The applications of next-generation sequencing in the field of human papillomavirus and associated neoplasias have extended beyond the accurate genotyping of human papillomavirus types. Next-generation sequencing is able to provide important information on the interactions of the cervicovaginal microbiome and environment with the virus, and the role that these factors play on its transmission and persistence. The advances in sequencing technologies have greatly contributed to the current knowledge of human cervicovaginal microbiome in recent years, allowing the assessment of microbiome variability between species, individuals and populations.

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