The finding, published in the Journal of the American Medical Association, could be pivotal for the prevention of cancers that form on the tonsils and tongue.
"Given the lack of universal HPV immunisation and the potential for the virus to evade the immune system even in individuals with detectable HPV in their blood, our findings could have far-reaching implications for identifying people at risk of developing HPV-related head and neck cancers and ultimately preventing them," said Matthew Miller, Associate Professor at the University of Rochester Medical Center in New York.
Only about five per cent of HPV-infected people go on to develop cancer of the mouth or throat, suggesting most people's immune systems can easily hold back HPV infections.
But why doesn't the immune system protect the five per cent who develop cancer?
Miller believes the answer lies in biofilms - thin, slimy sheets of bacteria.
The researchers found HPV encased in biofilms inside pockets on the tonsil surface, called tonsil crypts, which is where HPV-related head and neck cancers often originate.
They studied tissue samples from 102 patients who had elective tonsillectomies. A tonsillectomy is a surgical procedure to remove the tonsils.
Five of those samples contained HPV and four contained high risk strains, HPV 16 and 18. In every case, HPV was found in tonsil crypts biofilms.
The team believes HPV is shed from the tonsil during an active infection and gets trapped in the biofilm, where it may be protected from immune attack.
In the crypts, the virus likely lays in wait for an opportunity to reinstate infection or invade the tonsil tissue to develop cancer.
The research team now plans to investigate potential screening tools, such as an oral rinse, to detect HPV in the mouth and throat.
The next step would be to develop topical antimicrobials that would disrupt the biofilm and allow the immune system to clear the virus.
By mid-adulthood, most people get exposed to HPV. The same strains that cause cervical cancer (mainly HPV 16 and 18) cause head and neck cancers.
While verified tests exist to detect HPV in people before they develop cervical cancer, the same is not true for HPV-related head and neck cancers, which are expected to outnumber cervical cancer cases by 2020, University of Rochester Medical Center said in a statement.
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