Use of next-generation sequencing on HIV-1 DNA to assess archived resistance in highly treatment-experienced people with multidrug-resistant HIV under virological control: data from the PRESTIGIO Registry
Authors: Armenia Daniele , Spagnuolo Vincenzo , Bellocchi Maria C , Galli Laura , Duca Leonardo , Marchegiani Greta , Clemente Tommaso , Carioti Luca , Lolatto Riccardo , Calza Leonardo , Celesia Benedetto M , Cascio Antonio , Francisci Daniela , Saracino Annalisa , Torti Carlo , Zazzi Maurizio , Castagna Antonella , Santoro Maria M ,   PRESTIGIO Study Group, Castagna Antonella , Spagnuolo Vincenzo , Galli Laura , Maggiolo Franco , Calza Leonardo , Focà Emanuele , Lagi Filippo , Cenderello Giovanni , Di Biagio Antonio , Marchetti Giulia , Rusconi Stefano , Cervo Adriana , Gagliardini Roberta , Bonora Stefano , Cattelan Anna Maria , Zazzi Maurizio , Santoro Maria Mercedes , Zazzi Maurizio , Santoro Maria Mercedes , Galli Andrea , Saladini Francesco , Armenia Daniele , Carini Elisabetta , Bagaglio Sabrina , Galli Laura , Lolatto Riccardo , Diotallevi Sara , Tavio Marcello , Paggi Alessandra Mataloni , Vichi Francesca , Bellucci Alessio , Mirabelli Elisa , Saracino Annalisa , Balena Flavia , Maggiolo Franco , Comi Laura , Valenti Daniela , Suardi Claudia , Calza Leonardo , Malerba Federica , Castelli Francesco , Focà Emanuele , Minisci Davide , Pennati Francesca , Celotti Anna , Brognoli Francesca , Menzaghi Barbara , Farinazzo Maddalena , Cacopardo Bruno , Celesia Benedetto Maurizio , Raddusa Michele Salvatore Paternò , Giarratana Carmen , Torti Carlo , Fusco Paolo , Bruno Gabriele , Pan Angelo , Brambilla Paola , Fornabaio Chiara , Bartoloni Alessandro , Giachè Susanna , Corsi Paola , Kiros Seble Tekle , Lagi Filippo , Ducci Filippo , Santantonio Teresa , Caputo Sergio Lo , Ferrara Sergio , Narducci Marianna , Pontali Emanuele , Feasi Marcello , Sarà Antonio , Bassetti Matteo , Di Biagio Antonio , Blanchi Sabrina , Castagna Antonella , Spagnuolo Vincenzo , Carini Elisabetta , Bagaglio Sabrina , Galli Laura , Lolatto Riccardo , Galli Andrea , Clemente Tommaso , Borjesson Rebecka Papaioannu , Diotallevi Sara , Antinori Spinello , Formenti Tiziana , Giacomelli Andrea , Marchetti Giulia , Gazzola Lidia , De Flaviis Federica , Puoti Massimo , Moioli Cristina , D’Amico Federico , Mussini Cristina , Cervo Adriana , Enrica Roncaglia , Giulia Nardini , Beghetto Barbara , Manzillo Elio , Lanzardo Amedeo , Cattelan Anna Maria , Mazzitelli Maria , Cascio Antonio , Trizzino Marcello , Fronti Elisa , Laccabue Diletta , Gulminetti Roberto , Zuccarini Andrea , Francisci Daniela , Schiaroli Elisabetta , De Socio Giuseppe , Garlassi Elisa , Corsini Romina , Gagliardini Roberta , Fusto Marisa , Sarmati Loredana , Malagnino Vincenzo , Lamonica Silvia , Di Giambenedetto Simona , Mulas Tiziana , Cenderello Giovanni , Pincino Rachele , Tumbarello Mario , Fabbiani Massimiliano , Panza Francesca , Rancan Ilaria , Di Perri Giovanni , Bonora Stefano , Ferrara Micol , Fantino Silvia , Malena Marina , Fiscon Marta 
Published: July 2024

Abstract

Background
To clarify whether next-generation sequencing (NGS) can be useful for resistance assessment in virologically suppressed highly treatment-experienced (HTE) individuals with MDR HIV.

Methods
Ninety-one participants from the PRESTIGIO Registry were included. NGS was performed on HIV-DNA at 1%, 5% and 20% cut-offs; major drug resistance mutations (DRMs) were evaluated and compared with those detected in historical plasma genotypic resistance testing (h-GRT). APOBEC editing was also characterized.

Results
Participants had a complex and long treatment history [median 23 (IQR 21–25) years of ART exposure) and had been virologically suppressed since a median of 3 (IQR 2–5) years. Among all major DRMs detected by HIV-DNA NGS and/or h-GRT, 30% were exclusively found through NGS. The highest detection rate of historical major DRMs was reached with NGS set at 1%, but unusual substitutions and extensive APOBEC hypermutations suggest technical issues and poor clinical relevance in the 1%–5% interval. At NGS set at 5%, 67.2% of historical major DRMs were detected. The number of major DRMs detected exclusively by DNA-NGS as minority variants (frequency 5%–20%) was significantly higher in individuals who later experienced virological rebound compared with those who maintained virological control [median 2 (IQR 1–3) versus 1 (0–2), P = 0.030] and positively correlated with viraemia levels at rebound (rho = 0.474, P = 0.030).

Conclusions
In non-viraemic people with an MDR virus, HIV-1 DNA NGS set at 5% is an acceptable technical cut-off that might help to reveal mutations with a potential clinical relevance. Moreover, the number of minority resistance mutations additionally detected by NGS might be associated with loss of virological control.