Molecular epidemiology of HIV in Israel

On the origin of HIV-1 subtype C in South America

OBJECTIVE

Our aim was to investigate the monophyletic status of the HIV-1C that circulates in South America and its phylogenetic relationships with other HIV-1C populations around the world in order to shed light on its the geographic origins as well as the place of introduction in the continent.

METHODS

Fifty-one sequences from South America and 46 from non-South American countries, including samples from Africa and Asia, were obtained from the Los Alamos National Laboratory. The data analyzed corresponded to the entire protease and two-thirds of the polymerase domain from the reverse transcriptase. Phylogenetic analyses using maximum likelihood and Bayesian inference were performed in Phylogenetic Analysis Using Parsymony, PHYlogenetic inferences using Maximum Likelihood, and MrBayes.

RESULTS

Samples from South America formed a monophyletic group independent of the method used. The bootstrap support of South American HIV-1C was higher than 60% in maximum likelihood trees and its posterior probability was 99% in the Bayesian analysis. These results indicate the monophyletic nature of the South American HIV-1C. Moreover, in all trees estimated, a sequence from Kenya was the most closely related to the South American clade, followed by two from Ethiopia. All South American sequences from countries other than Brazil showed closer phylogenetic relatedness to Brazilian samples, indicating that HIV-1C was introduced in South America in Brazil.

CONCLUSION

Our results indicate that the entry of HIV-1C in South America occurred in a single episode or in multiples episodes of genetically related viruses, possibly from an eastern African country. HIV-1C was then disseminated to the remaining South American countries from Brazil.

Absence of HIV-associated nephropathy in Ethiopians

BACKGROUND

Population-based epidemiological surveys in several countries have shown approximately 10- to 15-fold increased susceptibility to human immunodeficiency virus (HIV)-associated nephropathy (HIVAN) for populations of recent African ancestry. Accordingly, we sought to determine whether a similar or different pattern of susceptibility was evident among Ethiopians followed up in an HIV clinic in Israel.

METHODS

One hundred seventy-six consecutive patients (126 Ethiopians, 50 non-Ethiopian Israelis) followed up at the HIV clinic of Rambam Medical Center in northern Israel were examined for the presence of proteinuria and/or decreased glomerular filtration rate. HIV viral load, CD4 count, and treatment modality also were determined.

RESULTS

Overall, 73% of patients were treated with highly active antiretroviral therapy, and there was no difference between Ethiopians and non-Ethiopian Israelis in this regard. Mean CD4 count in Ethiopians was 288 +/- 140/microL, significantly less than the corresponding CD4 count of 398 +/- 190/microL for non-Ethiopian Israelis. Mean viral loads were greater in Ethiopians compared with non-Ethiopian Israelis. None of 176 HIV-infected patients fulfilled clinical criteria for HIVAN as delineated in this study.

CONCLUSION

HIV-infected individuals of Ethiopian descent have a level of susceptibility to HIVAN similar to that of non-Ethiopian Israelis, which is strikingly less than that reported for other populations for recent African ancestry. This does not appear to be attributable to differences in HIV infection control or viral subtype and most likely represents population-based differences in host genetic factors. This finding emphasizes the importance of avoiding generalizations with respect to phylogeographic ancestry in disease-susceptibility studies.

Comparative performance of the Amplicor HIV-1 monitor assay versus NucliSens EasyQ in HIV subtype C-infected patients

In facing global programs for treating HIV-infected patients in the developing countries, there is a real need for viral load assays that are accurate for the local subtypes. The present study was designed to evaluate viral load measurements using the newer version of the NASBA assay in subtype C-infected patients. The performances of this new version, a real-time nucleic acid sequence-based amplification HIV-1 assay (NucliSens EasyQ), were compared to Amplicor HIV-1 Monitor Assay version 1.5 in 79 samples of subtype C-infected patients originating from Ethiopia. Twenty HIV-1 subtype B-infected patients served as a control group. Blood samples from patients in both groups were tested by both assays. The results were compared by a paired, two-tailed Student's t-test. The disparity between the results of the two viral load assays was highly significant in subtype C samples (P = 0.005), such that in the vast majority, higher values of viral load were obtained by the Amplicor assay. However, no differences between the two assays were found in subtype B samples (P = 0.77). CD4 measurements were available for 78 samples of subtype C-infected patients. Of these, a CD4-to-viral load discrepancy (CD4 <or= 200, viral load <or=5,000 IU/ml) was found in 11.5% of the samples when using the EasyQ assay, compared with 5.1% of the samples using the Amplicor assay. In conclusion, the performance of the NucliSens EasyQ assay was inferior to that of the Amplicor assay in assessing viral load levels in subtype C-infected patients. This difference may have a significant bearing on patient care.

Measurement of HIV RNA in patients infected by subtype C by assays optimized for subtype B results in an underestimation of the viral load

Quantitation assays of HIV-1 RNA used currently were designed and optimized for subtype B viruses. However, infection with non-B HIV viruses has become more common worldwide. Unfortunately, little information is available regarding the suitability of these assays for measurement of viral load in specific non-B subtypes. The performance of two commercial HIV-1 RNA quantitation assays was evaluated in 82 HIV subtype C-infected patients and in 43 HIV-1 subtype B-infected patients. Blood samples were tested by the Amplicor HIV-1 Monitor Assay, Version 1.5, and by the nucleic acid sequence-based amplification HIV-1 assay (NucliSens). The results were compared by using a paired, two-tailed Student's t-test; the difference between the assays was found to be significant only for subtype C. Discordant results (>0.5 log difference) between the two assays were detected in 39% of subtype C samples, compared to 23.2% of subtype B samples. In all cases in which a discordant result was detected, the lower results were obtained by the NucliSens assay. Discordant results between CD4 and viral load (CD4 < 200 cells/ml with a viral load <5,000 copies/ml) were observed in eight of the subtype C-infected patients when a viral load was measured by NucliSens (9.7%), compared to three patients (3.6%) when measured by the Amplicor assay. In conclusion, in patients with HIV subtype C infection, measurement of HIV RNA by the NucliSens assay resulted in a significant underestimation of the viral load as compared to the Amplicor assay. As a consequence, such an underestimation may result in sub-optimal care of patients infected with HIV subtype C.

Genotypic variation of HIV-1 reverse transcriptase and protease: comparative analysis of clade C and clade B

OBJECTIVE

To compare drug-resistant variants from untreated (naive) and treated patients infected with clade B or C virus.

METHODS

Consecutive samples (165) from patients throughout Israel were analyzed. All those in the treated group were failing highly active antiretroviral therapy.

RESULTS

There were 87 clade B (14 naive) and 78 clade C (20 naive) [corrected] with significant differences in the prevalence of known drug-resistance mutations between the clades: in naive patients in the protease region M36I 7% and 95% (P < 0.0001), K20R 0% and 27% (P = 0.063), A71V 18% and 0% (P = 0.063), M46I 0% and 13%, and V77I 18% and 0% (P = 0.063), respectively, and in the reverse transcriptase region A98G/S 0% and 20% (P = 0.12), respectively. Most clade C viruses also showed significant differences from clade B consensus sequence at additional protease sites: R41K 100%, H69K/Q 85%, L89M 95% and I93L 80% (P < 0.0001). There were also significant differences (P < 0.03 to < 0.0001) in treated patients in clades B and C: in the protease region L10I 40% and 12%, M36I 26% and 95%, L63P 67% and 40%, A71I 38% and 7%, G73I and V77I 18% and 0%, I84V 16% and 3%, and L90M 40% and 12%, respectively; in the reverse transcriptase M41L 41% and 17%, D67N 41% and12%, K70R 30% and 7%, T215Y 48% and 29%, K219Q 21% and 7%, and A98G/S 3% and 24%, respectively.

CONCLUSION

Significantly differences between clade B and C viruses may be associated with development of differing resistance patterns during therapy and may affect drug utility in patients infected with clade C.

Low levels of HIV-1 plasma viral load in patients infected with HIV-1 subtype b and advanced immunosuppression

OBJECTIVES

Some HIV-1 infected patients show low levels of viraemia despite having advanced immunosuppression. Cases with falsely undetectable viraemia by conventional PCR have been reported when patients were infected with non-B subtypes. The aim of this study was to investigate whether this immunovirological discordance can be due to the presence of HIV-1 non-B subtypes, and whether a modified PCR procedure can yield different HIV viraemia values in these cases.

METHODS

Fifteen HIV-infected patients either naive for antiretroviral drugs or under treatment, with HIV plasma viraemia below 1000 copies/mm(3)and CD4+ cell counts lesser than 500 or 300 cells/mm(3), respectively, were included. Serotyping, genotyping and HIV plasmatic viraemia determinations were performed in all individuals.

RESULTS

In five out of six treatment-naive patients the virus was categorized as non-B subtype by serotyping, although only one case was confirmed by genotyping as HIV-2. Eight out of nine patients under antiretroviral therapy were subtype B carriers by serotyping and confirmed by genotyping. The remaining patient was determined as a subtype A carrier by both procedures. A modified PCR procedure (Amplicor HIV Monitor Test version 1.5) did not yield higher viral load levels than the former version.

CONCLUSIONS

The presence of HIV-1 subtypes non-B can explain a minority of cases of this immunovirological discordance, but in most of them the reason is still unknown. Likewise, a PCR procedure adapted for detecting HIV-1 non-B subtypes fails to find higher plasma viraemia in patients with such a discordance.

Human immunodeficiency virus (HIV)-positive sera obtained shortly after seroconversion neutralize autologous HIV type 1 isolates on primary macrophages but not on lymphocytes

The aim of this study was to analyze the role of humoral immunity in early human immunodeficiency virus (HIV) infection. As neutralizing activities in HIV-positive sera are rarely detectable earlier than 9 to 12 months after infection using primary lymphocytes as target cells in neutralization assays, humoral immunity is generally thought not to contribute significantly to early virus control in the patients. Besides lymphocytes, cells of the monocyte/macrophage lineage are known to be important target cells for HIV in vivo during the establishment of the infection. Therefore, we studied the neutralization of early primary HIV isolates by autologous serum samples using primary macrophages as target cells in the neutralization assays. We analyzed neutralizing activities against the autologous HIV-1 isolates in 10 patients' sera taken shortly after seroconversion, both on primary macrophages and, for comparison, on lymphocytes. Viruses were isolated and expanded in primary mixed cultures containing macrophages and lymphocytes in order to avoid selection for one particular cell type. All viruses replicated to different degrees in macrophages and lymphocytes; nine had a nonsyncytium-inducing phenotype, and one was syncytium inducing. The detection of neutralizing antibodies in acute primary HIV infection depended on the target cells used. Confirming previous studies, we did not find neutralizing activities on lymphocytes at this early time point. In contrast, neutralizing activities were detectable in the same sera if primary macrophages were used as target cells. Differences in neutralizing activities on macrophages and lymphocytes were not due to different virus variants being present in the different cell systems, as gp120 sequences derived from both cell types were homogeneous. Neutralization activities on macrophages did not correlate with the amount of beta-chemokines in the sera. As affinity-purified immunoglobulin G preparations from an early patient serum also exhibited neutralization of the autologous virus isolate on primary macrophages, but not on lymphocytes, neutralization is very likely due to antibodies against viral epitopes necessary for infection of macrophages but not for infection of lymphocytes. Our data suggest that, along with cell-mediated immunity, humoral immunity may contribute to the reduction of primary viremia in the patient. This was further supported by a certain association between neutralizing antibody titers on macrophages and viral load in the patients.

Recombinant human immunodeficiency viruses type 1 circulating in Spain

The protease, reverse transcriptase (RT), and envelope (env) genes of human immunodeficiency virus type 1 (HIV-1) clinical isolates from 13 immigrants (mainly of African origin) living in Spain were examined. Phylogenetic analyses were performed, taking as reference a panel of 25 HIV-1 sequences representing various subtypes. A discrepant topology was recognized in comparing the protease, RT, and/or env phylogenetic trees in 10 isolates, in which sequences clustering in 2 or 3 different HIV-1 subtypes were found. In eight of these strains, the discrepant region was env with respect to concordant pol genes. Five of nine patients harboring subtype G sequences at the protease and RT genes showed discrepant env sequences, being subtype A (three) or B (two). In addition, one recombinant H/A strain, one recombinant H/B isolate, and a triple recombinant, A/D/C, variant were found. This work represents the first phylogenetic characterization of HIV-1 recombinant clinical isolates in Spain.

Silent mutation in the V3 region characteristic of HIV type 1 env subtype B strains from injecting drug users in the former Soviet Union

New independent states of the former Soviet Union are facing a rapidly growing epidemic of HIV-1 among injecting drug users (IDUs). This epidemic is caused by three HIV-1 populations, one belonging to HIV-1 subtype A (IDU-A), another to subtype B (IDU-B), and the third being a recombinant of the IDU-A and IDU-B viruses (IDU-A/B, gagA/envB). Each of these populations is characterized by a high level of genetic homogeneity. We identified a unique synonymous nucleotide substitution in the first isoleucine codon at the IHIGPGR motif (ATT), which was observed in the env subtype B V3 sequences derived from IDUs in Russia and the Ukraine. This substitution was observed in none of 179 sequences obtained from IDUs in western Europe, northern America, and Asia. Molecular epidemiological analysis of HIV-1 strains based on this sequence pattern could be useful for tracing the origin and spread of the IDU-B viruses to other countries and risk groups.

Serologic and genetic characterization of HIV type 1 subtypes on Reunion Island

The aim of this study was to determine the HIV subtypes present on Reunion Island, a French island located in the Indian Ocean, where the first case of AIDS was diagnosed in 1987. Paired sera and blood samples were collected between September 1996 and September 1997 from 53 HIV-1-positive patients. Subtyping was performed by serotyping with a previously described subtype-specific enzyme immunoassay (SSEIA) and by genotyping with the heteroduplex mobility assay (HMA). When samples gave uninterpretable results with either of the methods, or discordant results, the V3 env region was sequenced and genetic subtypes were determined by phylogenetic analysis. Genetic subtyping showed that 48 of 53 patients were infected with HIV-1 subtype B (90.5%). This high prevalence of subtype B on Reunion Island is probably due to the regular exchanges with metropolitan France. The other five patients were infected with subtype A (9.5%); they had been directly linked to African populations. Of the 48 subtype B samples, 44 (91.7%) were correctly subtyped by SSEIA and 43 (89.6%) by HMA. However, the SSEIA did not allow the subtyping of A strains in three of five patients. Thus, the SSEIA could be an alternative routine technique for screening subtype B versus nonsubtype B HIV-1 strains.

Selection of HIV-1 genotypes by cultivation in different primary cells

OBJECTIVES

To determine the representation of particular HIV-1 genotypes during cultivation in different primary cell-culture systems compared with the spectrum of the quasispecies in vivo.

METHODS

Primary isolates of HIV-1 were recovered by isolation in cultures of lymphocytes, mixed mononuclear cells (MNC), and monocytes/macrophages. Nucleotide sequence determination of the C2-V3 region of gp120 of HIV was performed on 10-20 independently isolated clones derived by polymerase chain reaction from the culture systems, the uncultured peripheral blood MNC (PBMC) as well as plasma.

RESULTS

Several predominant HIV genotypes were found in the uncultured PBMC from each of the patients. The most frequent genotypes in PBMC were also the most frequent types in plasma. In addition, lymphocytes, macrophages or mixed MNC cultures allowed the outgrowth of variants that were underrepresented in uncultured PBMC. We showed that the virus cultivation systems used in this study selected differently for the genetic variants. Whereas some genotypes were present in all three culture systems, although at different frequencies, others were exclusively found in a specific culture system.

CONCLUSIONS

These results demonstrate that monocyte/macrophage and mixed MNC culture systems complement the standard lymphocyte culture in terms of the spectrum of genotypically different virus variants obtained in vitro.

HIV type 1 V3 serotyping of Tanzanian samples: probable reasons for mismatching with genetic subtyping

HIV-1 V3 serotyping is used to classify immunodeficiency viruses on the basis of antibody binding to V3 peptides derived from env genetic subtypes. Although it shows a reasonable overlap, it has been reported to be distinct from viral genetic subtypes. The aim of this study is to determine the feasibility of HIV-1 serotyping to predict genetic subtypes in an East African setting, where multiple HIV-1 subtypes have coexisted for many years. HIV-1 genetic subtypes of 86 AIDS patients in Mbeya Town, southwest Tanzania, were determined, using env nucleic acid sequencing as the basis for comparison. Those data were compared with V3 serotyping results obtained by four different methodologies. Four HIV-1 genetic subtypes were identified, including A (25, 29%), C (47, 55%), D (13, 15%), and G (1, 1%). The sensitivity and specificity of those serotyping assays varied considerably: sensitivity for genetic subtype A (40-48%), C (52-96%), and D (9-31%); and specificity for genetic subtype A (77-95%), C (46-63%), and D (97-100%). We further tried to identify reasons for the discrepancies between serotyping results and genetic subtypes. By means of logistic regression analysis three amino acid residues within the V3 loop (positions 12, 13, and 19; V, H, and A for serotype A, I, R, and T for serotype C) were found to be most important for antibody binding; a deviation from the subtype-specific amino acids was highly related to mismatched results. In addition, we have shown that phenetic analysis of V3 amino acid sequence data could be used to predict the majority of V3 serotypes (93-94%). Our data demonstrated that for the majority of specimens HIV-1 V3 serotyping results closely match the subtype of the analyzed sample as revealed by the V3 loop amino acid sequence. However, our data demonstrate that HIV-1 serotyping is not sufficiently accurate to predict genetic subtypes in Tanzania, where subtypes A, C, D, and G are circulating. This was due to highly similar amino acid sequences throughout the prevalent genetic subtypes, which caused the inability of HIV-1 V3 serotyping to differentiate subtype A from C as well as D from C. Instead, the serotyping results reflect the frequency distribution of V3 serotypes. To investigate HIV-1 genetic subtypes in population-based studies in this African setting additional or modified algorithms are needed.