Epidemiologically linked transmission of HIV-1 illustrates the impact of host genetics on virological outcome
Streeck, Hendrika,*; Jessen, Heikob,*; Kuecherer, Claudiac; Li, Bina; Jessen, Arne Bb; Dupke, Stephand; Baumgarten, Axeld; Stahmer, Ingride; van Lunzen, Jane; Altfeld, Marcusa; Walker, Bruce Da,f,g; Allen, Todd Ma
aPartners AIDS Research Center, Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, USA
bHIV Clinic Dres. Jessen, Jessen, Stein, Berlin, Germany
cRobert Koch Institute, Berlin, Germany
dHIV Clinic Baumgarten, Carganico, Dupke, Berlin, Germany
eUniversity Medical Center Hamburg-Eppendorf, Infectious Diseases Unit, Germany
fHeinrich Pette Institute for Experimental Virology and Immunology, Hamburg, Germany
gHoward Hughes Medical Institute, Chevy Chase, Maryland, USA.
* These authors contributed equally.
Correspondence to Todd M. Allen, PhD, MGH-East, CNY 6625, 149 13th Street, Charlestown, MA 02129, USA. Tel: +1 617 726 7846; fax: +1 617 724 8586; e-mail: firstname.lastname@example.org
The diversity of HIV-1 and human genetics complicates our ability to determine the impact of treatment during primary HIV-1 infection on disease outcome. Here, we show, in a small group infected with virtually identical HIV-1 strains and treated during primary HIV-1 infection, that patients expressing protective human leucocyte antigen alleles had lower viral loads following treatment discontinuation. These data suggest that genetic factors play an important role in the outcome of HIV-1 infection despite early therapy.
Although patients with primary HIV-1 infection (PHI) present with distinct clinical syndromes, only a fraction of patients are diagnosed at this early stage of infection. However, it is during this initial phase that antiviral CD8+ T cell responses first emerge and high-level HIV-1 viremia is controlled by several logs to a set point [1,2]. It is a matter of ongoing debate that therapeutic intervention initiated during PHI may alter the immune response of the host to HIV-1 and therefore allow for subsequent immune control of disease progression [3–9].
One of the strongest predictors of HIV-1 disease progression is host genetic factors [10,11], which may also play a key role in influencing the control of viral replication following short-term treatment during the acute phase of the infection. For example, patients expressing the major histocompatibility complex alleles, human leucocyte antigen (HLA)-B57, HLA-B27, HLA-B51 and HLA-A11, which dictate the specificity of the CD8+ T cell response, demonstrate an unusual ability to control viral replication regardless of early therapeutic interventions [10,12]. In addition to host factors, viral genetics have been shown to play a substantial role in clinical outcome [13–15]. Therefore, differences in both host and viral genetics can contribute substantially to disease progression in the setting of HIV-1 infections.
Unfortunately, however, the relative impact of an early therapeutic intervention during PHI in the presence of multifaceted and heterogeneous factors such as host genetics and viral diversity remains difficult to interpret. In the present study, we report on a small epidemiologically linked group, infected with virtually identical strains of HIV-1, in whom we had the rare opportunity to examine immune control and disease progression following treatment during PHI.
All participants were enrolled at the HIV clinic Jessen, Berlin, Germany (approved by the respective institutional review boards).
Autologous gag and pol was sequenced from plasma RNA using population sequencing, as described previously . A neighbor-joining phylogenetic tree was constructed using ClustalX [accession no. FJ179456-FJ179459; FJ185106-FJ185128 of the German HIV-1 seroconverterstudy (Robert Koch-Institute) and reference sequences: K03455 B.FR.83.HXB2, U63632 B.US.86.JRFL, U21135 B.US.90.WEAU 160, U88824 D.UG.94.94, U46016 C.ET.86.ET].
All participants were HLA typed using the SSP Unitray system (Invitrogen, Carlsbad, California, USA). Screening for chemokine (C-C motif) receptor 5 (CCR5), chemokine (C-C motif) receptor 2 (CCR2) and stromal cell-derived factor-1 (SDF-1) polymorphisms were performed by PCR as previously described .
HIV-1-specific cytotoxic T lymphocyte (CTL) responses were quantified by the IFN-γ–Elispot assay using previously described optimal epitopes . A response was considered positive if more than 55 spot-forming cells (SFC)/106 cells and at least three times higher than mean background activity.
Three patients with PHI (≤3 western blot bands positive) were suspected of having been serially infected within 3 months from a chronically infected index patient following unprotected sex (Fig. 1a). The status of the source person was unknown, but they did test HIV negative 5 years previously. To verify the presumed linked transmission events, the gag and pol genes from each patient were amplified and sequenced from plasma RNA. Nearly identical HIV-1 clade B sequences were identified in each patient, with a mean pairwise nucleotide sequence identity between these sequences of 99.6% (±0.2%) (Fig. 1b). These data strongly support the transmission of highly related strains of HIV-1 between these epidemiologically linked patients over a short period of time.
All patients immediately initiated highly active antiretroviral therapy (HAART) for a period of 6 months, achieving suppression of viral replication (Fig. 1a). Within 6 months of cessation of therapy, patient ‘A’, who had already established chronic infection at the time of HAART initiation, and patient ‘C’ exhibited viral load set points of 9 × 104 and 6 × 105 copies/ml, respectively, whereas patients ‘B’ and ‘D’ exhibited lower viral load set points of 7 × 103 and 3.3 × 104 copies/ml, respectively (Fig. 1a). Thus, viral loads in patients ‘A’ and ‘C’ ranged in the upper quartile, which is predictive of more rapid progression of disease, whereas patients ‘B’ and ‘D’ ranged in the second and third quartiles, associated with slower progression of disease according to the Multicenter AIDS Cohort Studies . These data indicate that patients infected with an identical viral strain, and receiving HAART during the early phase of the infection, can have a substantially different viral set point after treatment discontinuation, suggesting that additional factors may be responsible for the distinct clinical courses.
To examine whether differences in host genetics might account for these differences in viral set points between patients, we examined multiple genetic loci previously identified to contribute to the susceptibility to HIV-1 infection and the rate of progression to AIDS . In the present study, we assessed differences in HLA class I alleles , as well as polymorphisms within the chemokine receptors . Although multiple promotor mutations in CCR5, CCR2 and SDF-1 were observed in this cluster of individuals, only patient ‘B’ was found to be homozygous for the potential protective A59029G polymorphism in CCR5  (Fig. 1a). Notably, patients ‘B’ and ‘D’ also expressed the HLA alleles, HLA-B57 and HLA-A11, respectively, which are associated with control of HIV-1 replication and a more favorable disease progression . In addition, both patients immunodominantly targeted specific CTL epitopes [HLA-B57HW9 (Nef) HTQGYFPDW, HLA-B57-TW10 (Gag) TSTLQEQIGW, HLA-A11-AK11 (Gag) ACQGVGGPGHK], which have been previously associated with control of viral replication [22,23] (data not shown). The immunodominant response B51-TI8(Pol) in patient ‘C’, with a substantial higher viral load was, in contrast, not present because an escape mutation had been transmitted within this epitope to patient ‘C’. In summary, these data suggest that the expression of protective HLA alleles and the immunodominant targeting of key responses by these alleles had a strong impact on the control of viral replication following cessation of therapy.
The identification of tightly linked transmission cases of HIV-1 provides a unique opportunity to understand the different influences of host genetics and early antiretroviral therapy on disease progression. In the current study, we present data documenting the rapid transmission of a strain of HIV-1 clade B within four individuals with different genetic backgrounds, which resulted in distinctly different virologic and immunological outcomes. The high degree of similarity of sequences derived from each patient suggested that little viral diversification had taken place within the first few weeks of infection and, therefore, was not substantially contributing to differences in viral control.
After treatment discontinuation, only patients ‘B’ and ‘D’ maintained relative control of viral replication after cessation of HAART, in contrast to patients ‘A’ and ‘C’. Both patients ‘B’ and ‘D’ expressed HLA alleles – especially HLA-B57 associated with control of HIV-1 – and they mounted immune responses against immunodominantly targeted CD8+ epitopes, which have previously been associated with slower disease progression [22,23]. This observation is emphasized by revisiting the ‘Berlin patient’, the first described case of spontaneous control of viral replication following short-term treatment interruption during primary HIV-1 infection . Several subsequent studies have investigated the role of early treatment during acute HIV-1 infection with or without interruptions but have provided contradictory results [6,7,9,24,25]. A reanalysis of host genetic factors of the ‘Berlin patient’, who, to the present date, exhibits control of viral replication, has recently revealed expression of the HLA-B57 haplotype (unpublished data). Therefore, it is likely that the expression of HLA-B57 may have been at least one major contributor to the sustained control of HIV-1 replication in this patient, questioning the role of early interventional strategies for the sustained containment of HIV-1 following cessation of therapy. Taken together, these data suggest that host genetic factors should be included in trials investigating the impact of treatment initiation during acute HIV-1 infection in order to accurately discern the relative contribution of early treatment on HIV-1 clinical outcome.
We would like to thank the participants in this study. We also would like to thank Mary Carrington and Yuko Yuki from the NCI Frederick, Andreas Carganico from the HIV Clinic Dupke, Carganico, Baumgarten in Berlin, Zabrina Brumme, Chanson Brumme and Adrianne Gladden from the Partners AIDS Research Center, Boston for their outstanding help to realize this project. This study was funded by NIH grants R01-AI054178 to Todd M. Allen and U01-AI052403 to Todd M. Allen, Bruce D. Walker, and Marcus Altfeld. Hendrik Streeck is supported by the Deutscher Akademischer Austauschdiensts.
Authors' contributions: Hendrik Streeck, Todd M. Allen, Claudia Kuecherer, Marcus Altfeld and Bruce D. Walker designed the experiments/the study. Heiko Jessen and Arne B. Jessen identified and enrolled the patients of the cluster. Heiko Jessen, Arne B. Jessen, Stephan Dupke and Axel Baumgarten were treating physicians of the patients and collected clinical data. Bin Li, Todd M. Allen and Claudia Kuecherer generated viral sequence data. Hendrik Streeck generated immunological data. Hendrik Streeck, Bin Li, Claudia Kuecherer, Todd M. Allen, Jan van Lunzen and Ingrid Stahmer collected data or did experiments for the study. Hendrik Streeck and Todd M. Allen wrote the first draft of the paper. Hendrik Streeck, Heiko Jessen, Todd M. Allen, Bruce D. Walker, Claudia Kuecherer and Marcus Altfeld contributed to writing the paper.
1. Kassutto S, Rosenberg ES. Primary HIV type 1 infection. Clin Infect Dis 2004; 38:1447–1453.
2. Kahn JO, Walker BD. Acute human immunodeficiency virus type 1 infection. N Engl J Med 1998; 339:33–39.
3. Lori F, Jessen H, Lieberman J, Finzi D, Rosenberg E, Tinelli C, et al. Treatment of human immunodeficiency virus infection with hydroxyurea, didanosine, and a protease inhibitor before seroconversion is associated with normalized immune parameters and limited viral reservoir. J Infect Dis 1999; 180:1827–1832.
4. Lisziewicz J, Rosenberg E, Lieberman J, Jessen H, Lopalco L, Siliciano R, et al. Control of HIV despite the discontinuation of antiretroviral therapy. N Engl J Med 1999; 340:1683–1684.
5. Lori F, Lewis MG, Xu J, Varga G, Zinn DE, Crabbs C, et al. Control of SIV rebound through structured treatment interruptions during early infection. Science 2000; 290:1591–1593.
6. Rosenberg ES, Altfeld M, Poon SH, Phillips MN, Wilkes BM, Eldridge RL, et al. Immune control of HIV-1 after early treatment of acute infection. Nature 2000; 407:523–526.
7. Streeck H, Jessen H, Alter G, Teigen N, Waring MT, Jessen A, et al. Immunological and virological impact of highly active antiretroviral therapy initiated during acute HIV-1 infection. J Infect Dis 2006; 194:734–739.
8. Kinloch-de Loes S, Hoen B, Smith DE, Autran B, Lampe FC, Phillips AN, et al. Impact of therapeutic immunization on HIV-1 viremia after discontinuation of antiretroviral therapy initiated during acute infection. J Infect Dis 2005; 192:607–617.
9. Kaufmann DE, Lichterfeld M, Altfeld M, Addo MM, Johnston MN, Lee PK, et al. Limited durability of viral control following treated acute HIV infection. Plos Med 2004; 1:e36.
10. Carrington M, O'Brien SJ. The influence of HLA genotype on AIDS. Annu Rev Med 2003; 54:535–551.
11. Berger EA, Murphy PM, Farber JM. Chemokine receptors as HIV-1 coreceptors: roles in viral entry, tropism, and disease. Annu Rev Immunol 1999; 17:657–700.
12. Altfeld M, Addo MM, Rosenberg ES, Hecht FM, Lee PK, Vogel M, et al. Influence of HLA-B57 on clinical presentation and viral control during acute HIV-1 infection. AIDS 2003; 17:2581–2591.
13. Price DA, Goulder PJ, Klenerman P, Sewell AK, Easterbrook PJ, Troop M, et al. Positive selection of HIV-1 cytotoxic T lymphocyte escape variants during primary infection. Proc Natl Acad Sci USA 1997; 94:1890–1895.
14. Feeney ME, Tang Y, Pfafferott K, Roosevelt KA, Draenert R, Trocha A, et al. HIV-1 viral escape in infancy followed by emergence of a variant-specific CTL response. J Immunol 2005; 174:7524–7530.
15. Allen TM, Altfeld M, Yu XG, O'Sullivan KM, Lichterfeld M, Le Gall S, et al. Selection, transmission, and reversion of an antigen-processing cytotoxic T-lymphocyte escape mutation in human immunodeficiency virus type 1 infection. J Virol 2004; 78:7069–7078.
16. Altfeld M, Allen TM, Yu XG, Johnston MN, Agrawal D, Korber BT, et al. HIV-1 superinfection despite broad CD8+ T-cell responses containing replication of the primary virus. Nature 2002; 420:434–439.
17. Kostrikis LG, Huang Y, Moore JP, Wolinsky SM, Zhang L, Guo Y, et al. A chemokine receptor CCR2 allele delays HIV-1 disease progression and is associated with a CCR5 promoter mutation. Nat Med 1998; 4:350–353.
18. Altfeld M, Kalife ET, Qi Y, Streeck H, Lichterfeld M, Johnston MN, et al. HLA alleles associated with delayed progression to AIDS contribute strongly to the initial CD8(+) T cell response against HIV-1. PLoS Med 2006; 3:e403.
19. Mellors JW, Rinaldo CR Jr, Gupta P, White RM, Todd JA, Kingsley LA. Prognosis in HIV-1 infection predicted by the quantity of virus in plasma. Science 1996; 272:1167–1170.
20. Carrington M, Nelson GW, Martin MP, Kissner T, Vlahov D, Goedert JJ, et al. HLA and HIV-1: heterozygote advantage and B*35-Cw*04 disadvantage. Science 1999; 283:1748–1752.
21. Kaslow RA, Carrington M, Apple R, Park L, Munoz A, Saah AJ, et al. Influence of combinations of human major histocompatibility complex genes on the course of HIV-1 infection. Nat Med 1996; 2:405–411.
22. Frater AJ, Brown H, Oxenius A, Gunthard HF, Hirschel B, Robinson N, et al. Effective T-cell responses select human immunodeficiency virus mutants and slow disease progression. J Virol 2007; 81:6742–6751.
23. Navis M, Schellens IM, Swieten PV, Borghans JA, Miedema F, Kootstra NA, et al. A nonprogressive clinical course in HIV-infected individuals expressing human leukocyte antigen B57/5801 is associated with preserved CD8(+) T lymphocyte responsiveness to the HW9 epitope in Nef. J Infect Dis 2008; 197:871–879.
24. Kinloch-De Loes S, Hirschel BJ, Hoen B, Cooper DA, Tindall B, Carr A, et al. A controlled trial of zidovudine in primary human immunodeficiency virus infection. N Engl J Med 1995; 333:408–413.
25. Hecht FM, Wang L, Collier A, Little S, Markowitz M, Margolick J, et al. A multicenter observational study of the potential benefits of initiating combination antiretroviral therapy during acute HIV infection. J Infect Dis 2006; 194:725–733.
© 2009 Lippincott Williams & Wilkins, Inc.