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Defective proviruses rapidly accumulate during acute HIV-1 infection

Abstract

Although antiretroviral therapy (ART) suppresses viral replication to clinically undetectable levels, human immunodeficiency virus type 1 (HIV-1) persists in CD4+ T cells in a latent form that is not targeted by the immune system or by ART1,2,3,4,5. This latent reservoir is a major barrier to curing individuals of HIV-1 infection. Many individuals initiate ART during chronic infection, and in this setting, most proviruses are defective6. However, the dynamics of the accumulation and the persistence of defective proviruses during acute HIV-1 infection are largely unknown. Here we show that defective proviruses accumulate rapidly within the first few weeks of infection to make up over 93% of all proviruses, regardless of how early ART is initiated. By using an unbiased method to amplify near-full-length proviral genomes from HIV-1-infected adults treated at different stages of infection, we demonstrate that early initiation of ART limits the size of the reservoir but does not profoundly affect the proviral landscape. This analysis allows us to revise our understanding of the composition of proviral populations and estimate the true reservoir size in individuals who were treated early versus late in infection. Additionally, we demonstrate that common assays for measuring the reservoir do not correlate with reservoir size, as determined by the number of genetically intact proviruses. These findings reveal hurdles that must be overcome to successfully analyze future HIV-1 cure strategies.

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Figure 1: Proviral sequences in chronically treated subjects are highly defective.
Figure 2: Defective proviruses accumulate rapidly during the course of HIV-1 infection.
Figure 3: Expanded clones identified in chronically and acutely treated subjects are grossly defective.
Figure 4: Current assays substantially underestimate or overestimate the size of the latent reservoir.

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Acknowledgements

We thank the study participants who have made this research possible. We also thank G. Laird for critical advice and discussion, L. Alston, H. McHugh and D. Xu for assistance with study participants, V. Walker-Sperling for providing the Ba-L virus, C. Pohlmeyer for providing a sample from a viremic subject, and all of the members of the Siliciano laboratory for valuable discussion and advice. This work was supported by the Genomics and Sequencing Core at the UCSD Center for AIDS Research (P30AI036214 (D.D.R.)), the Pendleton Charitable Trust (D.D.R.), the VA San Diego Healthcare System (D.D.R.), the Veterans Medical Research Foundation (D.D.R.), the Martin Delaney CARE and DARE Collaboratories (US National Institutes of Health (NIH) grants AI096113 (M.C.S., D.D.R. and R.F.S.) and 1U19AI096109 (S.G.D. and R.F.S.)), an ARCHE Collaborative Research Grant from the Foundation for AIDS Research (amFAR 108165-50-RGRL (R.F.S.)), the Johns Hopkins Center for AIDS Research grant P30AI094189 (R.F.S.), the NIH grants 43222 (R.F.S.) and R21AI113147-02 (J.D.S.), the Howard Hughes Medical Institute (R.F.S.), and the Bill and Melinda Gates Foundation (R.F.S.).

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K.M.B., R.A.P., S.G.D. and R.F.S. designed the experiments; K.M.B., A.J.M., R.A.P., M.G.S., A.A.C., J.L., M.C.S. and S.M.L. performed the experiments; K.M.B., A.J.M., S.B.L., Y.-C.H., D.D.R., J.D.S. and R.F.S. analyzed the data; R.H. and A.A.C. managed study participant recruitment; S.G.D. provided patient samples; and K.M.B. and R.F.S. wrote the manuscript.

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Correspondence to Robert F Siliciano.

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Bruner, K., Murray, A., Pollack, R. et al. Defective proviruses rapidly accumulate during acute HIV-1 infection. Nat Med 22, 1043–1049 (2016). https://doi.org/10.1038/nm.4156

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