Background: Human T-lymphotropic virus 1 (HTLV-1) integrates into host DNA, resulting in life-long infection that underlies malignancy, inflammatory disease, and early all-cause mortality. HTLV-1 subtype-C endures as an endemic infection in Central Australia, and is associated with pulmonary disease. The cellular and viral features driving HTLV-1c pathogenesis remain poorly understood. Methods: We recruited a cohort of 41 First Nations participants from Alice Springs Hospital in Central Australia. We analysed plasma biomarker sVCAM1, and three circulating CD4⁺ T-cell phenotypes by flow cytometry: Lung-homing (TLH, CCR4⁺CC49d⁺Integrinβ7⁻), regulatory T-cells (TREG, CCR4⁺CD49d⁻CD127⁻) and CCR4⁻ (TCCR4−). We determined the proviral load by ddPCR. Haplotype resolved proviruses were assembled from 6 donors using single provirus amplification and long-read sequencing (SPA-ONT-seq). Analysis of CD4⁺ T-cell phenotypes and the proviral landscape was also performed in a humanised mouse model of HTLV-1c infection. Findings: All HTLV-1c+ participants showed expansion of chronically activated TLH cells. These cells were highly infected with HTLV-1c provirus and enriched in the lung tissue of humanised mice, confirming pulmonary trafficking. Despite extensive structural diversity in the proviral landscape, defective proviruses in participants with pulmonary disease preferentially retain virulence factor hbz. Defective proviruses were detected in the sputum of HTLV-1c+ participants. We discovered chimeric HTLV-1c:human proviruses containing internalised host DNA segments, and implicated them in modulating host gene expression. Interpretation: HTLV-1c likely contributes to pulmonary disease through lung-homing of chronically activated CD4⁺ T-cells harbouring defective proviruses that retain hbz. CD49d and hbz could represent potential therapeutic targets. Single-provirus sequencing revealed previously unrecognised structural complexity, including functional viral-host chimeras, with implications for HTLV-1 pathogenesis. Funding: This work was supported by NHMRC, Mater Foundation, ACH4, and Miller Foundation PhD Scholarship.

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Natasha Jansz

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Department of Microbiology and Immunology

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Natasha Jansz

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