As ZIKV RNA can be detected in the saliva, can the saliva be used as an alternative sample for routine ZIKV RNA detection. And what are the disadvantages?
As far as I'm aware, the recent detection of Zika virus within saliva is the first reporting of its kind - very little is known at this stage as to if ZKV infection can be transmitted from human to human through saliva itself, and further testing would be required to determine this.
Relating back to your question, I imagine that it would depend on what the viral load is within saliva compared to serum/traditional sample techniques, and if this is a high enough titre to be detected consistently.
Another thing to bear in mind is that viral RNA tends to be easier to detect in serum during the first 7 days of illness; viremia decreases over time. We would need to determine at what stage of zika infection viremia is detectable in saliva. It would indeed be interesting to see if testing of saliva samples result in a higher sensitivity/detection rate compared to traditional serum testing by RT-PCR.
I think it would be valuable to test saliva and other bodily fluids, and contribute to the body of literature. The CDC mentions it can do RT-PCR on saliva. http://www.cdc.gov/zika/hc-providers/body-fluids-collection-sumbission.html