Multivariate analysis of human immunodeficiency virus type 1 neutralization data

We report on the use of spectral map analysis of the inter- and intraclade neutralization data of 14 sera of human immunodeficiency virus type 1 (HIV-1)-infected individuals and 16 primary isolates, representing genetic clades A to H in group M and group O. This multivariate analysis has been used previously to study the interaction between drugs and receptors and between viruses and antiviral compounds. The analysis reveals the existence of neutralization clusters, not correlated with the known genetic clades. The structural factors that have been identified may correlate with the most important neutralization epitopes. Three key primary HIV-1 isolates, which allow discrimination of sera that are likely or unlikely to neutralize primary isolates from most of the genetic clades, were identified. Our method of analysis will facilitate the evaluation as well as the design of suitable HIV-1 vaccines, which induce high-titer interclade cross-neutralizing antibodies.

Isolation of HIV-1 RNA from plasma: evaluation of eight different extraction methods

The efficacy of eight different methods for the extraction of HIV-1 RNA from plasma was compared. The RNA preparation method that gave the best results by RT-PCR was the one described by Chomczynski and Sacchi (1987, Anal. Biochem. 162, 156-159). This method consists of a guanidine thiocyanate treatment followed by three phenol-chloroform-isoamylalcohol extractions and an ethanol precipitation. The disadvantage of this method is that it is time consuming and less suitable for the extraction of large series of samples. Moreover, due to the large number of procedural steps, there is a greater risk of sample mix-up or contamination. Of the single-step RNA purification methods, good results were obtained with the TRIzol method (Gibco Life Technologies, Paisley, UK) and with the extraction method offered by the NASBA kit (Organon Teknika, Turnhout, Belgium). The above single-step methods are recommended since both are sensitive enough to detect low copy numbers of HIV-RNA in the plasma of asymptomatic patients, and require only 2 h for completion. For most of the methods evaluated the inter-test variability was acceptable (mean variation coefficient between duplicate extraction varied between 17.3 and 47.3%). Inter-laboratory reproducibility was evaluated only for the TRIzol-method and found to be low (mean variation coefficient 63.4).

Epidemiological and molecular characteristics of HIV infection in Gabon, 1986-1994

OBJECTIVE

To describe trends in the prevalence of HIV-1 infection in different populations in Gabon, and the molecular characteristics of circulating HIV strains.

METHODS

Data were collected on HIV prevalence through sentinel surveillance surveys in different populations in Libreville (the capital) and in Franceville. In Libreville, a total of 7082 individuals (hospitalized patients, tuberculosis patients, pregnant women, asymptomatic adults, prisoners) were recruited between 1986 and 1994. In Franceville, we tested 771 pregnant women and 886 healthy asymptomatic adults (1986-1988). Sera were screened for HIV antibodies by enzyme-linked immunosorbent assay (ELISA) and confirmed by Western blot or line immunoassay (LIA). Reactive samples in ELISA were tested for the presence of antibodies to HIV-1 group O viruses by ELISA using V3 peptides from HIV-1 ANT-70 and HIV-1 MVP-5180 followed by confirmation by LIA and a specific Western blot. Seventeen HIV-1 strains were isolated (1988-1993) and a 900 base-pair fragment encoding the env region containing V3, V4, V5 and beginning of gp41 was sequenced and a phylogenetic tree was constructed.

RESULTS

HIV prevalence was relatively low and remained stable (0.7-1.6% in pregnant women, 2.1-2.2% in the general population). The prevalence was also stable among prisoners (2.1-2.6%). Among hospitalized and tuberculosis patients prevalence was higher and increased (1.8-12.7% and 1.5-16.2%, respectively). Only three sera had antibodies to HIV-1 group O. The 17 HIV-1 strains represent six different genetic subtypes including type O.

CONCLUSION

Our data from 1986 to 1994 show a stable and low HIV prevalence in Gabon, and a high genetic diversity of HIV-1 strains. This, also observed in Cameroon, is in contrast to that found elsewhere in Africa. Differences in rate of spread of HIV infection are probably explained by interplay between numerous factors. The role of different HIV subtypes in the dynamics of the HIV epidemic should be examined further.

Evaluation and comparison of the Amplicor HIV-1 PCR kit with an ‘in-house’ nested PCR

BACKGROUND

The polymerase chain reaction (PCR), a powerful gene amplification technique, is moving rapidly from the research laboratory into routine clinical use.

OBJECTIVES

To evaluate the specificity and sensitivity of a commercially available PCR kit, the Amplicor HIV-1 PCR kit (AMP) and to compare it with an in-house nested PCR, which amplified part of the POL gene (POL(n)).

STUDY DESIGN

A total of 517 samples were tested by AMP, including 159 fresh whole blood specimens from HIV-1 antibody positive Europeans and 358 archival samples (338 seropositive and 20 seronegative individuals) originating from 35 different countries in Africa and Europe. We compared the performance of AMP on the archival samples with POL(n).

RESULTS

The overall sensitivity and specificity as compared to HIV-1 serology were 93% and 100%, and 96% and 100%, for AMP and the in-house PCR, respectively. Repeat testing on co-cultured lymphocytes increased the sensitivity of AMP to 95%.

CONCLUSIONS

AMP is a rapid, and easy to use commercially available PCR kit, since only one amplification of the test sample is required. Moreover, the use of radioactivity is omitted, and reading of the test can be done with a spectrophotometer. The use of at least one additional primer pair may increase confidence in distinguishing a positive and negative sample by both PCR techniques.

Biological phenotypes of HIV-1 subtypes A and B strains of diverse origins

The identification of specific biologic phenotypic traits that can be correlated with different HIV-1 genetic subtypes was sought. The genetic subtypes were determined by either sequencing (Cameroonian strains, n = 18) or by the heteroduplex mobility assay (HMA) (Belgian strains, n = 21 and Ivorian strains, n = 25). Seventeen (81%) of the 21 Belgian isolates belonged to subtype B and 4 (17%) were subtype A strains. Subtype A variants were predominant in the two African countries studied; 11 (61%) of 18 strains from Cameroon and 23 (92%) of 25 strains from the Ivory Coast. Of the 64 isolates, 38 (58%) and 19 (29%) belonged to subtypes A and B, respectively. No significant difference was observed for biological phenotypes (slow/low and rapid/high) of both genetic subtypes. In symptomatic individuals, however, a significantly higher number of subtype B isolates were of rapid/high phenotype, compared with subtype A (5 of 10; 50%) vs. 2 of 22; 9%), respectively; X2 = 6.7, P = 0.02). The findings suggest that overall HIV-1 isolates belonging to genetic subtype B are not distinguishable from subtype A variants on the basis of their biological phenotypes. Syncytium-inducing variants were less prevalent regardless of the geographic origin of the isolates.

Reduced capacity of antibodies from patients infected with human immunodeficiency virus type 1 (HIV-1) group O to neutralize primary isolates of HIV-1 group M viruses

Neutralizing antibody patterns in sera of persons infected with human immunodeficiency virus type 1 (HIV-1) groups M and O to their homologous and heterologous primary isolates were determined in a peripheral blood mononuclear cell-based neutralization assay and correlated with their ability to bind to V3 loop synthetic peptides. Most HIV-1 group M sera (9/16) neutralized HIV-1 group O viruses, whereas fewer group O sera (3/13) only weakly neutralized HIV-1 group M viruses. Group M sera neutralizing HIV-1 group O viruses neutralized other HIV-1 group M viruses with titers of 1:10-1:1280. V3 loop binding capacity of sera did not reflect their neutralizing capacity of the homologous isolate. Despite the reduced neutralizing capacity of group O-infected patients' sera to group M viruses, some group M-infected patients' sera neutralized both HIV-1 group M and O isolates, suggesting that they share some conserved neutralizing epitopes.

Virologic and serologic characteristics of a natural chimpanzee lentivirus infection

This study set out to characterize the unique features of natural lentivirus infection in chimpanzees over time. The virologic and serologic characteristics of this infection were followed longitudinally in a naturally infected chimpanzee together with a small cohort of experimentally HIV-1-infected chimpanzees. The subsequent isolates from the naturally infected chimpanzee were all non-syncytium forming (NSI) versus syncytium forming in the experimentally infected animals. In contrast to HIV-1-infected chimpanzees virus load was higher and plasma viremia occurred but in a cyclic pattern. Serologic follow-up suggested the development of neutralizing antibodies with subsequent escape of new isolates. Interestingly, the sequence of the principal neutralizing (V3 loop) domain (of HIV-1) remained constant over time. Antibodies to peptides from the V3 loop were type specific. The occurrence of persistent, fluctuating plasma viremia and NSI-type virus variants of this natural lentivirus infection are unique characteristics not previously reported in experimentally infected chimpanzees.

Detection of HIV-1 RNA in plasma and serum samples using the NASBA amplification system compared to RNA-PCR

The presence of HIV-1 RNA in the plasma and serum of European and African patients was monitored using RNA-polymerase chain reaction (RNA-PCR) and the new isothermal NASBA nucleic acid amplification system encompassing a gel-based detection assay (ELGA). Identical RNA extraction procedures, provided by the NASBA amplification system, were used for both methods. The detection limit for HIV-1 RNA, measured on a 10-fold dilution series of spiked HIVIIIB in negative plasma, was about 0.05 CCID50 per test for both methods. Both NASBA and RNA-PCR were more sensitive than a p24 assay for the detection of circulating HIV-1 virus in blood: 17 of the 34 (50%) p24 antigen-tested seropositives were p24-positive while 32 (94%) were positive by NASBA and 30 (88%) by RNA-PCR. Among the 45 seropositives, 34 of which were tested for p24 antigen, 43 (96%) were positive by NASBA and 41 (91%) by RNA-PCR. Almost all seropositives had a detectable viral load in 100 microliters plasma. Lower viral loads were only encountered in some healthy seropositives with a higher CD4 count. There was no cross-reactivity with HIV-2 or HIV-I with both the RNA-PCR and NASBA. The extraction method used permitted the detection of HIV-1 RNA equally well in serum and in plasma with heparin or EDTA.

Standardisation of primers and an algorithm for HIV-1 diagnostic PCR evaluated in patients harbouring strains of diverse geographical origin. The Belgian AIDS Reference Laboratories

Eight Belgian AIDS Reference Laboratories established a multicentre quality control to evaluate the performance of their diagnostic human immunodeficiency virus type 1 (HIV-1) DNA polymerase chain reaction (PCR). A set of Belgian and African HIV-1 seropositive and seronegative patient samples, collected in Belgium, and the British Medical Research Council (MRC) HIV-1 PCR reference reagent kit, containing plasmid HIV-1 DNA at several dilutions in human carrier DNA with appropriate negative controls, were tested by the laboratories. No false positive results were reported. All laboratories were able to detect one to two copies of HIV-1 DNA. Among the 17 Belgian and African HIV-1 seropositives, some laboratories reported up to four indeterminate results, mainly due to failure of the SK38-39, SK68-69 (Ou et al. (1988) Science 239, 295-297) and/or gag881-882 (Simmonds et al. (1990) J. Virol. 64, 864-872) primers and a poorly performing algorithm. Only the H1POL4235-4538 nested pol primer set, developed by one of the laboratories, correctly identified all the tested HIV-1 positive and negative samples. Consequently, the laboratories decided to evaluate these pol primers as a reference primer set and to standardise the testing algorithm. All laboratories achieved a sensitivity and specificity of 100% on testing 10 additional Belgian and African patient samples, when adapting a standardised algorithm based on three HIV-1 primer sets, one of which is the H1POL4235-4538 primer set.

Risk factors for mother-to-child transmission of human immunodeficiency virus-1 infection

OBJECTIVE

Our aim was to examine maternal, obstetric, and infant characteristics of mother-to-child transmission of human immunodeficiency virus-1 in Nairobi, Kenya.

STUDY DESIGN

Proviral human immunodeficiency virus-1 was detected by polymerase chain reaction in peripheral blood samples taken between 6 weeks and 3 months of age from 107 children born to human immunodeficiency virus-1 seropositive women. The association of maternal, infant, and obstetric variables with human immunodeficiency virus-1 transmission was examined.

RESULTS

The mother-to-child transmission rate was 31% (95% confidence interval 21.6 to 40.2) as defined by the presence of proviral human immunodeficiency virus-1 in the infant. Variables associated with transmission in a univariate analysis included placental inflammation (7/12 in the transmitting group as compared with 2/22 in nontransmitters, p = 0.006), low maternal CD4 and high CD8 percentages (21% and 52%, respectively, in transmitting mothers and 32% and 40% in nontransmitting mothers; p = 0.001), and the gender of the neonate (20/29 infected neonates were female as compared with 26/65 noninfected children, p = 0.02). Sexually transmitted diseases were found more often in transmitting mothers but the differences were not significant. Birth weight and gestational age were not related to vertical transmission of human immunodeficiency virus-1.

CONCLUSION

Risk factors for mother-to-child transmission of human immunodeficiency virus-1 included chorioamnionitis, an impaired maternal immune status, and female gender.

Correlation between genetic and biological properties of biologically cloned HIV type 1 viruses representing subtypes A, B, and D

The relationship between the genetic variability in the V3 loop and the biological characteristics of 38 biological clones from 5 European and 7 African HIV-1 isolates belonging to 3 different subtypes (subtype A, B, and D) was investigated. Seventeen of 19 clones displaying a syncytium-inducing (SI) capacity had a positively charged amino acid located at position 11 and/or 25 in the V3 loop sequence. All 19 non-syncytium-inducing (NSI) virus clones lacked such a positive charge at the same positions (p < 0.001). The mean of net charge in the overall V3 loop sequences of the SI clones was higher than that of the NSI clones (p < 0.001). Within the same strains, the SI clones replicated faster/higher than the NSI clones in peripheral blood mononuclear cells (p < 0.01), but not in CD4+ T cell cultures (p > 0.1). All SI clones but only 5 of 19 NSI clones could replicate in human continuous T cell and monocytic cell lines (p < 0.001). A higher number of positively charged amino acid substitutions was found among the subtype D SI clones. Only one of eight autologous sera tested had the ability to neutralize the contemporaneously isolated NSI clones, but not the SI clones. This study indicates that the V3 loop amino acid sequences of HIV-1 biological clones from different origins belonging to different genetic subtypes are clearly correlated with viral syncytium-inducing capacity, cell tropism, and replication rate.

Detection of human immunodeficiency virus type 1 (HIV-1) in heel prick blood on filter paper from children born to HIV-1-seropositive mothers

The human immunodeficiency virus type 1 (HIV-1) DNA PCR results of 94 dried blood spot (DBS) samples on filter paper and corresponding venous blood in EDTA obtained from infants born to HIV-1-seropositive mothers were compared. In addition, the results of HIV-1 DNA PCR on DBS and the HIV-1 RNA PCR from plasma of 70 paired samples were compared. A 100% specificity and a 95% sensitivity for HIV-1 DNA PCR on DBS compared with results for venous blood were observed for the 94 paired samples. The results of the DBS HIV-1 DNA PCR and HIV-1 RNA PCR of 70 corresponding plasma samples correlated perfectly (100%). The DBS HIV-1 DNA PCR method proved reliable for HIV-1 detection.

Genotypic subtypes of HIV-1 in Cameroon

OBJECTIVE

The only two HIV-1 strains (ANT70 and MVP5180) reported to date from Cameroon are members of the outlier clade (group O). In this study, we assessed the prevalence of group O viruses and other HIV-1 subtypes in Cameroon.

DESIGN

A phylogenetic analysis of 18 HIV-1 strains isolated from seropositive individuals from Yaoundé and Douala, Cameroon.

METHODS

A 900 base-pair fragment of the env gene coding for V3, V4, V5, and the beginning of gp41 of 17 out of 18 HIV-1 isolates from Cameroon was amplified, cloned and sequenced using polymerase chain reaction. A phylogenetic tree was constructed.

RESULTS

The overall env nucleotide sequence divergence among the Cameroon isolates ranged from 6.1 to 27.5%. In a phylogenetic tree, six subtypes were identified when compared with 23 reference strains of different geographic origin. Of these 17 Cameroonian strains, 11 (61%) were of subtype A of which the interpatient distances at the sequence level varied from 6.1% to 18.3% (average, 11.9%). Three (17%) strains were of subtype F, and the other three strains (6% each) belonged to subtypes B, E and H, respectively. The remaining isolate was classified as belonging to group O, on the basis of the sequence of part of the pol gene. A very broad spectrum of different tetrameric amino-acid sequences was observed at the apex of the V3 loop. Eleven strains contained the tetrameric globally predominant GPGQ sequence at the tip of the V3 motif. Two strains had the GPGR sequence typical of the American and European HIV-1 strains. The remaining tetrameric sequences included GPGS, GSGQ, GRGQ, and GLGR.

CONCLUSION

These findings on a limited number of viruses suggest extensive env gene diversity of HIV-1 strains from Cameroon, and could have implications for vaccine development in Africa.

Isolation of simian immunodeficiency viruses from two sooty mangabeys in Côte d'Ivoire: virological and genetic characterization and relationship to other HIV type 2 and SIVsm/mac strains

OBJECTIVE

To search for the presence of SIV in sooty mangabeys and other monkey species in Côte d'Ivoire, West Africa, and to compare viral isolates with HIV-2 strains from the same region.

METHODS

Forty-three captive housed monkeys (28 African green monkeys, 6 sooty mangabeys, 6 baboons, and 6 patas monkeys) were tested for the presence of HIV and SIV antibodies. Virus was isolated from the peripheral blood lymphocytes of seropositive animals and from HIV-2 antibody-positive patients originating from Côte d'Ivoire, Ghana, Senegal, and Belgium. Viruses were characterized by Western blot and radioimmunoprecipitation assay. Proviral DNA was amplified by PCR, cloned, and sequenced to construct a phylogenetic tree.

RESULTS

One African green monkey and three sooty mangabeys had antibodies that cross-reacted with HIV-2. From two mangabeys lentiviruses were isolated and designated as SIVsmCI2 and SIVsmCI8. Serological, virological, and sequence data showed that these isolates are members of the HIV-2/SIVsm/SIVmac group of primate lentiviruses. Furthermore, in the phylogenetic tree, these two new viruses form a distinct subgroup that is equidistant to the HIV-2 strains and the previously described SIVsm/SIVmac viruses.

CONCLUSION

This study provides additional evidence that sooty mangabey monkeys can be infected with a lentivirus in their natural habitat. Within the SIVsm and SIVmac viruses extensive genetic variation is observed.

Genetic and antigenic variability of HIV type 1 in Brazil

Six Brazilian strains of human immunodeficiency virus type 1 (HIV-1) were isolated from infected individuals residing in different regions of Brazil between 1987 and 1989. Phylogenetic analysis based on an 860-base pair env fragment, including V3, V4, V5, and the beginning of gp41, classified the Brazilian strains significantly in genotype B, with interhost distances between 5.9 and 13.1% (mean value, 10%). Amino acid sequence analysis of the V3 loop revealed that three strains contained the North American/European GPGR motif as the tip of the loop whereas in the other three strains proline (P) was substituted by tryptophan (W), methionine (M), or phenylalanine (F). A consensus peptide, Bra-cons, was designed containing GWGR as the tip of the loop. Serological reactivity to the Bra-cons peptide and other V3 peptides (MN, SF2, HBX2, RF, MAL, ELI, Z6, and a Côte d'Ivoire peptide, CI-cons) was compared for 114 HIV-1-positive sera from Rio de Janeiro. Sixty-nine sera (60.5%) reacted with peptides belonging to genotype B, of which 10 sera also reacted with peptides belonging to genotype A (n = 7) and D (n = 3). Eighteen sera (15.8%) had binding antibodies to the Bra-cons peptide. A high number of sera (n = 43; 37.7%) had no antibodies to any of the V3 peptides tested. This result suggests that HIV-1 variants with aberrant V3 loops may circulate in Rio de Janeiro.

Design and evaluation of new, highly sensitive and specific primers for polymerase chain reaction detection of HIV-1 infected primary lymphocytes

Primer pairs in the HIV-1 POL and ENV genes were evaluated by performing a PCR on lysed peripheral blood mononuclear cells (PBMCs) from 96 HIV-1 seropositive and 40 seronegative individuals originating from 16 different geographical localities in Africa, Europe and Haiti. A single PCR using primer pairs to the LTR, GAG and ENV regions and detection by radioactively labelled oligonucleotide probes was compared to a nested PCR scheme using newly designed POL and ENV primers which used ethidium-bromide staining of the amplified product on agarose gel. The newly designed POL nested primer pair was shown to be highly sensitive (93%) and specific (100%) for the detection of HIV-1 proviral DNA of very diverse geographical and genetic origin, including highly aberrant HIV-1 isolates. The sensitivity of the newly designed ENV primers was 68.7%, which does not differ significantly from the sensitivity of the classical primers, SK 68/69. Both ENV primers were unable to amplify two SIVcpz isolates from naturally infected chimpanzees.

Cross-neutralizing antibodies to HIV-1ANT70 and HIV-1IIIB in sera of African and Belgian HIV-1-infected individuals

OBJECTIVES

To determine the neutralizing antibody patterns to HIV-1ANT70 (ANT70) and HIV-1IIIB (IIIB) in human sera obtained from HIV-1-infected individuals from different African countries and Belgium. Second, to correlate the presence of neutralizing antibodies in sera and their ability to bind to synthetic peptides derived from eight different HIV-1 V3 loop sequences.

DESIGN AND METHODS

Forty sera from Belgium and 88 obtained from seven countries in Africa were tested for their ability to neutralize ANT70 (one of the most genetically divergent HIV-1 isolates documented), and IIIB. Sera found to cross-neutralize both viruses were further challenged with four HIV-1 field isolates. All sera were tested on a panel of V3 loop peptides obtained from different HIV-1 genotypes.

RESULTS

Four patterns of sera were identified, including 33 (26%) sera not neutralizing any of the isolates, seven (5%) sera neutralizing only ANT70, 45 (35%) sera neutralizing only IIIB, and 43 (34%) sera cross-neutralizing both isolates. Sera capable of cross-neutralizing both ANT70 and IIIB consistently neutralized other field isolates tested, with a remarkable similarity in neutralizing antibody titre. A significantly higher number of sera cross-neutralizing both ANT70 and IIIB compared with sera lacking neutralizing antibodies, reacted simultaneously in enzyme-linked immunosorbent assays (ELISA) with three or more V3 loop peptides belonging to HIV-1 strains of different genotypes. However, none of the sera cross-neutralizing ANT70 and IIIB were reactive in ELISA with the ANT70 V3 loop peptide.

CONCLUSION

These results suggest that despite pronounced genomic variation of the HIV-1ANT70 isolate, there are strongly conserved neutralizing epitopes situated outside the V3 loop that are shared by other HIV-1 isolates. These findings suggest that genetic variation might be surmountable in the design of a polyvalent HIV vaccine, if neutralizing antibodies are found to be correlates of protection in HIV infection.

Quantification of human immunodeficiency virus in plasma by RNA PCR, viral culture, and p24 antigen detection

A semiquantitative PCR technique for detecting human immunodeficiency virus type 1 (HIV-1) RNA in plasma was compared with quantitative viral culture and p24 antigen detection in plasma. Ninety-three samples from 20 symptomatic, 10 asymptomatic, and 10 seronegative individuals were tested. For most of the seropositive patients, consecutives samples were examined. Viral RNA was extracted from plasma by the method described by Boom et al. (R. Boom, C.J. A. Sol, M. M. M. Salimans, C.L. Jansen, P. M. E. Wertheim-van Dillen, and J. van der Noordaa, J. Clin. Microbiol. 28:495-503, 1990). The RNA PCR was the most sensitive method (100 and 74% sensitivity for symptomatic and asymptomatic patients, respectively) and produced less divergent results with the consecutive samples from individual patients compared with the other techniques. All samples positive by viral culture or p24 antigen assay were also positive in the RNA PCR. For each of the three assays, the number of positive results obtained correlated with the disease stage. The estimated mean number of HIV-1 RNA copies was significantly higher in symptomatic patients (22,750 copies per ml) than in asymptomatic patients (1,820 copies per ml). It was also higher in samples positive for viral culture than in culture-negative samples. No close correlation was found between the amount of HIV-1 RNA and the amount of p24 antigen or the titer of infectious virus in plasma or between this titer and the level of p24 antigen. The plasma RNA PCR may be a useful additional marker of disease progression and may be valuable for monitoring the effects of antiviral therapy.

Effect of methodology on detection of HIV-1/HIV-2 dual infections in Côte d'Ivoire

Dual seroreactivity to the human immunodeficiency virus (HIV) types 1 and 2 is common in Côte d'Ivoire. To assess whether dual infection is the reason for dual seroreactivity, different methods for detection of HIV-1 and HIV-2 viruses were compared. PCR on primary uncultured lymphocytes of 56 dually seropositive samples revealed the presence of both HIV-1 and HIV-2 proviral DNA in 23 (41%) cases. In 7 other dual seropositive persons, PCR was carried out on the primary lymphocytes as well as on lymphocytes after 3 and 6 weeks of cocultivation. More cultures, 5/7 (71%), were positive for both viruses at 3 weeks compared to 0/7 at 6 weeks post cultivation. Moreover, 2 out of 3 samples, where only HIV-1 was detected in uncultured cells, were positive for both viruses after 3 weeks of cultivation. These data indicate that the sensitivity of HIV-2 detection can be increased by stimulation of patients' lymphocytes. A higher number of dual seropositive individuals (10/23 (48%)) had antibodies able to neutralize simultaneously both HIV-1 and HIV-2 prototype viruses than did HIV-1 antibody-positive sera (5/21 (24%)) or HIV-2 antibody positive sera (3/18 (17%)). The prevalence of dual seropositives being infected with both viruses is highly dependent on the method used to detect infection. There is a need to standardize virological markers in order to gain a better insight into the relative proportions of HIV-1, HIV-2 and HIV-1/HIV-2 dually infected persons.

Molecular phylogeny of part of the env gene of HIV-1 strains isolated in Côte d'Ivoire

OBJECTIVES

To examine the genetic variation of HIV-1 isolates in Abidjan, Côte d'Ivoire, and to determine the extent to which phylogenetic trees based on sequence information of part of the env gene containing the principal neutralizing domain are representative for documenting genetic variability.

DESIGN

Phylogenetic comparison of 13 HIV-1 strains isolated from patients in Abidjan with previously documented HIV-1 strains of different geographic origin.

METHODS

To sequence a 900 base-pair fragment of the env gene containing V3, V4, V5 and the beginning of gp41 of three to four clones per isolate. Phylogenetic tree analysis was performed with the software package TREECON.

RESULTS

Eleven HIV-1 isolates of Abidjan were classified as genotype A, while two were classed as genotypes B and D. Intra-genotype A distances at the nucleotide level were a maximum of 14.1%. Inter-genotype distances between genotype A and genotypes B, C, and D varied from 16.0 to 22.6%. Phylogenetic trees, based on sequence data of a 300 base-pair fragment containing the V3 loop, showed significant differences in tree topology and statistical confidence with phylogenetic trees based on sequence data of the 900 base-pair env fragment.

CONCLUSIONS

Genotype A Côte d'Ivoire HIV-1 strains, which comprise 11 out of 13 isolates, predominate in Abidjan, which may indicate a local burst of particular variants. Phylogenetic trees should be interpreted with caution when based on a more limited number of nucleotides, such as the V3 region.

Phylogenetic analysis of gag genes from 70 international HIV-1 isolates provides evidence for multiple genotypes

OBJECTIVE

To determine the extent of genetic variation among internationally collected HIV-1 isolates, to analyse phylogenetic relationships and the geographic distribution of different variants.

DESIGN

Phylogenetic comparison of 70 HIV-1 isolates collected in 15 countries on four continents.

METHODS

To sequence the complete gag genome of HIV-1 isolates, build multiple sequence alignments and construct phylogenetic trees using distance matrix methods and maximum parsimony algorithms.

RESULTS

Phylogenetic tree analysis identified seven distinct genotypes. The seven genotypes were evident by both distance matrix methods and maximum parsimony analysis, and were strongly supported by bootstrap resampling of the data. The intra-genotypic gag distances averaged 7%, whereas the inter-genotypic distances averaged 14%. The geographic distribution of variants was complex. Some genotypes have apparently migrated to several continents and many areas harbor a mixture of genotypes. Related variants may cluster in certain areas, particularly isolates from a single city collected over a short time.

CONCLUSIONS

The genetic variation among HIV-1 isolates is more extensive than previously appreciated. At least seven distinct HIV-1 genotypes can be identified. Diversification, migration and establishment of local, temporal 'blooms' of particular variants may all occur concomitantly.

Virological and polymerase chain reaction studies of HIV-1/HIV-2 dual infection in Côte d'Ivoire

Dual serological reactivity to the human immunodeficiency virus (HIV) types 1 and 2 is common in Côte d'Ivoire. To assess whether dual infection is the reason for dual seropositivity we sought HIV-1 and HIV-2 proviral DNA in primary uncultured peripheral blood mononuclear cells from selected seropositive patients in Côte d'Ivoire with the polymerase chain reaction (PCR). PCR on primary lymphocytes in 36 dually seropositive samples revealed the presence of both HIV-1 and HIV-2 proviral DNA in 12 cases and the presence of HIV-1 only in 24 cases. In 18 of these 36 samples a virus was isolated and identified by PCR. HIV-1 was isolated from the 9 specimens with only HIV-1 proviral DNA in the primary lymphocytes. Among dually PCR-positive samples, 2 viral isolates reacted with both HIV-1 and HIV-2 primers; and only HIV-2 (n = 1) or HIV-1 (n = 6) strains were isolated from the other samples. The findings show that surveys based on serology may overestimate the prevalence of mixed infections in areas where both HIV-1 and HIV-2 occur.

Isolation and characterization of a new chimpanzee lentivirus (simian immunodeficiency virus isolate cpz-ant) from a wild-captured chimpanzee

OBJECTIVE

To assess the prevalence of infection with simian immunodeficiency virus (SIV) isolate cpz, a lentivirus closely related to HIV-1, in chimpanzees, and to obtain new SIVcpz isolates.

METHODS

Forty-four wild-captured chimpanzees in Belgium and Côte d'Ivoire were tested for HIV and SIV antibodies. Virus was isolated from the peripheral blood lymphocytes of positive animals and characterized by electron microscopy, Western blot and radioimmunoprecipitation assay.

RESULTS

One animal had antibodies that cross-reacted with HIV-1. A lentivirus was isolated and referred to as SIVcpz-ant. With regard to molecular weight patterns, SIVcpz-ant differs from SIVcpz-gab' an HIV-1-related virus isolated from a wild-captured chimpanzee in Gabon. The major core protein, the transmembrane and outer membrane glycoproteins of the SIVcpz-ant strain consistently had higher molecular weights. Significantly more HIV-1-positive sera reacted with the envelope proteins of the Gabonese SIVcpz-gab strain than with the SIVcpz-ant strain.

CONCLUSIONS

This study shows that natural infection of wild-captured chimpanzees with an HIV-related virus may not be uncommon. The diversity of the two chimpanzee isolates, the different geographical origin and the absence of disease suggest that chimpanzees have not recently become SIVcpz-infected.

Evaluation of a line immunoassay for simultaneous confirmation of antibodies to HIV-1 and HIV-2

An anti-HIV-1/HIV-2 line immunoassay (LIA), using peptides and recombinant antigens was evaluated against commercially available Western blot tests for HIV-1 and HIV-2 antibodies. Two thousand one hundred and ten sera of European, African, and South American origin were used in the evaluation. The panel included 1066 sera with antibodies to HIV-1, 192 sera with antibodies to HIV-2, and 64 sera with antibodies to both. Using Western blot results interpreted according to the WHO criteria as a reference standard, the overall specificity obtained by this LIA was 100% and the sensitivity was 99.77% (97.51-100% for 95% confidence limits) when sera dually reactive in Western blot were included. Of the three sera negative in the LIA but positive in HIV-1 WB, two could be retested in a radioimmunoprecipitation assay and were negative. When dually reactive sera in the Western blot (WHO) were included, the LIA yielded 9.9% indeterminate results as compared with 15.5% for both assays (chi 2 = 29.30; p less than 0.001). Although only one HIV-2 specific peptide antigen (gp36) was used, the LIA yielded a specificity of 100% and a sensitivity of 100% as compared with the HIV-2 Western blot assay. When indeterminate results were included, the overall agreement between the LIA and the HIV-1 and HIV-2 Western blot (WHO criteria) was 89.9% and 90.1% respectively. These results indicate that the LIA provides reliable simultaneous detection of antibodies to HIV-1 and HIV-2, and at a cost which is substantially lower than the cost of Western blot tests.