Viroscope: Honing virus detection for the global plant trade


The destruction of plant crops from the propagation of plant pathogens, such as viruses, is a serious threat to global food security and human perpetuity. What’s more, the world’s governing bodies lack the tools for standardised and accurate virus detection.

The CEO and Founder of Multiplex startup, Dr Bernardo Pollak, and fellow researchers based in Chile have developed and tested a unique diagnostic pipeline, Viroscope, and demonstrated its functionality through a web application,

Read more in Research Features

Read the original research:


Image Source: Adobe Stock Images / Francescosgura




Hello and welcome to Research Pod! Thank you for listening and joining us today.


In this episode, we look at the work of Dr Bernardo Pollak, CEO and Founder of the startup Multiplex. They have developed a unique algorithm called Viroscope, which can detect pathogens that might be a threat to plant crops and, therefore, global food security.


A staggering volume of plant crops are lost to plant pests and vigorous diseases caused by plant pathogens, referring to organisms such as bacteria, fungi, and viruses – a primary threat to global food security. According to estimates from the Food and Agriculture Organization of the United Nations, plant diseases account for the loss of up to 40% of global crop production annually, costing the agricultural sector more than US$ 220 billion. With the increase in average global temperatures spurred by climate change, a growing human population, an increase in consumer food demand, and the subsequent import and export of plant materials from the global plant trade, the threat of propagating plant pathogens is of palpable concern.


The pervading threat to global food security posed by plant viral pathogens obviates the need for effective and expedient governmental phytosanitary programmes. The main goal of phytosanitary programmes is to stop the spread of diseases and pests that may decimate crops, forests, and other natural ecosystems and promote secure global plant trade.


Dr Bernardo Pollak, along with fellow researchers in Chile, has devised a sophisticated algorithm, called Viroscope, that can help improve the accuracy of virus detection. The unique diagnostic pipeline is supported by a cloud-based platform that broadens access to phytosanitary agencies across the globe through the provision of high-throughput sequencing data interpretation and consequent viral pathogen identification.


Although genetic analysis and detection tools such as high-throughput sequencing, known as HTS, are hailed as a gold standard for diagnosis and are becoming more affordable, several hurdles lie in the way of the technique’s wider adoption. These include the necessity for bioinformatics knowledge and processing power, inconsistent bioinformatics pipeline metrics, and the need for consistent criteria for viral identification, particularly in circumstances of low sequencing coverage.


In their 2022 paper, Pollak and his research team describe the Viroscope algorithm. It is comprised of four key steps: detection, analysis, interpretation, and diagnosis. First off, we begin with the biological material, which in this case are field samples from four sweet cherry plants. Ribose nucleic acid or RNA – a genetic component found in many organisms including viruses – is then extracted for further processing and analysis. Extracted RNA undergoes HTS, a contemporary technology for rapidly sequencing DNA or RNA molecules. This technique enables the parallel sequencing of millions to billions of RNA or DNA fragments.


In the analysis phase, Viroscope employs the process of read assignment to assign or map specific genetic sequences or fragments to a reference genome or, in this case, a curated database of viral targets. The team used three read assignment softwares to identify genomic or transcriptome regions from which each read was extracted. Only high-quality reads are retained for further processing in the Viroscope pipeline. Mapped RNA reads are gathered and used for creating longer contiguous sequences to calculate viral genome assembly coverage – representing the level of recovery of the viral genomes following sequencing.


Following this stage, the pipeline searches for the presence of protein sequences associated with virus replication – namely those proteins encoding polymerase and replicase enzymes – using an HTS alignment tool called Diamond with the help of Viral DataBase prot, a database that contains a compilation of viral proteins to aid identification. Replicases are enzymes necessary for the replication of RNA viruses. They support the reproduction of the virus inside host cells by producing new viral RNA genomes.


Finally, these measurements are employed to interpret viral presence in accordance with predetermined diagnostic cutoffs. Sweet cherry field samples, a simulation dataset, a mutation dataset, and external published datasets were utilised to validate the Viroscope pipeline.


Pollak and his team found viral genome assembly coverage  to be superior over read assignment for virus detection. False positives can result from read assignment, especially when host sequences include viral origins, such as endogenous viral components. For instance, the integration of reverse transcriptase domains by badnaviruses into the host genome isn’t always a sign of an ongoing infection. Badnaviruses are plant viruses that may induce disease in a variety of crops, impacting growth and yield. Locating badnavirus replicases is important since they may well be active and provide a systemic viral infection risk.


Furthermore, the researchers show that high-throughput sequencing based diagnostics exhibit greater sensitivity than real-time polymerase chain reaction – another analysis method – and can identify a wider variety of viruses.


Overall, the researchers demonstrate the significance of employing replicase identification and viral genome assembly coverage for enhancing the accuracy of virus detection through the Viroscope pipeline. Compared to traditional techniques like RT-PCR, Pollak and fellow researchers believe that their methodology offers greater sensitivity and accuracy concerning sequencing data-backed virus diagnosis.


Alongside Pollak, Morgante and colleagues conducted a large-scale study employing the web service for swift virus detection using high-throughput sequencing data to support efficient phytosanitary quarantine operations. Leaf samples provided by the  Chilean phytosanitary agency SAG, were analysed including a variety of species , such as apple, plum, sweet cherry olive, citrus, and avocado. The study compared Viroscope’s functional annotation with traditional methods utilised in phytosanitary quarantines, emphasising the additional insights it offers, particularly in situations where viral abundance is low. was used in the study to examine 145 plants for viruses; however, no quarantine viruses or viroids were discovered. The platform allows users to upload their data, initiate analyses, and select a predetermined panel of target viruses for detection.


High-throughput sequencing proved effective, showing presence of controlled and emerging viruses in 2.75%, and 29.6% of the samples,  respectively. Viroscope exceeded conventional technologies, providing exact detection, cost, and time reductions, as well as insight into viral physiology. Viroscope has been validated for real-life situations and is set to become a valuable tool for governmental phytosanitary programmes, one that can help expedite the quarantine process and safeguard global food security.


ResearchPod was privileged to discuss the research further with Pollack, who remarked that he and his team:


‘Identified that there was a need for better ways of ensuring that plants are healthy and that new technologies could enable safer and more precise detection of pathogens. These new methods reduce the risk of new pathogens being introduced through plant trade and can help us to determine disease-free plants for certification. This can ensure the planting of healthy orchards to achieve their maximum production capability, with less yield loss due to viruses and viroids.’


What’s more, Pollak outlined that the next steps were:


‘Developing methods for the identification of plant pathogenic bacteria and phytoplasmas, which are another kind of pathogens that are extremely damaging to plants and very tricky to identify. This is a tremendous challenge, but we are developing new strategies to approach the problem and have great data supporting our approach.’


And finally, Pollak states that:


‘Viroscope is a universal strategy for virus and viroid detection. We have tested it with over 20 plant species and made field tests with phytosanitary agencies, finding absolute agreement with conventional techniques. We have found even more viruses that are not present in the quarantine list and that have been described in the past year. We think it will be a fundamental tool for phytosanitary border vigilance, post-entry quarantines, and plant certification to guarantee food security from plant disease.’


That’s all for this episode – thanks for listening, and stay subscribed to Research Pod for more of the latest science.


See you again soon.

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