Paulina,

depending on the replication strategy of your virus you may try to find a needle in a bundle of hay. You may need to precise if you are dealing with an RNA virus or a DNA virus. I'll try to answer for both situation. The best method to visualise the RNA is molecular hybridization.

•the "old fashioned" northern blot will ensure you to detect the viral RNA using a specific probe. You can use random priming of a PCR product corresponding to a part of the genome to detect the vRNA. In the case of DNA virus, you may take into consideration that both strands could be transcribed. Then random priming probe will highlight 'two kinds' of RNAs from Crick strand and Watson strand. If you want to select only one transcript (or if you are not sure) use riboprobes (RNA labelled in vitro transcripts). This will need cloning in vectors having T7/T3/SP6 promoters flanking the cloning sites and unique restriction site to allow run-off transcription of the probe. In vitro labelling could be radioactive (very sensitive) or chemically labelled (Biotinylated nts). In all your experiments, add a mock control (non infected) in order to evaluate the background produced by your probe(s).

•the RT-PCR method : you will not visualise your viral RNA but amplicons/PCR products corresponding to the genome portion you selected with your primers. Here again, include a non infected control. Beware of this method since any traces of DNA will give you a signal. In the case of DNA virus, you may amplify genomic portion instead of cDNA. In case of RNA virus, this will not be an issue, except if you initiated the infection by the use of a cDNA copy of your vrial genome. Traces of this cDNA will be amplified !. If this is your situation, you need to DNase treat your samples (and include controls without reverse transcription) -> more samples to analyse.

I hope this helps

Best

D

Do you get the sequence of the virus? And are you sure the sample is infected by the virus? Before the RNA extracting, did you detected the sample whether it was infected? If you answers are "Yes", you can get a result by Northern Blot as David Gilmer said.

I find a paper said that they get a RNA virus genome band after the RNA extraction. The vRNA is protect by coat protien. So if I face this question, I will freeze and thaw my sample in PBS firstly to smash the sample and the cells. And then treat this homogenate with RNase by 37 degree for 30 min. And then extract the vRNA by Trizol. By this way, the RNA will be all from the RNA virus.