Genome-wide mRNA and miRNA analysis of peripheral blood mononuclear cells (PBMC) reveals different miRNAs regulating HIV/HCV co-infection.

Co-infection with human immunodeficiency virus (HIV) and hepatitis C virus (HCV) is common due to shared transmission routes. The genomic basis of HIV/HCV co-infection and its regulation by microRNA (miRNA) is unknown. Therefore, our objective was to investigate genome-wide mRNA expression and its regulation by miRNA in primary PBMCs derived from 27 patients (5 HCV - mono-infected, 5 HIV-mono-infected, 12 HCV/HIV co-infected, and 5 healthy controls). This revealed 27 miRNAs and 476 mRNAs as differentially expressed (DE) in HCV/HIV co-infection when compared to controls (adj p<0.05). Our study shows the first evidence of miRNAs specific for co-infection, several of which are correlated with key gene targets demonstrating functional relationships to pathways in cancer, immune-function, and metabolism. Notable was the up regulation of HCV-specific miR-122 in co-infection (FC>50, p=4.02E-06), which may have clinical/biological implications.

An examination of signs of disease progression in survivors of the Sydney Blood Bank Cohort (SBBC).

BACKGROUND: The Sydney Blood Bank Cohort (SBBC) was infected between 1981 and 1984 with a nef/LTR defective strain of HIV-1. Different responses to HIV-1 infection have emerged between cohort members in the last 5 years. Three recipients (C135, C64 and C49) remain asymptomatic, have normal CD4 T cell counts, below detection (BD) viral loads (VL), remain therapy naive and are termed long-term non-progressors (LTNP). The donor (D36) and the two recipients (C98 and C54) have significantly declining CD4 T cell counts, detectable VL and are now long-term survivors (LTS). In contrast, in the SA cohort, comparison study group for the SBBC, five of 24 remain therapy naïve after 15 years infection with HIV-1 and all have detectable VL. OBJECTIVES: This paper examines different outcomes to long-term infection with HIV-1 in the SBBC and provides a brief overview of the therapy naïve in a comparison study group, the SA cohort. STUDY DESIGN: Retrospective epidemiological follow-up of the SBBC and the SA cohort has been conducted for >15 years. Analysis of CD4 T cell counts, VL and intermittent monitoring of HIV-specific proliferative responses are reviewed. Viral sequence changes in the SBBC will be considered. RESULTS: Prior to therapy D36 had a CD4 T cell count of 160/mm(3) and plasma VL of 9900 copies/ml while C98 had a CD4 T cell count of 387/mm(3) and plasma VL of 11491 copies/ml. After 1 month of therapy, plasma VL was BD (<400 copies/ml) and both showed significant increase in CD4 T cell counts. Molecular changes have occurred in D36 and C98 viral strains, the most recently evolved quasispecies have larger deletions in the nef/LTR region. CONCLUSIONS: Infection with nef/LTR deleted HIV-1 has resulted in slower disease progression for the SBBC. The three LTNP have maintained normal low levels of activated CD8 T cells and strong HIV-specific proliferative responses to HIV-1 p24, which are associated with control of viral replication.

Changing epidemiology of HIV type 1 infections in India: evidence of subtype B introduction in Bombay from a common source.

India has experienced multiple introductions of diverse HIV-1 subtypes A, B, C, and E, along with subtype B of HIV-2 between the 1980s and early 1990s. In this study, we have carried out a molecular investigation of 21 heterosexually and vertically acquired HIV-infected individuals from the New Bombay area, who tested positive for HIV-1 by commercial enzyme-linked immunosorbent assay (ELISA) and Western blot assay. We have sequenced the proviral DNA segments from the uncultured PBMCs in the hypervariable env V(3) region (286 bp) and a full-length vpr gene (291 bp). Overall, phylogenetic clustering of all Indian strains and also their clustering with subtype B strains were evident from both V(3)- and vpr gene-based trees, strongly supporting their recent introduction from a common source. This is the first report on subtype B introduction in Bombay, a region where subtype C predominates. Overall, these subtype B strains from Bombay shared genetic closeness with subtype B strains from Europe, the United States, and Asia.

Varied tropism of HIV-1 isolates derived from different regions of adult brain cortex discriminate between patients with and without AIDS dementia complex (ADC): evidence for neurotropic HIV variants.

A number of infected individuals develop neuropathological disorders, such as AIDS dementia complex (ADC), as a consequence of HIV/AIDS. The biological features governing HIV entry and tropism in different brain cell types remain unclear, as do the genetics of the virus regulating these events and the neuropathogenic processes within the brain tissues. HIV-1 was isolated from the right and left parietal, occipital, and frontal lobes of the brain cortex of three HIV-1-infected patients: two with ADC and one without. The viral strains were studied from the innate tissues and various primary cell cultures. The kinetics and tropism of viral strains from different brain regions showed clear differences on various primary cell types (monocytes, monocyte-derived macrophages, and T cells), which could discriminate between biological behavior of HIV-1 strains from patients with and without ADC. The variable effect of different donor cells on tropism was also clearly evident. The majority (with a few exceptions) of isolates from different brain regions of all three patients used CCR5 as coreceptor for entry. The consistent CCR5 use, macrophage tropism, and non-syncytium-inducing phenotype were the main characteristics of the brain-derived HIV-1 strains from all three patients. Importantly, viral strains derived directly from innate brain tissue of the patient without ADC showed some differences from the cultured variants of the same patient, whereas those from brain tissue of the patients with ADC were more similar to the culture-adapted strains. This suggests that the emergence of primary cell type-adapted isolates during ADC may play a crucial role in the development and progression of the neuropathology associated with ADC. The different genotypes residing in different areas of brain combined with their differential tropism and coreceptor use suggest that neurotropic variants exist that may be governing the neurological manifestation of HIV disease in infected patients.

Molecular evidence for drug-induced compartmentalization of HIV-1 quasispecies in a patient with periodic changes to HAART.

OBJECTIVE: To perform molecular analysis of the predominant viral populations and drug-resistance mutations from plasma and peripheral blood mononuclear cell (PBMC) compartments over time from an HIV infected patient, who experienced virological failure while on different HAART regimens. MATERIALS AND METHODS: In a longitudinal study proviral and plasma HIV-1 sequences were amplified in the pol, protease and env genes and were sequenced directly and analysed phylogenetically. Virus was recovered from time points corresponding to viral load peaks using co-culturing techniques. The periodic failure of different highly active antiretroviral therapy (HAART) regimens was analysed sequencing. RESULTS: Longitudinal follow-up studies revealed four inflection peaks of plasma viraemia associated with the recovery of culturable virus in vitro, which indicated failure of the concurrent HAART regimen. Molecular analysis of viral strains revealed evidence of continual evolution and compartmentalization of drug-resistance mutants/quasispecies between plasma and PBMC, with the widest spectrum of mutations isolated from plasma. Importantly, these data show the periodic appearance and clearance of drug-resistance mutants concomitant with the introduction and withdrawal of zidovudine over time. CONCLUSION: This report is unique in showing drug-induced compartmentalization of viral quasispecies under the control of different HAART regimens in both plasma and PBMC. Introduction and withdrawal of zidovudine from the HAART regimen had direct bearing on the appearance and disappearance of specific zidovudine drug-resistance mutations in plasma-derived virus. This data has important implications for the management of HIV-infected patients with poor compliance with certain HAART regimens, and also in predicting the late emergence of drug-resistance mutations via the latent integrated provirus.

Evidence for late stage compartmentalization of HIV-1 resistance mutations between lymph node and peripheral blood mononuclear cells.

OBJECTIVE: To determine the overall distribution of drug-resistance mutations to nucleoside reverse transcriptase inhibitors of HIV strains recovered from the lymph nodes (LN) and peripheral blood mononuclear cell (PBMC) compartments of four HIV-infected patients receiving zidovudine and didanosine and to compare them with antiretroviral-naive patients. DESIGN: Molecular comparison of major and minor HIV-1 env and pol region variants residing in LN and PBMC compartments. MATERIALS AND METHODS: Proviral DNA sequences were amplified by PCR from both PBMC and LN compartments, cloned into PGEM-T II Easy vector and sequenced. The clones were subjected to molecular and phylogenetic analysis. RESULTS: Comparison of PBMC and LN-derived HIV-1 variants in the env V3 region showed that nucleotide and amino acid variability was a characteristic feature of LN-derived variants. In contrast, a majority of resistance mutations to reverse transcriptase inhibitors were localized in the PBMC compartment rather than in LN, which is thought to be a reservoir of HIV. CONCLUSIONS: Distinct compartmentalization or independent evolution of pol and env gene variants between LN and PBMC could be due to the differential selection pressure imposed by the combination drug regimen, hence the bimodal distribution of resistance variants between LN and PBMC compartments.

Molecular and biological interactions between two HIV-1 strains from a coinfected patient reveal the first evidence in favor of viral synergism.

An intravenous drug user was found to be dually infected with two genetically and phylogenetically distinct human immunodeficiency virus type 1 (HIV-1) subtype B strains (designated groups I and II). Viral isolation revealed a simultaneous copassaging of two strains in PBMC. The culture of viral strains on monocytes and monocyte-derived macrophages preferentially segregated the two viral strains. The group I strain utilized CXCR4 and group II used CCR5 coreceptor for entry. Sequencing of >100 clones from uncultured PBMC consistently showed the predominance of group II virus in vivo. Importantly, the group II virus alone could not productively infect PBMC, but when used together with group I virus for infection, the group II virus regained its high replication potential and predominance in cultured PBMC. These data are the first to provide direct evidence in favor of molecular and biological interaction between two infecting strains in a coinfected patient and show their differential pathogenic effects, tropism, and modes of entry. In addition, our data provide the first evidence for synergism between these two strains. Cumulatively, these data emphasize that in order to clearly interpret coreceptor usage, biological segregation of viral strains from primary isolates in vitro may be imperative.

HIV-1 strains from a cohort of American subjects reveal the presence of a V2 region extension unique to slow progressors and non-progressors.

OBJECTIVES: To determine the molecular nature of HIV-1 quasispecies and their evolution, in vivo over time, in an American cohort of 22 homosexual men [four rapid progressors (RP), 15 slow progressors (SP) and three long-term non-progressors (LTNP)], infected with HIV-1 between 1982 and 1983, and to assess the possible role of the HIV-1 V2 region extension in HIV disease progression. DESIGN: Genetic and phylogenetic analyses of the V3 region and the nef gene clones over time from uncultured peripheral blood mononuclear cells (PBMC) of American patients with varying HIV disease progression rates. METHODS: Proviral DNA from longitudinally collected uncultured PBMC were subjected to PCR amplification in the nef gene and env V2 and V3 regions, followed by cloning, sequencing and phylogenetic analysis to establish evolutionary relationships between HIV-1 strains over time. RESULTS: Analysis of multiple viral clones showed nef gene deletions/insertions in 10 out of 15 SP, along with the coexistence of intact and defective nef gene lineages in the same individual over time, whereas these nefgene abnormalities were absent from HIV-1 strains from LTNP. Increasing quasispecies diversity in HIV-1 strains, over time, abrogation of a V3 region N-linked glycosylation site in > 60% of the clones, and, importantly, an extended V2 region were unique features of HIV-1 strains from SP and LTNP. CONCLUSIONS: The V2 region extension was unique to only SP and LTNP, and so may have a role in slow progression or non-progression of HIV disease. Increasing genetic diversity in HIV-1 strains in SP and LTNP correlated with the immunocompetent status of the host.

Comparison of three commercial assays for the quantification of HIV-1 RNA in plasma from individuals infected with different HIV-1 subtypes.

BACKGROUND: Commercial human immunodeficiency virus 1 (HIV-1) ribonucleic acid (RNA) quantification assays vary in their ability to quantify different subtypes of HIV-1, a problem in regions where multipte HIV-1 subtypes may be circulating. OBJECTIVES: To assess commercial HIV-1 RNA quantification assays on two plasma panels. Panel 1 consisted of HIV-1 seronegative plasma 'spiked' with a known amount of cultured virus of different subtypes, and Panel 2 comprised plasma collected from individuals infected with different HIV-1 subtypes. STUDY DESIGN: The comparison involved the Amplicor HIV-1 reverse transcriptase-polymerase chain reaction (RT-PCR), Quantiplex branched DNA, and NucliSens HIV-1 QT assays. Panel 1 consisted of 11 plasma 'spiked' with cultured viruses of HIV-1 subtypes A-F, and Panel 2 included 33 plasma samples from 16 patients infected with subtypes A, B, C, E and G. RESULTS: In Panel 1, the Quantiplex branched deoxyribonucleic acid (bDNA) assay quantified subtypes A-F efficiently, comparable to published results from two other laboratories. The Amplicor RT-PCR assay quantified subtypes B, C, and D but was relatively less efficient with subtypes E, F, and did not or poorly quantified subtype A. Testing of Panel 2 showed some inter-assay differences. In contrast to Panel 1, the Amplicor RT-PCR assay performed variably with subtype A when compared with the Quantiplex bDNA and NucliSens QT assays, and higher viral load levels were generated with subtype E using the Amplicor RT-PCR assay. Subtypes B and C showed some inter-patient differences but the Quantiplex bDNA generally gave a lower quantification than the Amplicor RT-PCR and NucliSens QT assays. CONCLUSIONS: These studies confirm that commercial HIV-1 load assays vary in their ability to quantify different HIV-1 subtypes. This may be more apparent with individual patient samples than with 'spiked' panels. This variability emphasizes that it is preferable for patient samples to be tested with the same assay, and care should be taken where infection with unusual subtypes is suspected.

Significance of plasma and peripheral blood mononuclear cell derived HIV-1 sequences in establishing epidemiologic linkage between two individuals multiply exposed to HIV-1.

Establishing epidemiologic linkage in individuals multiply exposed to HIV can be a difficult task. To date, only peripheral blood mononuclear cell (PBMC)-derived sequences have been used in studying HIV-1 transmission between individuals. So far, the combined utility of plasma and PBMC-derived HIV-1 sequences has not been assessed in establishing epidemiologic linkage in people involved in transmission of HIV. In this study, both PBMC (DNA) and plasma (RNA) derived viral quasispecies was used in establishing epidemiologic linkage between two infected individuals (B-90 and B-69) multiply exposed to HIV-1 via injecting drug use. A detailed sequence, and phylogenetic analyses of HIV-1V3 region quasispecies derived from these two compartments clearly demonstrated compartmentalization of viral quasispecies between PBMC and plasma. More importantly, these data also demonstrate that in order to establish epidemiologic linkage between individuals multiply exposed to HIV-1, analyses of viral strains from both plasma and PBMC compartments may be necessary. The PBMC compartment alone may not provide sufficient information on epidemiologic linkage, overall diversification of viral quasispecies, replacement of older strains and the emergence of new viral recombinant strains in vivo. These are the first analyses that demonstrate the incremental value of plasma derived sequences, when used in conjunction with PBMC-derived sequences, in establishing the epidemiologic linkage between individuals multiply exposed to HIV parenterally. Further, the plasma derived HIV-1 sequences may prove to be invaluable in predicting a recent transmission between two epidemiologically-linked individuals.

Molecular evidence for transmission of human T-lymphotropic virus type II infection by a human bite.

Investigation of a human T-lymphotropic virus type II (HTLV-II) infection in a female Australian blood donor identified a human bite as the likely mode of transmission, confirmed by nucleotide sequencing of the proviral tax/rex from both donor and contact. We believe this to be the first report of the transmission of an HTLV by a human bite.

Unique HIV type 1 V3 region sequences derived from six different regions of brain: region-specific evolution within host-determined quasispecies.

HIV type 1 viral quasispecies were amplified by polymerase chain reaction (PCR) in the hypervariable V3 region of gp120 from six different regions of the brain (right and left frontal; right and left parietal; and right and left occipital) and from the peripheral blood mononuclear cells (PBMCs) of a patient who died of AIDS dementia complex (ADC). Cloning and sequencing of the entire V3 region suggested the presence of genetically unique sequences in different regions of the brain. In contrast, the blood-derived viral quasispecies carried homogeneous sequences that were characterized by a single octapeptide crest motif (HLGPGSAF), a motif important in viral fusion. The brain-derived viral strains showed extensive sequence heterogeneity and the presence of seven different octapeptide and four different tetrapeptide crest motifs (HIGPGRAF, RIGPGRAF, HIGPGSAI, HLGPGSAF, HIGPESAI, HLGPESAI, and YLRPGSAF). In addition, the brain-derived strains were also characterized by variable net V3 loop charge and hydrophilicity, along with distinct amino acid changes specific to different brain regions. Together, the sequence and phylogenetic analyses are unique in identifying the complexity of a viral quasispecies and its independent regional evolution within the brain compartment. Uniquely divergent viral strains were identified in the frontal regions and their presence was further supported by the presence of multinucleated giant cells (characteristic of HIV encephalopathy) predominantly in the left and right frontal regions. In summary, these analyses suggest that genetically different populations of HIV-1 may be present in different brain compartments and confirm that specific neurotropic variants may exist.

HIV infection of macrophages and pathogenesis of AIDS dementia complex: interaction of the host cell and viral genotype.

AIDS dementia complex (ADC) develops in only a third of HIV-infected patients who progress to AIDS. Macrophages and microglial cells are the major cellular sites of productive HIV replication in brain. Using 11 blood isolates of HIV from asymptomatic patients there was marked variation in tropism and the level of productive infection in recently adherent monocytes and monocyte-derived macrophages cultured in vitro. However, less variation was seen with 19 blood isolates from advanced HIV infection and 11 postmortem tissue isolates from brain, cerebrospinal fluid, spleen, and lung. Newly adherent monocytes expressed CCR5 in all seven patients tested, consistent with their susceptibility to infection but not explaining the above variability. There is, also marked regional variability in neuropathology in the brain of patients with ADC. We have demonstrated that there was marked variation in the V3 sequences of HIV clones from different regions of the cortex of a patient with ADC, suggesting independent evolution of HIV replication in brain. Furthermore, production of the neurotoxin quinolinic acid from HIV-infected macrophages varied, depending on the host and source of HIV isolate. Hence variations in viral genotype, production by infected macrophages, and subsequent toxin production may contribute to the variability in neuropathology between individuals and between different regions of the brain in the same individual.

Molecular analyses of human immunodeficiency virus type 1 V3 region quasispecies derived from plasma and peripheral blood mononuclear cells of the first long-term-nonprogressing mother and child pair.

Molecular analyses were done for the V3 region quasispecies of human immunodeficiency virus type 1 (HIV-1) strains from plasma and peripheral blood mononuclear cells of the first HIV-1-infected long-term-nonprogressing mother-child pair whose members have survived for >13 years with stable CD4 T cell counts. There was a predominance of lower V3 loop charge and the absence of genotypic changes that are critical in phenotypic determination and tropism during HIV-1 infection. The intrahost genetic diversity between HIV-1 strains from the mother-child pair compared with HIV-1 strains from slow and rapid progressors suggested that a high genetic heterogeneity in HIV-1 strains from this HIV-1-infected long-term-nonprogressing mother and child pair was directly proportional to the length of their immunocompetent period.