Wednesday, June 22, 2016

Plant virus detection

Plant viruses in the genus Begomovirus, family Geminiviridae often cause substantial crop losses. These viruses have been emerging in many locations throughout the tropics and subtropics. Like many plant viruses, they are often not recognized by plant diagnostic clinics due in large part to the lack of rapid and cost effective assays. 

When a plant gets infected with a pathogen, it often shows very general symptoms. An accurate diagnosis is essential to knowing which disease one is looking at. However, a number of different pathogens can cause the same symptoms and there are about 1,600 plant viruses out there. BEcause viruses can't be cultured, plant pathology labs use PCR and RT-PCR based tests to detect a part of the virus. Although used regularly in research these tests can be time-consuming and expensive. As a consequence diagnostic laboratories don't test for viruses, and the diseases go unmanaged or managed incorrectly, which is expensive for the grower. 

In a newly published study UF/IFAS scientists examined several ways to detect DNA of begomoviruses. These viruses have emerged over the last 30 years to become plant pathogens that threaten crop production in tropical and sub-tropical regions globally. The researchers found that recombinase polymerase amplification identified the cause of a disease faster and cheaper than commonly used assays.  RPA relies on the extension of primers induced by recombination proteins. These and DNA binding proteins bind the primers and scan for their target. The primers recombine with the target, and a mesophilic polymerase (Bacillus subtilis DNA polymerase I) extend the 3’ end of the invading primer using the opposite strand as a template. As opposed to PCR these reactions can be done at low temperatures (25 °C to 42 °C), with amplification in as short as 15 min which means that there won't be a need for thermocyclers.

The colleagues conclude: RPA could prove useful for the cost effective detection of plant viruses by plant diagnostic clinics. It can be performed in one hour or less with a reagent cost similar to that of PCR but with a lower labor cost, and with an acceptable level of sensitivity and specificity.

Perhaps something to look into not only for plant virus detection.

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