Intact HIV Proviruses Persist in Children 7-9 Years after Initiation of ART in the First Year of Life

Abstract

Background: In adults starting ART during acute infection, 2% of proviruses that persist on ART are intact (replication-competent) by sequence analysis. By contrast, a recent report in early treated children failed to detect sequence intact proviruses. We sought to detect and characterize proviral sequences in another cohort of early treated children after 6-9 years on suppressive ART. Methods: PBMCs from perinatally-infected children from the CHER study were analysed. Near full-length proviral amplification and sequencing (NFL-PAS) was performed at one time point after 6-9 years on ART. Amplicons with large internal deletions were excluded (<9kb). All amplicons ≥9kb were sequenced and analysed through a bio-informatic pipeline to detect indels, frameshifts, inactivating point mutations or hypermutations that would render them defective. Findings: In nine children who started ART at a median age of 2⋅3 (range: 1⋅7 - 11⋅1) months, 738 single NFL-PAS amplicons were generated. Of these, 538(72⋅9%) had large internal deletions, 175(23⋅7%) had hypermutation, 15(1⋅4%) had small internal deletions, 3(1%) had deletions in the packaging signal/major splice donor site and 7(0*9%) were sequence intact. These 7 intact sequences were from three children who initiated ART after 2⋅3 months of age; of whom one had two identical intact sequences, suggestive of a cell clone harbouring a replication-competent provirus. No intact proviruses were detected in five children who initiated ART before 2⋅3 months of age. Interpretation: Rare, intact proviruses can be detected in children who initiate ART after 2*⋅3 months of age. The frequency of intact proviruses is lower than (p<0*⋅05) reported for adults treated during early HIV infection. Funding Statement: NCI:1U01CA200441‐01, NIMH:1R01MH105134‐01, Polio Research Foundation; Leidos Biomedical Research Corporation(HHSN261200800001E); NIAID:5UM1AI126603 (Martin Delaney Collaboratory);SAMRC Collaborating Centre for HIV Laboratory Research. Support for the CHER study was provided by the US National Institute of Allergy and Infectious Diseases through the CIPRA network (GrantU19AI53217);Departments of Health of the Western Cape and Gauteng, South Africa; GlaxoSmithKline/Viiv Healthcare. Declaration of Interests: J.W. Mellors is a consultant for Gilead Sciences Inc., a shareholder of Cocrystal Pharma Inc., and has received research support from Gilead Sciences Inc. and Janssen Pharmaceuticals Inc. All other authors declare no competing interests. Ethics Approval Statement: Ethical approval was obtained from the Human Research Ethics Committee of Stellenbosch University (ethics numbers N13/04/046 and M14/07/029). Written informed consent was obtained from the parents or legal guardians on behalf of the study participants.