Abstract
A stable latent reservoir for HIV-1 in resting CD4+ T-cells precludes cure1–3. Curative strategies targeting the reservoir are being tested4,5 and require accurate, scalable reservoir assays. The reservoir was defined with quantitative viral outgrowth assays (QVOAs) for cells releasing infectious virus following one round of T-cell activation1. However, QVOAs and newer assays for cells producing viral RNA after activation6 may underestimate reservoir size because one round of activation does not induce all proviruses7. Many studies rely on simple PCR-based assays to detect proviral DNA regardless of transcriptional status, but the clinical relevance of these assays is unclear, as the vast majority proviruses are defective7–9. We describe a novel approach that separately quantifies intact and defective proviruses and show that the dynamics of cells carrying intact and defective proviruses are different in vitro and in vivo, a finding with implications for targeting the intact proviruses that are a barrier to cure.
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