Predictive Factors for Response to a Boosted Dual HIV-Protease Inhibitor Therapy with Saquinavir and Lopinavir in Extensively Pre-Treated Patients

Objective

To evaluate predictive factors for therapy outcome of a boosted double-protease inhibitor (PI) regimen in 58 extensively pre-treated patients with HIV.

Methods

Patients received lopinavir/ritonavir 400/100 mg and saquinavir 1,000 mg twice daily without reverse transcriptase inhibitors (RTI). The primary outcome parameter was HIV RNA <400 copies/ml at week 48, secondary parameters were HIV-1 RNA and CD4+ T-cell count changes from baseline to week 48. Pharmacokinetics, genotypic resistance and clinical and individual parameters were correlated with the clinical outcome in regression analyses. Covariates for the analyses were minimum plasma concentration (Cmin), maximum plasma concentration, area under the concentration versus time curve, half-life and clearance of lopinavir and saquinavir, the genotypic inhibitory quotients (GIQ) of archived (GIQarch) and baseline PI resistance mutations, previously taken antiretrovirals, archived and baseline viral resistance mutations, baseline HIV-1 RNA and CD4+ T-cell count.

Results

The analyses detected correlations between the primary outcome parameter and several factors: baseline CD4+ T-cell count ( P=0.001); absence of mutations at V82T/A/F/I/S plus I54M/V/L ( P=0.002) or K20M/R ( P=0.010); and lopinavir CminGIQarch ( P=0.046). This regression model had a predictability of 97.0% for response to therapy. Covariates for the decrease of HIV-1 RNA from baseline to week 48 were baseline HIV-1 RNA ( P<0.001), lopinavir CminGIQarch ( P=0.013), presence/absence of mutations at V82T/A/F/I/S or I84A/V plus L10I/R/V/F, I54M/V/L or L63P ( P=0.018), and previously taken antiretrovirals ( P=0.034).

Conclusions

Baseline HIV-1 RNA <5.0 log10 and CD4+ T-cell count >200 cells/μl, lopinavir CminGIQarch >2,000 ng/ml and the absence of viral resistance mutations at V82T/A/F/I/S and I54M/V/L are highly predictive for therapeutic success of a regimen of saquinavir/lopinavir/ ritonavir without RTI in a heterogenic cohort of patients with an extensive pre-treatment history and highly variable pharmacokinetics.

Novel approach for genotyping varicella-zoster virus strains from Germany

In this study, we present a novel genotyping scheme to classify German wild-type varicella-zoster virus (VZV) strains and to differentiate them from the Oka vaccine strain (genotype B). This approach is based on analysis of four loci in open reading frames (ORFs) 51 to 58, encompassing a total length of 1,990 bp. The new genotyping scheme produced identical clusters in phylogenetic analyses compared to full-genome sequences from well-characterized VZV strains. Based on genotype A, D, B, and C reference strains, a dichotomous identification key (DIK) was developed and applied for VZV strains obtained from vesicle fluid and liquor samples originating from 42 patients suffering from varicella or zoster between 2003 and 2006. Sequencing of regions in ORFs 51, 52, 53, 56, 57, and 58 identified 18 single-nucleotide polymorphisms (SNPs), including two novel ones, SNP 89727 and SNP 92792 in ORF51 and ORF52, respectively. The DIK as well as phylogenetic analysis by Bayesian inference showed that 14 VZV strains belonged to genotype A, and 28 VZV strains were classified as genotype D. Neither Japanese (vaccine)-like B strains nor recombinant-like C strains were found within the samples from Germany. The novel genotyping scheme and the DIK were demonstrated to be practical and simple and allow the highly efficient replication of phylogenetic patterns in VZV initially derived from full-genome DNA sequence analyses. Therefore, this approach may allow us to draw a more comprehensive picture of wild-type VZV strains circulating in Germany and Central Europe by high-throughput procedures in the future.

Association of saquinavir plasma concentrations with side effects but not with antiretroviral outcome in patients infected with protease inhibitor-susceptible human immunodeficiency virus type 1

The objective of this study was to identify parameters among saquinavir pharmacokinetics, patients' demographics or comedications, to be addressed for improved personalized therapy. The presence of human immunodeficiency virus type 1 (HIV-1) RNA at therapy week 48 (principal target parameter), CD4 cell count at week 48, infections and side effects during 48 weeks, indicators of liver toxicity and lipid abnormalities at week 48, and a 12-h saquinavir plasma concentration-versus-time profile were assessed in 56 patients receiving saquinavir-ritonavir (1,000 and 100 mg, respectively) twice daily (44 therapy-naïve and 12 antiretrovirally pretreated patients) for association with saquinavir plasma concentrations, demographics, baseline values of target parameters, and coadministered antiretrovirals. Antiretroviral failure was observed in 8 of the 56 patients in whom HIV-1 RNA was detectable at week 48. This therapeutic failure was not associated with individual saquinavir pharmacokinetics. More likely, therapeutic failure was related to incidences interfering with antiretroviral therapy, causing therapy interruptions or incompliance. Weak associations were, however, seen between high maximum saquinavir plasma concentrations and both CD4 counts of > or =200 cells microl(-1) at week 48 (P = 0.014) and constitutional side effects during 48 weeks (P = 0.002). However, patients with high CD4 counts and constitutional side effects were not identical (P = 0.53). Saquinavir therapeutic drug monitoring in patients infected with protease inhibitor-susceptible HIV-1 taking saquinavir-ritonavir (1,000 and 100 mg, respectively) is not demanded for improving the antiretroviral effect. It may be contemplated in cases with constitutional side effects or low CD4 counts with weak immune responses.

Quadruple Nucleoside Therapy with Zidovudine, Lamivudine, Abacavir and Tenofovir in the Treatment of HIV

Highly active antiretroviral therapy (HAART) has significantly reduced morbidity and mortality in HIV-infected patients. However, problems such as short-term or long-term toxicity and the development of drug resistance could necessitate a change in the therapy regimen. Whereas various HAART options with low pill burden and favourable long-term tolerability profiles are available for naive patients, treatment of experienced patients tends to be more complex and remains a challenge. Treatment with class sparing nucleoside-only regimens could be an option in this context, but the combination of zidovudine (AZT), lamivudine (3TC) and abacavir (ABC) has shown to be inferior in terms of virological efficacy compared with the standard regimen. More promising data were obtained when AZT, 3TC and ABC were intensified with tenofovir (TDF), resulting in a quadruple nucleoside therapy. This regimen has demonstrated comparable potency to a standard regimen with AZT, 3TC and efavirenz in treatment-naive patients. Additionally, it has shown to be an efficient treatment option especially in moderately pretreated patients. This is accredited to the potency of the single components and the antagonistic selection pressure of AZT and TDF. The presence of L210W, or at least two of the mutations 41L, 67N, 70R, 215F/Y or 219Q/E, at or before baseline seems to be a predictor of non-response, whereas the presence of M184V does not impede virological response and might even be advantageous. This review summarizes current data on the combined use of AZT, 3TC, ABC and TDF in regard to virological and immunological outcome as well as genotypic predictors of response.

Predictive factors for response to a boosted dual HIV-protease inhibitor therapy with saquinavir and lopinavir in extensively pre-treated patients

OBJECTIVE

To evaluate predictive factors for therapy outcome of a boosted double-protease inhibitor (PI) regimen in 58 extensively pre-treated patients with HIV.

METHODS

Patients received lopinavir/ritonavir 400/100 mg and saquinavir 1,000 mg twice daily without reverse transcriptase inhibitors (RTI). The primary outcome parameter was HIV RNA < 400 copies/ml at week 48, secondary parameters were HIV-1 RNA and CD4+ T-cell count changes from baseline to week 48. Pharmacokinetics, genotypic resistance and clinical and individual parameters were correlated with the clinical outcome in regression analyses. Covariates for the analyses were minimum plasma concentration (C(min)), maximum plasma concentration, area under the concentration versus time curve, half-life and clearance of lopinavir and saquinavir, the genotypic inhibitory quotients (GIQ) of archived (GI6(arch)) and baseline PI resistance mutations, previously taken antiretrovirals, archived and baseline viral resistance mutations, baseline HIV-1 RNA and CD4+ T-cell count.

RESULTS

The analyses detected correlations between the primary outcome parameter and several factors: baseline CD4+ T-cell count (P = 0.001); absence of mutations at V82T/A/F/I/S plus 154M/V/L (P = 0.002) or K20M/R (P = 0.010); and lopinavir C(min)GIQ(arch) (P = 0.046). This regression model had a predictability of 97.0% for response to therapy. Covariates for the decrease of HIV-1 RNA from baseline to week 48 were baseline HIV-1 RNA (P < 0.001), lopinavir C(min)GIQ(arch) (P = 0.013), presence/absence of mutations at V82T/A/F/I/S or 184A/V plus L10I/R/V/F, 154M/V/L or L63P (P = 0.018), and previously taken antiretrovirals (P = 0.034).

CONCLUSIONS

Baseline HIV-1 RNA < 5.0 log10 and CD4+ T-cell count > 200 cells/microl, lopinavir C(min)GIQ(arch) > 2,000 ng/ml and the absence of viral resistance mutations at V82T/A/F/I/S and 154M/V/L are highly predictive for therapeutic success of a regimen of saquinavir/lopinavir/ ritonavir without RTI in a heterogenic cohort of patients with an extensive pre-treatment history and highly variable pharmacokinetics.

Evolution of Resistance Mutations during Low-Level Viral Replication in HIV-1–Infected Patients Treated with Zidovudine/Lamivudine/Abacavir as a First-Line Regimen

Objective

Long-term evaluation of viral evolution in patients who continued first-line therapy with zidovudine/lamivudine/abacavir (Trizivir [TZV]) in the presence of low-level viral replication and assessment of the impact of mutational patterns selected under TZV on viral load (VL), CD4+ T-cell count (CD4) and subsequent therapeutic options.

Design

Analysis of viral evolution based on genotypic resistance tests (GRT) from samples collected during non-suppressive first-line therapy with TZV.

Methods

Patients from the Frankfurt HIV cohort with at least 3 months uninterrupted first-line therapy with TZV in whom VL and CD4 measurements were performed at baseline and at follow up were identified. Criteria for virological failure (VF) were two consecutive VL >400 copies/ml. GRTs were required at baseline, VF and last visit (LV).

Results

Initially, 23/119 patients were classified as VF; 4/23 were lost to follow up. Median time to VF was 48 weeks. Because of the observed virological and immunological benefit, patients continued TZV for a median of 87 weeks despite detectable viraemia. Median CD4 increase and VL reduction at LV were 120 cells/mm3 and 317,100 copies/ml, respectively, compared to baseline. After 54 weeks of treatment with detectable VL, three mutational patterns were observed: Group A ( n=4) characterized by M184V without further regimen-associated mutations, group B ( n=9) by M184V accompanied by one to three thymidine analogue mutations (TAMs), and group C ( n=6) by M184V and four to six TAMs. No virological or CD4 parameters correlated with these patterns. Group A remained unchanged, thus preserving activity of most nucleoside analogues (NA). However, in the majority of patients (groups B and C) accumulation of mutations at different rates was observed, leading to a sequential loss of NA options.

Conclusions

Continuous treatment with TZV in the presence of viral replication is associated with a stepwise accumulation of resistance mutations. M184V was present in all cases, not followed by further selection of TAMs in a small, unpredictable subgroup of patients. However, in the majority of patients selection of M184V was associated with accumulation of TAMs at different rates leading to a substantial loss of active NAs, despite continuous virological and immunological benefit when compared with baseline.

Quadruple nucleoside therapy with zidovudine, lamivudine, abacavir and tenofovir in the treatment of HIV

Highly active antiretroviral therapy (HAART) has significantly reduced morbidity and mortality in HIV-infected patients. However, problems such as short-term or long-term toxicity and the development of drug resistance could necessitate a change in the therapy regimen. Whereas various HAART options with low pill burden and favourable long-term tolerability profiles are available for naive patients, treatment of experienced patients tends to be more complex and remains a challenge. Treatment with class sparing nucleoside-only regimens could be an option in this context, but the combination of zidovudine (AZT), lamivudine (3TC) and abacavir (ABC) has shown to be inferior in terms of virological efficacy compared with the standard regimen. More promising data were obtained when AZT, 3TC and ABC were intensified with tenofovir (TDF), resulting in a quadruple nucleoside therapy. This regimen has demonstrated comparable potency to a standard regimen with AZT, 3TC and efavirenz in treatmentnaive patients. Additionally, it has shown to be an efficient treatment option especially in moderately pretreated patients. This is accredited to the potency of the single components and the antagonistic selection pressure of AZT and TDF. The presence of L210W, or at least two of the mutations 41L, 67N, 70R, 215F/Y or 219Q/E, at or before baseline seems to be a predictor of non-response, whereas the presence of M184V does not impede virological response and might even be advantageous. This review summarizes current data on the combined use of AZT, 3TC, ABC and TDF in regard to virological and immunological outcome as well as genotypic predictors of response.

Ultrasensitive monitoring of HIV-1 viral load by a low-cost real-time reverse transcription-PCR assay with internal control for the 5' long terminal repeat domain

BACKGROUND

Current HIV-1 viral-load assays are too expensive for resource-limited settings. In some countries, monitoring of antiretroviral therapy is now more expensive than treatment itself. In addition, some commercial assays have shown shortcomings in quantifying rare genotypes.

METHODS

We evaluated real-time reverse transcription-PCR with internal control targeting the conserved long terminal repeat (LTR) domain of HIV-1 on reference panels and patient samples from Brazil (n = 1186), South Africa (n = 130), India (n = 44), and Germany (n = 127).

RESULTS

The detection limit was 31.9 IU of HIV-1 RNA/mL of plasma (> 95% probability of detection, Probit analysis). The internal control showed inhibition in 3.7% of samples (95% confidence interval, 2.32%-5.9%; n = 454; 40 different runs). Comparative qualitative testing yielded the following: Roche Amplicor vs LTR assay (n = 431 samples), 51.7% vs 65% positives; Amplicor Ultrasensitive vs LTR (n = 133), 81.2% vs 82.7%; BioMerieux NucliSens HIV-1 QT (n = 453), 60.5% vs 65.1%; Bayer Versant 3.0 (n = 433), 57.7% vs 55.4%; total (n = 1450), 59.0% vs 63.8% positives. Intra-/interassay variability at medium and near-negative concentrations was 18%-51%. The quantification range was 50-10,000,000 IU/mL. Viral loads for subtypes A-D, F-J, AE, and AG yielded mean differences of 0.31 log(10) compared with Amplicor in the 10(3)-10(4) IU/mL range. HIV-1 N and O were not detected by Amplicor, but yielded up to 180 180.00 IU/mL in the LTR assay. Viral loads in stored samples from all countries, compared with Amplicor, NucliSens, or Versant, yielded regression line slopes (SD) of 0.9 (0.13) (P < 0.001 for all).

CONCLUSIONS

This method offers all features of commercial assays and covers all relevant genotypes. It could allow general monitoring of antiretroviral therapy in resource-limited settings.

Effect of first line therapy including efavirenz and two nucleoside reverse transcriptase inhibitors in HIV-infected children

OBJECTIVE

In an intent-to-treat study, reduction of viral load, increase in CD4 cell count, clinical benefit and adverse reactions were examined in HIV-infected children receiving first line therapy including efavirenz.

METHODS

The data of 10 perinatally infected children (median age: 5.8 years) were evaluated during a treatment period of 24 months. Viral load and CD4 cell count were measured every 4 - 8 weeks. Pharmacokinetic evaluations of efavirenz were performed in all patients at study onset. Adverse reactions were reported after obtaining interval history and examination.

RESULTS

At base line, median CD4 cell count was 378 cells/microl (21%) and median viral load was 350,000 copies/ml (5.5 log10 copies/ml). After 24 months of treatment, the median viral load reduction was > 3.5 log10 copies/ ml and HIV-1 RNA < 50 copies/ml was found in 8/10 children (80%). Median CD4 cell count increased to 721 cells/microl (24%) after 3 months and was maintained at a level of >1000 cells/microl (> 25%) after 24 months of treatment. Regarding efavirenz levels, C min. values ranged from 845 to 3550 ng/ml (median: 1845 ng/ml) and C max. values from 2380 to 24 200 ng/ ml (median: 3670 ng/ml). The most common adverse effect was a mild skin rash (4/10 children). CNS symptoms were recorded in one patient and no hyperlipidaemia was seen.

CONCLUSION

First line therapy with efavirenz and two NRTIs was well tolerated by HIV-1 infected children and the reduction of viral load seems to be similar to single protease inhibitor-containing regimens.

Comparative evaluation of the Cobas Amplicor HIV-1 Monitor Ultrasensitive Test, the new Cobas AmpliPrep/Cobas Amplicor HIV-1 Monitor Ultrasensitive Test and the Versant HIV RNA 3.0 assays for quantitation of HIV-1 RNA in plasma samples

BACKGROUND

There are several commercially available assays for the quantitation of HIV RNA. A new automated specimen preparation system, the Cobas AmpliPrep, was developed to automate this last part of the PCR.

OBJECTIVES AND STUDY DESIGN

We compared the results obtained by the Roche Cobas Amplicor HIV-1 Monitor Ultrasensitive Test (MCA, manual sample preparation) with those by the Versant HIV-1 RNA 3.0 assay (bDNA). Secondly we compared the MCA with the new Cobas AmpliPrep/Cobas Amplicor HIV Monitor Ultrasensitive Test (CAP/CA, automated specimen preparation) by investigating clinical patient samples and a panel of HIV-1 non-B subtypes. Furthermore, we assessed the assay throughput and workflow (especially hands-on time) for all three assays.

RESULTS

Seventy-two percent of the 140 investigated patient samples gave concordant results in the bDNA and MCA assays. The MCA values were regularly higher than the bDNA values. One sample was detected only by the MCA within the linear range of quantification. In contrast, 38 samples with results <50 copies/ml in the MCA showed in the bDNA results between 51 and 1644 copies/ml (mean value 74 copies/ml); 21 of these specimens were shown to have detectable HIV RNA < 50 copies/ml in the MCA assay. The overall agreement between the MCA and the CAP/CA was 94.3% (551/584). The quantification results showed significant correlation, although the CAP/CA generated values slightly lower than those generated by the manual procedure. We found that the CAP/CA produced comparable results with the MCA test in a panel of HIV-1 non-B subtypes.

CONCLUSIONS

All three assays showed comparable results. The bDNA provides a high sample throughput without the need of full automation. The new CAP/CA provides reliable test results with no HIV-subtype specific influence and releases time for other works in the laboratory; thus it is suitable for routine diagnostic PCR.

HBV reactivation after kidney transplantation

Recent studies suggest that reappearance of hepatitis B surface antigen (HBsAg) and loss of anti-HBs antibodies may be common events in bone marrow recipients and patients with chemotherapy. In this study, we reviewed the virologic laboratory records from kidney recipients. Out of 1512 patients, 228 had been diagnosed with resolved HBV infection (anti-HBc positive, HBsAg negative) but normal liver enzyme levels prior to kidney transplantation. Reappearance of HBsAg after kidney transplantation was observed in two (0.9%) of those patients, which may be attributed to reactivation of a latent infection or to a new HBV infection. In both of the patients, HBV infection may have been reactivated although immunosuppression was just on a low level over the whole period. We conclude that natural immunity to HBV may not protect against reactivation in patients with suppression of the immune system. Periodic follow-up of HBV serology for early diagnosis of reactivation is highly recommended in transplant recipients.

Variety of interpretation systems for human immunodeficiency virus type 1 genotyping: confirmatory information or additional confusion?

The emergence of drug resistance remains a major problem during antiretroviral treatment of patients infected with human immunodeficiency virus type 1 (HIV-1). As phenotypic drug resistance is laborious and expensive to determine, and because numerous specific mutations are known to be correlated with different resistance patterns, genotyping of the reverse transcriptase and protease genes of HIV is fast becoming an integral part of HIV management in industrialized countries. A number of software-based interpretation systems have been developed for the interpretation of the resulting complex nucleotide sequences. These programs either employ rule-based algorithms or are based on a genotype-phenotype database. This paper reviews recent publications that compare different such systems, trying to identify the degree of discordance between different systems and the reasons underlying such discrepant interpretations. The highest discordance rate was observed for nucleoside reverse transcriptase inhibitors (NRTIs) followed by protease inhibitors (PIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs). For the NRTIs, it is the role of nucleoside analogue associated mutations, for the PIs and for the NNRTIs, that of secondary mutations that causes most discrepancies. As the complexity of the mutation pattern is likely to increase further with new drugs becoming available, rule-based genotype interpretation algorithms need to be updated frequently. Whilst not recommending one particular system, the authors believe that the correlation of genotypic with clinical data is probably the best way to develop an optimal algorithm.

Severe acute respiratory syndrome (SARS)--paradigm of an emerging viral infection

An acute and often severe respiratory illness emerged in southern China in late 2002 and rapidly spread to different areas of the Far East as well as several countries around the globe. When the outbreak of this apparently novel infectious disease termed severe acute respiratory syndrome (SARS) came to an end in July 2003, it had caused over 8000 probable cases worldwide and more than 700 deaths. Starting in March 2003, the World Health Organization (WHO) organised an unprecedented international effort by leading laboratories working together to find the causative agent. Little more than one week later, three research groups from this WHO-coordinated network simultaneously found evidence of a hitherto unknown coronavirus in SARS patients, using different approaches. After Koch's postulates had been fulfilled, WHO officially declared on 16 April 2003 that this virus never before seen in humans is the cause of SARS. Ever since, progress around SARS-associated coronavirus (SARS-CoV) has been swift. Within weeks of the first isolate being obtained, its complete genome was sequenced. Diagnostic tests based on the detection of SARS-CoV RNA were developed and made available freely and widely; nevertheless the SARS case definition still remains based on clinical and epidemiological criteria. The agent's environmental stability, methods suitable for inactivation and disinfection, and potential antiviral compounds have been studied, and development of vaccines and immunotherapeutics is ongoing. Despite its grave consequences in humanitarian, political and economic terms, SARS may serve as an example of how much can be achieved through a well-coordinated international approach, combining the latest technological advances of molecular virology with more "traditional" techniques carried out to an excellent standard.

Laboratory diagnosis of norovirus: which method is the best?

Noroviruses (NV) are transmitted by fecally contaminated food, vomit, and person-to-person contact. They are one of the main causes of non-bacterial acute gastroenteritis in nursing, old people and children's homes. NV outbreaks are characterized by a short incubation period (12-48 h), nausea, vomiting and diarrhea, and high secondary attack rates. The illness is generally mild and self-limiting. The aim of diagnostic procedures in viral gastroenteritis is to avoid nosocomial infections on the one hand and unnecessary antibiotic treatment on the other. Diagnostic procedures for NV are based on the detection of virus in stool samples by (immune) transmission electron microscopy (TEM), antigen ELISA, or polymerase chain reaction (PCR). In our study, a total of 244 stool samples obtained from 227 patients between March and May 2002 were tested by TEM, antigen ELISA and in-house PCR. Our data showed that PCR has the highest sensitivity (94.1%), followed by TEM (58.3%), and ELISA (31.3%), while specificity was highest for TEM (98.0%), followed by ELISA (94.9%), and PCR (92.4%). All three methods tested (TEM, ELISA and PCR) are useful for epidemiological investigations in gastroenteritis outbreaks; however, to maximize diagnostic validity for individual cases, at least two of the methods should be combined.

A 6-base pair insertion in the protease gene of HIV type 1 detected in a protease inhibitor-naive patient is not associated with indinavir treatment failure

Insertions in the protease gene of HIV-1 were rarely found and are not associated with reduced effectiveness of protease inhibitors although they are thought to be selected by protease inhibitor therapy. This is the first report of a 6-basepair insertion in the protease gene prior to protease inhibitor therapy.

Modifications and substitutions of the RNA extraction module in the ViroSeq™ HIV-1 genotyping system version 2: Effects on sensitivity and complexity of the assay

Genotypic testing for HIV-1 resistance to anti-retroviral drugs has become accepted widely as a routine method to guide anti-retroviral therapy. However, implementation into routine high-throughput laboratory diagnosis is difficult due to the complexity of the assay. A commercially available assay is the ViroSeq HIV-1 Genotyping System (Applied Biosystems, Weiterstadt, Germany). We modified and substituted the RNA extraction module to optimize the proportion of samples amplified successfully as follows: 1 ml plasma was concentrated by ultracentrifugation and extracted according to the manufacturer's instructions (Kit), by substituting the lysis buffer (Roche, Roche Diagnostics GmbH, Mannheim, Germany), and by using the QIAamp Viral RNA Kit (Qiagen GmbH, Hilden, Germany) with elution volumes of 60 (Q60) or 50 micro l (Q50). Overall Q50 showed a higher success rate (97%) than the other extraction modules used (range 88-91%). In samples with a viral load range of 1,000-4,999 copies/ml, Q50 was superior (95 vs. 65% to 83%), while in samples with a viral load range of 5,000-9,999 copies/ml or those with 10,000 or more copies/ml, the success rate of the extraction procedures showed no significant differences. In 18 samples, which were negative using the Kit or Roche extraction, Q60 resulted in 7/18 positive results; in addition the Q50 was successful in amplifying 7/10 of the Q60 negative samples. When investigating samples with a measurable viral load of less than 1,000 copies/ml or lower, Q50 had the highest success rate with 80% compared to the other procedures (33-63%). A statistically significant new cut-off could be defined for Q50 at a value of 250 copies/ml. The results showed clearly that the ViroSeq System is suitable for analyzing the HIV-1 genotype over a wide range of viral loads but could be improved significantly when substituting the RNA extraction module with Q50 without using a nested PCR protocol. This is of great importance as it avoids further time- and cost-intensive steps.

Prions and orthopedic surgery

Prions are a novel class of infectious agents that cause subacute encephalopathy in man and animals as human Creutzfeldt-Jakob disease (CJD), sheep scrapie and bovine spongiform encephalopathy (BSE). Previously, prions were shown to be transmitted by neuro- and ophthalmosurgical measures and by application of brain-derived therapeutic hormones. Recently, prions have been detected in blood specimens of experimentally infected monkeys indicating a principal threat to transfusion medicine, furthermore in human or bovine materials used in reconstructive surgery. In this article the risk of prion transmission from the surgeon to the patient or vice versa during (orthopedic) surgery is reevaluated including the issues of blood transfusion. This is accomplished based on recent epidemiologic findings and biometric calculations on the spread of prions in animals and humans as well as in terms of experimental data on artificially contaminated medical materials and devices. The overall risk of prion transmission in orthopedic surgery is considered very low if adequately prepared and sterilized materials and devices are used.

Comparison of nine resistance interpretation systems for HIV-1 genotyping

HIV-1 genotyping has become a widely accepted tool for monitoring antiretroviral therapy. However, the benefit of genotyping is limited by the need to interpret the mutation pattern in order to obtain a prediction regarding susceptibility to each antiretroviral drug. Several different interpretation systems are currently available, commercially or free of charge; some are in combination with the genotyping test system used. In this study, we compared the results obtained on patient samples, using nine different resistance interpretation systems for HIV-1 genotype, and identified mutation patterns responsible for discordances between these systems. HIV-1 genotypes from 26 patients were obtained using the ViroSeq HIV-1 Genotyping System (Applied Biosystems). Nine resistance interpretation systems were used: the 'virtual phenotype' systems VirtualPhenotype (Virco) and Geno2Pheno (http://cartan.gmd.de/geno2pheno.html), the rule-based resistance algorithms Antiretroviral Drug Resistance Report (Applied Biosystems), Stanford HIV-SEQ program (http://hivdb.stanford.edu/) and the ViroScorer system (ABL; including ANRS AC11, Detroit Medical Center, Grupo de Aconselhamento Virológico, CHL, and Rega). Discordance was defined as the same sequence being interpreted as resistant and sensitive to a substance by different systems, with intermediate scores being regarded as neutral. Results for lopinavir were not available from some interpretation systems. None of the 26 patient samples had concordant results for all drugs. The highest degree of concordance was found for the resistance scoring of lamivudine (25/26), followed by nelfinavir (23/26), indinavir, ritonavir, saquinavir (all 22/26), zidovudine, nevirapine (all 21/26), lopinavir, efavirenz (all 18/26), amprenavir, delavirdine (all 17/26), stavudine, abacavir (all 13/26), zalcitabine (7/26) and didanosine (5/26). In most cases, it was only one interpretation system that gave an interpretation different from the others. If this interpretation system was omitted, the overall discordance rate decreased by a statistically significant degree. There exists, therefore, an urgent need for standardization of interpretation algorithms for HIV-1 genotyping.

Identification of a novel coronavirus in patients with severe acute respiratory syndrome

BACKGROUND

The severe acute respiratory syndrome (SARS) has recently been identified as a new clinical entity. SARS is thought to be caused by an unknown infectious agent.

METHODS

Clinical specimens from patients with SARS were searched for unknown viruses with the use of cell cultures and molecular techniques.

RESULTS

A novel coronavirus was identified in patients with SARS. The virus was isolated in cell culture, and a sequence 300 nucleotides in length was obtained by a polymerase-chain-reaction (PCR)-based random-amplification procedure. Genetic characterization indicated that the virus is only distantly related to known coronaviruses (identical in 50 to 60 percent of the nucleotide sequence). On the basis of the obtained sequence, conventional and real-time PCR assays for specific and sensitive detection of the novel virus were established. Virus was detected in a variety of clinical specimens from patients with SARS but not in controls. High concentrations of viral RNA of up to 100 million molecules per milliliter were found in sputum. Viral RNA was also detected at extremely low concentrations in plasma during the acute phase and in feces during the late convalescent phase. Infected patients showed seroconversion on the Vero cells in which the virus was isolated.

CONCLUSIONS

The novel coronavirus might have a role in causing SARS.

Correlation of phenotypic zidovudine resistance with mutational patterns in the reverse transcriptase of human immunodeficiency virus type 1: interpretation of established mutations and characterization of new polymorphisms at codons 208, 211, and 214

Zidovudine resistance (ZDV-R) is associated with classic genotypic changes at codons 41, 67, 70, 210, 215, and 219 of the human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) gene as well as with the multinucleoside resistance (MNR) complexes (Q151M MNR complex; 6-bp insertion/A62V complex). In addition, enhanced resistance to ZDV in the context of the classic ZDV mutations plus the M184V mutation has been associated with additional mutations at positions 208, 211, 214, and 333. In this study we investigated phenotypic ZDV-R determined by a recombinant virus assay (Antivirogram; Virco) in 223 clinical samples in relation to the above genotypic changes. 150 out of 223 clinical samples had the M184V mutation. Phenotypic ZDV-R ranged from 0.3- to 5,338-fold. Sixteen samples (15 with high ZDV-R ranging from 90- to 3,571-fold) contained MNR-associated patterns. Analysis of classic mutational patterns broadly demonstrated increasing ZDV-R with increasing number of ZDV mutations. A comparable correlation was obtained when ZDV-R was analyzed only relative to the T215Y/F mutation. Site-directed mutagenesis experiments investigating the influence of the additional mutations H208Y, R211K, and L214F on ZDV-R resulted in a 7.4- or 21-fold increase in ZDV-R when the R211K/L214F or H208Y/R211K/L214F mutations, respectively, were added to a highly ZDV-R virus. In the clinical sample data set we analyzed, the combination of R211K/L214F appeared most frequently. The H208Y change was detected only in highly ZDV-R viruses, whereas the G333E/D change was distributed equally. All changes were independent of the M184V mutation. A 2.4- or 8-fold increase in ZDV-R was observed in the clinical samples with high ZDV-R containing the R211K/L214F or H208Y/R211K/L214F mutations, respectively. We have shown that the combination of the additional mutations H208Y, R211K, and L214F in HIV-1 RT may influence ZDV-R and should be considered when assessing ZDV-R.

Evaluation of the LiPA HIV-1 RT assay version 1: comparison of sequence and hybridization based genotyping systems

BACKGROUND

Specific mutations in the reverse transcriptase (RT) gene of HIV-1 are associated with reduced activity of nucleoside inhibitors used in the antiretroviral treatment of infected patients. The appearance of these mutations may result in therapy failure. Therefore, HIV-1 genotyping is an important tool for monitoring antiretroviral therapy. At present different assay systems are used to obtain information about the changes in the viral genome.

OBJECTIVE

The aim of this study was to evaluate the LiPA HIV-1 RT assay version 1 for monitoring drug resistance mutations in comparison to full-length sequencing.

STUDY DESIGN

Two hundred and forty-four samples were analyzed using the LiPA HIV-1 RT assay version 1 and were compared with full RT gene sequences obtained by in-house sequencing.

RESULTS

In 129/244 (52.9%) samples full concordance between both systems was found, in 86/244 (35.2%) samples at least one position was not detected by the LiPA assay, in 19/244 (7.8%) samples the results were contradictory, and in 10/244 (4.1%) contradictory as well as absent signals from the LiPA assay were found. Analyzing total codons, missing signals were observed at 137 codons, mainly found at positions 41 (40/137) and 215 (41/137). The 32 contradictions between LiPA and sequencing were equally distributed across all codons except for position 184 with only one case. The main reason for missing signals is the heterogeneity of the HIV genome, which could not be fully covered by the LiPA probes, e.g. unusual mutations or polymorphisms in the vicinity of the relevant positions. The same is the case for some contradictions, although most of them are not evident (19/32 positions).

CONCLUSIONS

We analyzed a patient population with partly multiple therapy failures. The LiPA HIV-1 RT assay version 1 gives a high degree of samples with at least one missing signal (39.4%) in our cohort and this is not acceptable for a diagnostic tool. However, the LiPA assay might work better in untreated patients and could, therefore, still be used for screening.

Evaluation of the Cobas AmpliPrep/Cobas Amplicor HIV-1 Monitor Ultrasensitive Test: comparison with the Cobas Amplicor HIV-1 Monitor test (manual specimen preparation)

In this preliminary study, we evaluated the performance of the Cobas AmpliPrep/Cobas Amplicor HIV-1 Monitor Ultrasensitive Test (CAP; Roche Molecular Systems, Branchburg, NJ) for automated specimen preparation and quantitative detection of human immunodeficiency virus type 1 (HIV-1) RNA and compared it to the Cobas Amplicor HIV-1 Monitor Ultrasensitive Test (MCA; Roche), which includes a manual sample preparation protocol. A dilution panel of a patient sample was prepared. Additionally, 584 EDTA plasma samples were collected from HIV-1 infected patients. Reproducibility was estimated with six assay runs using the dilution panel. The inter-assay coefficient of variation ranged from 39.4 to 48.4% (CAP assay) and from 34.3 to 45.6% (MCA assay), whereas the intra-assay coefficient of variation ranged from 6.2 to 58.0% (CAP assay) and from 4.4 to 57.3% (MCA assay). Comparison of CAP assay results with the HIV-1 copy number of the dilution panel determined by the MCA assay resulted in a good agreement, although the CAP results were found to be slightly lower. A significant correlation between both test systems was found when clinical samples were analyzed. The mean viral load of 152 samples, which were within the linear range of both tests, was 3.70 log(10) HIV-1 copies/ml by the CAP assay compared to 3.73 by the MCA assay. In conclusion, we could demonstrate that the new Cobas AmpliPrep/Cobas Amplicor HIV Monitor Ultrasensitive Test is reproducible and sensitive. In comparison to the assay with manual extraction, no significant difference in HIV-1 RNA copy numbers was observed.