JCM Accepted Manuscript Posted Online 1 July 2015 J. Clin. Microbiol. doi:10.1128/JCM.00893-15 Copyright © 2015, American Society for Microbiology. All Rights Reserved.

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Genotypic Tropism Testing in HIV-1 Proviral DNA Can Provide Useful Information at Low-

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Level Viremia

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Running title: Genotypic Tropism Testing in HIV-1 Proviral DNA

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Lavinia Fabeni,a# Giulia Berno,a# Valentina Svicher,b Francesca Ceccherini-Silberstein,b Caterina

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Gori,a Ada Bertoli,b,c Cristina Mussini,d Miriam Lichtner,e Mauro Zaccarelli,a Adriana Ammassari,a

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Carmela Pinnetti,a Stefania Cicalini,a Claudio Maria Mastroianni,e Massimo Andreoni,c Andrea

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Antinori,a Carlo Federico Perno,a Maria Mercedes Santorob*

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National Institute for Infectious Diseases L. Spallanzani - IRCCS, Rome, Italya; University of Rome

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Tor Vergata, Rome, Italyb; University Hospital Tor Vergata, Rome, Italyc; University of Modena

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and Reggio Emilia School of Medicine, Modena, Italyd; Infectious Diseases Unit, Sapienza

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University, Polo Pontino, Latina, Italye

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# Lavinia Fabeni and Giulia Berno contributed equally to this work

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Keywords: HIV-1, genotypic tropism testing, proviral DNA, low-level viremia, CCR5 inhibitors

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*Address correspondence to:

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Maria Mercedes Santoro;

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e-mail: [email protected];

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Tel: +39-06-72596572; Fax: +39-06-72596039

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ABSTRACT

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The possibility of doing genotypic tropism testing (GTT) on proviral DNA (pvDNA) even during

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suppressed viremia would facilitate the use of CCR5 inhibitors as part of switching, simplification,

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or intensification strategies. Thus, we aimed at evaluating the GTT concordance between plasma

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RNA and pvDNA and at assessing which factors could affect the possible discrepancy between the

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two compartments. GTT was determined using both plasma RNA and pvDNA from 55 paired

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samples from drug-experienced patients. Potential differences between the two compartments were

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evaluated by analyzing co-receptor usage and genetic variability. Paired samples were also stratified

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in three viremia levels (500 copies/mL). Overall, comparison of Geno2Pheno

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FPRs in both compartments showed a good correlation (r=0.72). A high concordance in tropism

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prediction was found in the two compartments (46/55 paired samples, 83.6%). Among the 9 paired

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samples with discordant tropism, a higher proportion of pvDNA harboring X4/dual-mixed tropic

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viruses was found in comparison to plasma RNA (88.9% vs. 11.1%, p=0.0034). Discordant samples

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were characterized by a higher genetic variability than concordant samples. When stratifying the

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paired samples according to different viremia levels, the prevalence of discordant samples increased

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when decreasing viremia (

Genotypic Tropism Testing in HIV-1 Proviral DNA Can Provide Useful Information at Low-Level Viremia.

The possibility of performing genotypic tropism testing (GTT) with proviral DNA (pvDNA) even during suppressed viremia would facilitate the use of CCR...
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