Performance of different sample types for high-risk human papillomavirus testing and genotyping for the detection of high grade cervical intraepithelial neoplasia

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ABSTRACT This application is being submitted in response to the Notice of Special Interest (NOSI) identified as NOT-CA- 22-036. Invasive cervical cancer (ICC) remains a public health problem among vulnerable populations in both high and low-and-middle income countries (LMICs).1 Annually, about 342,000 die from ICC worldwide, with over 85% of deaths occurring in LMICs.1 ICC is preventable through human papillomavirus (HPV) vaccination, screening, and treatment for cervical intraepithelial neoplasia 2 or higher (CIN2+).2 However, access to these ICC prevention strategies remains limited, particularly in LMICs, and is compounded in sub-Saharan Africa (SSA) by HIV since women living with HIV (WLWH) are at increased risk of persistent HPV infection, cervical intraepithelial neoplasia 2 or higher (CIN2+), and ICC.3–5 Malawi, a country in SSA, has the world’s highest ICC mortality.6 HIV prevalence is 11% among females age 15-49 years,7 and HPV infection is currently estimated at 39% among WLWH.8 In 2019, Malawi launched a national HPV vaccination program for adolescent girls following a pilot demonstration project.9,10 However, for the near future, most Malawian women will be vaccine-ineligible due to their age and thus will remain unvaccinated. Even if widespread HPV vaccination of adolescents is achieved, the consequent decline in ICC mortality is not anticipated for decades. Rapid HPV testing is attracting interest as it allows for same day screen-and-treat strategies for ICC prevention. The AmpFire® HPV Genotyping System is a unique nucleic acid amplification technology developed by Atila Biosystems, Inc. that genotypes 15 hrHPV subtypes.23,24 It uses a low-cost portable instrument that provides HPV test results in approximately one hour and can be used on dry swabs. Thus, hrHPV genotyping for same- day HPV screen-and-treat programs in LMICs is feasible with AmpFire®. Therefore, for this supplemental research project, we plan to evaluate the performance of different sample types for hrHPV testing using AmpFire® HPV genotyping and explore which individual genotypes by sample type have the highest sensitivity for CIN2+ among a subset of 331 hrHPV+ among the 627 WLWH in Lilongwe, Malawi. These women are already enrolled and being followed up in our U54-funded study (U54CA254564), which evaluates the performance of another potential triage test, S5 methylation, for the detection of CIN2+ in WLWH.25 To achieve our goals, we have the following Specific Aims: Aim 1: Evaluate and compare urine, self- collected cervicovaginal, and provider-collected cervical samples for the detection of different high-risk HPV genotypes among WLWH. Aim 2: Explore which individual hrHPV genotypes detected on urine, self-collected cervicovaginal, and provider-collected cervical samples have the highest sensitivity for detecting CIN2+. Aim 3: Explore which individual hrHPV genotypes detected on urine, self-collected cervicovaginal, and provider-collected cervical samples are associated with thermal ablation treatment failure.