Repurposing GeneXpert® for rapid diagnosis of HPV-associated anal cancer: a case report of an unusually large lesion

BACKGROUND: Human papillomavirus (HPV)-associated anal squamous cell carcinoma (SCC) is strongly linked to persistent infection with high-risk HPV genotypes, particularly in people living with human immunodeficiency virus (HIV), who experience higher rates of viral persistence and oncogenic progression. The burden of HPV-related malignancies is disproportionately higher in low-resource settings, where limited access to screening, histopathology, and specialist care contributes to delayed diagnosis and advanced-stage presentation. In such contexts, rapid molecular diagnostic tools may help overcome diagnostic delays and support earlier clinical decision-making. CASE PRESENTATION: , exceeding sizes typically reported in the literature and reflecting prolonged disease progression. High-risk HPV type 16 was detected using a GeneXpert® assay applied to solid tissue, an approach rarely described, as most available evidence and current guidelines focus on swab-based specimens. Histopathological confirmation of HPV-associated squamous cell carcinoma was delayed due to limited local pathology services. In the interim, molecular HPV testing contributed to early diagnostic orientation and clinical planning. Imaging findings raised suspicion for advanced disease, although definitive metastatic staging could not be established due to incomplete diagnostic workup. CONCLUSIONS: This case highlights the potential utility of tissue-based GeneXpert HPV testing as a rapid adjunctive diagnostic tool in resource-limited settings where access to histopathology is delayed. Early molecular identification of high-risk HPV may support timely clinical decision-making and facilitate linkage to care. However, its clinical impact remains constrained in the context of advanced disease at presentation, underscoring the importance of addressing structural barriers to early diagnosis and sustained HIV and cancer care in underserved regions.