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Defective proviruses rapidly accumulate during acute HIV-1 infection

Nature Medicine volume 22, pages 1043–1049 (2016)Cite this article

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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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References

  1. Finzi, D. et al. Identification of a reservoir for HIV-1 in patients on highly active antiretroviral therapy. Science 278, 1295–1300 (1997).

    Article  CAS  PubMed  Google Scholar 

  2. Chun, T.W. et al. Presence of an inducible HIV-1 latent reservoir during highly active antiretroviral therapy. Proc. Natl. Acad. Sci. USA 94, 13193–13197 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Wong, J.K. et al. Recovery of replication-competent HIV despite prolonged suppression of plasma viremia. Science 278, 1291–1295 (1997).

    Article  CAS  PubMed  Google Scholar 

  4. Siliciano, J.D. et al. Long-term follow-up studies confirm the stability of the latent reservoir for HIV-1 in resting CD4+ T cells. Nat. Med. 9, 727–728 (2003).

    Article  CAS  PubMed  Google Scholar 

  5. Ruelas, D.S. & Greene, W.C. An integrated overview of HIV-1 latency. Cell 155, 519–529 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Ho, Y.-C. et al. Replication-competent non-induced proviruses in the latent reservoir increase barrier to HIV-1 cure. Cell 155, 540–551 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Finzi, D. et al. Latent infection of CD4+ T cells provides a mechanism for lifelong persistence of HIV-1, even in patients on effective combination therapy. Nat. Med. 5, 512–517 (1999).

    Article  CAS  PubMed  Google Scholar 

  8. Crooks, A.M. et al. Precise quantitation of the latent HIV-1 reservoir: implications for eradication strategies. J. Infect. Dis. 212, 1361–1365 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Archin, N.M. & Margolis, D.M. Emerging strategies to deplete the HIV reservoir. Curr. Opin. Infect. Dis. 27, 29–35 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Deeks, S.G. HIV: shock and kill. Nature 487, 439–440 (2012).

    Article  CAS  PubMed  Google Scholar 

  11. Archin, N.M. et al. Administration of vorinostat disrupts HIV-1 latency in patients on antiretroviral therapy. Nature 487, 482–485 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Siliciano, J.D. & Siliciano, R.F. Enhanced culture assay for detection and quantitation of latently infected, resting CD4+ T cells carrying replication-competent virus in HIV-1-infected individuals. Methods Mol. Biol. 304, 3–15 (2005).

    PubMed  Google Scholar 

  13. Laird, G.M. et al. Rapid quantification of the latent reservoir for HIV-1 using a viral outgrowth assay. PLoS Pathog. 9, e1003398 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Strain, M.C. et al. Highly precise measurement of HIV DNA by droplet digital PCR. PLoS One 8, e55943 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Rouzioux, C., Mélard, A. & Avéttand-Fénoël, V. in Human Retroviruses (eds. Vicenzi, E. & Poli, G.) 1087, 261–270 (Humana Press, 2013).

    Article  CAS  Google Scholar 

  16. Henrich, T.J., Gallien, S., Li, J.Z., Pereyra, F. & Kuritzkes, D.R. Low-level detection and quantitation of cellular HIV-1 DNA and 2-LTR circles using droplet digital PCR. J. Virol. Methods 186, 68–72 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Eriksson, S. et al. Comparative analysis of measures of viral reservoirs in HIV-1 eradication studies. PLoS Pathog. 9, e1003174 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Günthard, H.F. et al. Antiretroviral treatment of adult HIV infection: 2014 recommendations of the International Antiviral Society–USA Panel. J. Am. Med. Assoc. 312, 410–425 (2014).

    Article  CAS  Google Scholar 

  19. Archin, N.M. et al. Immediate antiviral therapy appears to restrict resting CD4+ cell HIV-1 infection without accelerating the decay of latent infection. Proc. Natl. Acad. Sci. USA 109, 9523–9528 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Jain, V. et al. Antiretroviral therapy initiated within 6 months of HIV infection is associated with lower T cell activation and smaller HIV reservoir size. J. Infect. Dis. 208, 1202–1211 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Deng, K. et al. Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations. Nature 517, 381–385 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Delviks-Frankenberry, K. et al. Mechanisms and factors that influence high-frequency retroviral recombination. Viruses 3, 1650–1680 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Jetzt, A.E. et al. High rate of recombination throughout the human immunodeficiency virus type 1 genome. J. Virol. 74, 1234–1240 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Yu, H., Jetzt, A.E., Ron, Y., Preston, B.D. & Dougherty, J.P. The nature of human immunodeficiency virus type 1 strand transfers. J. Biol. Chem. 273, 28384–28391 (1998).

    Article  CAS  PubMed  Google Scholar 

  25. Hwang, C.K., Svarovskaia, E.S. & Pathak, V.K. Dynamic copy choice: steady state between murine leukemia virus polymerase and polymerase-dependent RNase H activity determines frequency of in vivo template switching. Proc. Natl. Acad. Sci. USA 98, 12209–12214 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Yu, Q. et al. Single-strand specificity of APOBEC3G accounts for minus strand deamination of the HIV genome. Nat. Struct. Mol. Biol. 11, 435–442 (2004).

    Article  CAS  PubMed  Google Scholar 

  27. Kieffer, T.L. et al. G–>A hypermutation in protease and reverse transcriptase regions of human immunodeficiency virus type 1 residing in resting CD4+ T cells in vivo. J. Virol. 79, 1975–1980 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Pierson, T.C. et al. Molecular characterization of preintegration latency in human immunodeficiency virus type 1 infection. J. Virol. 76, 8518–8531 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Pillai, S.K. et al. Role of retroviral restriction factors in the interferon-α-mediated suppression of HIV-1 in vivo. Proc. Natl. Acad. Sci. USA 109, 3035–3040 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Harper, M.S. et al. Interferon-α subtypes in an ex vivo model of acute HIV-1 infection: expression, potency and effector mechanisms. PLoS Pathog. 11, e1005254 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Stacey, A.R. et al. Induction of a striking systemic cytokine cascade prior to peak viremia in acute human immunodeficiency virus type 1 infection, in contrast to more modest and delayed responses in acute hepatitis B and C virus infections. J. Virol. 83, 3719–3733 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Kearney, M.F. et al. Origin of rebound plasma HIV includes cells with identical proviruses that are transcriptionally active before stopping of antiretroviral therapy. J. Virol. 90, 1369–1376 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Maldarelli, F. et al. HIV latency. Specific HIV integration sites are linked to clonal expansion and persistence of infected cells. Science 345, 179–183 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Wagner, T.A. et al. HIV latency. Proliferation of cells with HIV integrated into cancer genes contributes to persistent infection. Science 345, 570–573 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Schröder, A.R.W. et al. HIV-1 integration in the human genome favors active genes and local hotspots. Cell 110, 521–529 (2002).

    Article  PubMed  Google Scholar 

  36. Cohn, L.B. et al. HIV-1 integration landscape during latent and active infection. Cell 160, 420–432 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Simonetti, F.R. et al. Clonally expanded CD4+ T cells can produce infectious HIV-1 in vivo. Proc. Natl. Acad. Sci. USA 113, 1883–1888 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Bosque, A., Famiglietti, M., Weyrich, A.S., Goulston, C. & Planelles, V. Homeostatic proliferation fails to efficiently reactivate HIV-1 latently infected central memory CD4+ T cells. PLoS Pathog. 7, e1002288 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Massanella, M., Gianella, S., Lada, S.M., Richman, D.D. & Strain, M. Quantification of total and 2-LTR (long terminal repeat) HIV DNA, HIV RNA and herpesvirus DNA in PBMCs. Bio Protoc. 5, e1492 (2015).

    Article  PubMed  Google Scholar 

  40. Lorenzo-Redondo, R. et al. Persistent HIV-1 replication maintains the tissue reservoir during therapy. Nature 530, 51–56 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Rose, P.P. & Korber, B.T. Detecting hypermutations in viral sequences with an emphasis on G–> A hypermutation. Bioinformatics 16, 400–401 (2000).

    Article  CAS  PubMed  Google Scholar 

  42. Kim, M. et al. A primary CD4+ T cell model of HIV-1 latency established after activation through the T cell receptor and subsequent return to quiescence. Nat. Protoc. 9, 2755–2770 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Rosenbloom, D.I.S. et al. Designing and interpreting limiting dilution assays: general principles and applications to the latent reservoir for human immunodeficiency virus-1. Open Forum Infect. Dis. 2, ofv123 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

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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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Authors and Affiliations

  1. Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

    Katherine M Bruner, Alexandra J Murray, Ross A Pollack, Mary G Soliman, Sarah B Laskey, Adam A Capoferri, Jun Lai, Ya-Chi Ho, Janet D Siliciano & Robert F Siliciano

  2. Howard Hughes Medical Institute, Baltimore, Maryland, USA

    Adam A Capoferri & Robert F Siliciano

  3. Department of Medicine, University of California, San Diego (UCSD), San Diego, California, USA

    Matthew C Strain & Douglas D Richman

  4. Veteran's Affairs (VA) San Diego Healthcare System, San Diego, California, USA

    Steven M Lada & Douglas D Richman

  5. Department of Medicine, University of California, San Francisco (UCSF), San Francisco, California, USA

    Rebecca Hoh & Steven G Deeks

  6. Department of Pathology, University of California, San Diego, San Diego, California, USA

    Douglas D Richman

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Contributions

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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