I found some plant viruses in human brain sample through Rna-seq analysis. I know it's some kind of weird, but I do find some evidence that plant viruses can infect human. Even there is a very new review paper discussed "Can plant virus cross the kingdom border and be pathogenic to human". My question focus on how to evaluate the virus. The mapping analysis can only show some reads can be mapped to some virus. But "Does the virus exactly exist in my brain sample?" is still a unanswered question. Do anyone have great ideas to evaluate it?
My little idea is to detect the fusion sites, but what if they didn't integrate into our genome?
My pipeline is as follows:
First, map RNA reads against human reference. Second, align unmapped reads against all viruses genomes. Third, extract those highly expressed viruses according to PPM or RPKM.
For example, in one sample with about 60,000,000 unmapped reads(against human reference), there are 470,000 reads can be mapped to 'Poinsettia mosaic virus', which is a plant virus. And it seems not like contaminants because this virus are not detected in other samples.
Any advices are appreciated.