A diagnostic HIV-1 tropism system based on sequence relatedness

Area of Science:

• Virology
• Molecular Diagnostics
• Biotechnology

Background:

• HIV tropism testing is crucial for selecting effective coreceptor antagonist therapies.
• Current genotypic tests often analyze only dominant viral sequences, potentially missing important viral diversity.
• Phenotyping tests, while accurate, can be complex and time-consuming.

Purpose of the Study:

• To introduce XTrack, a novel, non-sequencing-based diagnostic test for determining HIV tropism.
• To evaluate the performance and capabilities of the XTrack system in clinical settings.
• To demonstrate XTrack's ability to detect mixed viral populations and analyze samples with low viral loads.

Main Methods:

• The XTrack system utilizes the unique electrophoretic mobility of heteroduplexes formed by HIV-1 env V3 loop probes hybridized to clinical specimens.
• A rigorous optimization process identified specific probe candidates with high diagnostic accuracy across diverse HIV-1 subtypes.
• Validation was performed using a replicative phenotyping system and comparison with established tests like TrofileES and Geno2Pheno.

Main Results:

• XTrack demonstrated high concordance with the commercial TrofileES test (84.9%) and Geno2Pheno (83.0%).
• The system successfully identified mixed virus populations and analyzed specimens with viral loads below 200 copies/ml.
• The test proved effective on proviral DNA extracted from leukocytes, indicating broad applicability.

Conclusions:

• The XTrack test is a viable and efficient option for routine HIV tropism diagnostics.
• Its ability to detect viral minorities and mixed populations offers a significant advantage over some existing methods.
• The underlying platform principles hold potential for adaptation to other sequence-divergent pathogens like Hepatitis B and C viruses.