Virus Identification

[aftabac]

Hi dear fellows
for the identification of some unknown bacteria we commonly do ribotyping using 16S rRNA gene and for eukaryoties we commonly do 5S or 18S rRNA gene sequencing and then BLAST it to find out homology.
For the identification of some unknown virus, what is the marker used for identification.
IS it sequencing of particular region or some other feature identification??

waiting


aftab ahmad

[JackieS]

As viruses are quite small, if you sequence their RNA you should easily have enough to find out by BLAST or search what exactly they are.

Many viruses are RNA so I am not exactly sure how you would sequence them. Make cDNA first?

[aftabac]

i am still doutful about virus identification in some unknown samples, so if someone has more informations then please forward to forum.

waiting

aftab

[admin]

Hi Aftabac,
Is this the same virus that you want to identify in many samples or just a virus you want to find the sequence of?

If you will be analyzing hundreds of samples an ELISA assay would be best, although for a few samples I would go the route of either southern blotting, northern blotting with probes against the virus, or somehow trying to sequence cDNA from isolates...

This is an intruiging problem. I will also get back to you.

[BlessedOne]

Anyone familiar with an OAN9 as a virus number?

[aftabac]

Yes we do ELISA, probe, PCR or even microarray for viruses but if there is unknow virus that is not reported before, what way we should move to identify the unknown virus? I think the way which is usually opted is to sequence it and if it does not match with the existing sequences then a new name is given to it....

it will be nice if someone elaborate it more