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High-throughput sequencing (HTS) technologies have the potential to become one of the most significant advances in molecular diagnostics. Their use by researchers to detect and characterize plant pathogens and pests has been growing steadily for more than a decade and they are now envisioned as a routine diagnostic test to be deployed by plant pest diagnostics laboratories. Nevertheless, HTS technologies and downstream bioinformatics analysis of the generated datasets represent a complex process including many steps whose reliability must be ensured. The aim of the present guidelines is to provide recommendations for researchers and diagnosticians aiming to reliably use HTS technologies to detect plant pathogens and pests. These guidelines are generic and do not depend on the sequencing technology or platform. They cover all the adoption processes of HTS technologies from test selection to test validation as well as their routine implementation. A special emphasis is given to key elements to be considered: undertaking a risk analysis, designing sample panels for validation, using proper controls, evaluating performance criteria, confirming and interpreting results. These guidelines cover any HTS test used for the detection and identification of any plant pest (viroid, virus, bacteria, phytoplasma, fungi and fungus-like protists, nematodes, arthropods, plants) from any type of matrix. Overall, their adoption by diagnosticians and researchers should greatly improve the reliability of pathogens and pest diagnostics and foster the use of HTS technologies in plant health.

The advances in high-throughput sequencing (HTS) technologies and bioinformatic tools have provided new opportunities for virus and viroid discovery and diagnostics. Hence, new sequences of viral origin are being discovered and published at a previously unseen rate. Therefore, a collective effort was undertaken to write and propose a framework for prioritizing the biological characterization steps needed after discovering a new plant virus to evaluate its impact at different levels. Even though the proposed approach was widely used, a revision of these guidelines was prepared to consider virus discovery and characterization trends and integrate novel approaches and tools recently published or under development. This updated framework is more adapted to the current rate of virus discovery and provides an improved prioritization for filling knowledge and data gaps. It consists of four distinct steps adapted to include a multi-stakeholder feedback loop. Key improvements include better prioritization and organization of the various steps, earlier data sharing among researchers and involved stakeholders, public database screening, and exploitation of genomic information to predict biological properties. [ABSTRACT FROM AUTHOR]

Plantain virus X was first recognized by the ICTV as a species in the genus Potexvirus in 1982. However, because no sequence was available for plantain virus X (PlVX), abolishing the species was proposed to the Flexiviridae working group of the ICTV in 2015. This initiated efforts to sequence the original isolates from Plantago lanceolata samples. Here we report the full‐genome sequencing of two original isolates of PlVX, which demonstrate that the virus is synonymous to Actinidia virus X, a species previously reported from kiwifruit (Actinidia sp.) and blackcurrant (Ribes nigrum). PlVX was previously noted to be widespread in the UK in P. lanceolata. This report additionally presents novel data on the distribution and diversity of PlVX, collected at the same site as the original UK isolates, and from three independent surveys, two in the Netherlands and one in Belgium. This study also includes two new host records for PlVX, Browallia americana and Capsicum annuum (sweet pepper), indicating the virus is more widespread and infects a broader range of hosts than previously reported. This stresses the importance of surveys of noncultivated species to gain insight into viral distribution and host range. This study also demonstrates the value of generating sequence data for isolates retained in virus collections. Additionally, it demonstrates the potential value in prepublication data sharing for giving context to virus detections such as the four independent studies here which, when combined, give greater clarity to the identity, diversity, distribution, and host range of plantain virus X. [ABSTRACT FROM AUTHOR]

Pollen morphology has played a major role in elucidating infrafamiliar-level systematics and evolution within Annonaceae, especially within the African genera. The Monodora clade is composed of five genera, Asteranthe, Hexalobus, Isolona, Monodora and Uvariastrum, which are restricted to Africa and contain together c. 50 species. A molecular phylogeny of the family showed that the monophyly of the Monodora clade is strongly supported and that it is part of a larger clade of 11 African genera. In order to support classification a detailed survey was made of the pollen morphological variation within the Monodora clade, using scanning and transmission electron microsopy. For the two most species-rich genera, Isolona and Monodora, a molecular species-level phylogeny was used to assess the taxonomic usefulness of the pollen characters. The survey showed a wide range of pollen morphological diversity. The most conspicuous variation concerned the occurrence of monads without a thicker outer foliation in the basal exine layer in Isolona in contrast to tetrads with a thicker outer foliation in Asteranthe, Hexalobus, Monodora and Uvariastrum. At the infrageneric level, Hexalobus, Isolona and Monodora showed the largest diversity, with various pollen types based on tectum morphology. Hexalobus is exceptional with three types within only five species. The pollen types defined in this study are hardly useful in characterizing major groups identified within both Isolona and Monodora, but they do illustrate relationships within smaller groups. [ABSTRACT FROM AUTHOR]

Tomato brown rugose fruit virus (ToBRFV) is regulated as a quarantine pest in many countries worldwide. To assess whether ToBRFV is present in cultivations, plants or seed lots, testing is required. The interpretation of test results, however, can be challenging. Reverse transcription‐quantitative (real‐time) PCR results, even though considered “positive”, may not always signify plant infection or indicate the presence of infectious virus, but could be due to the presence of viral residues in the environment. Here, case studies from the Netherlands, Belgium, and the United Kingdom address questions regarding the detection of ToBRFV in various settings, and the infectiousness of ToBRFV‐positive samples. These exploratory analyses demonstrate widespread detection of ToBRFV in diverse samples and environments. ToBRFV was detected inside and around greenhouses with no prior history of ToBRFV infection, and on different materials and surfaces, including those that were untouched by individuals, plants or objects. This suggested the dispersal of viral residues through aerosols. ToBRFV or its residues were more often detected in regions with nearby tomato production, yet were also found in a wider environment extending beyond infected crops. ToBRFV originating from environmental contamination may or may not be infectious, adding complexity to decision‐making in response to positive test results. Contextual information, such as the origin of the sample and the likelihood of residues from prior cultivations and/or the broader environment, is important for interpreting test results. A nuanced approach is crucial to correctly interpret ToBRFV test results, necessitating further research to support risk assessment. [ABSTRACT FROM AUTHOR]

In 2014, Physostegia chlorotic moitié virus (PhCMoV) was discovered in Austria in Physostegia virginiana. Subsequent collaborative efforts established a link between the virus and severe fruit symptoms on important crops such as tomato, eggplant, and cucumber across nine European countries. Thereafter, specific knowledge gaps, which are crucial to assess lhe risks PhCMoV can pose for production and how to manage it, needed to be addressed. In this study, the transmission, prevalence, and disease severity of PhCMoV were examined. This investigation led to lhe identification of PhCMoV presence in a new country, Switzerland. Furthermore, our research indicates that the virus was already present in Europe 30 years ago. Bioassays demonstrated PhCMoV can result in up to 100% tomato yield losses depending on the phenological stage of the plant at the lime of infection. PhCMoV was found to naturally infect 12 new host plant species across eight families, extending its host range to 21 plant species across 15 plant families. The study also identified a polyphagous leafhopper (genus Anaceratagallia) as a natural vector of PhCMoV. Overall, PhCMoV was widespread in small-scale diversified vegetable farms in Belgium where tomato is grown in soil under tunnels, occurring in approximately one-ihird of such farms. However, outbreaks were sporadic and were associated al least once with the cultivation in tomato tunnels of perennial plants that can serve as a reservoir host for the virus and its vector. To further explore this phenomenon and manage the virus, studying the ecology of the vector would be beneficial. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]