RNA Viruses sequencing strategy

[Etherella]

Hello! My question is about whether there is a certain strategy to sequence an RNA virus provided the input material is a biological sample (host cells). Is there a method to separate viral RNA from the rest of the genomic material? The virus genome sequence is completely unknown, that is to say we're trying to indentify what kind of a virus it is.

[kopi-o]

I've heard that in some RNA viruses, the capsid protects the viral RNA against RNases, so you can use RNase to deplete non-viral RNA ... but if you don't know what kind of virus it is this might be a bit optimistic.

You could always try to sequence the sample and isolate out the viral RNA bioinformatically, i e filter out suspected host RNA, de novo assemble what is left and BLAST the contigs against NT, for instance.

[dpryan]

There are also virus purification kits that you can just buy. The alternative is to determine the various centrifugation steps yourself to just manually purify things. There are a number of papers on that, so I imagine there are some standard tricks to be found.

[JamieHeather]

Another option is using some kind of targeted pulldown/bait approach, eg SureSelect, which I imagine would be relatively less cost-prohibitive for some of the smaller RNA viruses.