Multiple Viral Infections Detected in by Total and Small RNA Sequencing.

Marine oomycetes have recently been shown to be concurrently infected by (-)ssRNA viruses of the order . In this work, even higher virus variability was found in a single isolate of , a recently described member of phylogenetic Clade 6a, which was isolated from brackish estuarine waters in southern Portugal. Using total and small RNA-seq the full RdRp of 13 different potential novel bunya-like viruses and two complete toti-like viruses were detected. All these viruses were successfully confirmed by reverse transcription polymerase chain reaction (RT-PCR) using total RNA as template, but complementarily one of the toti-like and five of the bunya-like viruses were confirmed when dsRNA was purified for RT-PCR. In our study, total RNA-seq was by far more efficient for de novo assembling of the virus sequencing but small RNA-seq showed higher read numbers for most viruses. Two main populations of small RNAs (21 nts and 25 nts-long) were identified, which were in accordance with other species. To the best of our knowledge, this is the first study using small RNA sequencing to identify viruses in spp.