The data are cause for alarm because of increasing rates of oral cancer, a portion of which are caused by the virus. HPV is best known for its connection to cervical cancer, which affects more than 12,000 women each year, according to the CDC. The agency reported that about 7,100 develop HPV-related throat cancers each year, but the study noted that if present trends continue, oral cancers may overtake cervical cancer as the leading source of HPV-related tumors by 2020.
In October, Gillison published a study showing that the number of HPV-related oral cancers shot up from 16 percent to 72 percent in a 20-year period.
But experts emphasize that the link between oral cancer and HPV is still scientifically shaky.
"The vast majority of infections will never lead to any sort of relevant disease, let alone cancer," said Dr. Mark Einstein, head of the HPV Vaccine Clinic at Montefiore Medical Center in Bronx, N.Y. "Just because it's there doesn't mean it's doing anything or causing any cellular damage."
Experts say the study provides another strong argument for vaccinating both boys and girls against HPV, a move recommended by the CDC in 2011. By 2008, only about 30 percent of women and even fewer men had gotten the vaccine, which has been approved for both men and women ages 9 to 26.
HPV vaccines like Merck's Gardasil and Glaxo SmithKline's Cervarix have so far only been tested for their effectiveness against the virus that causes cervical, vulvar and anal cancer. The vaccines work against several strains of the virus, including HPV-16, which Gillison noted is responsible for about 90 percent of oral HPV cases, as opposed to about 57 percent of cervical HPV infections.
"We have every reason to be optimistic that it will work against oral HPV, but we don't know directly because it's never been studied," she said.
Dr. Hans Schlecht, an assistant professor of infectious diseases at Drexel University College of Medicine in Philadelphia, said it will probably take at least a decade to know whether the vaccines are effective against oral HPV.
"It does work in the genital area, but we don't know anything about the mouth yet," Schlecht said. "It makes sense, but right now it's just guesswork."
Experts say protection against oral HPV begins by practicing safe oral sex and quitting smoking.
Schlecht added that doctors should be increasingly vigilant about looking for signs of oral cancers in their patients, which can include earache, difficulties with speaking or swallowing, and lumps in the neck.