Well-mixed plasma and tissue viral populations in RT-SHIV-infected macaques implies a lack of viral replication in the tissues during antiretroviral therapy

Retrovirology

Zandrea Ambrose⁴  John M. Coffin³  John W. Mellors⁴  Jonathan Spindler¹  Christopher Kline⁴  Nicholas Johnson¹  Wei Shao²  Luke Smith¹  Charles Coomer¹  Elizabeth M. Anderson¹  Mary F. Kearney¹ 

[1]HIV Dynamics and Replicaton Program, National Cancer Institute at Frederick, 1050 Boyles Street, Building 535, Room 109, Frederick 21702-1201, MD, USA

[2]Advanced Biomedical Computing Center, SAIC, Frederick, USA

[3]Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, USA

[4]Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA

关键词: SIV or HIV reservoir;    HIV persistence;    HIV compartmentalization;    Antiretroviral therapy;    Nonhuman primate model;    Single genome sequencing (SGS);    HIV diversity;    SIV or HIV evolution;    RT-SHIV;   

Others  :  1232029
DOI  :  10.1186/s12977-015-0212-2

 received in 2015-09-10, accepted in 2015-10-01,  发布年份 2015

【 摘 要 】

Background

Determining the anatomic compartments that contribute to plasma HIV-1 is critical to understanding the sources of residual viremia during combination antiretroviral therapy (ART). We analyzed viral DNA and RNA populations in the plasma and tissues from macaques infected with SIV containing HIV-1 RT (RT-SHIV) to identify possible sources of persistent viremia and to investigate the effect of ART on viral replication in tissues. Tissues were collected at necropsy from four pigtailed macaques infected for 30 weeks with a diverse population of RT-SHIV. Two animals (6760 and 8232) were untreated and two animals (8030 and 8272) were treated with efavirenz, tenofovir, and emtricitabine for 20 weeks.

Results

A total of 1800 single-genome RT-SHIV pol and env DNA and RNA sequences were analyzed from the plasma, PBMCs, axillary and mesenteric lymph nodes, spleen, thymus, small intestine, bone marrow, lung, and brain. Analyses of intracellular DNA and RNA populations revealed that the majority of proviruses in tissues from untreated animal 8232 were not expressed, whereas a greater proportion of proviruses in tissues were expressed from 6760. Few intracellular RNA sequences were detected in treated animals and most contained inactivating mutations, such as frame shifts or large deletions. Phylogenetics showed that RT-SHIV DNA populations in tissues were not different from virus in contemporary plasma samples in the treated or untreated animals, demonstrating a lack of anatomic compartmentalization and suggesting that plasma viremia is derived from multiple tissue sources. No sequence divergence was detected in the plasma or between tissues in the treated animals after 20 weeks of ART indicating a lack of ongoing replication in tissues during treatment.

Conclusions

Virus populations in plasma and tissues did not differ significantly in either treated or untreated macaques, suggesting frequent exchange of virus or infected cells between tissues and plasma, consistent with non-compartmentalized and widely disseminated infection. There was no genetic evidence of ongoing replication in tissues during suppressive ART.

【 授权许可】

   
2015 Kearney et al.

【 图 表 】

Fig.1.

Figure 3.

Fig.3.

Fig.4.

Fig.5.

Fig.6.

Fig.7.

Fig.8.

【 参考文献 】

• [1]Shiu C, Cunningham CK, Greenough T, Muresan P, Sanchez-Merino V, Carey V, Jackson JB, Ziemniak C, Belzer M, Ray SC, Luzuriaga K, Persaud D. Identification of ongoing HIV-1 replication in residual viremia during recombinant HIV-1 poxvirus immunizations in patients with clinically undetectable viral loads on durable suppressive HAART. J Virol. 2009; 83:9731-9742.
• [2]Chun TW, Nickle DC, Justement JS, Meyers JH, Roby G, Hallahan CW, Kottilil S, Moir S, Mican JM, Mullins JI et al.. Persistence of HIV in gut-associated lymphoid tissue despite long-term antiretroviral therapy. J Infect Dis. 2008; 197:714-720.
• [3]Gunthard HF, Wong JK, Ignacio CC, Guatelli JC, Riggs NL, Havlir DV, Richman DD. Human immunodeficiency virus replication and genotypic resistance in blood and lymph nodes after a year of potent antiretroviral therapy. J Virol. 1998; 72:2422-2428.
• [4]Benito JM, Lopez M, Lozano S, Martinez P, Gonzalez-Lahoz J, Soriano V. CD38 expression on CD8 T lymphocytes as a marker of residual virus replication in chronically HIV-infected patients receiving antiretroviral therapy. AIDS Res Hum Retroviruses. 2004; 20:227-233.
• [5]Cohen Stuart JW, Hazebergh MD, Hamann D, Otto SA, Borleffs JC, Miedema F, Boucher CA, de Boer RJ. The dominant source of CD4+ and CD8+ T-cell activation in HIV infection is antigenic stimulation. J Acquir Immune Defic Syndr. 2000; 25:203-211.
• [6]Martinez E, Arnedo M, Giner V, Gil C, Caballero M, Alos L, Garcia F, Holtzer C, Mallolas J, Miro JM et al.. Lymphoid tissue viral burden and duration of viral suppression in plasma. Aids. 2001; 15:1477-1482.
• [7]Ruiz L, van Lunzen J, Arno A, Stellbrink HJ, Schneider C, Rull M, Castella E, Ojanguren I, Richman DD, Clotet B et al.. Protease inhibitor-containing regimens compared with nucleoside analogues alone in the suppression of persistent HIV-1 replication in lymphoid tissue. AIDS. 1999; 13:F1-F8.
• [8]Martinez MA, Cabana M, Ibanez A, Clotet B, Arno A, Ruiz L. Human immunodeficiency virus type 1 genetic evolution in patients with prolonged suppression of plasma viremia. Virology. 1999; 256:180-187.
• [9]Josefsson L, von Stockenstrom S, Faria NR, Sinclair E, Bacchetti P, Killian M, Epling L, Tan A, Ho T, Lemey P et al.. The HIV-1 reservoir in eight patients on long-term suppressive antiretroviral therapy is stable with few genetic changes over time. Proc Natl Acad Sci USA. 2013; 110:E4987-E4996.
• [10]Maldarelli F, Palmer S, King MS, Wiegand A, Polis MA, Mican J, Kovacs JA, Davey RT, Rock-Kress D, Dewar R et al.. ART suppresses plasma HIV-1 RNA to a stable set point predicted by pretherapy viremia. PLoS Pathog. 2007; 3:e46.
• [11]Bailey JR, Sedaghat AR, Kieffer T, Brennan T, Lee PK, Wind-Rotolo M, Haggerty CM, Kamireddi AR, Liu Y, Lee J et al.. Residual human immunodeficiency virus type 1 viremia in some patients on antiretroviral therapy is dominated by a small number of invariant clones rarely found in circulating CD4+ T cells. J Virol. 2006; 80:6441-6457.
• [12]Palmer S, Maldarelli F, Wiegand A, Bernstein B, Hanna GJ, Brun SC, Kempf DJ, Mellors JW, Coffin JM, King MS. Low-level viremia persists for at least 7 years in patients on suppressive antiretroviral therapy. Proc Natl Acad Sci USA. 2008; 105:3879-3884.
• [13]Dinoso JB, Kim SY, Wiegand AM, Palmer SE, Gange SJ, Cranmer L, O’Shea A, Callender M, Spivak A, Brennan T et al.. Treatment intensification does not reduce residual HIV-1 viremia in patients on highly active antiretroviral therapy. Proc Natl Acad Sci USA. 2009; 106:9403-9408.
• [14]Shen L, Siliciano RF. Viral reservoirs, residual viremia, and the potential of highly active antiretroviral therapy to eradicate HIV infection. J Allergy Clin Immunol. 2008; 122:22-28.
• [15]Siliciano RF. Scientific rationale for antiretroviral therapy in 2005: viral reservoirs and resistance evolution. Top HIV Med. 2005; 13:96-100.
• [16]Kieffer TL, Finucane MM, Nettles RE, Quinn TC, Broman KW, Ray SC, Persaud D, Siliciano RF. Genotypic analysis of HIV-1 drug resistance at the limit of detection: virus production without evolution in treated adults with undetectable HIV loads. J Infect Dis. 2004; 189:1452-1465.
• [17]Fourati S, Lambert-Niclot S, Soulie C, Malet I, Valantin MA, Descours B, Ait-Arkoub Z, Mory B, Carcelain G, Katlama C et al.. HIV-1 genome is often defective in PBMCs and rectal tissues after long-term HAART as a result of APOBEC3 editing and correlates with the size of reservoirs. J Antimicrob Chemother. 2012; 67:2323-2326.
• [18]Kearney MF, Spindler J, Shao W, Yu S, Anderson EM, O’Shea A, Rehm C, Poethke C, Kovacs N, Mellors JW et al.. Lack of detectable HIV-1 molecular evolution during suppressive antiretroviral therapy. PLoS Pathog. 2014; 10:e1004010.
• [19]Maldarelli F, Wu X, Su L, Simonetti FR, Shao W, Hill S, Spindler J, Ferris AL, Kearney JW, Coffin MF, Carcelain JM, Hughes SH. Specific HIV integration sites are linked to clonal expansion and persistence of infected cells. Science. 2014; 345:179-183.
• [20]Fourati S, Lambert-Niclot S, Soulie C, Wirden M, Malet I, Valantin MA, Tubiana R, Simon A, Katlama C, Carcelain G et al.. Differential impact of APOBEC3-driven mutagenesis on HIV evolution in diverse anatomical compartments. Aids. 2014; 28:487-491.
• [21]Rozera G, Abbate I, Vlassi C, Giombini E, Lionetti R, Selleri M, Zaccaro P, Bartolini B, Corpolongo A, D’Offizi G et al.. Quasispecies tropism and compartmentalization in gut and peripheral blood during early and chronic phases of HIV-1 infection: possible correlation with immune activation markers. Clin Microbiol Infect Off Publ Eur Soc Clin Microbiol Infect Dis. 2014; 20:O157-O166.
• [22]Penton PK, Blackard JT. Analysis of HIV quasispecies suggests compartmentalization in the liver. AIDS Res Hum Retroviruses. 2014; 30:394-402.
• [23]Stam AJ, Nijhuis M, van den Bergh WM, Wensing AM. Differential genotypic evolution of HIV-1 quasispecies in cerebrospinal fluid and plasma: a systematic review. AIDS Rev. 2013; 15:152-161.
• [24]Pou C, Codoner FM, Thielen A, Bellido R, Perez-Alvarez S, Cabrera C, Dalmau J, Curriu M, Lie Y, Noguera-Julian M et al.. HIV-1 tropism testing in subjects achieving undetectable HIV-1 RNA: diagnostic accuracy, viral evolution and compartmentalization. PLoS One. 2013; 8:e67085.
• [25]Falcone EL, Adegbulugbe AA, Sheikh V, Imamichi H, Dewar RL, Hammoud DA, Sereti I, Lane HC. Cerebrospinal fluid HIV-1 compartmentalization in a patient with AIDS and acute varicella-zoster virus meningomyeloradiculitis. Clin Infect Dis Off Publ Infect Dis Soc Am. 2013; 57:e135-e142.
• [26]Blackard JT. HIV compartmentalization: a review on a clinically important phenomenon. Curr HIV Res. 2012; 10:133-142.
• [27]Heath L, Fox A, McClure J, Diem K, van’t Wout AB, Zhao H, Park DR, Schouten JT, Twigg HL, Corey L, et al. Evidence for limited genetic compartmentalization of HIV-1 between lung and blood. PLoS One. 2009;4:e6949.
• [28]Reeve AB, Patel K, Pearce NC, Augustus KV, Domingues HG, O’Neil SP, Novembre FJ. Reduced genetic diversity in lymphoid and central nervous system tissues and selection-induced tissue-specific compartmentalization of neuropathogenic SIVsmmFGb during acute infection. AIDS Res Hum Retroviruses. 2009; 25:583-601.
• [29]Harrington PR, Schnell G, Letendre SL, Ritola K, Robertson K, Hall C, Burch CL, Jabara CB, Moore DT, Ellis RJ et al.. Cross-sectional characterization of HIV-1 env compartmentalization in cerebrospinal fluid over the full disease course. AIDS. 2009; 23:907-915.
• [30]Diem K, Nickle DC, Motoshige A, Fox A, Ross S, Mullins JI, Corey L, Coombs RW, Krieger JN. Male genital tract compartmentalization of human immunodeficiency virus type 1 (HIV). AIDS Res Hum Retroviruses. 2008; 24:561-571.
• [31]Caragounis EC, Gisslen M, Lindh M, Nordborg C, Westergren S, Hagberg L, Svennerholm B. Comparison of HIV-1 pol and env sequences of blood, CSF, brain and spleen isolates collected ante-mortem and post-mortem. Acta Neurol Scand. 2008; 117:108-116.
• [32]van Marle G, Gill MJ, Kolodka D, McManus L, Grant T, Church DL. Compartmentalization of the gut viral reservoir in HIV-1 infected patients. Retrovirology. 2007; 4:87. BioMed Central Full Text
• [33]Harrington PR, Connell MJ, Meeker RB, Johnson PR, Swanstrom R. Dynamics of simian immunodeficiency virus populations in blood and cerebrospinal fluid over the full course of infection. J Infect Dis. 2007; 196:1058-1067.
• [34]Philpott S, Burger H, Tsoukas C, Foley B, Anastos K, Kitchen C, Weiser B. Human immunodeficiency virus type 1 genomic RNA sequences in the female genital tract and blood: compartmentalization and intrapatient recombination. J Virol. 2005; 79:353-363.
• [35]Smit TK, Brew BJ, Tourtellotte W, Morgello S, Gelman BB, Saksena NK. Independent evolution of human immunodeficiency virus (HIV) drug resistance mutations in diverse areas of the brain in HIV-infected patients, with and without dementia, on antiretroviral treatment. J Virol. 2004; 78:10133-10148.
• [36]Petito CK. Human immunodeficiency virus type 1 compartmentalization in the central nervous system. J Neurovirol. 2004; 10 Suppl 1:21-24.
• [37]Ohagen A, Devitt A, Kunstman KJ, Gorry PR, Rose PP, Korber B, Taylor J, Levy R, Murphy RL, Wolinsky SM, Gabuzda D. Genetic and functional analysis of full-length human immunodeficiency virus type 1 env genes derived from brain and blood of patients with AIDS. J Virol. 2003; 77:12336-12345.
• [38]Kemal KS, Foley B, Burger H, Anastos K, Minkoff H, Kitchen C, Philpott SM, Gao W, Robison E, Holman S et al.. HIV-1 in genital tract and plasma of women: compartmentalization of viral sequences, coreceptor usage, and glycosylation. Proc Natl Acad Sci USA. 2003; 100:12972-12977.
• [39]Korber BT, Kunstman KJ, Patterson BK, Furtado M, McEvilly MM, Levy R, Wolinsky SM. Genetic differences between blood- and brain-derived viral sequences from human immunodeficiency virus type 1-infected patients: evidence of conserved elements in the V3 region of the envelope protein of brain-derived sequences. J Virol. 1994; 68:7467-7481.
• [40]Bull ME, Heath LM, McKernan-Mullin JL, Kraft KM, Acevedo L, Hitti JE, Cohn SE, Tapia KA, Holte SE, Dragavon JA et al.. Human immunodeficiency viruses appear compartmentalized to the female genital tract in cross-sectional analyses but genital lineages do not persist over time. J Infect Dis. 2013; 207:1206-1215.
• [41]Swanstrom R, Coffin J. HIV-1 pathogenesis: the virus. Cold Spring Harb Perspect Med. 2012; 2:a007443.
• [42]North TW, Higgins J, Deere JD, Hayes TL, Villalobos A, Adamson L, Shacklett BL, Schinazi RF, Luciw PA. Viral sanctuaries during highly active antiretroviral therapy in a nonhuman primate model for AIDS. J Virol. 2010; 84:2913-2922.
• [43]Kline C, Ndjomou J, Franks T, Kiser R, Coalter V, Smedley J, Piatak M, Mellors JW, Lifson JD, Ambrose Z. Persistence of viral reservoirs in multiple tissues after antiretroviral therapy suppression in a macaque RT-SHIV model. PLoS One. 2013; 8:e84275.
• [44]Petravic J, Vanderford TH, Silvestri G, Davenport M. Estimating the contribution of the gut to plasma viral load in early SIV infection. Retrovirology. 2013; 10:105. BioMed Central Full Text
• [45]Lay MD, Petravic J, Gordon SN, Engram J, Silvestri G, Davenport MP. Is the gut the major source of virus in early simian immunodeficiency virus infection? J Virol. 2009; 83:7517-7523.
• [46]Rothenberger MK, Keele BF, Wietgrefe SW, Fletcher CV, Beilman GJ, Chipman JG, Khoruts A, Estes JD, Anderson J, Callisto SP et al.. Large number of rebounding/founder HIV variants emerge from multifocal infection in lymphatic tissues after treatment interruption. Proc Natl Acad Sci USA. 2015; 112:E1126-E1134.
• [47]Ambrose Z, Palmer S, Boltz VF, Kearney M, Larsen K, Polacino P, Flanary L, Oswald K, Piatak M, Smedley J et al.. Suppression of viremia and evolution of human immunodeficiency virus type 1 drug resistance in a macaque model for antiretroviral therapy. J Virol. 2007; 81:12145-12155.
• [48]Ambrose Z, Boltz V, Palmer S, Coffin JM, Hughes SH, Kewalramani VN. In vitro characterization of a simian immunodeficiency virus-human immunodeficiency virus (HIV) chimera expressing HIV type 1 reverse transcriptase to study antiviral resistance in pigtail macaques. J Virol. 2004; 78:13553-13561.
• [49]Kearney M, Spindler J, Shao W, Maldarelli F, Palmer S, Hu SL, Lifson JD, KewalRamani VN, Mellors JW, Coffin JM, Ambrose Z. Genetic diversity of simian immunodeficiency virus encoding HIV-1 reverse transcriptase persists in macaques despite antiretroviral therapy. J Virol. 2011; 85:1067-1076.
• [50]Achaz G, Palmer S, Kearney M, Maldarelli F, Mellors JW, Coffin JM, Wakeley J. A robust measure of HIV-1 population turnover within chronically infected individuals. Mol Biol Evol. 2004; 21:1902-1912.
• [51]Patterson KB, Prince HA, Stevens T, Shaheen NJ, Dellon ES, Madanick RD, Jennings S, Cohen MS, Kashuba AD. Differential penetration of raltegravir throughout gastrointestinal tissue: implications for eradication and cure. AIDS. 2013; 27:1413-1419.
• [52]Ho YC, Shan L, Hosmane NN, Wang J, Laskey SB, Rosenbloom DI, Lai J, Blankson JN, Siliciano JD, Siliciano RF. Replication-competent noninduced proviruses in the latent reservoir increase barrier to HIV-1 cure. Cell. 2013; 155:540-551.
• [53]Kim M, Hosmane NN, Bullen CK, Capoferri A, Yang HC, Siliciano JD, Siliciano RF. 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. 2014; 9:2755-2770.
• [54]Chomczynski P, Mackey K. Short technical reports. Modification of the TRI reagent procedure for isolation of RNA from polysaccharide- and proteoglycan-rich sources. Biotechniques. 1995; 19:942-945.
• [55]Kearney M, Maldarelli F, Shao W, Margolick JB, Daar ES, Mellors JW, Rao V, Coffin JM, Palmer S. Human immunodeficiency virus type 1 population genetics and adaptation in newly infected individuals. J Virol. 2009; 83:2715-2727.