Question: Finding Reads from a DNA Virus
0
gravatar for nickeener
7 weeks ago by
nickeener0
nickeener0 wrote:

Hi, I'm trying to locate viral reads from a DNA virus in Drosophila sequencing data from NCBI's SRA and was unsure whether using RNA-seq experiments would be productive or not. Obviously the virus must transcribe its DNA into RNA in order to have its viral proteins translated, but my question is: since there will be both viral RNA and viral DNA in infected cells, should I look for sequencing runs where the genomic DNA was sequenced or would using RNA-seq runs give me better results? Or should I consider both?

Thanks

rna-seq virus detection sra • 195 views
ADD COMMENTlink modified 6 weeks ago by darren.obbard20 • written 7 weeks ago by nickeener0
2
gravatar for darren.obbard
6 weeks ago by
UK, University of Edinburgh
darren.obbard20 wrote:

Both DNA and RNA will work. In our experience virus (genomic) copy number can be several hundred-fold higher than the host genome-copy number, so on experimental cultures/ infections DNA will work well. On the other hand, DNA can be prone to false positives, as large DNA viruses often contain microsatellite sequences.

RNA reads would imply active transcription, but at least some genes are expressed at high levels compared to fly mRNAs in active infections.

See https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1007050

If you're looking for known Drosophila viruses, see http://obbard.bio.ed.ac.uk/data/Updated_Drosophila_Viruses.fas.gz, which includes several unpublished DNA viruses.

Best wishes,

Darren

ADD COMMENTlink written 6 weeks ago by darren.obbard20
0
gravatar for Istvan Albert
7 weeks ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

since the DNA is covered relatively evenly whereas the RNA depends on the copy number of each transcript detecting from DNA ought to work more effectively. Especially if you can poinpoint the location of the insertion.

Another way to say this is that the amount of viral RNA in the sample is probably at trace levels, whereas the DNA should end up at the same coverage as all the other DNA.

ADD COMMENTlink written 7 weeks ago by Istvan Albert ♦♦ 80k

There are no integrating retroviruses (other than TEs!) outside of vertebrates. Other insertions will not be active (infectious) viruses.

ADD REPLYlink written 6 weeks ago by darren.obbard20

I was not aware of that - thanks for the information

ADD REPLYlink written 6 weeks ago by Istvan Albert ♦♦ 80k
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