Virus disease outbreaks occur globally, causing damage varying from small-scale losses to total crop failure. They diminish the growth and vigour of plants and decrease the yield and quality of their produce (Bos, 1982; Thresh, 1982; Thresh, 2004; Jones, 2006; Thresh, 2006a; Hull, 2014; Jones and Naidu, 2019). They damage all types of cultivated plants, including those grown to feed humans and their livestock, such as grains, oilseeds, roots, tubers, fruits and vegetables, and those grown for fibre, ornamental and medicinal purposes. Moreover, since they damage staple food crops of crucial importance for food-insecure world regions, such as maize, wheat, rice, potato, cassava, sweet potato and banana, minimizing the losses they cause is vital to achieving global food security (Thresh, 2004; Fargette et al., 2006; Thresh, 2006a; Loebenstein and Thottappilly, 2013; Hull, 2014; Jones and Naidu, 2019; Jones, 2020; Jones, 2021). In addition to plants grown as monocultures, virus diseases also damage plants growing amongst plant species mixtures in diverse situations. These include intercropping, mixed cropping, smallholder, market garden and subsistence farming (Thresh, 1982; Thresh, 2006b; Jones, 2009; Boudreau, 2013; Hull, 2014; Chai et al., 2021; Jones, 2022), and managed pastures (Edwardson and Christae, 1986; Barbetti et al., 1996; McLaughlin et al., 1996; Jones, 2012; Jones, 2022). They also damage wild plants growing in disturbed and undisturbed wild plant ecosystems, and at the interface between natural and managed vegetation (Bos, 1981; Thresh, 1981; Malmstrom et al., 2005a; Malmstrom et al., 2005b; Cooper and Jones, 2006; Webster et al., 2007; Alexander et al., 2014; Jones and Coutts, 2015; Malmstrom and Alexander, 2016). In managed pastures and natural vegetation, they diminish the fitness of plant species sensitive to infection. This reduces their ability to compete with non-host species and leads to alterations in the plant species balance (McLaughlin et al., 1992; Friess and Maillet, 1996; Jones and Nicholas, 1998; Maskell et al., 1999; Coutts and Jones, 2002; Malmstrom et al., 2005a; Malmstrom et al., 2005b; Cooper and Jones, 2006; Alexander et al., 2017; Jones, 2022). Wild plants also serve as an important infection reservoir from which viruses spread to crops (Bos, 1981; Thresh, 1981; Hull, 2014). In 2014, plant viruses were estimated to cause a worldwide economic impact of more than US$30 billion annually (Sastry and Zitter, 2014), which is likely to have grown considerably since then. Furthermore, since the world’s population is projected to increase to approximately 10 billion by 2050, the need to feed this burgeoning human population is paramount.

Factors driving the increasing threat posed by plant virus diseases worldwide include expansion of: (i) agricultural intensification, extensification and diversification; (ii) globalisation; and (iii) disturbance and fragmentation of natural vegetation (Thresh, 1980; Thresh, 1982; Fargette et al., 2006; Thresh, 2006a; Thresh, 2006b; Thresh, 2006c; Jones, 2009; Jones and Naidu, 2019 Jones, 2020; Jones, 2021). Furthermore, unpredictable weather conditions and global warming from climate change make plant virus diseases more difficult to control and alter their global distributions (Canto et al., 2009; Jones, 2009; Jones and Barbetti, 2012; Jones, 2016; Trebicki, 2020). Frequent reports of new and emerging viral diseases have elevated plant viruses to become an increasingly important global biosecurity challenge (Anderson et al., 2004; Fargette et al., 2006; Jones, 2009; Elena et al., 2014; Fereres, 2015; Gilbertson et al., 2015; Jones and Naidu, 2019). Agricultural diversification involving dissemination of crops away from their centres of origin and domestication has important consequences with respect to virus diseases. Firstly, due to virus infection in the seed or other planting material introduced, viruses that evolved in crop domestication centres become introduced inadvertently to new world regions, and then spread to local crops and native vegetation, neither of which have encountered them previously. Secondly, the newly introduced crops become invaded by viruses they never encountered before, which spread to them from infected crops occurring locally and native vegetation. Both scenarios lead to rapid virus evolution resulting in new viral variants or strains and host species jumps, which sometimes cause severe crop losses, major epidemics and even global pandemics (Thresh, 1980; Thresh, 2004; Jones, 2006; Thresh, 2006a; Thresh, 2006b; Jones, 2009; Dombrovsky et al., 2017; Jones and Naidu, 2019; Jones, 2020; Jones, 2021). The first scenario also damages natural ecosystems (Alexander et al., 2014; Vincent et al., 2014; Jones and Coutts, 2015). Under these circumstances, preventing incursions of damaging viruses and their virus vectors, and eradicating or containing any that establish successfully, is becoming an increasingly difficult challenge for biosecurity authorities located within different world regions and countries. Fortunately, rapid technological advances that improve the effectiveness of virus diagnosis in preborder, border and postborder situations are providing new opportunities to detect viruses earlier and more reliably (Jones, 2014; Martin et al., 2016; Kreuze, et al., 2023; Waite et al., 2022; Adams and Fox, 2016; Barrero et al., 2017; Pecman et al., 2017; Bronzato-Badial et al., 2018; FAO, 2019; Piper et al., 2019; Liefting et al., 2021; Maina et al., 2021; Whattam et al., 2021; Gauthier et al., 2022; Lelwala et al., 2022; Mackie et al., 2022; Alcalá Briseño et al., 2023).

Viruses are transmitted from virus-infected to healthy plants in diverse ways depending upon the pathosystem involved. These include transmission via insect, mite, nematode or fungal vectors, contact, vegetative propagules, seed, pollen, water, soil, and parasitic plants (Hull, 2014; Jones, 2018). This means that distinct pathways exist by which they can be introduced from one location to another. The most significant pathway for long-distance plant virus dissemination is via virus-infected vegetative planting material, fruits and seeds distributed via trade supply chains involving ship, plane, railway or road transport. However, international germplasm exchange for plant breeding purposes also contributes (Thresh, 1980; Thresh, 1982, Bos, 1992; Lapierre and Signoret, 2004; Jones, 2009; Sastry, 2013; Jones, 2020; Jones, 2021; Whattam et al., 2021; Lenzen et al., 2023). Moreover, the movement via trade supply chains of viruliferous arthropod vectors adhering to vegetative planting material and cut flowers, or viruliferous nematode vectors and resting spores of fungal vectors in infested soils, constitutes another major pathway for long-distance plant virus dissemination (Lecoq et al., 2003; Jones, 2009; Jones and Barbetti, 2012; Fereres, 2015; Wamaitha et al., 2018; Jones and Naidu, 2019). Furthermore, viruses and their vectors can also be disseminated over large distances when viruliferous arthropod vectors are transported by major wind currents including jet winds (Thresh, 1982; Irwin and Thresh, 1988; Maina et al., 2017a; Maina, 2018; Maina et al., 2018a; Maina et al., 2018b; Maina et al., 2019);. Dissemination also occurs when airline, ship or railway passengers unknowingly, or deliberately, carry virus-infected fruits, seeds, vegetative planting material or virus-infested soil in their luggage (Swain et al., 1952; Crooks et al., 1983; Alvarez Quinto et al., 2023).

Australia differs from other continents and major world regions regarding the threat virus diseases pose to its agriculture. It has a unique situation in the world because of being an island continent where the only plants cultivated during the limited agriculture practiced for thousands of years before Europeans first settled in 1788 were derived from Australian native plants (Gerritsen, 2010). Therefore, before its colonisation the continent lacked the numerous virus and virus vector introductions that occurred elsewhere in the world when seeds and vegetative propagules of cultivated plants were moved between continents (Gibbs et al., 2008; Jones, 2009). Furthermore, since the Australian Quarantine Service commenced with the Quarantine act of 1908, a national biosecurity framework has gradually been developed that minimizes the likelihood of incursions by viral pathogens that damage cultivated plants and native flora in other parts of the world (Rodoni, 2009; Burgman et al., 2014; Barrero et al., 2017; Davis et al., 2021; Jones et al., 2021c; Whattam et al., 2021). For these reasons, Australia remains free of many damaging viral diseases and virus vectors found elsewhere. Nevertheless, its quarantine barrier is sometimes breached and the ensuing post border operations may fail to eradicate or contain virus and vector incursions. For example, this occurred when two seed-borne viruses entered via infected seeds: wheat streak mosaic virus (WSMV) which arrived around 1999 (Dwyer et al., 2007; Jones et al., 2022), and cucumber green mottle mosaic virus which arrived in 2014 (Dombrovsky et al., 2017; Kehoe et al., 2022; Mackie et al., 2022). It also occurred when the insect ‘supervectors’ Franklinella occidentalis (western flower thrips) and Bemisia tabaci Biotype MEAM1 (silverleaf whitefly) arrived in 1993 and 1994, respectively (Malipatil et al., 1993; Gunning et al., 1995). Moreover, Australia’s northern coastline is near to the coastlines of its neighbouring countries of Indonesia, East Timor and Papua New Guinea (PNG). It is, therefore vulnerable to virus and vector incursions from wet season monsoonal wind currents carrying insect vectors (Maina et al., 2017a; Maina, 2018; Maina et al., 2019; Davis et al., 2021). It is also vulnerable to virus incursions via migrating birds bringing infected seeds, and vessel landings which inadvertently introduce virus-infected seeds and/or virus-infected or vector-infested vegetative propagules, fruits or soils (Gibbs et al., 2008; Horwood et al., 2018; Davis et al., 2021; Jones et al., 2021c).

The Australian continent has diverse climatic zones ranging from temperate to tropical, which allow production of a wide diversity of grain crops grown mainly for export (Henzell, 2007; Brown et al., 2020). Grain crop cultivation is a major Australian economic activity worth $16.7 billion annually (ABARES, 2022). As the world’s population continues to increase, the importance of Australia’s grain exports in helping to satisfy the ever-growing demand for food worldwide is likely to increase further. Consequently, ongoing prevention of plant virus introductions is fundamental to mitigate viral disease impacts on Australian grain crops and safeguard its economy. Here, after describing Australian plant biosecurity procedures in relation to virus and vector interceptions and incursions, we describe advancements in detection technologies, innovative tools and database analytics which can improve Australian plant virus disease diagnosis and surveillance, and highlight areas that warrant further investigation. Examples of virus biosecurity threats to Australian cereal and oilseed crops were provided in two recent reviews (Davis et al., 2021; Jones et al., 2021c). Therefore, the examples used here mostly involve biosecurity threats to the legume component of the continent’s grain crops. Our primary objective in writing this review is to enhance the effectiveness of Australian plant biosecurity at (i) intercepting damaging grain viruses when they first arrive in the country, and (ii) providing the extensive background information its post entry surveillance activities require to detect, assess and manage new virus and vector incursions in grain crops.

Currently more than 1.8 million hectares of grain legumes are grown in Australia, an average 2.2 million metric tonnes being produced annually (AEGIC, 2020). The principal grain legumes grown are chickpea (Cicer arietinum), field pea (Pisum sativum), faba bean (Vicia faba), lentil (Lens culinaris), lupin (Lupinus spp.), mungbean (Vigna radiata), common bean (Phaseolus vulgaris), cowpea (Vigna unguiculata), soybean (Glycine max), and peanut (Arachis hypogea) (AEGIC, 2020). The main grain legume crops in tropical northern Australia are chickpea, mungbean, soybean, peanut, cowpea, common bean and cowpea. Those grown within Australia’s subtropical northern grainbelt are mungbean, soybean, peanut, lupin, field pea, chickpea and lentil, while those grown in the Mediterranean and temperate climates of its southern grainbelt are lupin, chickpea, faba bean, lentil and field pea (AEGIC, 2020; Brown et al., 2020; Jones et al., 2021c).

Examples of more important grain legume viruses absent from Australia are shown in Table 2 , which lists information for each of them on the main crops they affect, their principal vectors, whether they are seed-borne, and their global distributions, disease impacts and entry risks. Figures 2A–H illustrate the disease symptoms some of them cause in grain legume foliage and seeds. The losses these viral pathogens engender within grain legume crops growing elsewhere in the world vary from devastating, e.g., groundnut rosette disease in sub-Saharan Africa ( Figures 2A, B ; Naidu et al., 1999) and faba bean necrotic yellows disease in the Middle East and North Africa ( Figures 2C, D ; Makkouk, 2020), to major losses only occurring sporadically (e.g. bean dwarf mosaic disease in South America and pea early browning disease in Europe) ( Table 2 ). Nine of the virus examples in Table 2 are seed-borne so these are therefore of greater concern for Australian biosecurity authorities than those only likely to enter Australia via vegetative propagule imports. Moreover, three of the viruses in Table 2 , bean common mosaic necrosis virus (BCMNV), groundnut bud necrosis virus (GBNV) and mungbean yellow mosaic India virus (MBYMIV), have been found in the neighbouring countries of Indonesia or East Timor closest to Australia’s northern coastline. Amongst these, BCMNV is both found in East Timor (Maina et al., 2016) and seed-borne so likely to enter Australia via birds or insect vectors crossing the ocean or directly via introduction of virus-contaminated seed (see previous Section). Since they are not seed-borne, GBNV and MBYMIV are more likely to arrive in northern Australia from Indonesia (Damayanti and Naidu, 2009; Hema et al., 2014) via insect vectors crossing the ocean. In the 1970s, the seed-borne viruses broad bean stain virus (BSV; Figure 2H ) and broad bean true mosaic virus were found infecting faba bean seeds sourced in the Australian Capital Territory and the state of South Australia (Moghal and Francki, 1974; Randles and Dube, 1977; Buchen-Osmond et al., 1988). However, there have been no further detections in Australia, so both are deemed no longer present and, therefore, still considered to be biosecurity threats ( Table 2 ).

Amongst some of the grain legume viruses already present in Australia, there are virulent strains which have not yet arrived but pose a threat to Australia’s grain legume crops. For example, two virulent strains of bean common mosaic virus (BCMV) fit this category. These are its peanut stripe (BCMV-PSt) and blackeye cowpea mosaic virus (BCMV-BICMV) strains, both of which were formerly considered distinct viruses. Moreover, BCMV-BICMV already occurs in Indonesia, and BCMV-PSt in both Indonesia and PNG (Green et al., 1988; Akin, 1997; Davis et al., 2002; Davis et al., 2021). Therefore, both are likely to enter Australia via birds or insect vectors crossing the ocean or directly via introduction of virus-contaminated seed. In 2013, an eastern Australian study reported finding a seed-borne PSbMV strain in seed of lentil germplasm imported from the USA and demonstrated that it belonged to PSbMV pathotype 2 ( Figure 2I ; Van Leur et al., 2013). This report considered this PSbMV strain to be a major biosecurity threat to the Australian lentil industry and ways of avoiding its establishment in commercial lentil crops were proposed. However, in 2001 an earlier study in south-western Australia had reported finding PSbMV-infected plants with atypically severe foliage symptoms growing within plots of field pea breeding lines ( Figure 2J ; Latham and Jones, 2001). This report suggested that these plants were infected with a severe PSbMV strain introduced via field pea germplasm from overseas. Soon afterwards, virus isolate W1 obtained from these plants was found to belong to PSbMV pathotype 2 to which the virulent lentil strain of PSbMV, sometimes called the lentil strain (L-1, Alconero et al., 1986), also belongs (Coutts et al., 2008; Wylie et al., 2011). Moreover, in a field experiment PSbMV isolate W1 infection decreased lentil seed yield by 96% and was seed-borne in 6% of seedlings grown from harvested lentil seed (Coutts et al., 2008). Therefore, the PSbMV variants found first in field pea breeding plots in south-western Australia and later in imported lentil seed in eastern Australia might both be representatives of the same virulent seed-borne lentil strain, which has apparently not yet spread within commercial crops belonging to the Australian lentil industry.

Recent advances in high-throughput sequencing (HTS) and bioinformatic analysis have provided considerable opportunities to upgrade virus surveillance for plant health services and virus discovery, so this subject has recently received considerable worldwide attention (Massart et al., 2014; Adams and Fox, 2016; Massart et al., 2017; Pecman et al., 2017; Adams et al., 2018; Villamor et al., 2019; EPPO, 2022; Lebas et al., 2022; Alcalá Briseño et al., 2023; Fontdevila Pareta et al., 2023), including within Australia (Barrero et al., 2017; Piper et al., 2019; Maina et al., 2021; Whattam et al., 2021; Gauthier et al., 2022; Lelwala et al., 2022; Mackie et al., 2022; Maina et al., 2022). Moreover, the cost of HTS is declining at a significant rate due to advances in sequencing technology, so its application as a routine diagnostic tool is becoming increasing attractive (Villamor et al., 2019; Lebas et al., 2022). Indeed, it has been endorsed as a robust testing tool for screening viral pathogens in inter-country commodity trading by both the World Trade Organisation and Food and the Agriculture Organisation of the United Nations (FAO, 2019). Furthermore, its integration is recommended for critical sample testing within healthy stock, seed and crop certification programs around the world to enhance the availability of virus-tested plant material in a timely manner (Villamor et al., 2019). However, despite these benefits its main drawback remains that, in addition to known viral pathogens, it also reveals presence of potential viral pathogens that exist only as sequences lacking any biological data (Massart et al., 2017; Jones et al., 2021b; Whattam et al., 2021). In 2017 in Europe, a collective framework was devised to provide guidelines designed to help both plant inspection agencies and biosecurity and plant health authorities with their collection of the biological data needed to establish whether such potential viral pathogens pose any actual economic risks to the agricultural sector (Massart et al., 2017). However, the biological data obtained from following these guidelines was insufficient for meaningful biosecurity PRAs to be performed on each potential viral pathogen. This was because they required comprehensive information for each virus about its incidence, distribution, symptomatology, pathogenicity, vectors, host range, genetic diversity and epidemiology. Therefore, this framework was expanded to make it sufficiently comprehensive to guide these agencies and authorities toward assembling all the biological data necessary for their PRAs to be effective (Adams et al., 2018; Olmos et al., 2018; Fontdevila Pareta et al., 2023). Figure 2 of Fontdevila Pareta et al. (2023) provides an up-to-date, detailed, explanatory diagram of the most recent version of the European PRA framework, which illustrates all its different components and how they relate to the other. This revised framework will help greatly with the collection of biological data needed to strengthen the effectiveness of biosecurity PRAs employed in Australia (see the Australian Plant Biosecurity Section above).

In the pre-sequencing era, there was far greater focus on the provision of extensive biological data about plant viruses than currently. Sequencing virus isolates preserved in historical plant virus collections, and establishing whether the sequences obtained match those of recently found potential viral pathogens existing only as sequences, can, in instances where there is a match, help provide access to otherwise missing but extensive biological baseline data needed for biosecurity PRAs (Jones et al., 2021b). It will also help establish when apparently newly found viruses have been provided inadvertently with incorrect names, because they had actually been studied and named in the past. This scenario is also important for biosecurity and other plant health authorities to be aware of when conducting their PRAs. Nevertheless, over the last ten years, the demand for HTS in global plant health diagnostics has remained high. Notably, whole genome sequencing can be costly when used for routine massive parallel sequencing. Therefore, over the last five years, considerable efforts have been underway in Australia to explore the possible integration of rapid diagnostics innovation involving HTS genome based smart tools into plant health and biosecurity programs (Barrero et al., 2017; Piper et al., 2019; Maina et al., 2021; Whattam et al., 2021; Gautier et al., 2022; Lelwala et al., 2022; Mackie et al., 2022). The following Sections describe examples of the most promising, cost-effective approaches suitable for use by plant biosecurity and other plant health authorities.

Machine learning and deep learning algorithms for big data analyses, and remote sensing technologies, such as hyperspectral, multispectral, thermal, and other types of optical sensing, hold considerable promise toward achieving more effective virus disease and virus vector surveillance (Jones, 2014; Jones and Naidu, 2019; Oerke, 2020; Ahmad Loti et al., 2021; Khan et al., 2022; Gollapudi et al., 2023; Sarkar et al., 2023). Moreover, the combined use of ground with aerial remote sensing increases the accuracy and precision of virus disease or vector detection (Jones, 2014; Neupane and Baysal-Gurel, 2021; Rhodes et al., 2022; Wang et al., 2022). Furthermore, these innovations are becoming increasingly successful at distinguishing virus-infected or insect vector-infested plants from healthy plants (Griffel et al., 2018; Nansen et al., 2019; Abd El-Ghany et al., 2020; Terentev et al., 2022; Wang et al., 2022). During searches for new virus and vector incursions, adopting such technologies can strengthen the effectiveness and efficiency of different kinds of surveillance activities. This applies not only to NAQS activities in northern Australia, but also to post entry biosecurity eradication and containment programs in affected regions throughout Australia. It also applies to other plant health activities such as healthy stock and seed schemes and large-scale seed crop certification inspections. Such imaging would be applied on different scales depending on what it is being used for, ranging from very intensive during eradication programs to moderate or infrequent, as appropriate, during NAQS or containment activities.

Database surveillance networks could serve as an effective way of sharing datasets to help track viral genome mutations and variants of concern as they enter Australia. For this, a prospective virus genomic-surveillance system would be combined with an interoperable virus database adhering to standard practices. These practices would guide the process of creating and submitting sequence metadata records for standardization across different Australian biosecurity and plant health agencies. A dedicated high-performance computing system would be built in partnership with computing system administrators with extensive computing expertise, and both virology and virus vector researchers with strong virus biology and bioinformatics linkages. Database and surveillance systems would facilitate tracking viruses of biosecurity or plant health concern using sequence predictive tools to identify lineages and the origins of different incursions ( Figure 1 ). Nextstrain (Hadfield et al., 2018) proved a successful approach with which real-time phylogenetic information was used to track variants within SARS-2 (COVID-19) populations. By revealing virus evolutionary trends, geographical origins and diversity, the development of such phylogenetic inference tools would help with tracking Australian grain virus incursions. This information would ensure more effective surveillance thereby enabling more effect virus management during eradication and containment programs.

Notably, as explained in the ‘High Throughput Sequencing’ Section above, historical virus specimen collections can help with understanding more recent virus incursions and their subsequent spread (Jones et al., 2021b). Likewise, building and enhancing Australian virus specimen collections, would provide a significant baseline data contribution to future virus biosecurity and plant health programs. These collections need to be sequenced, and the datasets obtained linked back to surveillance databases. Doing this would not only support the accurate identification of damaging viral variants linked to new incursions, but also help to ensure that all virus species identifications and classifications based on sequences are correct.

Here we explain the critical importance of grain industry exports to the Australian economy, the reasons why the continent lacks many of the virus diseases that damage grain crops in other continents and the importance of having a stringent biosecurity program in place to prevent their introduction and establishment. We also specify the different pathways by which damaging grain viruses and their vectors can reach Australia, and the measures currently in place to prevent their introduction and establishment. Next, we explain how Australian biosecurity programs currently test seeds, vegetative propagules or other plant imports after their arrival for the presence of viruses of concern. When such viruses are found the consignment is destroyed. When these efforts fail to detect threatening viruses, and an affected consignment is inadvertently released, an incursion occurs. In these circumstances, PRAs are done to provide an estimate of the risk of economic loss likely to occur if no further action is taken. In this context, we recommend using the most recent European framework providing comprehensive guidelines to help biosecurity and plant health authorities assemble all the biological data required to conduct effective PRAs. When the estimated risk level justifies the cost of taking action, an eradication campaign is authorised. Although such campaigns normally involve taking drastic measures, they sometimes fail to eliminate the incursion. When this transpires, a decision is made to continue to localise the distribution of the viral pathogen with a containment exercise or accept its presence and manage its epidemics in the same way as those of established viruses. Similar procedures to those used with virus threat arrivals also apply to incoming virus vectors.

Fortunately, exciting recent advances in technological innovation provide major opportunities to improve the effectiveness and reduce the costs of Australian biosecurity detection, diagnosis and surveillance procedures that target threatening grain crop viruses and their vectors. Where appropriate, they also provide opportunities to improve other Australian plant health activities. These include the effectiveness of future virus surveillance during healthy stock and seed programs, and crop certification. We recommend increasing their adoption, and continuous investment in future research innovations in Australian grains biosecurity to enhance their effectiveness and reduce the costs of virus testing and surveillance activities. In particular, we advocate more widespread integration of HTS genome based smart tools and research on their application into PEQ testing and other biosecurity testing of imported seeds, vegetative propagules, and further planting material. Additionally, these technologies offer major advantages for testing NAQS surveillance samples collected in the field. Where appropriate, we also suggest their use to ensure accurate diagnosis of viruses present in critical surveillance samples collected during eradication and containment activities, healthy stock and seed program inspections and seed crop health certification. This is because conventional plant biosecurity techniques are less adaptable to the detection of distinct viruses than HTS. This challenge underscores the necessity of undertaking future innovation focused on developing effective broad-spectrum HTS detection methods for use in detecting the growing number of virus biosecurity threats to the Australian grain industry. Globally, HTS has revolutionized the identification and characterization of plant viruses. Its high robustness has enabled the discovery of many viruses which have been fully or partially characterized subsequently. This has improved diagnostic procedures, disease diagnosis, and the understanding of virus diseases of unknown etiology. HTS has superseded conventional detection methods, due to its ability to identify both known and unknown viruses without prior knowledge of their presence, and in a reduced timeframe. The greater comprehensiveness of HTS compared to conventional detection methods means that it can profile multiple viruses present in a single biological sample, including viruses co-existing within a synergistic complex.

Illumina technology significantly reduces errors and missed base calls associated with homopolymers and other experimental stochasticity. It provides high quality short reads and has a massive multiplexing capability. These are all desirable cost-effective features especially suited for screening large number of samples for targets of low abundance viruses. However, future research innovation should focus on developing faster and shorter robust library preparation procedures and the capability to stop/pause the run as soon as enough data has accumulated to allow initial analysis. Further, future on board platforms should have the ability to allow analysis of base called datasets in real time sequencing. This could dramatically reduce grain virus biosecurity diagnostics associated costs and shorten critical biosecurity decision-making timelines. The ONT MinION portable sequencer is ideally suited to circumstances where few samples need to be tested rapidly by a cheaper method. Combining real-time nanopore sequencing with multiplexed barcoded loop-mediated amplification and transposase library preparation (LamPORE) increases accuracy, reduces virus diagnostic costs and shortens decision-making timelines. ONT future innovation should strive to develop robust library preparation procedures which incorporate both rRNA depletion and reverse transcription, for example in direct RNA-Seq and cDNA-PCR approaches, and higher quality score sequencing procedures which lead to a considerable increase in obtaining accurate results in virus detection. Such a portable tool would be ideally suited to on farm virus genomic surveillance.

TG-Seq is a targeted HTS approach that maximises the sensitivity and specificity of virus assays, decreases sequencing costs and simplifies downstream bioinformatic analyses. Likewise, VgSkim-Seq offers an effective and low-cost tool for use in routine viral genome sequencing. Moreover, inclusion of metabarcoding in an HTS platform such as the NovaSeq system makes it efficient and cost effective for use in surveillance for new virus vector incursions in the field. To further optimise the effectiveness of virus surveillance activities, we recommend widespread adoption of machine learning and deep learning algorithms for big data analyses, and both surface and aerial remote sensing technologies. Combining in-field machine learning high throughput phenotyping and real-time genotyping, will help track vector arrivals, viral genome mutations and virus variants of concern as they enter Australia. We also recommend using these technologies along with database surveillance networks that combine virus genomic-surveillance systems with an interoperable virus database. Finally, we recommend, enhancing and HTS of Australian virus specimen collections to help ensure all virus species identifications based on sequences are correct and viral variants linked to new incursions are identified accurately. These recommendations will help improve Australian grain biosecurity and plant health policy planning and grain virus and vector research. They will also help towards bettering both virus diagnosis and virus and virus vector data collection, thereby upgrading not only post entry virus interceptions but also background virus and vector surveillance information. In turn, this will reduce the frequency of new incursions, improve virus management during eradication, containment and other plant health activities, and help towards safeguarding the Australian grains industry and achieving more profitable Australian grain production.

The original contributions presented in the study are included in the article. Further inquiries can be directed to the corresponding author.

SM: Conceptualization, Funding acquisition, Investigation, Project administration, Writing – original draft, Writing – review & editing. RJ: Conceptualization, Investigation, Supervision, Visualization, Writing – original draft, Writing – review & editing.