A paper by Richard S Funk, Rachel E Marschang, Inna Romanova, and Maha Degan Abbas titled "A survey of native Arizona rattlesnakes for viral infections ," will be published in "The Biology of Rattlesnakes" which is In Press. Probably will be published in next several months.
If you are looking for indications of previous infections in healthy animals, you should consider serology rather than (or in addition to) virus detection methods. Attached is a paper on detection of antibodies against various atadenoviruses in reptiles (including rattlesnakes). The paper coming out in "The Biology of Rattlesnakes" covers other viruses as well.
The papers found under the links may also be of interest.
There are multiple other studies available with information on antibody detection in various other (wild caught) reptile species in the Americas.