Advances in clonality analysis of human T-cell leukemia virus type 1-infected cells: from Southern blotting to high-throughput sequencing

Human T-cell leukemia virus type 1 (HTLV-1) causes persistent infection and can lead to adult T-cell leukemia-lymphoma (ATL), a hematological malignancy with a poor prognosis. In ATL patients, monoclonal expansion of HTLV-1-infected cells is observed. Each HTLV-1-infected clone harbors a unique proviral integration site. Based on this feature, various methods have been developed to detect and characterize HTLV-1-infected clones. Traditional Southern blotting detects monoclonal proliferation; however, it lacks sensitivity for detecting minor clones. Polymerase chain reaction (PCR)-based approaches, including inverse PCR and linker-mediated PCR, enhance sensitivity and can detect clonal proliferation even in asymptomatic carriers. The advent of high-throughput sequencing has enabled high-resolution quantitative analysis of the clonality of HTLV-1-infected cells based on proviral integration sites. Additionally, HTLV-1 DNA capture-seq allows simultaneous identification of the proviral structure and the degree of clonal abundance of the expanded infected clones. The modified non-restrictive linear amplification-mediated PCR and sequencing is a rapid and cost-effective tool for integration site analysis that is suitable for clinical application. These approaches could help analyze HTLV-1 pathogenesis, monitor clonal dynamics, and improve patient care strategies.