Serendipitomics: A New Virus Found on an RNA-Seq Library

The Papaya Ringspot Virus (PRSV) is a Potyvirus transmitted nonpersistently by aphid vectors and, like other Potyvirus, has a linear single-stranded positive sense RNA genome of about 10.3 Kb. There are two major strains of the virus, the type P which affects papaya and the type W which affects curcubits but not papaya. This is an economical important virus as plants infected at a young stage will show high yield loss. We describe here the whole genome sequence of a new PRSV species of the type W, found on an RNA-seq library made of fruits of Fevillea cordifolia (Cucurbitaceae, known as Javillo or Antidote Caccoon). The F. cordifolia fruits had no symptoms of infection. However, PRSV represented 5.4 % of all sequences on this library, showing an abundance of 65,696 FPKM. Comparatively, the DNA-directed RNA polymerase subunit RPABC4 found on this same library showed an abundance of 1,389 FPKM. RNA virus have a very high mutation rate, this is expected to generate many quasispecies of the virus. We were able to identify at least 2 distinct quasispecies on our sample.