent a distinct group.