Lengthy phytosanitary cleaning and screening procedures, used to prevent the spread of diseases through the distribution of plant material, are obstacles to the rapid dissemination and use of improved cultivars and genetic gain in clonal crops such as sweetpotato, yam, and cassava. Owing to the need for iterative phytosanitary therapy and indexing cycles until ‘clean’, these procedures significantly delay the testing and release of improved varieties, often resulting in a failure to meet critical planting windows. Methodologies for rapid cleaning and streamlined disease detection are therefore critical to certify that material is virus free.