Genetic divergence of tomato ringspot virus

et al. 2019

EFS2

Following a request from the EU Commission, the Panel on Plant Health performed a pest categorisation of 17 viruses and viroids, herein called viruses, of Cydonia Mill., Malus Mill. and Pyrus L. determined as being either non‐EU or of undetermined standing in a previous EFSA opinion. These viruses belong to different genera and are heterogeneous in their biology. They can be detected by available methods and are efficiently transmitted by vegetative propagation techniques, with plants for planting representing a major long‐distance spread mechanism and, potentially, a major entry pathway. Depending on the viruses, additional pathway(s) can also be seed, pollen and/or vector transmission. Most of the viruses categorised here are known to infect only one of few related plant genera, but some of them have a wider host range, thus extending the possible entry pathways. Three viruses (apple necrotic mosaic virus, cherry rasp leaf virus, temperate fruit decay‐associated virus) and one viroid (apple fruit crinkle viroid) satisfy all the criteria to be considered as Union quarantine pests. Five viruses (apple green crinkle‐associated virus, blackberry chlorotic ringspot virus, eggplant mottled crinkle virus, tobacco ringspot virus and tomato ringspot virus) and one viroid (apple scar skin viroid), satisfy the criteria to be considered as Union quarantine pests with the possible exception of being absent from the EU territory or having a restricted presence and being under official control. The remaining six viruses (apple geminivirus, apple latent spherical virus, apple‐associated luteovirus, Pyrus pyrifolia cryptic virus, Pyrus pyrifolia partitivirus 2 and Tulare apple mosaic virus) and one viroid (apple hammerhead viroid) were not found to satisfy one or more of these criteria. The Panel highlights that for several viruses, especially those recently discovered, the categorisation is associated with high uncertainties mainly linked to the absence of data on biology and distribution. Since this opinion addresses specifically the non‐EU viruses, in general these viruses do not meet the criteria assessed by EFSA to qualify as a potential Union regulated non‐quarantine pests.

Section: Pest Categorisationmentioning

confidence: 99%

Pest categorisation of non‐EU viruses and viroids of Cydonia Mill., Malus Mill. and Pyrus L.

Bragard¹,

et al. 2019

EFS2

“…This is likely due to competition among the diverse genomic variants generated as a consequence of the error-prone viral replication system (higher in RNA than in DNA viruses) and the ensuing selection of the most fit variant distributions in a given environment (Domingo et al, 2012). As an example, high intraspecific divergence has been observed in the X4 domain of the ToRSV RNA2 between different virus strains (Jafarpour and Sanfac ßon, 2009;Rivera et al, 2016). This genetic variability may interfere with the efficiency of detection methods, especially when they are based on polymerase chain reaction (PCR), thus generating uncertainties on the reliability and/or sensitivity of the detection for all the existing viral variants.…”

Section: Intraspecific Diversitymentioning

confidence: 99%

“…This genetic variability may interfere with the efficiency of detection methods, especially when they are based on polymerase chain reaction (PCR), thus generating uncertainties on the reliability and/or sensitivity of the detection for all the existing viral variants. As an example, high intraspecific divergence has been observed in the X4 domain of the ToRSV RNA2 between different virus strains (Jafarpour and Sanfac ßon, 2009;Rivera et al, 2016). However, for the other viruses of Fragaria spp.…”

Section: Intraspecific Diversitymentioning

confidence: 99%

Pest categorisation of non‐EU viruses of Fragaria L.

Bragard¹,

et al. 2019

EFS2

Following a request from the EU Commission, the Panel on Plant Health addressed the pest categorisation of the viruses and viroids of Fragaria L. determined as being either non-EU or of undetermined standing in a previous EFSA opinion. These infectious agents belong to different genera and are heterogeneous in their biology. With the exclusion of strawberry latent virus and strawberry latent C virus for which very limited information exists, the pest categorisation was completed for 12 viruses having acknowledged identities and available detection methods. All these viruses are efficiently transmitted by vegetative propagation techniques, with plants for planting representing the major pathway for long-distance dispersal and thus considered as the major pathway for entry. Depending on the virus, additional pathway(s) can also be Fragaria seeds, pollen and/or vector(s). Most of the viruses categorised here are known to infect only one or few plant genera, but some of them have a wide host range, thus extending the possible entry pathways. Strawberry chlorotic fleck-associated virus, strawberry leaf curl virus, strawberry necrotic shock virus, strawberry pallidosis-associated virus, strawberry vein banding virus (SVBV) and tomato ringspot virus meet all the criteria evaluated by EFSA to qualify as potential Union quarantine pests (QPs). For SVBV, the Panel considered that following its entry and establishment into the EU territory, an impact of uncertain magnitude is expected mainly because a synergistic effect may occur in strawberry in case of mixed infections with viruses already present in the EU. Strawberry crinivirus 3, strawberry crinivirus 4 and strawberry polerovirus 1 meet all criteria for being considered as potential Union QPs, except for the impact in the EU territory, on which the Panel was unable to conclude. Fragaria chiloensis cryptic virus, Fragaria chiloensis latent virus and strawberry pseudo mild yellow edge virus do not meet the criterion of having potential negative impact in the EU. For several viruses, especially those recently discovered, the categorisation is associated with high uncertainties mainly because of the absence of data on their biology, distribution and impact. Since this opinion addresses specifically the non-EU viruses, in general, these viruses do not meet the criteria assessed by EFSA to qualify as potential Union regulated non-quarantine pests.

“…This genetic variability may interfere with the efficiency of detection methods, especially when they are based on the amplification of variable genomic viral sequences, thus generating uncertainties on the reliability and/or sensitivity of the detection for all the existing viral variants. As an example, high intraspecific divergence has been observed in the X4 domain of the ToRSV RNA2 among different virus strains (Jafarpour and Sanfac ßon, 2009;Rivera et al, 2016). Highlighting intraspecific diversity of AVCaV, Marais et al (2015b) characterised three non-EU isolates (from sources outside EU) with a longer genome than the Italian isolate due to an insertion in the RdRp coding sequence.…”

Section: Cannot Be Excludedmentioning

confidence: 99%

Pest categorisation of non‐EU viruses and viroids of Prunus L.

Bragard¹,

et al. 2019

EFS2

Following a request from the EU Commission, the Panel on Plant Health addressed the pest categorisation of the viruses and viroids of Prunus L. determined as being either non-EU or of undetermined standing in a previous EFSA opinion. These infectious agents belong to different genera and are heterogeneous in their biology. With the exclusion of Ilarvirus S1 and Ilarvirus S2, for which very limited information exists, the pest categorisation was completed for 26 viruses and 1 viroid having acknowledged identities and available detection methods. All these viruses are efficiently transmitted by vegetative plant propagation techniques, with plants for planting representing the major pathway for long-distance dispersal and thus considered as the major pathway for entry. Depending on the virus, additional pathway(s) can also be Prunus seeds, pollen and/or vector(s). Most of the viruses categorised here are known to infect only one or few plant genera, but some of them have a wide host range, thus extending the possible entry pathways. Apple scar skin viroid, American plum line pattern virus, cherry mottle leaf virus, cherry rasp leaf virus, cherry rosette virus, cherry rusty mottle-associated virus, cherry twisted leaf-associated virus, peach enation virus, peach mosaic virus, peach rosette mosaic virus, tobacco ringspot virus and tomato ringspot virus meet all the criteria evaluated by EFSA to qualify as potential Union quarantine pests (QPs). With the exception of impact in the EU territory, on which the Panel was unable to conclude, apricot vein clearing virus, Asian prunus virus 1, Asian prunus virus 2, Asian prunus virus 3, Caucasus prunus virus, cherry virus B, Mume virus A, nectarine stem pitting-associated virus, nectarine virus M, peach chlorotic mottle virus, peach leaf pitting-associated virus, peach virus D, prunus virus F and prunus virus T satisfy all the other criteria to be considered as potential Union QPs. Prunus geminivirus A does not meet the criterion of having negative impact in the EU. For several viruses, especially those recently discovered, the categorisation is associated with high uncertainties mainly because of the absence of data on their biology, distribution and impact. Since this opinion addresses specifically the non-EU viruses, in general these viruses do not meet the criteria assessed by EFSA to qualify as potential Union regulated non-quarantine pests.