Demonstrating pest-freedom from avocado sunblotch viroid with a smartphone app and improved detection methods

By Dr Louisa Parkinson and Dr Lara-Simone Pretorius, Queensland Alliance for Agriculture and Food Innovation (QAAFI), and A/Prof Andrew Geering, The University of Queensland

Avocado sunblotch viroid (ASBVd) has the potential to disrupt trade in fresh fruit, particularly to pest-free countries such as New Zealand. As such, a new biosecurity surveillance project (AV18007) for demonstrating pest-freedom from ASBVd is underway in Australia.

This project aims to map all avocado orchards and nurseries in the country, testing thousands of trees and conducting statistical analyses to demonstrate pest-freedom at farm or regional-level, so that growers can meet export conditions and nurseries can obtain NIASA accreditation.

We are collaborating with experts in epidemic modelling from Cambridge University in the UK and in disease management from South Africa.

In collaboration with CSIRO, we are also trialing a novel surveillance strategy using honeybees, which do the leg work by collecting pollen samples from dozens of trees. If the viroid is present, it should be detectable in the pollen samples using our highly sensitive molecular diagnostic tools. A key industry partner for us is AgKonect Pty Ltd, which has made large-scale surveillance and data recording simple and accessible for researchers and growers. Outcomes of the project will be that the Australian avocado industry can enter new export markets and will be better equipped to respond to all types of biosecurity threat.

Symptoms and mode of spread of ASBVd

Symptoms of ASBVd include abnormally shaped fruit with deep scarring beginning at the petiole; variegation, bleaching and deformation of the leaves; a stunted and decumbent growth habit; and in some cases, bark cracking or ‘crocodile skin’ on the trunk and branches (Figure 1). There are also asymptomatic strains of the viroid that nevertheless, still result in yield losses. Root grafting is thought to be the principal mode of transmission in the field, although there is likely inefficient transmission of the viroid on sap-contaminated pruning blades. The major point of infection is in the nursery, as the viroid is transmitted at a very high rate through seed, and can also be introduced through use of infected budwood. Growers are recommended to use NIASA (previously ANVAS) certified nursery plants.

Figure 1. Symptoms of ASBVd infection. Malformed fruit and yellow sunblotch streaking at the stem (left); yellow streaking and curving of leaves (right).

How is surveillance conducted with AgKonect?

We identified that data management would present some challenges in the project: in capturing field data, tracking diagnostic samples, reconciling results with tree observations, analysing and presenting the data, and reporting back to growers. Thus our surveys are conducted in collaboration with Brisbane company AgKonect Pty Ltd, which provides custom software for agriculture, with the QLUMP national avocado farm layer (a map of all avocado orchards and nurseries in Australia) already added to their software platform.

AgKonect is a software program that simplifies field work using custom forms in a map-driven smartphone app. The software enables users to create customisable survey forms on a computer (Figure 2) and subsequently capture all data, photos, precise GPS locations and sample details in the field using a smartphone or tablet (Figure 3).

Figure 2. Screenshot of computer software interface where the survey form can be created and edited. The smartphone image (right) displays the survey form interface on the app.

The AgKonect app is user-friendly, making collecting data in the field quick and easy, eliminating sources of error; the user does not have to juggle paper records, cameras, GPS equipment and writing instruments while collecting data in the field. The app also has data caching capabilities, allowing the app to be used in remote, poor mobile coverage areas (Figure 3). Once in the field, GPS points are created for each tree and saved as colour-coded dots on the map (Figure 3). When sampling is complete, data is synced from the phone to the computer software where the data can be exported as an excel spreadsheet for further analysis or record keeping.

Figure 3. Smartphone screenshots of the app interface with a GPS point recorded for an individual tree (red dot).

AgKonect is used in our project for precisely tracking the GPS location of every single tree that is tested so we have an auditable record of the tree location and label, observations made, samples taken, photographs of symptoms and diagnostic test results. The software also enables growers to collect samples for testing and directly input the data, and for the diagnostic team to link results as they are obtained. Industry-wide use of the app can enable our research team to collect detailed and accurate data for demonstrating freedom from ASBVd.

We are exploring further uses for the app and another advantage of AgKonect is its customisable features for traceability – its use can be applied for almost any kind of data collection or record keeping. For research or on-farm records, it can be customised for recording dates and details of field sprays; which trees have pest and disease issues; nursery records such as sources of budwood and what screening tests have been done prior to dispatch; and finally, record-keeping for fruit in the supply chain. The app can be used by pathologists for routine inspections or used by growers to demonstrate that industry standard protocols are being followed. Moreover, the NIASA certification form has been converted into a digital format using AgKonect, and could potentially enable NIASA accreditors to complete an inspection and certify on-site.

Implementing improved diagnostic methods

The highly sensitive and specific molecular test for ASBVd, a reverse transcription quantitative PCR assay (RT-qPCR), was developed by A/Prof Andrew Geering and has become a global industry standard. Dr Lara Pretorius, a new member of our research team, has developed an improved nucleic acid extraction method (the first step in the molecular diagnostic test), utilising filter paper. The viroid nucleic acids have high binding affinity to the cellulose fibres in the filter paper under high salt conditions, but are reversibly eluted under low salt conditions (Figure 4). This extraction technique improves the sensitivity of the molecular test and enables fast, inexpensive, high-throughput processing of a large number of plant samples, making testing of thousands of trees feasible by a small research team.

Figure 4. Extraction procedure with avocado leaf tissue and filter paper disks for use in the ASBVd molecular diagnostic test.

Another diagnostic component of our project is to trial the use of honeybees for monitoring the incidence of ASBVd in avocado-growing regions. When managed honeybee hives are used for horticultural crops to deliver pollination, the bees can also provide valuable pathogen surveillance services by effectively ‘sampling’ entire crops as they collect pollen and nectar. Research by Dr John Roberts (CSIRO) has demonstrated that a wide diversity of viruses can be detected in pollen samples, and exotic viruses can be discovered before they are recognised using traditional methods of surveillance. We will be trialling the usefulness of this surveillance method in South Africa where ASBVd is widespread, and as well as in the Tristate area of Australia, which historically has had the most records of ASBVd in the country. We are also collaborating with citrus pathologists in New South Wales to validate the method using citrus viroids.

Interested in having your orchard or nursery tested for ASBVd?

Please contact our research team (Dr Louisa Parkinson, for your orchard or nursery to be tested for ASBVd. For further information about using AgKonect in your orchard or nursery, please contact Dr Peter Whittle (


This project has been funded by Hort Innovation, using the avocado research and development levy and contributions from the Australian Government.

Hort Innovation - Strategic Levy Investment (Avocado Fund)

This article was prepared for the Autumn 2020 edition of Talking Avocados.



Author: Dr Louisa Parkinson, Dr Lara-Simone Pretorius, A/Prof Andrew Geering
Date Published: 17/04/2020