Some studies have evidenced the role of human polyomaviruses in head and neck squamous cell carcinoma. BK, JC and SV40 human polyoma viruses are widely recognized as etiological agents associated with malignancies. The aim of this study was to analyse the prevalence of BK, IC and SV40 in tonsillar microbiota in a group of Afghan volunteers. A sample of the tonsillar microbiota was taken from a single site using a sterile oral swab paper stick. A fixed volume of purified DNA from each sample was tested by quantitative real-time polymerase chain reactions to evaluate the number of human cells and the number of viral genomes in each sample. The cell number was evaluated via the quantification of a single copy genomic sequence, which is located in the HMBS locus. The median analyzed cell number in each reaction was 4343 (interquartile range 2074-8470). SV40 was never detected, while prevalence rate was 0.11 (C.I. 0.06-0.20) for BK and 0.10 (C.I. 0.05-0.19) for JC. Further studies are necessary to clarify whether polyomaviruses can be considered a risk factor of oral, oropharyngeal and laryngeal malignancies.
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