Take a look at the existing literature, folks have already been studying exactly this question.

Using informatics I test for 331 viral genomes of all the viruses known or suspected of being part of the malignant phenotype. I believe that these viruses could be therapeutic targets for the treatment of the cancer. Indeed the literature has 25 articles that antiviral drugs improve cancer outcomes. In my research SV40 is present in 0-30 percent of tumors but the Roseola viruses (herpesviruses 6A, 6B and 7) are consistently present in 60-100% and I've examined lung, colorectal, prostate and ovarian cancers. The best antiviral drug for this is Brincidofovir but SymBio Pharmaceuticals unfortunately will not initiate trials. There are other drugs that could be tried.

The Immunization Safety Review Committee of the Institute of Medicine (IOM) reviewed this topic in 2002. The present review of recent studies showed that the earlier results describing the recovery of SV40 DNA sequences from a large proportion of the above tumors were not reproducible and that most studies were negative. Contamination with laboratory plasmids was identified as a possible source of false positive results in some previous studies. The low-level immunoreactivity of human sera to SV40 was very likely the result of cross-reactivity with antibodies to the SV40-related human polyomaviruses BKV and JCV, rather than of authentic SV40 infection. SV40 sero-reactivity in patients with the suspect tumors was no greater than that in controls. In epidemiologic studies, the increased incidence of some of the suspect tumors in the 1970s to 1980s was not related to the risk of exposure to SV40-contaminated vaccines. In summary, the most recent evidence does not support the notion that SV40 contributed to the development of human cancer@

Methodology is important. With samtools I can extract the sequences/reads from the STAR aligner sorted BAM. Then I confirm the virus diagnosis by pasting the reads into BLAST and make sure that there are no identical human sequences by pasting into BLAT. I found 10/27 prostate cancers to contain reads from SV40. Out of 28 ovarian tumors so far only 1 is positive. The tumors are flash frozen right after excision so there is no opportunity for contamination with plasmids. Many of the tumors were negative for SV40 so it is unlikely reagents were contaminated. In the prostate cancers I also found about the same percentage of CMV, Herpesvirus 1 and Merkel Cell polyomavirus.