Human papillomavirus genotype distribution and concordance between vaginal and prior lower genital tract neoplasia: a tissue-based study

Women previously treated for HPV-associated lower genital tract neoplasia remain at increased risk of developing vaginal intraepithelial neoplasia (VaIN). However, data on HPV genotype concordance based on direct tissue analysis remain limited. We evaluated HPV genotype distribution and concordance between HPV-associated VaIN2+ (VaIN2, VaIN3, or invasive vaginal carcinoma) and previous HPV-associated lower genital tract neoplasia using lesion-specific HPV genotyping of archived tissue specimens. This retrospective single-center cohort study included women with histologically confirmed and HPV-associated VaIN2+​. HPV genotyping was performed on formalin-fixed, paraffin-embedded tissue using a multiplex real-time PCR assay. HPV genotype distributions were compared between women with and without previous HPV-associated lower genital tract neoplasia. Genotype concordance between paired lesions and factors associated with VaIN3+ were also evaluated. Of 72 eligible women, 39 (54.2%) had previous lower genital tract neoplasia. The vaginal lesion was genotyped in 56 women (30 with, 26 without previous neoplasia); both lesions were evaluable and HPV-positive in 28. HPV16 predominated, detected in 51.8% of the lesions with a valid result. HPV16 and/or HPV18 positivity was more frequent in women with previous neoplasia (66.7% vs. 38.5%; p = 0.059), as was VaIN3+ (66.7% vs. 42.3%; p = 0.106); neither remained below 0.05 after adjustment for multiplicity. HPV16 was independently associated with VaIN3+ (adjusted OR 3.84, 95%CI: 1.22–12.93; p = 0.024). Among the 28 paired cases, concordance was complete in 23 (82.1%), partial in four (14.3%) and absent in one (3.6%); 27 (96.4%) shared at least one genotype. The interval between lesions reached 31.8 years. Direct tissue-based HPV genotyping showed a high frequency of shared HPV genotypes between VaIN2 + and previous HPV-associated LGT neoplasia. This is consistent with long-term persistence or reactivation of the same HPV genotype, although reinfection with the same genotype cannot be excluded and a common clonal origin was not assessed. Women with previous neoplasia more often had HPV16 and/or HPV18 positivity and VaIN3+, but these exploratory differences were imprecise. The findings support long-term surveillance after treatment of cervical high-grade lesions. Institution: University Hospital Královské Vinohrady, Prague, Czech Republic; reference number EK-VP/34/00/2025; approved 7 May 2025.