An enhanced-sensitivity branched-DNA assay for quantification of human immunodeficiency virus type 1 RNA in plasma

Simultaneous runs of the Bayer VERSANT HIV-1 version 3.0 and HCV bDNA version 3.0 quantitative assays on the system 340 platform provide reliable quantitation and improved work flow

Branched DNA (bDNA) assays to quantify human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) consist of three distinct steps, including sample processing, hybridization, and detection, and utilize the System 340 platform for plate incubation and washing. Sample processing differs: HIV-1 from 1 ml of plasma is concentrated by high-speed centrifugation, whereas HCV plasma or serum samples are used without concentration. The first step of hybridization involves viral lysis at 63 degrees C: HIV-1 is performed in a heat block, whereas HCV is performed in System 340. The remaining hybridization and detection steps are similar for HIV-1 and HCV and executed on System 340. In the present study, the HIV-1 bDNA assay was adapted for viral lysis in the System 340 platform. The adaptation, test method 2, includes a 20-s vortex of concentrated viral pellet and lysis working solution, transfer of viral lysate to the 96-well capture plate, and transfer to System 340 programmed for HCV assay specifications. With test method 2, specificity and quantification were within assay specifications. HCV bDNA methodology remains unchanged. Hence, an HIV-1 and an HCV bDNA can be run simultaneously on System 340. With simultaneous testing, laboratories can run full plates, as well as combinations of full and partial plates. Also, simultaneous HIV-1 and HCV bDNA permits labor consolidation and improved workflow while maintaining multitasking and rapid patient result turnaround.

Multiplexed genetic analysis using an expanded genetic alphabet

Background: All states require some kind of testing for newborns, but the policies are far from standardized. In some states, newborn screening may include genetic tests for a wide range of targets, but the costs and complexities of the newer genetic tests inhibit expansion of newborn screening. We describe the development and technical evaluation of a multiplex platform that may foster increased newborn genetic screening.

Methods: MultiCode® PLx involves three major steps: PCR, target-specific extension, and liquid chip decoding. Each step is performed in the same reaction vessel, and the test is completed in ∼3 h. For site-specific labeling and room-temperature decoding, we use an additional base pair constructed from isoguanosine and isocytidine. We used the method to test for mutations within the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The developed test was performed manually and by automated liquid handling. Initially, 225 samples with a range of genotypes were tested retrospectively with the method. A prospective study used samples from >400 newborns.

Results: In the retrospective study, 99.1% of samples were correctly genotyped with no incorrect calls made. In the perspective study, 95% of the samples were correctly genotyped for all targets, and there were no incorrect calls.

Conclusions: The unique genetic multiplexing platform was successfully able to test for 31 targets within the CFTR gene and provides accurate genotype assignments in a clinical setting.

Nucleic acid analysis using an expanded genetic alphabet to quench fluorescence

Organic chemistry has made possible the synthesis of molecules that expand on Nature's genetic alphabet. Using the previously described nonstandard DNA base pair constructed from isoguanine and 5-methylisocytosine, we report a highly specific and sensitive method that allows for the fast and specific quantitation of genetic sequences in a closed tube format. During PCR amplification, enzymatic site-specific incorporation of a quencher covalently linked to isoguanine allows for the simultaneous detection and identification of multiple targets. The specificity of method is then established by analysis of thermal denaturation or melting of the amplicons. The appropriate functions of all reactions are further verified by incorporation of an independent target into the reaction mixture. We report that the method is sensitive down to the single copy level, and specificity is demonstrated by multiplexed end-point genotypic analysis of four targets simultaneously using four separate fluorescent reporters. The method is general enough for quantitative and qualitative analysis of both RNA and DNA using previously developed primer sets. Though the method described employs the commonly used PCR, the enzymatic incorporation of reporter groups into DNA site-specifically should find broad utility throughout molecular biology.

Comparison of LCx with other current viral load assays for detecting and quantifying human immunodeficiency virus type 1 RNA in patients infected with the circulating recombinant form A/G (CRF02)

LCx was compared to other assays in measuring human immunodeficiency virus type 1 (HIV-1) CRF02 viremia. LCx showed significant but low correlation with the other methods. Values of <2.60 log(10) cp/ml were observed in 29.6% of specimens with LCx and in only 14.8% with bDNA and PCR, suggesting suboptimal performance of LCx with CRF02.

Virus concentration using sulfonated magnetic beads to improve sensitivity in nucleic acid amplification tests

To enhance the sensitivity of virus detection by polymerase chain reaction (PCR) and reverse-transcriptional (RT)-PCR, we developed a novel virus-concentration method using sulfonated (SO-) magnetic beads in the presence of divalent cations. In the presence of either Zn(2+) or Cu(2+) ions, we showed that SO-magnetic beads were able to concentrate non-enveloped model viruses, such as porcine parvovirus (PPV) and poliovirus, which were not concentrated by polyethyleneimine (PEI)-magnetic beads.(1)) Using the SO-magnetic beads, the sensitivity of virus genome detection by PCR or RT-PCR can be enhanced. Therefore, an efficient virus concentration method using either SO-magnetic beads or PEI-magnetic beads enhances the sensitivity of virus detection by PCR or RT-PCR.

Memory in retroviral quasispecies: experimental evidence and theoretical model for human immunodeficiency virus

Viral quasispecies may possess a molecular memory of their past evolutionary history, imprinted on minority components of the mutant spectrum. Here we report experimental evidence and a theoretical model for memory in retroviral quasispecies in vivo. Apart from replicative memory associated with quasispecies dynamics, retroviruses may harbour a "cellular" or "anatomical" memory derived from their integrative cycle and the presence of viral reservoirs in body compartments. Three independent sets of data exemplify the two kinds of memory in human immunodeficiency virus type 1 (HIV-1). The data provide evidence of re-emergence of sequences that were hidden in cellular or anatomical compartments for extended periods of infection, and recovery of a quasispecies from pre-existing genomes. We develop a three-component model that incorporates the essential features of the quasispecies dynamics of retroviruses exposed to selective pressures. Significantly, a numerical study based on this model is in agreement with the experimental data, further supporting the existence of both replicative and reservoir memory in retroviral quasispecies.

Nucleic acid capture assay, a new method for direct quantitation of nucleic acids

Technologies allowing direct detection of specific RNA/DNA sequences occasionally serve as an alternative to amplification methods for gene expression studies. In these direct methods the hybridization of probes takes place in complex mixtures, thus specificity and sensitivity still limit the use of current technologies. To address these challenges, we developed a new technique called the nucleic acid capture assay, involving a direct multi-capture system. This approach combines a 3'-ethylene glycol scaffolding with the incorporation of 2'-methoxy deoxyribonucleotides in the capture sequences. In our design, all nucleotides other than those complementary to the target mRNA have been replaced by an inert linker, resulting in significant reductions in non-specific binding. We also provide a versatile method to detect the presence of captured targets by using specific labeled probes with alkaline phosphatase-conjugated anti-label antibodies. This direct, flexible and reliable technique for gene expression analysis is well suited for high-throughput screening and has potential for DNA microarray applications.

Sustained high proportion of zidovudine-resistant HIV variants despite prolonged substitution of zidovudine by other nucleoside reverse transcriptase inhibitors

The consequences of zidovudine (ZDV) replacement by other nucleoside reverse transcriptase inhibitors on the expression of resistance mutations at codons 215 and 41 of the reverse transcriptase (RT) gene was investigated prospectively in 66 patients harboring mutant genotypes who were changed to an effective two- or three-drug combination antiretroviral regimen. Quantitation of mutant (MUT) viral populations at codon 215 by means of RT-PCR with differential hybridization of amplicons specific for MUT and wild (WT) variants revealed no difference in the proportion of 215 MUT variants prior to (93.5 +/- 2.4%) and 12 to 20 months after (96.9 +/- 1.9%) ZDV replacement, independently of a therapeutic change for stavudine. The fitness of the variants harboring the ZDV-resistant MUT 215 genotype following drug withdrawal was calculated to be 96 to 99% of that of the variants harboring the WT 215 genotype. The apparent stability of ZDV-resistant variants in the study population may have two main complementary explanations: persistent selective pressure secondary to partial cross-resistance due to the new regimens given after the therapeutic alteration and suppression of viral replication after the therapeutic alteration that could have hampered the replacement of less fit variants by fitter variants. These findings indicate that, at least within 15 months following discontinuation of ZDV, an effective antiretroviral therapy is insufficient to allow for ZDV-resistant strains to disappear, and thus to allow for the safe re-introduction of the drug.

HIV-1 subtype J recombinant viruses in Spain

Genetic characterization of HIV-1 was carried out in two women who originated in Cameroon and Equatorial Guinea, respectively, and who were diagnosed more recently as HIV-1 seropositive in Madrid, Spain. Phylogenetic studies showed that the protease-encoding gene from both individuals clustered with subtype J sequences with a high bootstrap. However, env sequences clustered with subtypes A and C, respectively. This work represents the first characterization of HIV-1 containing subtype J-like genomic regions in Spain.

Comparative analysis of HIV-1 viral load assays on subtype quantification: Bayer Versant HIV-1 RNA 3.0 versus Roche Amplicor HIV-1 Monitor version 1.5

Quantification of HIV-1 subtypes is essential for appropriate clinical management. Whereas viral load assays were initially developed to accurately quantify subtype B, the recent worldwide spread of non-B subtypes and the introduction of treatment programs in regions with non-B subtypes have prompted adaptations of these assays. The Bayer Versant HIV-1 RNA 3.0 Assay (branched DNA [bDNA] 3.0) and the Roche Amplicor HIV-1 Monitor version 1.5 (Amplicor 1.5) assays are reported to quantify all subtypes in group M; however, evaluation of performance characteristics remains limited. In this study, we evaluated the accuracy and reliability of bDNA 3.0 and Amplicor 1.5 on multiple serially diluted viral isolates from HIV-1 group M, subtypes A through F. Testing was conducted on both assay systems in two independent laboratories. Comparative pansubtype quantification from regression analysis showed that quantification by bDNA 3.0 was approximately 0.3 log-fold lower than that by Amplicor 1.5. Comparative pansubtype accuracy analysis showed data points more closely distributed about their respective regression lines and thus showing greater reliability by bDNA 3.0 than by Amplicor 1.5.

The effect of antiretroviral therapy on HTLV infection

No effective treatment for TSP/HAM has been described so far. Interventions with corticosteroids, plasmapheresis, interferon and, more recently, with antiretroviral drugs have been tried with poor results. The main HTLV replication mechanism is thought to be through clonal expansion of HTLV-infected cells, which excludes the involvement of the reverse transcriptase (RT) enzyme. However, a virological and clinical improvement has been noticed in HTLV-I carriers suffering from TSP/HAM receiving zidovudine or lamivudine. Herein, we describe the virological and clinical outcome in two TSP/HAM patients infected with HTLV-I treated with zidovudine plus lamivudine, and in two HTLV-II/HIV-1 co-infected patients receiving triple combinations including lamivudine. While, one TSP/HAM patient experienced a 2 log decrease in HTLV-I proviral load, an increase of 1 log was observed in another patient after several months of treatment with zidovudine plus lamivudine. The two HTLV-II/HIV-1 co-infected patients showed an initial increase in HTLV-II proviral load after beginning HAART followed by a slight decline a few months later. Plasma HIV-1 RNA fell to <50 copies/ml in both patients after beginning therapy. None of the four HTLV positive patients developed genetic changes at the conserved YMDD domain within their respective RT genes, which could be related to lamivudine resistance. No clinical improvement was observed in one TSP/HAM patient after more than 1 year on treatment with nucleoside analogues. The inhibition of the HTLV RT along with the cytostatic effect of some nucleoside analogues, including zidovudine, could reduce HTLV replication, and therefore reduce HTLV proviral load. The clinical consequences of this effect need to be further examined.

Single-copy gene detection using branched DNA (bDNA) in situ hybridization

We have developed a branched DNA in situ hybridization (bDNA ISH) method for detection of human papillomavirus (HPV) DNA in whole cells. Using human cervical cancer cell lines with known copies of HPV DNA, we show that the bDNA ISH method is highly sensitive, detecting as few as one or two copies of HPV DNA per cell. By modifying sample pretreatment, viral mRNA or DNA sequences can be detected using the same set of oligonucleotide probes. In experiments performed on mixed populations of cells, the bDNA ISH method is highly specific and can distinguish cells with HPV-16 from cells with HPV-18 DNA. Furthermore, we demonstrate that the bDNA ISH method provides precise localization, yielding positive signals retained within the subcellular compartments in which the target nucleic acid sequences are localized. As an effective and convenient means for nucleic acid detection, the bDNA ISH method is applicable to the detection of cancers and infectious agents. (J Histochem Cytochem 49:603-611, 2001)

Comparative performance of three viral load assays on human immunodeficiency virus type 1 (HIV-1) isolates representing group M (subtypes A to G) and group O: LCx HIV RNA quantitative, AMPLICOR HIV-1 MONITOR version 1.5, and Quantiplex HIV-1 RNA version 3.0

The performance of the LCx HIV RNA Quantitative (LCx HIV), AMPLICOR HIV-1 MONITOR version 1.5 (MONITOR v1.5), and Quantiplex HIV-1 RNA version 3.0 (bDNA v3.0) viral load assays was evaluated with 39 viral isolates (3 A, 7 B, 6 C, 4 D, 8 E, 4 F, 1 G, 4 mosaic, and 2 group O). Quantitation across the assay dynamic ranges was assessed using serial fivefold dilutions of the viruses. In addition, sequences of gag-encoded p24 (gag p24), pol-encoded integrase, and env-encoded gp41 were analyzed to assign group and subtype and to assess nucleotide mismatches at primer and probe binding sites. For group M isolates, quantification was highly correlated among all three assays. In contrast, only the LCx HIV assay reliably quantified group O isolates. The bDNA v3.0 assay detected but consistently underquantified group O viruses, whereas the MONITOR v1.5 test failed to detect group O viruses. Analysis of target regions revealed fewer primer or probe mismatches in the LCx HIV assay than in the MONITOR v1.5 test. Consistent with the high level of nucleotide conservation is the ability of the LCx HIV assay to quantify efficiently human immunodeficiency virus type 1 group M and the genetically diverse group O.

Evaluation of a second-generation nucleic acid sequence-based amplification assay for quantification of HIV type 1 RNA and the use of ultrasensitive protocol adaptations

Accurate assessment of plasma HIV RNA levels at low concentrations is clinically important. We evaluated a second-generation quantitative HIV RNA assay (NucliSens HIV-1 QT), and three simple adaptations of the NucliSens standard protocol to lower the lower cutoff level. The assays were evaluated in constructed panels with known HIV RNA concentrations and in clinical samples. Results were compared with those obtained with the first generation (NASBA HIV-1 QT) and with two other commercially available assays: the Amplicor HIV Monitor test and the Quantiplex assay. In a constructed panel, results obtained by NASBA QT were on average 0.13 log(10) copies/ml (SD 0.15) higher than those of NucliSens. The NucliSens assay could quantify HIV RNA in at least 50% of the samples down to 518 (2.71 log(10)) copies/ml and NASBA QT to 5.80 x 10(3) (3.76 log(10)) copies/ml). Both assays correlated well with the known input (R NucliSens = 0.99; R NASBA QT = 0.996), but results were more variable at lower input levels. With the three different ultrasensitive NucliSens adaptations, HIV RNA could be quantified in at least 50% of the samples down to 100 (2.00 log(10)), 46 (1.66 log(10)), and 10 (1.00 log(10)) copies/ml, respectively. In patient samples, Amplicor results were on average 0.11 (SD 0.20) log(10) copies/ml above, NucliSens 0.02 (SD 0.29) copies/ml above, and Quantiplex 0.13 (SD 0.19) copies/ml below the mean of the three assay results per sample. The variation remained the same over the range of RNA levels with all three assays. The NucliSens assay can quantify HIV RNA at lower levels than the NASBA QT and is comparable to other commercially available assays. The lower cutoff of the NucliSens can be lowered down to 10 copies/ml.

Evaluation of the abbott LCx HIV-1 RNA quantitative, a new assay for quantitative determination of human immunodeficiency virus type 1 RNA

A new quantitative reverse transcription (RT)-PCR assay for human immunodeficiency virus type 1 (HIV-1) RNA (Abbott LCx HIV RNA Quantitative assay) has been compared with the Organon NucliSens assay on 521 retrospective samples obtained from HIV-1-positive patients monitored during highly active antiretroviral therapy, 79 of whom were assayed also by the Chiron Quantiplex 3.0 system and on characterized panels. The LCx system showed a moderate correlation (r = 0.795) and gave higher results than the NucliSens system on 245 of 327 concordant positive samples, with similar sensitivity. Correlation with Quantiplex system results was higher (r = 0.943). LCx reproducibility was very good; the procedure was simple, well controlled, and rapid (up to 48 results in 7 h). The HIV RNA quantitative assay on the LCx system is suitable for routine use.

Protease gene analysis of HIV type 1 non-B subtypes in Spain

The protease gene of human immunodeficiency virus type 1 (HIV-1) clinical isolates found in 15 immigrants (most of African origin) living in Spain was examined. Phylogenetic analyses were performed, taking as reference a panel of 26 HIV protease gene sequences deposited with GenBank. All specimens belonged to four distinct HIV-1 non-B subtypes: C (three cases), F (one), G (nine), and H (two). Five patients harboring subtype G strains were further classified within the IbNg recombinant clade. A high degree of genetic polymorphism at the protease gene was seen in all subtypes. Moreover, changes at positions associated with drug resistance were seen in subtype G viruses carried by patients who had not been exposed to protease inhibitors. Plasma viremia was lower than expected for some samples, according to the clinical features and the CD4+ cell count, suggesting that viral load titers were underestimated by all three commercially available techniques. This work represents the first genetic characterization of subtypes C, F, G, and H in Spain.

Quantification of HIV-1 group M (subtypes A-G) and group O by the LCx HIV RNA quantitative assay

Human immunodeficiency virus type 1 (HIV-1) genetic diversity presents a challenge to nucleic acid-based assays with regard to sensitivity of detection and accuracy of quantification. The Abbott LCx HIV RNA Quantitative assay (LCx(R) HIV assay), a competitive RT-PCR targeting the pol integrase region, was evaluated using a panel of 297 HIV-1 seropositive plasma samples from Cameroon, Uganda, Brazil, Thailand, Spain, Argentina and South Africa. The panel included group M subtypes A-G, mosaics, and group O based on sequence analysis of gag p24, pol integrase, and env gp41. The LCx HIV assay quantified 290 (97.6%) of the samples, including all the group O samples tested. In comparison, the Roche AMPLICOR HIV-1 MONITOR test versions 1.0 and 1.5 quantified 67.3 and 94.6% of the samples, respectively. No group O specimens were quantified by either version of AMPLICOR HIV-1 MONITOR. Seven specimens were below the detectable limits of all the three assays. The LCx HIV assay had fewer nucleotide mismatches at primer/probe binding sites as compared with both AMPLICOR HIV-1 MONITOR tests. The high degree of nucleotide conservation within the pol target region enables the LCx HIV assay to efficiently quantify the HIV-1 subtypes A-G and the most genetically diverse HIV-1, group O.

Evaluation of performance of the Gen-Probe human immunodeficiency virus type 1 viral load assay using primary subtype A, C, and D isolates from Kenya

Accurate and sensitive quantification of human immunodeficiency virus type 1 (HIV-1) RNA has been invaluable as a marker for disease prognosis and for clinical monitoring of HIV-1 disease. The first generation of commercially available HIV-1 RNA tests were optimized to detect the predominant HIV-1 subtype found in North America and Europe, subtype B. However, these tests are frequently suboptimal in detecting HIV-1 genetic forms or subtypes found in other parts of the world. The goal of the present study was to evaluate the performance of a new viral load assay with non-subtype B viruses. A transcription-mediated amplification method for detection and quantitation of diverse HIV-1 subtypes, called the Gen-Probe HIV-1 viral load assay, is under development. In this study we examined the performance of the Gen-Probe HIV-1 viral load assay relative to that of the commonly used commercial HIV-1 RNA assays using a panel of primary isolates from Kenya. For comparison, we included several subtype B cloned viruses, and we quantified each virus using an in-house quantitative-competitive reverse transcriptase PCR (QC-RT-PCR) method and gag(p24) antigen capture. The Gen-Probe HIV-1 viral load assay and a version of the Roche AMPLICOR HIV-1 MONITOR test (version 1.5) that was designed to detect a broader range of subtypes were both sensitive for the quantification of Kenyan primary isolates, which represented subtype A, C, and D viruses. The Gen-Probe HIV-1 viral load assay was more sensitive for the majority of viruses than the Roche AMPLICOR HIV-1 MONITOR test version 1.0, the Bayer Quantiplex HIV RNA 3.0 assay, or a QC-RT-PCR method in use in our laboratory, suggesting that it provides a useful method for quantifying HIV-1 RNAs from diverse parts of the world, including Africa.

In vivo fluctuation of HTLV-I and HTLV-II proviral load in patients receiving antiretroviral drugs

HTLV-I and HTLV-II infect T lymphocytes. A high HTLV-I proviral load in peripheral blood mononuclear cells (PBMCs) has been associated with a higher risk of neurologic disease. For HTLV-II, large numbers of infected lymphocytes might contribute to accelerate the immunodeficiency and increase the risk of neuropathy in HTLV-II/HIV-1 coinfected people. We have examined the impact of antiretroviral drugs on HTLV proviral load, testing longitudinal samples collected from 1 HTLV-I infected patient suffering HTLV-I-associated myelopathy (HAM), and two HTLV-II/ HIV-1 coinfected subjects. The HAM patient showed a reduction greater than 2 log in the peripheral proviral load after being treated with zidovudine and lamivudine. In contrast, potent antiretroviral treatment in HIV-1/HTLV-II coinfected carriers produced an initial increase in the HTLV proviral load, which was followed by a reduction greater than 1 log thereafter. In conclusion, antiretroviral drugs seem to reduce HTLV proviral load, although in HIV-1 coinfected persons a transient increase in HTLV proviral load could reflect the rapid blocking of HIV-1 replication occurring in response to therapy, thus causing an increase in the number of circulating T lymphocytes carrying HTLV proviral DNA.

Clearance of human herpesvirus type 8 viraemia in HIV-1-positive patients with Kaposi's sarcoma treated with liposomal doxorubicin. Caelyx/KS Spanish Study Group

OBJECTIVE

To assess the impact of liposomal doxorubicin on human herpesvirus type 8 (HHV-8) cell viraemia in HIV-infected patients with Kaposi's sarcoma.

DESIGN

Prospective, non-controlled, multicenter study.

METHODS

The presence of HHV-8 DNA was investigated by polymerase chain reaction in peripheral blood mononuclear cells from 46 HIV-positive patients with Kaposi's sarcoma. Samples were tested at baseline and every 3 months during treatment with liposomal doxorubicin. CD4 cell counts, plasma HIV RNA, and clinical outcome were recorded at baseline and at follow-up visits.

RESULTS

HHV-8 sequences were detected in 32 (70%) patients at baseline. No significant differences were found between subjects with HHV-8 positive and negative results. The proportion of patients with positive HHV-8 viraemia decreased to 38% (10 of 26) after 3 months of treatment with liposomal doxorubicin (P < 0.01). Overall, 12 of 22 (57%) subjects with positive HHV-8 cell viraemia at baseline became negative during the treatment period. However, in one of them HHV-8 reappeared 8 months later despite being on therapy. On the other hand, six of eight subjects with negative HHV-8 at baseline remained negative thereafter. There were no significant changes in plasma HIV RNA, total lymphocyte, or CD4 cell counts during the treatment period. Clinical response of Kaposi's sarcoma to liposomal doxorubicin and clearance of HHV-8 viraemia did not correlate well.

CONCLUSIONS

HHV-8 cell viraemia significantly decreased during treatment with liposomal doxorubicin in HIV-infected patients with Kaposi's sarcoma, although the clinical response and HHV-8 clearance did not correlate well.

Blinded, multicenter quality control study for the quantification of human immunodeficiency virus type 1 RNA in plasma by the Belgian AIDS reference laboratories

OBJECTIVE

In order to evaluate the interlaboratory variation of HIV-1 RNA measurements in plasma, the Belgian AIDS reference laboratories organized a blinded multicenter quality control study.

METHODS

Atest panel of coded spiked HIV-1 plasma samples reflecting the dynamic range of the assay was composed and distributed. The HIV-1 RNA concentration of these samples was determined by the eight Belgian AIDS reference laboratories by means of the Amplicor HIV-1 Monitor version 1.5 assay.

RESULTS

Analysis of the results demonstrated that there was little interlaboratory variation for the high concentration range (4.0-5.7 log10 copies/mL), never exceeding 0.2 log10 copies/mL. However the standard deviation for the low concentration range (2.6-3.9 log10 copies/mL) reached up to 0.22 log10 copies/mL.

CONCLUSIONS

Since interlaboratory variability never reached 0.5 log10 copies/mL and each of the laboratories was able to detect four-fold differences in plasma HIV-1 RNA levels, the Amplicor assay can be used in multicenter studies without a centralized analysis of samples. Furthermore, this well-characterized proficiency panel of spiked plasma samples could be used as a standard in the study of interassay comparisons.

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.

Quantitative and cost comparison of ultrasensitive human immunodeficiency virus type 1 RNA viral load assays: Bayer bDNA quantiplex versions 3.0 and 2.0 and Roche PCR Amplicor monitor version 1.5

Quantification of human immunodeficiency virus type 1 (HIV-1) RNA as a measure of viral load has greatly improved the monitoring of therapies for infected individuals. With the significant reductions in viral load now observed in individuals treated with highly active anti-retroviral therapy (HAART), viral load assays have been adapted to achieve greater sensitivity. Two commercially available ultrasensitive assays, the Bayer Quantiplex HIV-1 bDNA version 3.0 (bDNA 3.0) assay and the Roche Amplicor HIV-1 Monitor Ultrasensitive version 1.5 (Amplicor 1.5) assay, are now being used to monitor HIV-1-infected individuals. Both of these ultrasensitive assays have a reported lower limit of 50 HIV-1 RNA copies/ml and were developed from corresponding older generation assays with lower limits of 400 to 500 copies/ml. However, the comparability of viral load data generated by these ultrasensitive assays and the relative costs of labor, disposables, and biohazardous wastes were not determined in most cases. In this study, we used matched clinical plasma samples to compare the quantification of the newer bDNA 3.0 assay with that of the older bDNA 2.0 assay and to compare the quantification and costs of the bDNA 3.0 assay and the Amplicor 1.5 assay. We found that quantification by the bDNA 3.0 assay was approximately twofold higher than that by the bDNA 2.0 assay and was highly correlated to that by the Amplicor 1.5 assay. Moreover, cost analysis based on labor, disposables, and biohazardous wastes showed significant savings with the bDNA 3.0 assay as compared to the costs of the Amplicor 1.5 assay.

Comparative evaluation of two branched-DNA human immunodeficiency virus type 1 RNA quantification assays with lower detection limits of 50 and 500 copies per milliliter

We have comparatively evaluated Quantiplex version 3.0 and version 2. 0 on 133 plasma samples and a repetitive dilution series. Version 3. 0 yielded higher human immunodeficiency virus RNA values, and the ratio of version 3.0 results to version 2.0 results decreased from 3. 47 below 1,000 copies/ml to 1.97 above 50,000 copies/ml [linear regression, log (version 3.0) = 0.915 + 0.871 x log (version 2.0); r(2) = 0.952].

Performance of five different assays for the quantification of viral load in persons infected with various subtypes of HIV-1. Swiss HIV Cohort Study

Five methods for the assessment of plasma viral load (VL) were evaluated in 103 seropositive patients infected with various subtypes of HIV-1. The methods included three RNA-based assays (Amplicor Monitor 1.5, Quantiplex version 2.0, NucliSens), one ultrasensitive reverse transcriptase (PERT) assay and one "boosted" p24 antigen (Ag) enzyme immunoassay (EIA). Subtyping was based on sequencing in env. The sensitivities were, in decreasing order, Amplicor > PERT > p24 Ag > NucliSens > Quantiplex. The low sensitivity of NucliSens was related to the missing of several non-B (A, E, F, G) or recombinant strains, whereas that of Quantiplex did not depend on subtype. In the 1 group O sample and 4 group M samples, only PERT assay or p24Ag EIA produced a positive result. In the quantitative range, correlation was best between Amplicor and Quantiplex (r = 0.8848), fair between Amplicor and NucliSens (r = 0.7064) or PERT assay (r = 0.7266), lowest between Amplicor and p24Ag EIA (r = 0.3989). Amplicor underestimated VL in 1 subtype E sample. Thus, Amplicor performed best in terms of sensitivity (compared with all other assays) and accuracy (compared with NucliSens, PERT assay, and p24Ag) for non-B subtypes in group M samples. PERT assay appears useful for VL assessment in infections by group O or other highly divergent viruses.

Dynamics of dominance of a dipeptide insertion in reverse transcriptase of HIV-1 from patients subjected to prolonged therapy

A small proportion (0.8%) of individuals of a cohort of HIV-1 infected patients subjected to prolonged therapy with nucleoside analogues included a recently recognised dipeptide insertion in their RT (Ser-Ser or Ser-Gly between RT codons 69 and 70). To study the dynamics of dominance of genomes with this genetic change, sequential HIV-1 isolates from two patients were analyzed with regard to consensus sequences and complexity of mutant spectra. The two patients displayed completely different, complex evolutionary patterns leading to temporary dominance of dipeptide insertions. In one patient, a virus very closely related to an ancestor virus from the same patient overtook the population at late times, displacing genomes encoding a Ser-Ser insertion. In another patient the sequential dominance of genomes with Ser-Ser insertion-->no insertion-->Ser-Gly insertion was observed. These three types of genomes coexisted in the mutant spectrum of one HIV-1 isolate. Complexity was also reflected in the shape of phylogenetic trees derived with genomes from the mutant spectrum at each time point. The results suggest that HIV-1 genomes encoding a dipeptide insertion between RT codons 69 and 70 do not show a clear selective advantage over other genomes lacking the insertion. Such an absence of a clear selective advantage will favor that such genomes encoding this RT insertion become dominant only in a transient fashion, and following disparate kinetics in different patients.

Sociodemographic and psychological variables influencing adherence to antiretroviral therapy

OBJECTIVE

To assess the degree of compliance with antiretroviral therapy in HIV-infected patients, and identify which sociodemographic and psychological factors influence it, in order to develop strategies to improve adherence.

DESIGN AND SETTING

Cross-sectional study in a reference HIV/AIDS institution located in Madrid, Spain.

PATIENTS AND METHODS

A total of 366 HIV-infected patients who were on treatment with antiretroviral drugs were invited to complete a questionnaire which recorded sociodemographic data and psychological variables in relation to compliance with the prescribed medication. Clinical information was extracted from the hospital records. The Beck Depression Inventory was used to assess depression, while adherence to treatment was evaluated using patient's self report and the pill count method.

RESULTS

A good adherence to antiretroviral therapy (> 90% consumption of the prescribed pills) was recorded in 211 (57.6%) patients. A good concordance for assessing adherence was found using the patient's self-report and the pill count method in a sub-group of patients. Predictors of compliance in the univariate analysis were age, transmission category, level of studies, work situation, CD4 cell count level, depression and self-perceived social support. In the multivariate model, only age, transmission category, CD4 cell count level, depression, self-perceived social support, and an interaction between the last two variables predicted compliance to treatment; adherence to antiretroviral therapy was better among subjects aged 32-35 years [odds ratio (OR), 2.31; 95% confidence interval (CI), 1.21-4.40], in non-intravenous drug users (IVDUs) (OR, 2.05; 95% CI, 1.28-3.29), subjects with CD4 cell counts from 200-499 x 10(6) cells/l at enrolment (OR, 2.78; 95% CI, 1.40-5.51) and in subjects not depressed and with a self-perceived good social support (OR, 1.86; 95% CI, 0.98-3.53).

CONCLUSIONS

Sociodemographic and psychological factors influence the degree of adherence to antiretroviral therapy. Overall, IVDUs and younger individuals tend to have a poorer compliance, as well as subjects with depression and lack of self-perceived social support. An increased awareness of these factors by practitioners attending HIV-infected persons, recognizing and potentially treating some of them, should indirectly improve the effectiveness of antiretroviral therapy.

Immunologic and viral markers of HIV-1 disease progression: implications for dentistry

BACKGROUND

Current medical care for patients infected with the human immunodeficiency virus type 1, or HIV-1, involves monitoring laboratory assays for CD4+ lymphocyte cell count and plasma viral load.

TYPES OF STUDIES REVIEWED

The authors reviewed recent medical and dental studies that contribute to our current understanding of these immunologic and viral markers and their relevance to systemic and oral health.

RESULTS

Dramatic reduction in plasma viral load resulting from more potent antiretroviral drug combinations is the goal of medical management for HIV. These protease inhibitor-containing regimens, although complex, expensive and associated with substantial side effects, have decreased the morbidity and mortality associated with HIV in the United States. Although reduction in viral load can result in increases in CD4+ counts, which restores some level of immune competence, a cure for AIDS has not yet been found.

CLINICAL IMPLICATIONS

Patients with low CD4+ cell counts (and often high viral loads) are more likely to develop destructive periodontal infections and other oral manifestations of HIV. Partial recovery of the immune system after viral load reduction may affect both the prognosis and oral disease experience of these patients.

Detection of Yersinia pestis using branched DNA

In contrast to target amplification methods, e.g. polymerase chain reaction, the branched DNA (bDNA) signal amplification method quantitates target nucleic acid at physiological levels, involving a series of hybridization reactions without thermal cycling. In this report, we describe a modification of the bDNA assay in which a <<concatenated>> preamplifier oligonucleotide (206 mer) is used in concert with ELISA and light addressable potentiometric sensor (LAPS) formats to detect the plasminogen activator (pla) gene of Yersinia pestis, the etiological agent of plague. Pla is encoded by a 9.6-kb plasmid pPCP, which is essential for virulence. The detection limit of the bDNA-ELISA and LAPS assays is less than 10 000 and 1000 molecules of Y. pestis plasmid DNA, respectively.

Branched DNA signal amplification for direct quantitation of nucleic acid sequences in clinical specimens

In this chapter I have reviewed the development of bDNA as a method for quantitation of nucleic acid targets and the application of this technology to the study of infectious diseases and cell biology. The ability to quantify viral nucleic acids in clinical specimens has led to a better understanding of the pathogenesis of chronic viral infections such as HIV-1, HCV, and HBV. The information provided by these methods can also be important in the management of patients with these infections. The prognostic value of a single baseline HIV-1 RNA level rivals that surgical staging procedures for cancer, which are among the most powerfully predictive tests in medicine (Mellors et al., 1996). These methods have been used to assess rapidly the effects of antiviral therapy, which has both expedited the development of antiviral drugs and improved the management of patients with HIV-1 and HCV infections. bDNA has several characteristics that distinguish it from the quantitative target amplification systems, including better tolerance of target sequence variability, more direct measurement of target, simpler sample preparation, and less sample-to-sample variation. However, the first- and second-generation bDNA assays lacked sensitivity compared with the target amplifications systems. The changes incorporated into the third-generation assays have effectively increased the signal-to-noise ratio to such a high level that the analytical sensitivity of system 8 bDNA approaches that of PCR. In theory, bDNA can be made even more sensitive by increasing both the sample volume and the signal-to-noise ratio. Nonspecific hybridization can be further reduced by finding more effective blockers for the solid phase or by redesigning the amplifier molecule or the solid phase itself. The increased sensitivity may create new applications for the technology in filter and in situ hybridization assays.

Effect of potentially interfering substances on the measurement of HIV-1 viral load by the bDNA assay

As high heterogeneity of plasma composition may be responsible for interference with HIV-1 viral load determination by the bDNA assay, the potential interference caused by a number of plasma components was examined. Among the biochemical substances assayed, cholesterol, bilirubin, and triglycerides did not affect viral load quantification. Hemoglobin did not interfere with the assay at concentrations lower than or equal to 14 g/dl. Above this concentration, measurements decreased by up to 0.78 log, but these hemoglobin levels do not usually occur in the clinical setting. None of the antiretroviral drugs assayed (AZT, dDC, d4T, 3TC and Indinavir) interfered with the measurement. HIV bDNA is a robust assay even in those frequent circumstances in which plasma composition differs notably from normal.

Reproducibility and performance of the second-generation branched-DNA assay in routine quantification of human immunodeficiency virus type 1 RNA in plasma

We examined the reproducibility of a second-generation branched-DNA (bDNA) assay (Quantiplex HIV RNA 2.0) for quantification of human immunodeficiency virus type 1 (HIV-1) RNA in plasma by retesting 325 specimens on separate runs and on different lots. The performance of the bDNA test was also assessed by data analysis obtained during routine testing of 15,365 specimens. Upon retesting, 96 and 86% of specimens displaying RNA levels above 5,000 and between 500 and 5, 000 copies/ml, respectively, showed less than a 0.3 log10 (twofold) difference with their initial values. Assay variability was found to increase as viral load decreased. Overall, the bDNA version 2.0 assay was found to be a reproducible and efficient test for routine quantification of HIV-1 RNA in plasma.

Efficiency of Drug Resistance Genotypic Tests in Specimens with Low HIV Viral Load

The early recognition of resistance to antiretroviral agents could allow a rapid switch in therapy and therefore avoid the accumulation of mutations and reduce the risk of cross-resistance. However, the efficiency of genotypic tests in specimens with low viral load (VL) is severely compromised since human immunodeficiency virus (HIV) RNA in these samples often goes unrecognized. The frequency of results provided by a line probe assay (LiPA, Murex), a commercially available drug resistance test and a home-made point mutation assay (PMA) for recognizing the codon 151 multidrug-resistance mutation was examined in 664 plasma samples stratified with respect to VL values. Overall, 421 (63%) samples could be interpreted by both LiPA and PMA. The sensitivity decreased as plasma VL lowered: 89% for samples with VL >10000 HIV RNA copies/ml, 77% for those with VL between 500 and 10000 HIV RNA copies/ml and 37% for specimens with VL <500 HIV RNA copies/ml. A good agreement existed comparing the sensitivity of the home-made PMA and LiPA. Although the former tends to produce more results, the difference did not achieve statistical significance. Our results support that new, more sensitive, HIV RNA extraction methods need to be implemented for the rapid recognition of drug-resistant mutants in patients experiencing an early rebound in plasma viraemia.

Clinical evaluation of an in-house reverse transcription-competitive PCR for quantitation of human immunodeficiency virus type 1 RNA in plasma

An in-house reverse transcription (RT)-competitive PCR (RT-cPCR) for the quantitation of human immunodeficiency virus type 1 (HIV-1) RNA in plasma samples was developed and validated. The procedure involves (i) extraction of RNA with spin columns, (ii) ready-to-use bead-mediated RT, (iii) competitive PCR in a microtiter plate, (iv) agarose gel electrophoresis of the reaction products, and (v) densitometric analysis of the digitized image of the gel. Quadruplicate tests and dilution studies showed that the sensitivity and intertest coefficient of variability of the RT-cPCR are comparable to those of the reference AMPLICOR HIV-1 MONITOR test. The results obtained by the two assays with a panel of 45 clinical samples were in good agreement (mean difference, 0.36 +/- 0.25 log units). Analysis of 1,982 clinical samples by the in-house RT-cPCR yielded the typical range of plasma HIV-1 RNA levels with the expected inverse correlation between CD4 counts and HIV-1 RNA titers. In addition, testing of plasma from 36 subjects at weeks 0 and 4 with respect to the time of initiation of protease inhibitor therapy detected a significant decrease in HIV-1 viremia. The mean reduction in the HIV-1 RNA level was 0.914 log unit for those receiving saquinavir (P = 0.0210), 1.584 log units for those receiving indinavir (P = 0.0047), and 1.904 log units for those receiving ritonavir (P < 0.0001). The in-house RT-cPCR assay is simple to develop and perform and allows quantitation of HIV-1 RNA in 100 to 200 samples per operator per week. Since the cost is 1/8 to 1/10 of those of reference commercial assays, this procedure could be conveniently used in medium-scale laboratories.

Presence of Genotypic Resistance in Nucleoside Analogue-Treated HIV-1-Infected Patients with Undetectable Viral Load

Patients harbouring drug-resistant viruses usually suffer a rise in serum viraemia after a variable period of time. We have investigated the relationship between the appearance of resistant genotypes and the viral load of each patient after treatment. Our objective was to assess the association between human immunodeficiency virus (HIV) RNA plasma levels and the number of drug resistance-associated point mutations after treatment. A total of 150 patients from three reference centres in Spain (Madrid, Barcelona and Seville) from a previous study (Erase Study) were included. Patients had at that time undergone antiretroviral treatment with nucleoside analogues for at least 1 year (zidovudine/didanosine; zidovudine/zalcitabine; zidovudine/zalcitabine/lamivudine; zidovudine/didanosine/lamivudine). In this study, plasma viraemia in these patients was quantified and a line probe assay was used to determine the genotype of the virus. Viral load was significantly higher in patients harbouring virus with more than three mutations than in those individuals who harboured wild-type strains ( P<0.05). Surprisingly, when patients with viral load <500 copies/ml (13/150) were analysed, only two carried wild-type strains, whereas three had virus with more than three point mutations. The viral load of six samples was assayed using an ultrasensitive test (detection limit <20 copies/ml). Of the three samples where viral load was <20 copies/ml, one patient harboured wild-type virus, whereas two carried mutant virus strains. These results suggest that even in patients with undetectable viral loads by conventional methods, viral replication may continue and mutations develop. Therefore, standard values of plasma viraemia for measuring the effectiveness of the treatment should be reconsidered when patients are on antiviral regimens of just two or three nucleoside analogues.

Immune activation in HIV-infected African individuals. Italian-Ugandan AIDS cooperation program

OBJECTIVE

Immune activation induced by chronic infections, dietary limitations, and poor hygienic conditions is suggested to be present in African HIV infection and is at the basis of the hypothesis that HIV infection in Africa could be prevalently associated with immunopathogenetic mechanisms. Very limited data are nevertheless available supporting this theory, and in particular no data are reported on functional and phenotypic analyses performed on fresh peripheral blood mononuclear cells (PBMC) of African HIV-infected patients living in Africa.

DESIGN

Immunological and virological parameters were analysed in fresh PBMC of HIV-infected African and Italian patients with advanced HIV disease and comparable CD4 and CD8 counts, sex, and age. Both functional (antigen- and mitogen-stimulated cytokine production) and phenotypic (activation markers; markers preferentially expressed by T helper (Th) type 2 cells or by memory and naive cells) analyses were performed. Results were compared with those of HIV-seronegative African and Italian controls. HIV plasma viraemia was analysed by competitive polymerase chain reaction (PCR) and branched DNA techniques.

RESULTS

(1) The production of mitogen-stimulated IFN-gamma and TNF-alpha as well as the production of env peptide-stimulated IFN-gamma, TNF-alpha, and IL-10 are increased in African HIV infection; (2) the expression of activation and Th2-associated markers is augmented in African HIV infection as is the memory/naive ratio; (3) mitogen-stimulated IFN-gamma and IL-10 production, as well as the expression of activation and Th2-associated markers and the memory/naive ratio, are augmented in African compared with Italian controls; and (4) plasma viraemia is reduced in African compared with Italian HIV-infected individuals.

CONCLUSIONS

These results, which are the first to be reported on fresh material from African HIV-infected patients living in Africa, indicate that HIV disease is associated with an abnormal immune hyperactivation and may be accompanied in these patients by lower loads of virus, and show that such activation is present even in HIV-seronegative controls.

Amplicor HIV monitor, NASBA HIV-1 RNA QT and quantiplex HIV RNA version 2.0 viral load assays: a Canadian evaluation

BACKGROUND

HIV-1 viral load quantitation is now recognized as a useful tool to monitor the efficiency of antiviral treatment and a powerful predictor of disease outcome. Three HIV-1 viral load quantitation methods have been currently available as commercial kits in Canada since 1996.

OBJECTIVE

To evaluate the ability to quantify HIV-1 RNA in plasma of the Amplicor HIV Monitor Test, the NASBA HIV-1 RNA QT Assay and the Quantiplex HIV RNA Assay, version 2.0, at comparable lower detection limits.

STUDY DESIGN

Blood was collected from 50 HIV-1-infected patients at various stages of infection and therapy. CD4+ cell count were estimated by flow cytometry. Plasma was isolated and tested in duplicate on four occasions using viral load kits from a single lot. HIV RNA data, performance, sensitivity and intra- and inter-assay variability were compared.

RESULTS

RNA could be quantified in 33 patients by each technique. An inverse correlation was observed between viral load level and CD4+ cell counts in patients with counts below 200. Monitor could detect RNA in 94% of patients, but it showed the greatest variability and failure rate. Quantiplex 2.0 could detect HIV-1 RNA in 78%, and NASBA in 88% of the patients at theoretically equivalent lower detection limits, suggesting that the detection limit of Quantiplex 2.0 may be higher than 500 HIV-1 RNA copies per ml. NASBA had the fewest invalid tests and good reproducibility, comparable to that of Quantiplex 2.0. The mean values from NASBA and Monitor were the most similar but the best correlation was observed between Monitor and Quantiplex 2.0 results.

CONCLUSIONS

Monitor, NASBA and Quantiplex results were comparable, although those obtained by Quantiplex were significantly lower. Performing this study at comparable detection limits showed that the detection limit of Quantiplex 2.0 may be higher than stated by the manufacturer.

Association of HLA profiles with early plasma viral load, CD4+ cell count and rate of progression to AIDS following acute HIV-1 infection. Multicenter AIDS Cohort Study

BACKGROUND

Host genetic factors, such as HLA alleles, play an important role in mediating the course of HIV-1 disease progression through largely undefined mechanisms.

OBJECTIVES

To examine the association of HLA markers with HIV-1 RNA plasma viral load and other factors associated with course of disease progression in HIV-1 infection.

DESIGN AND METHODS

A group of 139 HIV-1 seroconverters from the Multicenter AIDS Cohort Study had been typed for a variety of HLA markers. HIV-1 RNA plasma viral load was measured from frozen plasma specimens obtained approximately 9 months following seroconversion. CD4+ cell counts were available from the same study visit. Statistical analysis was performed using survival techniques and linear regression models to quantify the relative associations of an HLA score profile, HIV-1 RNA plasma viral load, CD4+ cell count and age with each other and with rate of progression to AIDS and death.

RESULTS

Cox proportional hazards models showed statistically significant differences in time to AIDS by HLA score profile category per unit increase [relative hazard (RH), 0.64; P < 0.0001], HIV-1 RNA plasma viral load per 10-fold increase (RH, 2.04; P = 0.0003), and CD4+ cell count per 100 cell (x 10(6)/l) increase (RH, 0.90; P = 0.02). Multivariate linear regression showed that viral load was 39% lower (P = 0.0001) for each unit increase in HLA score profile and 13% lower (P = 0.002) for each 100 cell (x 10(6)/l) increase in CD4+ cell count.

CONCLUSION

The means by which the HLA score profile influences the time to AIDS is probably through immunologic responses that affect the rate of HIV-1 replication, as manifested by the HIV-1 RNA plasma viral load during the first 6-12 months following acute infection.

Comparison of the QUANTIPLEX HIV-1 RNA 2.0 assay with the AMPLICOR HIV-1 MONITOR 1.0 assay for quantitation of levels of human immunodeficiency virus type 1 RNA in plasma of patients receiving stavudine-didanosine combination therapy

We compared the QUANTIPLEX HIV-1 RNA 2.0 assay with the AMPLICOR HIV-1 MONITOR 1.0 assay for quantitation of human immunodeficiency virus type 1 (HIV-1) RNA in plasma in the Stadi trail, which evaluated a stavudine plus didanosine combination therapy in 52 patients. HIV-1 RNA baseline values measured with AMPLICOR HIV-1 MONITOR 1.0 were significantly higher than those measured with QUANTIPLEX HIV-1 RNA 2.0, and decreases in HIV-1 RNA levels from baseline were also found to be significantly higher when measured with the AMPLICOR HIV-1 MONITOR 1.0 assay. The frequency of HIV-1 RNA levels below the lower limit of quantitation was significantly higher with QUANTIPLEX HIV-1 RNA 2.0 than with AMPLICOR HIV-1 MONITOR 1.0. Reanalysis of these results by an ultrasensitive procedure of AMPLICOR HIV-1 MONITOR 1.0 or by a modified version of the test that included additional primers adapted for non-B HIV-1 clades yielded greater differences between the QUANTIPLEX HIV-1 RNA 2.0 assay and the AMPLICOR HIV-1 MONITOR 1.0 assay. Our results indicate that a valid comparison of the virological efficacies obtained with different antiretroviral drug regimens requires the use of the same viral load quantitation procedure; further standardization between the different HIV-1 RNA quantitation kits is therefore needed.

Evaluation of the Nuclisens HIV-1 QT assay for quantitation of human immunodeficiency virus type 1 RNA levels in plasma

Nuclisens HIV-1 QT is a new version of the NASBA HIV-1 QT assay for quantitation of human immunodeficiency virus type 1 (HIV-1) RNA in plasma. The specificity of this assay was 100% in one laboratory and 99%-with nonrepeatability of the initial false positive-in another. The test was linear between 2.0 and 6.0 log RNA copies per ml. According to the input HIV-1 RNA concentration, accuracy varied from -0.11 to +0.10 log RNA copy per ml and precision varied from 0.66 to 0.14 log RNA copy per ml. Reproducibility decreased when the HIV-1 RNA level was near the lower limit of quantitation of the test. HIV-1 RNA could be quantitated by Nuclisens HIV-1 QT in 36% (laboratory 1) and 24% (laboratory 2) of clinical samples with HIV-1 RNA levels lower than the lower limit of quantitation by NASBA HIV-1 QT. Nuclisens HIV-1 QT was not suitable for measurement of RNA from clade G and group O HIV-1 strains.

Influence of delayed viral production on viral dynamics in HIV-1 infected patients

We present and analyze a model for the interaction of human immunodeficiency virus type 1 (HIV-1) with target cells that includes a time delay between initial infection and the formation of productively infected cells. Assuming that the variation among cells with respect to this 'intracellular' delay can be approximated by a gamma distribution, a high flexible distribution that can mimic a variety of biologically plausible delays, we provide analytical solutions for the expected decline in plasma virus concentration after the initiation of antiretroviral therapy with one or more protease inhibitors. We then use the model to investigate whether the parameters that characterize viral dynamics can be identified from biological data. Using non-linear least-squares regression to fit the model to simulated data in which the delays conform to a gamma distribution, we show that good estimates for free viral clearance rates, infected cell death rates, and parameters characterizing the gamma distribution can be obtained. For simulated data sets in which the delays were generated using other biologically plausible distributions, reasonably good estimates for viral clearance rates, infected cell death rates, and mean delay times can be obtained using the gamma-delay model. For simulated data sets that include added simulated noise, viral clearance rate estimates are not as reliable. If the mean intracellular delay is known, however, we show that reasonable estimates for the viral clearance rate can be obtained by taking the harmonic mean of viral clearance rate estimates from a group of patients. These results demonstrate that it is possible to incorporate distributed intracellular delays into existing models for HIV dynamics and to use these refined models to estimate the half-life of free virus from data on the decline in HIV-1 RNA following treatment.

Use of multiple competitors for quantification of human immunodeficiency virus type 1 RNA in plasma

Quantification of human immunodeficiency virus type 1 (HIV-1) RNA in plasma has rapidly become an important tool in basic HIV research and in the clinical care of infected individuals. Here, a quantitative HIV assay based on competitive reverse transcription-PCR with multiple competitors was developed. Four RNA competitors containing identical PCR primer binding sequences as the viral HIV-1 RNA target were constructed. One of the PCR primers was fluorescently labeled, which facilitated discrimination between the viral RNA and competitor amplicons by fragment analysis with conventional automated sequencers. The coamplification of known amounts of the RNA competitors provided the means to establish internal calibration curves for the individual reactions resulting in exclusion of tube-to-tube variations. Calibration curves were created from the peak areas, which were proportional to the starting amount of each competitor. The fluorescence detection format was expanded to provide a dynamic range of more than 5 log units. This quantitative assay allowed for reproducible analysis of samples containing as few as 40 viral copies of HIV-1 RNA per reaction. The within- and between-run coefficients of variation were <24% (range, 10 to 24) and <36% (range, 27 to 36), respectively. The high reproducibility (standard deviation, <0.13 log) of the overall procedure for quantification of HIV-1 RNA in plasma, including sample preparation, amplification, and detection variations, allowed reliable detection of a 0.5-log change in RNA viral load. The assay could be a useful tool for monitoring HIV-1 disease progression and antiviral treatment and can easily be adapted to the quantification of other pathogens.