High throughput sequencing and RT-qPCR assay reveal the presence of rose cryptic virus-1 in the United Kingdom

Rose cryptic virus-1 (RoCV1) also known as Rosa multiflora cryptic virus is a partitivirus affecting roses, one of the most important ornamental crops worldwide. RoCV1 has previously been reported in the US, Canada and New Zealand, and has now been identified in the United Kingdom for the first time. Using High Throughput Sequencing (HTS) RoCV1 sequences were found in two samples collected in 2007 and 2012. This discovery led to the development of a RT-qPCR (TaqMan) assay for the detection of this virus. As part of a rose virus survey in the UK, 251 samples were analysed using the newly developed RoCV1 RT-qPCR test, following ELISA analysis for other common rose viruses. The results of the RT-qPCR test were confirmed using published conventional PCR primers and Sanger sequencing of amplified products. Results suggest that RoCV1 could have been infecting roses in the UK since at least 2007, with a large number of recently collected samples (43%) found to be infected. Cryptoviruses are not thought to cause direct economic losses in their plant host, although it is not clear what impact they might have in mixed infections.