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

We undertook a longitudinal study of SBBC SP and LTNP. The clinical history of the study subjects from infection to 1998 has been described (17). Subjects C54, C98, C49, C64, and C135 were referred to previously as recipients 13, 7, 12, 9, and 4, respectively (17). Subjects C54 and C98 have since died from causes unrelated to HIV-1 infection. An update on the results of laboratory studies and clinical history of these two subjects and of the surviving SBBC members studied in this report is summarized in Table 1 and detailed below.

SBBC subjects with slowly progressing HIV-1 infection include the donor (D36) and transfusion recipient C98. D36 commenced highly active antiretroviral therapy (HAART) in January 1999 following HIV-associated dementia that coincided with a fall in the CD4 cell count to <200 cells/μl and the presence of high plasma and cerebrospinal fluid (CSF) HIV-1 RNA levels (4, 5). As reported previously, C98 commenced prednisone for treatment of asthma in 1995 (17). C98 was diagnosed with pulmonary amyloidosis in 1998. C98 commenced HAART in November 1999 after experiencing a steady decline in his CD4⁺ T-cell count and a gradual increase in HIV-1 RNA from below-detectable levels to 1,500 RNA copies/ml. During 2001 his CD4⁺ T-cell count declined and fluctuated between 213 and 484 cells/μl despite the continuance of HAART and a viral load below detectable levels. He died at the age of 64 in March 2002 of amyloidosis, which was not HIV-1 related.

Nonprogressing SBBC subjects include transfusion recipients C49, C54, C64, and C135; these subjects have experienced steady CD4⁺ T-cell counts since infection was first identified, with median values of >900, >1,000, >900, and > 500 cells/μl, respectively. HIV-1 RNA levels have remained consistently low or below detectable levels in these subjects despite being infected for up to 20 years without antiretroviral intervention. Patient C54 died aged 73 from a myocardial infarct in September 2001. C135 was not included in the present study because of the lack of consistent amplification of HIV-1 DNA.

Peripheral blood mononuclear cells (PBMC) were obtained at each of the times indicated in Table 1 according to guidelines endorsed by the Australian Red Cross Blood Service human ethics committee. The nef/LTR region of the HIV-1 genome was amplified from PBMC by nested PCR, as described previously (4, 20). The products of six independent PCRs were pooled and cloned into pGEM-T-Easy (Promega, Madison, WI), and the nucleotide sequences of multiple independent clones were determined using a SequiTherm EXCEL II DNA sequencing kit (Epicenter Technologies, Madison, WI) and a model 4000L LI-COR DNA sequencer (LI-COR, Lincoln, NE). Nucleotide sequences were aligned and analyzed using DNAMAN software (Lynnon, Quebec, Canada).

Intersubject nef/LTR sequences cloned from the earliest available PBMC samples were heterogenous but contained a number of common mutations (Fig. 1A): (i) deletions of various lengths in the amino terminus of the nef gene, (ii) at least one deletion in the nef/LTR overlap region, and (iii) duplication and/or rearrangement of nuclear factor-κB (NF-κB) and specificity factor 1 (Sp-1) binding sites in the LTR (Fig. 1B). The 3′-most deletion in the nef/LTR overlap region shared by all viruses is thought to have been present in the transmitted virus, as none of the subjects has antibodies to a peptide of the corresponding region in the Nef protein (9). None of the viruses are capable of encoding Nef, carrying either an in-phase termination codon (D36) or lacking the nef ATG. The duplicated or rearranged region of the LTR was unique to each of the cohort members and varied with respect to the number and arrangement of NF-κB and Sp-1 sites inserted (Fig. 1). Thus, despite the common origin of the viruses, the nef/LTR regions differed from subject to subject.

Sequential analysis of nef/LTR sequences spanning a 4- to 10-year period demonstrated a further loss of nef sequence that differed in magnitude between subjects (Fig. 2). A large deletion of 128 bp emerged in D36, effectively removing the entire nef gene with the exception of the region surrounding the nef start codon, the polypurine tract which contains terminal signals for HIV-1 integration, and a 90-bp region of the nef/LTR overlap region surrounding the negative regulatory element. The basal promoter and enhancer elements of the LTR were retained, but a 44-bp deletion appeared in the rearranged or duplicated NF-κB/Sp-1 motif. The pattern of nef sequence loss in C98 was remarkably similar to that which occurred in D36. The pattern of nef sequence loss in C54 was also similar but was less extensive than that observed in D36 and C98. However, the additional loss of nef sequence in C64 was comparatively minimal. Thus, viruses harbored by D36, C54, C98, and C64 appear to be evolving in a convergent fashion toward a highly deleted, minimal nef/LTR structure containing only sequence elements that are absolutely essential for HIV-1 replication. The convergent nature of the nef/LTR evolution is further illustrated in Fig. 3, where sequences from the earliest and most recent nef/LTR clones from each subject are compared. The convergent nature of the nef/LTR sequence changes implies the presence of strong selection pressures that maintain the ability of defective HIV-1 genomes to persist in vivo.

The highly evolved nef/LTR sequences harbored by D36, C54, and C98 are strikingly similar to those that have remained dominant in C49 for at least 10 years (Fig. 2). The presence of Nef antibodies directed against peptides spanning the entire Nef protein (with the exception of the common, 3′-most deletion in the nef/LTR overlap region) in C49 (9) suggests that prior to 1994 a near-complete nef sequence existed and that the bulk of nef/LTR evolution occurred during the first 10 years after infection. C49 has had below-detectable HIV-1 RNA levels since February 1994 (Table 1) and persistent HIV-1 cytotoxic T-cell responses since monitoring of the SBBC began in 1992 (2, 8, 17). Thus, our findings suggest that the highly evolved nef/LTR structure is stable and, in the case of C49, does not increase pathogenicity.

In this study, we demonstrated a progressive loss of nef/LTR sequence in an epidemiologically-linked cohort of long-term survivors who have been infected with attenuated HIV-1 for up to 25 years. The intersubject evolution of nef/LTR sequence loss appears convergent, tending toward retention of only those sequence elements that are absolutely required for HIV-1 replication. The highly evolved, minimal nef/LTR structure appears stable, being present as the dominant strain in C49 for at least 10 years. Its persistence in this subject, who has consistently had a below-detectable viral load in the absence of HAART (Table 1), initially suggested that evolution to the minimal nef/LTR sequence may result in a further-attenuated, even less-pathogenic virus. However, we found no association between evolution toward the minimal nef/LTR sequence and the clinical status of the subject. For example, both progressing (D36, C98) and nonprogressing (C54, C49) subjects harbored highly evolved forms of nef/LTR, and a nonprogressing subject (C64) harbored a significantly less evolved nef/LTR. Thus, other viral and/or host factors are likely to contribute to modulating the in vivo pathogenicity of HIV-1 strains with nef/LTR deleted.

Reversion to pathogenicity by SIV with nef deleted has been associated with restoration of a truncated Nef protein (21), acquisition of further deletions in the nef/LTR overlap region (1), and/or duplications of NF-κB binding sites in the LTR (1). In contrast to the SIV studies, the in vivo evolution of HIV-1 with nef/LTR was unidirectional toward a smaller nef/LTR sequence and the majority of the additional sequence loss was within the nef-alone region. Furthermore, none of the clones were capable of encoding Nef. In addition, the presence of duplicated NF-κB binding sites in the LTR was not associated with the clinical status of the SBBC subjects. Therefore, it is likely that any viral factors that modulate the in vivo pathogenicity of HIV-1 with nef/LTR deleted will be distinct from those in SIV with nef deleted. Interestingly, the unidirectional evolution toward the minimal nef/LTR sequence observed in SBBC members is strikingly similar to the pattern of evolution in a slow progressor infected with a nef/LTR deletion variant of HIV-1 circulating recombinant form 01_AE (15). The convergent pattern of nef/LTR evolution among viruses harbored by SBBC members is therefore unlikely to be due to a unique property of the infecting strain but rather likely reflects an intrinsic instability of HIV-1 with nef/LTR defects that is common across clades.

The molecular mechanisms underlying the increased or acquired pathogenicity of nef/LTR-deleted HIV-1 harbored by slow progressors D36 and C98 remain to be determined, but possibilities include changes in LTR or Env function that may contribute to increasing replicative capacity or cytopathicity, respectively. In support of this hypothesis, enhanced transcriptional activity of LTR clones isolated from CSF of D36 was shown to contribute to high CSF HIV-1 RNA levels and the development of HIV-associated dementia (4). Moreover, enhanced coreceptor usage by HIV-1 isolated from D36 when CD4⁺ cell counts fell below 200/μl contributed to enhanced cell killing in ex vivo human tissue cultures (12). Further studies on the function of sequential LTR and Env clones from SBBC subjects are in progress to elucidate their role in the pathogenesis of nef/LTR-deleted HIV-1 infection.

In conclusion, while our studies affirm that nef is important for HIV-1 pathogenesis, convergent evolution of HIV-1 in vivo toward a minimal and apparently stable nef/LTR structure via extensive loss of nef sequence was not associated with HIV-1 progression. Factors other than nef sequence therefore contribute significantly to HIV-1 progression in the SBBC of long-term survivors.

The nef/LTR nucleotide sequences reported here have been assigned GenBank accession numbers DQ287272 to DQ287311.

We thank Dale McPhee for helpful comments.

This study was supported by grants from the Australian National Center for HIV Virology Research to M.J.C. and N.J.D. and grants from the Australian National Health and Medical Research Council (NHMRC) (251520) and National Institutes of Health and the National Institute of Allergy and Infectious Diseases (1-R21-AI054207-01-A1) to P.R.G. P.R.G. is a recipient of an NHMRC R. Douglas Wright Biomedical Career Development Award.