Objectives To identify the prevalence of human papillomavirus genotypes – as a single infection or co-infection – not included in the 9-valent (9v) HPV vaccine among women with cervical intraepithelial neoplasia (CIN 2–3).

Methods Retrospective study of 1700 women referred due to abnormal cytology to Sant Joan de Deu Hospital. We selected 849 patients with CIN 2 or CIN 3 diagnosis confirmed by biopsy. An HPV test, a second cytology, and colposcopy were performed on all patients.Those with abnormal colposcopy underwent cervical biopsy. Patients with abnormal cytology and normal colposcopy or transformation zone type 3 underwent endocervical curetage. Conization was performed if punch biopsy or endocervical curetage confirmed CIN 2–3 or if a CIN 1 lesion persisted (diagnosed by biopsy) over 2 years in patients over 25 years of age. Comparisons for qualitative variables were analyzed with the chi-squared test. Analysis of variance was used for comparisons involving more than two samples.

Results HPV was detected in 746 of 849 patients (87.9%) and in 306 (41%) of those where more than one HPV genotype was present. The more frequent genotypes detected as single infection were: HPV-16 (267/849%–31.4%), HPV 31 (34/849–4%), HPV-33 (20/849%–2.4%), HPV-58 (17/849%–2%), HPV-51 (15/849%–1.8%), and HPV-53 (12/849%–1.4%). The more frequent genotypes isolated including multiple HPV infection were HPV-16 (427/849%–50.2%), HPV-31 (108/849%–12.7%), HPV-51 (79/849%–9.3%), HPV-33 (67/849%–7.8%), HPV-58 (67/849%–7.8%), and HPV-52 (59/849%–6.9%). In total, 78% of women diagnosed with CIN 2 or CIN 3 had an infection by a HPV genotype included in the 9v vaccine. Of the 849 women diagnosed with CIN 2 or CIN 3, 103 (12.1%) tested negative for HPV and 106 (12.4%) tested positive for low-risk HPV types.

Conclusions Inclusion of HPV-51, 53, 66, and 35 in a new vaccine may not be advisable as most are detected as coinfection with other high-risk genotypes that are already included in the current vaccines.