Evidence that an Unnamed Isometric Virus Associated with Potato Rugose Disease in Peru Is a New Species of Genus Torradovirus.

A previously uncharacterized torradovirus species infecting potatoes was detected by high-throughput sequencing from field samples from Peru and in customs intercepts in potato tubers that originated from South America in the United States of America and the Netherlands. This new potato torradovirus showed high nucleotide sequence identity to an unidentified isometric virus (SB26/29), which was associated with a disease named potato rugose stunting in southern Peru characterized over two decades ago. Thus, this virus is tentatively named potato rugose stunting virus (PotRSV). The genome of PotRSV isolates sequenced in this study were composed of two polyadenylated RNA segments. RNA1 ranges from 7,086 to 7,089 nt and RNA2 from 5,228 to 5,230 nt. RNA1 encodes a polyprotein containing the replication block (helicase-protease-polymerase), whereas RNA2 encodes a polyprotein cleaved into a movement protein and the three capsid proteins (CPs). Pairwise comparison among PotRSV isolates revealed amino acid identity values greater than 86% in the protease-polymerase (Pro-Pol) region and greater than 82% for the combined CPs. The closest torradovirus species, squash chlorotic leaf spot virus, shares amino acid identities of ∼58 and ∼41% in the Pro-Pol and the combined CPs, respectively. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

African eggplant-associated virus: Characterization of a novel tobamovirus identified from Solanum macrocarpon and assessment of its potential impact on tomato and pepper crops.

A novel tobamovirus was identified in a fruit of Solanum macrocarpon imported into the Netherlands in 2018. This virus was further characterized in terms of host range, pathotype and genomic properties, because many tobamoviruses have the potential to cause severe damage in important crops. In the original fruit, two different genotypes of the novel virus were present. The virus was able to infect multiple plant species from the Solanaceae family after mechanical inoculation, as well as a member of the Apiaceae family. These species included economically important crops such as tomato and pepper, as well as eggplant and petunia. Both tomato and pepper germplasm were shown to harbor resistance against the novel virus. Since most commercial tomato and pepper varieties grown in European greenhouses harbor these relevant resistances, the risk of infection and subsequent impact on these crops is likely to be low in Europe. Assessment of the potential threat to eggplant, petunia, and other susceptible species needs further work. In conclusion, this study provides a first assessment of the potential phytosanitary risks of a newly discovered tobamovirus, which was tentatively named African eggplant-associated virus.

List of non-EU viruses and viroids infecting potato (Solanum tuberosum) and other tuber-forming Solanum species.

The European Commission requested a pest categorisation of the non-EU viruses and viroids of potato (hereafter referred to as viruses). As a first step, a systematic literature and database search was carried out to identify the viruses reported to naturally infect Solanum tuberosum and other tuber-forming Solanum spp (hereafter referred to as potato). Based on the global distribution and on the prevalence inside the European Union (EU), the Panel identified 40 non-EU viruses known to occur only outside the EU or with only a limited presence in the EU (reported in only one or few Member States (MSs) and/or with restricted distribution, outbreaks). Twenty-seven viruses were identified as having a significant presence in the EU (known to occur in several MSs, frequently reported in the EU, widespread in several MSs) or reported only from the EU so far, and will be excluded from further categorisation in the frame of the present mandate. Five viruses remained with an undetermined standing because the available information did not allow their allocation to one of the above groups. The viruses considered non-EU and those with undetermined standing will be further categorised if not addressed by EFSA in previous scientific opinions. Seven viruses for which non-European isolates are specifically regulated in Annex I of directive 2000/29/EC will be categorised separately. The main knowledge gaps and uncertainties of this grouping concern the natural host status of potato, the taxonomy, and/or information on the geographical distribution and prevalence of some of the analysed viruses.

Pest categorisation of non-EU viruses and viroids of potato.

Following a request from the EU Commission, the Panel on Plant Health has addressed the pest categorisation of those viruses and viroids (hereafter referred to as viruses) of Solanum tuberosum and other tuber-forming Solanum spp. (hereafter referred to as potato) which are considered to be either non-EU or of undetermined standing based on a previous EFSA opinion. These viruses belong to different families and genera and either have an established identity or produce consistent symptoms. Plants for planting is the main pathway for entry for all categorised viruses as they can all be transmitted by vegetative propagation. Several categorised viruses have a relatively wide host range and/or are vector-transmitted, increasing the potential for entry. The information currently available on geographical distribution, biology, epidemiology, impact and potential entry pathways has been evaluated with regard to the criteria to qualify as potential Union quarantine pest or as Union regulated non-quarantine pest (RNQP). Since this opinion addresses specifically the non-EU potato viruses, in general these viruses do not meet the criteria assessed by EFSA to qualify as potential Union regulated non-quarantine pests. The following viruses meet the criteria to qualify as potential Union quarantine pest: APLV, APMMV, APMoV, ChiLCV, CYSDV, PAMV, PBRSV, PVH, PVP, PVT, PYDV, PYMV, PYV, PYVV, RCVMV, SALCV, SB26/29, ToCV, ToLCNDV, ToMHaV, ToMoTV, ToSRV and ToYVSV. With the exception of the criterion regarding the potential for consequences in the EU territory, for which the Panel is unable to conclude because of lack of information, AVB, CPSbV, PaLCrV, PapMV, PVB, PVU, SB41 and TVBMV meet all the other criteria to qualify as potential Union quarantine pest. PotLV and WPMV do not qualify as potential Union quarantine pest, since they are not reported to have any impact. For most of the categorised viruses, the conclusions of the Panel have inherent uncertainties, due to the lack of quantitative data on their impact and/or absence or limited availability of information on the biology, epidemiology and geographical distribution.

Pest categorisation of potato virus M (non-EU isolates).

Following a request from the EU Commission, the Panel on Plant Health has addressed the pest categorisation of non-EU isolates of potato virus M (PVM). The information currently available on geographical distribution, biology, epidemiology, potential entry pathways, potential additional impact compared to the current situation in the EU and availability of control measures of non-EU isolates of PVM has been evaluated with regard to the criteria to qualify as a potential Union quarantine pest. Because non-EU isolates of PVM are absent from the EU, they do not meet one of the requirements to be regulated as a regulated non-quarantine pest (RNQP) (presence in the EU); as a consequence, the Panel decided not to evaluate the other RNQP criteria for these isolates. Populations of PVM can be subdivided into two strains: the ordinary strain (PVM-O) is present in the EU, while the divergent strain (PVM-D) is absent from the EU or considered to have at most a limited distribution in the EU. Non-EU isolates of PVM-O are not expected to have an additional impact in the EU compared to EU isolates and therefore do not meet the corresponding criterion to qualify as a potential Union quarantine pest. The Panel is unable to conclude on the potential impact of non-EU PVM-D isolates in the EU territory, but PVM-D isolates meet all the other criteria to qualify as a potential Union quarantine pest.

Pest categorisation of potato virus S (non-EU isolates).

Following a request from the EU Commission, the Panel on Plant Health has addressed the pest categorisation of non-EU isolates of potato virus S (PVS). The information currently available on geographical distribution, biology, epidemiology, potential entry pathways, potential additional impact compared to the current situation in the EU, and availability of control measures of non-EU isolates of PVS has been evaluated with regard to the criteria to qualify as potential Union quarantine pest. Because non-EU isolates of PVS are absent from the EU, they do not meet one of the requirements to be regulated as an RNQP (presence in the EU); as a consequence, the Panel decided not to evaluate the other RNQP criteria for these isolates. Populations of PVS can be subdivided into two strains: the ordinary strain (PVS-O) with a worldwide distribution (including the EU), and the Andean strain (PVS-A) which is absent from the EU or considered to have at most a limited distribution in the EU. Two additional divergent isolates (PVS-A/PVS-O recombinants and PVS-arracacha) have also been categorised. Non-EU isolates of PVS-A are expected to have an additional impact as compared to the PVS isolates currently present in the EU, and therefore meet all the criteria to qualify as potential Union quarantine pests; the magnitude of the additional impact is, however, unknown. Non-EU isolates of PVS-A/PVS-O recombinants and of PVS-arracacha also meet these criteria, with the exception of the criterion regarding the potential additional consequences in the EU territory for which the Panel was unable to conclude. Non-EU PVS-O isolates are not expected to have an additional impact in the EU as compared to EU isolates and therefore do not meet the corresponding criterion.

Pest categorisation of potato virus A (non-EU isolates).

Following a request from the EU Commission, the Panel on Plant Health has addressed the pest categorisation of non-EU isolates of potato virus A (PVA). The information currently available on geographical distribution, biology, epidemiology, potential entry pathways, potential additional impact over the current situation and availability of control measures of non-EU isolates of PVA has been evaluated with regard to the criteria to qualify as potential Union quarantine pest. Because non-EU isolates of PVA are absent from the EU, they do not meet one of the requirements to be regulated as a regulated non-quarantine pest (RNQP) (presence in the EU); as a consequence, the Panel decided not to evaluate the other RNQP criteria for these isolates. This categorisation was performed considering two groups of isolates: those reported in Solanum betaceum (PVA-TamMV, not reported from the EU) and all other isolates (hereafter referred to as PVA, worldwide distribution). Non-EU isolates of PVA and of PVA-TamMV do not meet one of the criteria evaluated by EFSA to be regarded as a potential Union quarantine pest, since they are not expected to have an additional impact in the EU.

Pest categorisation of potato virus V (non-EU isolates).

Following a request from the EU Commission, the Panel on Plant Health has addressed the pest categorisation of non-EU isolates of potato virus V (PVV). The information currently available on geographical distribution, biology, epidemiology, potential entry pathways, potential additional impact and availability of control measures of non-EU isolates of PVV has been evaluated with regard to the criteria to qualify as a potential Union quarantine pest. Because non-EU isolates of PVV are absent from the EU, they do not meet one of the requirements to be regulated as a regulated non-quarantine pest (RNQP) (presence in the EU); as a consequence, the Panel decided not to evaluate the other RNQP criteria for these isolates. This categorisation was performed considering two lineages, PVV-I (present in and outside the EU) and PVV-II (not reported in the EU), and isolate PVV-PA4 (unknown distribution). Non-EU isolates of PVV-I and PVV-PA4 do not meet one of the criteria evaluated by EFSA to be regarded as a potential Union quarantine pest, since they are not expected to have an additional impact in the EU. With the exception of the criterion regarding the potential consequences in the EU territory, for which the Panel is unable to conclude, non-EU isolates of PVV-II meet all the other criteria to qualify as a potential Union quarantine pest.

Pest categorisation of potato virus X (non-EU isolates).

Following a request from the EU Commission, the Panel on Plant Health has addressed the pest categorisation of non-EU isolates of potato virus X (PVX). The information currently available on geographical distribution, biology, epidemiology, potential entry pathways, potential additional impact and availability of control measures of non-EU isolates of PVX has been evaluated with regard to the criteria to qualify as a potential Union quarantine pest. Because non-EU isolates of PVX are absent from the EU, they do not meet one of the requirements to be regulated as a regulated non-quarantine pest (RNQP) (presence in the EU); as a consequence, the Panel decided not to evaluate the other RNQP criteria for these isolates. On the basis of their ability to overcome potato resistance genes, PVX isolates can be divided into several pathotypes. PVX isolates that are not able to overcome resistance genes and PVX isolates that are able to overcome the Nb and/or Nx resistance genes are already present in the EU. Isolates able to overcome the Rx resistance gene have only been reported from South America. These Rx breaking isolates could potentially have an additional impact over the current situation in the EU and therefore meet all the criteria to qualify as a potential Union quarantine pest. All other non-EU isolates, should they be introduced, are not expected to have additional impact and therefore do not meet this criterion to qualify as a potential Union quarantine pest.

Pest categorisation of potato virus Y (non-EU isolates).

Following a request from the EU Commission, the Panel on Plant Health has addressed the pest categorisation of non-EU isolates of potato virus Y (PVY). The information currently available on geographical distribution, biology, epidemiology, potential entry pathways and potential additional impact of non-EU isolates of PVY, has been evaluated with regard to the criteria to qualify as a potential Union quarantine pest. Because non-EU isolates of PVY are absent from the EU, they do not meet one of the requirements to be regulated as a regulated non-quarantine pest (RNQP) (presence in the EU); as a consequence, the Panel decided not to evaluate the other RNQP criteria for these isolates. Populations of PVY can be subdivided into several strains and groups of isolates: strain C (PVY-C), strain N (PVY-N), strain O (PVY-O) and a wide range of recombinant isolates (PVY-recombinants) which have a worldwide distribution (including the EU). Two groups of isolates, i.e. the Brazilian (PVY-Br) and Chilean (PVY-Ch) isolates, are considered absent from the EU. Non-EU isolates of PVY-C, PVY-N, PVY-O and PVY-recombinants identified so far are not expected to have an additional impact in the EU compared to the PVY isolates already present and, therefore, do not meet the corresponding criterion to qualify as a potential Union quarantine pest. The Panel is unable to conclude on the potential additional impact of isolates of PVY-Br and PVY-Ch in the EU territory, but these isolates meet all the other criteria to qualify as potential Union quarantine pests.

Pest categorisation of potato leafroll virus (non-EU isolates).

Following a request from the EU Commission, the Panel on Plant Health has addressed the pest categorisation of non-EU isolates of potato leafroll virus (PLRV). The information currently available on geographical distribution, biology, epidemiology, potential entry pathways, potential additional impact and availability of control measures of non-EU isolates of PLRV has been evaluated with regard to the criteria to qualify as a potential Union quarantine pest. Because non-EU isolates of PLRV are absent from the EU, they do not meet one of the requirements to be regulated as a regulated non-quarantine pest (RNQP) (presence in the EU); as a consequence, the Panel decided not to evaluate the other RNQP criteria for these isolates. This categorisation was performed considering two groups of PLRV isolates: those associated with the tomato yellow top disease (PLRV-TYTV), not reported from the EU, and all other isolates (hereafter referred to as PLRV), with a worldwide distribution. Isolates of PLRV-TYTV could potentially have an additional impact over the current situation in the EU and therefore meet all the criteria to qualify as a potential Union quarantine pest. All other non-EU PLRV isolates, should they be introduced, are not expected to have additional impact and therefore do not meet this criterion to qualify as a potential Union quarantine pest.