Adapting the geno2pheno[coreceptor] tool to HIV-1 subtype CRF01_AE by phenotypic validation using clinical isolates from South-East Asia

Nina Marty; Siriphan Saeng-Aroon; Eva Heger; Alexander Thielen; Martin Obermeier; Nico Pfeifer; Rolf Kaiser; Thomas Klimkait

doi:10.1016/j.jcv.2021.104755

Adapting the geno2pheno[coreceptor] tool to HIV-1 subtype CRF01_AE by phenotypic validation using clinical isolates from South-East Asia

J Clin Virol. 2021 Mar:136:104755. doi: 10.1016/j.jcv.2021.104755. Epub 2021 Feb 9.

Authors

Nina Marty¹, Siriphan Saeng-Aroon², Eva Heger³, Alexander Thielen⁴, Martin Obermeier⁵, Nico Pfeifer⁶, Rolf Kaiser³, Thomas Klimkait⁷

Affiliations

¹ Molecular Virology, Department Biomedicine-Petersplatz, University of Basel, Petersplatz 10, 4055 Basel, Switzerland. Electronic address: nina.marty@unibas.ch.
² Hazardous Pathogen Laboratory, National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand.
³ Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.
⁴ Seq-It GmbH & Co. KG, Kaiserslautern, Germany.
⁵ Medizinisches Infektiologiezentrum Berlin, Berlin, Germany.
⁶ Max Planck Institute for Informatics, Saarland Informatics Campus E1 4, Saarbruecken, Germany.
⁷ Molecular Virology, Department Biomedicine-Petersplatz, University of Basel, Petersplatz 10, 4055 Basel, Switzerland.

PMID: 33639408
DOI: 10.1016/j.jcv.2021.104755

Abstract

Objectives: Geno2pheno[coreceptor] is a widely used tool for the prediction of coreceptor usage (viral tropism) of HIV-1 samples. For HIV-1 CRF01_AE, a significant overcalling of X4-tropism is observed when using the standard settings of Geno2pheno[coreceptor]. The aim of this study was to provide the experimental backing for adaptations to the geno2pheno[coreceptor] algorithm in order to improve coreceptor usage predictions of clinical HIV-1 CRF01_AE isolates STUDY DESIGN: V3-sequences of 20 clinical HIV-1 subtype CRF01_AE samples were sequenced and analyzed by geno2pheno[coreceptor]. In parallel, coreceptor usage was determined for these samples by replicative phenotyping in human cells in the presence of specific X4- or R5-inhibitors.

Results: The sole introduction of the CRF01_AE V3 region into a full-length otherwise subtype B provirus failed to produce replication-competent viral progeny. A successive genome-replacement strategy revealed that also CRF01_AE derived gag and pol sequences are necessary to generate HIV genomes with sufficient replication competence. Subsequent phenotypic analysis confirmed overcalling of X4-tropism for CRF01_AE viruses using the current version and the standard cut-off at 10% false positive rate (FPR) of geno2pheno[coreceptor]. Lowering the FPR cut-off to 2.5% reduced the X4-overcalling in our sample collection, while still allowing a safe administration of Maraviroc (MCV).

Conclusion: This study demonstrates the successful adjustment of geno2pheno[coreceptor] rules for subtype CRF01_AE. It also supports the unique strength of combining complementing methods, namely phenotyping and genotyping, for validating new bioinformatics tools prior to application in diagnostics.

Keywords: Coreceptor; HIV-1; Phenotyping; Subtype CRF01_AE; Tropism; geno2pheno.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Asia, Eastern
Genotype
HIV Infections*
HIV-1* / genetics
Humans
Viral Tropism