Author(s): Gonçalves, Fátima ; Cabanas, Joaquim ; Costa, Inês ; Veloso, Margarida ; Ribeiro, Marta ; Fernandes, Sandra ; Diogo, Isabel ; Sebastião, Cruz S. ; Pingarilho, Marta ; Pimentel, Victor ; Abecasis, Ana ; Gomes, Perpétua
Date: 2025
Persistent ID: http://hdl.handle.net/10362/188697
Origin: Repositório Institucional da UNL
Subject(s): DRM; Hybrid NGS (Ion torrent); PLHIV-2; Sanger; Virology; SDG 3 - Good Health and Well-being
Funding Information: Researchers from GHTM|IHMT, CNIC, CISA, or INIS received financial support from FCT-Foundation for Science and Technology (MARVEL project - PTDC/SAU-PUB/4018/2021), FCG-Calouste Gulbenkian Foundation (HITOLA project - N\u00BA.250466), PDCT-Science and Technology Development Project (N\u00BA.36 MESCTI/PDCT/2022), GHTM-UID/04413/2020 and LA-REAL-LA/P/0117/2020. Egas Moniz Center for Interdisciplinary Research (CiiEM) has provided support through Project 10.54499/UIDB/04585/2020, funded by FCT The funders have no role in the conceptualization, design, data collection, analysis, decision to publish, or preparation of the manuscript. Publisher Copyright: © 2025 The Authors
HIV-2 affects over 1 million people globally and can lead to AIDS if untreated. Treating people living with HIV-2 (PLHIV-2) is challenging because the virus is inherently resistant to some drugs. Effective treatment monitoring, particularly drug resistance testing, is critical for managing therapeutic failure. Without commercial tests to identify drug resistance mutations (DRM), laboratories have felt the need to develop in-house methods. NGS provides improved sensitivity for detecting minority DRM, which is crucial for effectively treating individuals, especially with limited therapeutic options. This study aimed to evaluate the effectiveness of a hybrid NGS Ion Torrent protocol for the detection of DRM in PLHIV-2 and its use in clinical practice. One hundred samples from PLHIV-2 collected from hospitals across Portugal were analyzed using a hybrid NGS protocol. Of these, 48 samples were also subjected to Sanger sequencing for comparative purposes. NGS successfully amplified 92 % of protease, 91 % of reverse transcriptase, and 49 % of integrase regions. The two sequencing methods agreed on the majority of DRM identified, with the only difference in two samples for the reverse transcriptase, which NGS identified as K70E and M184V, while Sanger did not. Hybrid NGS was able to identify DRM, demonstrating strong statistical agreement. In conclusion, hybrid NGS detected all DRM identified by Sanger, with the added ability to detect minority variants. The implementation of NGS-based protocol can provide clinicians with more comprehensive data, allowing for adjustments to ART regimens, and ultimately improving patient outcomes and quality of care for PLHIV-2.
