Title: Cross-platform protocol for HTLV-1 whole-genome sequencing using nanopore and Illumina technologies
Authors: Lima A, de Moraes L, Amorim R, Cucco M, Silva R, Giovanetti M, Rego F, Araújo T, Fonseca V, Khouri R, Alcantara L, Santos L, Barreto F.
Journal: Next Research, 3:101110 (2026)
Abstract
Abstract
Human T-lymphotropic virus type 1 (HTLV-1) is associated with several diseases, such as HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), adult T-cell leukemia/lymphoma, and infectious dermatitis. However, the mechanisms behind its diverse clinical manifestations remain poorly understood. Despite its global health impact, complete HTLV-1 genome sequences are limited, hindering progress in research and treatment development. In this study, we develop and validate a tiling amplicon-based sequencing protocol compatible with both Illumina and Oxford Nanopore platforms for generating HTLV-1 genomes. The protocol produced near-complete HTLV-1 genomes with up to 98.67 % coverage. BBMap (Illumina) and the Sup basecalling model (Nanopore) yielded the best results. Hac provided an optimal balance between processing time and accuracy. Our protocol is efficient, versatile, and suitable for broad implementation. Its dual-platform compatibility facilitates genomic surveillance and enhances the availability of high-quality HTLV-1 genomic data, supporting advances in viral pathogenesis, evolution, and transmission research.
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Citation: Lima A, de Moraes L, Amorim R, Cucco M, Silva R, Giovanetti M, Rego F, Araújo T, Fonseca V, Khouri R, Alcantara L, Santos L, Barreto F. Cross-platform protocol for HTLV-1 whole-genome sequencing using nanopore and Illumina technologies Next Research, 3:101110 (2026).