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Recently, I have been researching about DNA and I know the most popular method for detecting viruses is based on DNA. After learning about proteins, I wonder why we do not detect viruses based on virus proteins?

If it becomes true we can save a lot of money, instead of doing a PCR reaction, we can detect more than one disease in a single reaction.

For example, when I have the sequence of a virus from NCBI Genebank, I can know how many proteins the target organism produces and I can calculate the molecular weight of each protein. Then running it in a SDS-PAGE gel to see what the bands look like, may be that I can know the target organism is present or not?

For example, HIV produces 9 proteins and the molecular weight of each protein is different. So after doing electrophoresis, I have 9 bands. Based on the distance between each band and based on the molecular weight, it's possible to know HIV is present or not?

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Put simply, the answer is that you could seek to detect viral proteins, but because these proteins would be very minor components of your sample, you would have to use an immunoblotting technique to detect a specific viral protein. While immunoblotting is quite a sensitive technique, I think its fair to say that it can be technically demanding. In contrast a PCR reaction is exquisitely sensitive and is fairly robust. PCR is also technically more staightfoward because DNA is generally easier to work with than are proteins.

Before the advent of PCR, immunoblotting would have been the method of choice.

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    $\begingroup$ also many viruses will have nearly the same molecular weight and therefore a nearly identical SDS PAGE pattern. $\endgroup$ – shigeta Jul 14 '13 at 14:28
  • $\begingroup$ @AlanBoyd point, comment removed. $\endgroup$ – terdon Jul 15 '13 at 17:45
  • $\begingroup$ Absolutely correct. And to the advantage of "more than one disease" this can, and routinely is done, with qPCR, with a much higher sensitivity that can reasonably be obtained via western or even ELISA (which is a viable detection system often based on protein). $\endgroup$ – Atl LED Jul 16 '13 at 0:39

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