HIV-1 testing in the context of expanding PrEP modalities
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Updated: Aug 5, 2026

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3
Published on: December 27, 2010
Urvi M Parikh1, Jana L Jacobs1, Njambi Njuguna2
1Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
Introduction:
Multiple effective antiretroviral-based pre-exposure prophylaxis (PrEP) modalities for HIV-1 prevention are now available or under investigation but their safe rollout requires implementable HIV-1 testing strategies that accurately identify rare cases of HIV-1 acquisition. Current PrEP testing guidelines and testing algorithms in PrEP studies are varied, using single or combinations of rapid antibody-based diagnostic testing, qualitative or quantitative nucleic acid testing, and/or sample collection for retrospective analyses with sensitive research assays for HIV-1 nucleic acid detection. The objective of this commentary is to summarize current and alternative HIV testing approaches for PrEP implementation to guide best practices for individual programmes.
Discussion:
Diagnosing HIV-1 in PrEP users is challenging because (1) rarity of breakthrough HIV-1 in individuals on PrEP that increases the risk of a false-positive test; (2) modification of acute HIV infection by PrEP; and (3) PrEP delivery in community settings with inadequate testing infrastructure. Current best practices indicate the use of rapid diagnostic tests or self-testing as recommended by national testing algorithms and the World Health Organization (WHO). The use of nucleic acid testing such as plasma HIV-1 RNA polymerase chain reaction may allow earlier detection of HIV-1 but feasibility and risk of false positive are downsides. Sensitive tests to detect single-copy HIV-1 RNA in plasma and integrated proviral DNA in blood mononuclear cells may be important methods to resolve ambiguous HIV-1 diagnosis in research settings. Delayed diagnoses could lead to drug resistance emergence under long-acting PrEP selection, whereas single unconfirmed false-positive tests could create diagnostic challenges in users of long-acting PrEP. The cost, feasibility and positive predictive value of HIV tests are important considerations for PrEP programmes.
Conclusions:
Optimal strategies to detect HIV-1 acquisition among users of different PrEP modalities are evolving. While new guidance from the WHO recommends HIV-1 testing by serological assays or self-testing with PrEP use, feasible plans for clinical management of rare cases of breakthrough on PrEP and ambiguous diagnoses are still needed. The data from PrEP studies and scale-up will help us assess the value of different tests and testing approaches for their inclusion in HIV detection algorithms across PrEP modalities.

