Development of a one-step RT-qPCR assay for the detection of Citrus concave gum-associated virus in apples

The yield and quality of apples are affected by diseases caused by bacteria, fungi, viruses, and virus-like organisms. Several viruses are known to cause or be associated with diseases of economic importance which impact apple production. Citrus concave gum-associated virus (CCGaV; order Bunyavirales, family Phenuiviridae, genus Coguvirus) is a negative-stranded RNA virus, with a bipartite genome of negative-stranded RNA1 and an ambisense RNA2. In recent years, CCGaV was identified in apple germplasm collections in a number of countries. Although identified in apple trees showing decline, CCGaV could not be implicated in disease causation due to the presence of other coinfecting viruses. As a precautionary measure, virus elimination programs have included CCGaV in the list of viruses that should be eliminated from the propagative material before distribution to its stakeholders. Detection of tree fruit viruses in woody hosts is difficult as compared to annual crops, due to the low titer, irregular distribution, and the occurrence of mixed infections. Sensitive and specific virus detection methods are critical part of virus elimination programs, first to identify virus infected plants that need to be treated and then to certify virus-free status of after virus elimination treatments. In this study, an RT-qPCR assay was developed for sensitive and specific detection of CCGaV in apples.