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Genome sequencing leaves plant viruses no place to hide

Agriculture Victoria’s Dr Solomon Maina is working to develop new genome sequencing methods to screen for plant viruses.
Photo: Dr Piotr Trebecki

Key points

  • New genome sequencing techniques will enable faster testing of a broader range of plant viruses to enhance accuracy for quarantine and biosecurity investigations
  • Agriculture Victoria is leading the world in developing these new techniques for the grains industry

New genome sequencing methods bolster plant quarantine screening through the rapid identification of multiple viruses.

The 2020 COVID-19 pandemic has taught us much about the potential impact of viruses on humans. Similarly, plant viruses can reduce the yield, quality, competitiveness and marketability of broadacre crops, yet once a crop is infected there is little a grower can do to limit the damage.

While the Australian grains industry has always been at risk from the inadvertent introduction of plant viruses through imported seed, it has a long-standing and rigorous approach to post-entry quarantine and diagnostics.

The potential for this defence to be strengthened further may come from advances being made in the development of high-throughput genome sequencing diagnostics for viruses in grains. This is being developed by researchers at Agriculture Victoria with GRDC investment. If successful, it will allow the detection of new pathogens that could be missed with traditional testing methods.

Researchers at Agriculture Victoria have developed an Australian first – a high-throughput genome sequencing diagnostic method for viruses in grains.

Genome sequencing methods enable researchers to detect multiple viruses – even those with high genetic variability. These tools are especially valuable when it is not known which pathogens might be present in a grain sample.

Traditional methods, by comparison, rely on the use of antibodies, which are limited by antisera availability, and may not detect viruses with highly variable genomes.


The main route for long-distance spread of new viruses is through inadvertent introduction via imported seed. Some may arrive on our shores through illegal importation of plant material or by natural means such as wind. While it might be tempting to close borders to material such as seed, Australian plant breeders and researchers must have access to new germplasm. This is why the onus is on a stringent process of legal importation followed by post-entry quarantine.

Virus screening at the Australian Grains Genebank (AGG) quarantine facility in Horsham, Victoria, enables the legal importation of new germplasm and also supports biosecurity investigations. While the risk of virus introduction can never be completely eliminated, improved testing procedures significantly reduce the risk.

First runs

After five years of research, a targeted genome sequencing approach has successfully detected the exotic pea early browning virus and three endemic viruses at the same time and proved substantially more sensitive than traditional methods.

The ability to detect multiple virus targets allows widespread identification of damaging plant viruses across multiple grains, oilseeds and pulse crops, and at a reduced cost.

While genome sequencing tools have been adopted for different crops in the US and parts of Europe as part of their genetic certification programs, Australia is leading this approach for grains.

These new testing regimes may one day provide comprehensive universal pathogen surveillance that will also protect market access for Australia grains.

More information: Dr Solomon Maina, 0469 356 000,

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