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JAIDS Journal of Acquired Immune Deficiency Syndromes:
doi: 10.1097/QAI.0b013e31815aba08
Brief Report: Basic Science

Replication-Dependent Pathogenicity of Attenuated nef-Deleted HIV-1 In Vivo

Gorry, Paul R PhD*†‡; Churchill, Melissa PhD*; Learmont, Jennifer§; Cherry, Catherine MBBS, PhD*†∥; Dyer, Wayne B PhD§¶; Wesselingh, Steven L MBBS, PhD*†‡; Sullivan, John S PhD, MPH§¶

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From the *Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, Australia; †Department of Medicine, Monash University, Melbourne, Victoria, Australia; ‡Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia; §Australian Red Cross Blood Service, Sydney, New South Wales, Australia; ∥Infectious Diseases Unit, The Alfred Hospital, Melbourne, Victoria, Australia; and the ¶Faculty of Medicine, University of Sydney, Sydney, New South Wales, Australia.

Received for publication May 10, 2007; accepted September 10, 2007.

Supported by a grant from the Australian Center for HIV Virology Research to M.J. Churchill and, in part, by grants from the Australian National Health and Medical Research Council (NHMRC) (433915) and National Institutes of Health/National Institute for Allergy and Infectious Diseases (AI054207-01-A1) to P.R. Gorry. P.R. Gorry is the recipient of an NHMRC R. Douglas Wright Biomedical Career Development Award.

Correspondence to: Paul R. Gorry, PhD, Macfarlane Burnet Institute for Medical Research and Public Health, GPO Box 2284, Melbourne 3001, Victoria, Australia (e-mail:

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Background: The Sydney Blood Bank Cohort (SBBC) of long-term survivors consists of 8 individuals infected with an attenuated nef-deleted strain of HIV-1 by means of contaminated blood products donated from a common blood donor between 1981 and 1984. We report the outcome of a 26-year prospective study documenting the clinical course of nef-deleted HIV-1 infection in 7 SBBC members.

Methods: CD4 T-cell counts and plasma HIV-1 RNA levels were measured by flow cytometry and the COBAS AMPLICOR HIV-1 monitor version 1 or 1.5 (Roche Molecular Diagnostic Systems, Branchburg, NJ), respectively. Changes in these parameters with time were determined by least-squares analysis using STATA (StataCorp, College Station, TX) statistical software.

Results: Four subjects had persistent low-level viremia. Of these, progression to AIDS and/or evidence of CD4 T-cell loss occurred in 3; the fourth viremic individual died of non-HIV-1-related causes in 1995, only 12 years after infection. Three subjects have persistently undetectable plasma HIV-1 RNA levels and remain long-term nonprogressors.

Conclusions: Our study shows that even weakened highly attenuated HIV-1 strains with nef deletions are ultimately pathogenic in humans unless replication is completely and persistently suppressed in vivo. This finding underscores the importance of aiming to achieve nothing less than complete and sustained suppression of HIV-1 replication by antiretroviral drugs and vaccines.

The nef gene is a major determinant of virulence in primate lentiviruses. Mutations in nef attenuate replication capacity and pathogenicity of simian immunodeficiency virus,1-6 and long-term survival of HIV-1 infection has been noted in rare cases of infection with nef-defective HIV-1.7-11 The largest described cohort of long-term survivors infected with nef-defective HIV-1 is the Sydney Blood Bank Cohort (SBBC), which consists of 8 individuals who became infected with HIV-1 by means of contaminated blood products obtained from a common donor between 1981 and 1984.12,13 Viral attenuation has been attributed to common deletions in the nef and long-terminal repeat (LTR) regions of the HIV-1 genome.7,14 Thus, the SBBC provides an unprecedented opportunity to study the in vivo pathogenicity of nef-deleted HIV-1 in a naturally occurring human setting. We report the outcome of a 26-year prospective study documenting the clinical course of nef-deleted HIV-1 infection in 7 SBBC members.

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Blood samples were taken according to guidelines endorsed by the Australian Red Cross Blood Service Human Ethics Committee. CD4 T-cell counts were determined by flow cytometry. HIV-1 RNA levels were determined using the COBAS AMPLICOR HIV-1 monitor version 1 or 1.5. HIV-1 RNA levels <400 copies/mL (version 1) or <50 copies/mL (version 1.5) were considered to be lower than detection. Changes in CD4 T-cell counts and plasma HIV-1 RNA levels with time were assumed to be linear, and regressions were determined by least-squares analysis. Statistical analyses were performed with STATA statistical software (version 9.2; StataCorp, College Station, TX). All reported P values are 2-sided. P values <0.01 were considered statistically significant.

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The clinical history and laboratory studies of the subjects from when they were first identified as SBBC members until 1998 have been described previously.13 The clinical course of a number of subjects has changed significantly since 1998, including progression to AIDS in 1 subject and 2 additional non-HIV-1-related deaths. The clinical history and laboratory studies through 2006 are detailed here and summarized in Figure 1 and Table 1.

Figure 1
Figure 1
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Table 1
Table 1
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Between December 1984 and April 1994, the SBBC blood donor D36 had a stable CD4 T-cell count but subsequently experienced CD4 T-cell loss at an average rate of 97.48 cells/μL/y until diagnosis of HIV-associated dementia (HIVD) was made in December 1998.15,16 CD4 T-cell loss was accompanied by a steady increase in plasma HIV-1 RNA levels at an average rate of 3408 RNA copies/mL/y, peaking at approximately 20,000 copies/mL in August 1998. At diagnosis of HIVD, cerebrospinal fluid (CSF) HIV-1 RNA levels were recorded at >750,000 copies/mL. After commencement of highly active antiretroviral therapy (HAART),15,16 plasma and CSF HIV-1 RNA were suppressed to lower than detectable levels. D36 subsequently experienced neurologic improvement and CD4 T-cell recovery to approximately 700 cells/μL in August 2006. D36 remains clinically well.

C98 died of non-HIV-1-related causes at the age of 64 years but experienced significant CD4 T-cell loss before death. This individual commenced prednisone for treatment of asthma in 199513 and was diagnosed with pulmonary amyloidosis in 1998. With this background, C98 commenced HAART in November 199914 because of CD4 T-cell loss at an average rate of approximately 60 cells/μL/y. CD4 T-cell loss was accompanied by low steady-state plasma HIV-1 RNA levels, with the median level between December 1994 and August 1999 recorded at 690 copies/mL. Plasma HIV-1 RNA levels were suppressed to lower than detectable levels on HAART, but the decline in CD4 T-cell count continued. C98 died of amyloidosis in March 2002.

C54 died from a myocardial infarction in September 2001 aged 73 years,14 17 years after infection. This subject had previously undergone splenectomy, accounting for an overall elevation in lymphocyte count.17 C54 never required antiretroviral therapy but had persistently detectable plasma HIV-1 RNA levels, with the median level between November 1994 and May 2001 recorded at 1700 copies/mL. C54 experienced an overall loss of CD4 T cells at an average rate of 46 cells/μL/y between June 1987 and May 2001. The percentage of CD4 T cells also fell significantly between November 1993 and May 2001 (P < 0.001; data not shown).

C18 died from causes unrelated to HIV-1 infection in 1995 and has been described in detail previously.13 Although asymptomatic and with a preserved CD4 T-cell count before death, this subject had persistently detectable plasma HIV-1 RNA levels, with the median level between July 1994 and October 1995 recorded at 1400 copies/mL.13

Subjects C49, C64, and C135 have been infected for 23, 24, and 26 years, respectively, without antiretroviral therapy, and they have consistently had undetectable plasma HIV-1 RNA levels. C49 suffers with type II diabetes and chronic alcoholism. For the first 14 years after infection, C49 had stable CD4 T-cell counts,13 but inclusion of more recent data demonstrated a marginal decline in CD4 T cells that was not considered significant. The median CD4 T-cell count since June 1987 was recorded at 918 cells/μL. C64 and C135 have had steady CD4 T-cell counts, with median values since December 1987 and January 1996 recorded at 968 and 503 cells/μL, respectively. Of note, C135 carries the heterozygous CCR5Δ32 and HLA-B57 genotypes,18,19 both of which are associated with slow HIV-1 progression.20,21 Thus, the host genotype of C135 may have contributed to further attenuated infection.

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Our studies show that D36, C98, and C54, who had persistently detectable plasma HIV-1 RNA, all experienced HIV-1 progression highlighted by significant CD4 T-cell losses over time. Progression was more dramatic in D36, who experienced HIVD as an initial AIDS-defining illness. The neurologic improvement and restoration of CD4 T-cell count in D36 by inhibiting the in vivo HIV-1 replication kinetics with HAART unequivocally demonstrates the pathogenic potential of nef-deleted HIV-1. Thus, eventual HIV-1 disease progression was demonstrated in 3 of 4 subjects who had persistent low-level viremia. The other viremic individual, C18, died after only 12 years of infection.13 Although C18 showed no evidence of CD4 T-cell loss before death, our results suggest that persistently detectable plasma HIV-1 RNA levels placed this individual at risk of eventual HIV-1 progression had death not occurred from unrelated causes. In contrast, 3 of 3 subjects with persistently undetectable HIV-1 RNA levels remain long-term nonprogressors 23 to 26 years after infection. Two additional SBBC subjects not reported here, C83 and C124, died before 1995.13 A lack of laboratory measures from C83 and C124, including plasma HIV-1 RNA levels, prevents assessment of whether HIV-1 infection was progressive in these subjects. SBBC subjects harbor closely related HIV-1 variants.7 Furthermore, detailed longitudinal studies of the evolution of nef/LTR sequences,14 HIV-1 coreceptor use,22 envelope gene diversity,23 and rev sequence/function24 were unable to segregate SBBC nonprogressors from progressors. Together, these studies suggest that nef-deleted HIV-1 may be nonpathogenic in humans only if additional host factors are present to suppress replication persistently to lower than detectable levels.

Analysis of host immune mechanisms suppressing nef-deleted virus in SBBC nonprogressors may provide insights relevant for HIV-1 vaccine design. Previous studies of HIV-1 nonprogressor cohorts harboring nef-intact virus showed a predominance of Gag-specific CD8 T-cell responses.25,26 In contrast, a strong CD8 T-cell response to HIV-1 Pol antigens is dominant in all SBBC members, and that against HIV-1 Gag is present in only a subset of SBBC nonprogressors (W. Dyer et al, manuscript in preparation). Nevertheless, persistent and strong T-helper proliferative responses to HIV-1 p24 antigen were present in all SBBC nonprogressors but were lacking in the viremic subjects throughout the course of the study.27 These data suggest that T-helper responses may contribute to control of viremia in SBBC nonprogressors.

Together, these studies provide valuable insights into the long-term pathogenicity of nef-deleted HIV-1. Importantly, we show that even weakened highly attenuated HIV-1 strains with nef deletions are ultimately pathogenic in humans unless replication is completely and persistently suppressed in vivo. Furthermore, only low-level persistent viremia was necessary to mediate the long-term pathogenic effects of nef-deleted virus. Thus, our studies underscore the importance of aiming to achieve nothing less than complete and sustained suppression of HIV-1 replication by antiretroviral drugs and vaccines.

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11. Kondo M, Shima T, Nishizawa M, et al. Identification of attenuated variants of HIV-1 circulating recombinant form 01_AE that are associated with slow disease progression due to gross genetic alterations in the nef/long terminal repeat sequences. J Infect Dis. 2005;192:56-61.

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14. Churchill MJ, Rhodes DI, Learmont JC, et al. Longitudinal analysis of human immunodeficiency virus type 1 nef/long terminal repeat sequences in a cohort of long-term survivors infected from a single source. J Virol. 2006;80:1047-1052.

15. Churchill M, Sterjovski J, Gray L, et al. Longitudinal analysis of nef/long terminal repeat-deleted HIV-1 in blood and cerebrospinal fluid of a long-term survivor who developed HIV-associated dementia. J Infect Dis. 2004;190:2181-2186.

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18. Geczy AF, Kuipers H, Coolen M, et al. HLA and other host factors in transfusion-acquired HIV-1 infection. Hum Immunol. 2000;61:172-176.

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20. O'Brien SJ, Moore JP. The effect of genetic variation in chemokines and their receptors on HIV transmission and progression to AIDS. Immunol Rev. 2000;177:99-111.

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22. Verity E, Zotos D, Wilson K, et al. Viral phenotypes and antibody responses in long term survivors infected with attenuated human immunodeficiency virus type 1 containing deletions in the nef/long terminal repeat region. J Virol. 2007;81:9268-9278.

23. Gray L, Churchill MJ, Sterjovski J, et al. Phenotype and envelope gene diversity of nef-deleted HIV-1 isolated from long term survivors infected from a single source. Virology J. 2007;4:75.

24. Churchill M, Chiavaroli L, Wesselingh SL, et al. Persistence of attenuated HIV-1 rev alleles in an epidemiologically linked cohort of long-term survivors infected with nef-deleted virus. Retrovirology. 2007;4:43.

25. Pontesilli O, Klein MR, Kerkhof-Garde SR, et al. Longitudinal analysis of human immunodeficiency virus type 1-specific cytotoxic T lymphocyte responses: a predominant gag-specific response is associated with nonprogressive infection. J Infect Dis. 1998;178:1008-1018.

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27. Gorry PR, McPhee DA, Verity E, et al. Pathogenicity and immunogenicity of attenuated, nef-deleted HIV-1 strains in vivo. Retrovirology. 2007;4:66.

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attenuated; HIV-1; long-term nonprogressor (LTNP); nef-deleted

© 2007 Lippincott Williams & Wilkins, Inc.


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