Standardized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA

Patients with COVID-19 shed SARS-CoV-2 RNA in stool, sometimes well after their respiratory infection has cleared. This may be significant for patient health, epidemiology, and diagnosis. However, methods to preserve stool, and to extract and quantify viral RNA are not standardized. We test the performance of three preservative approaches at yielding detectable SARS-CoV-2 RNA: the OMNIgene-GUT kit, Zymo DNA/RNA shield kit, and the most commonly applied, storage without preservative. We test these in combination with three extraction kits: QIAamp Viral RNA Mini Kit, Zymo Quick-RNA Viral Kit, and MagMAX Viral/Pathogen Kit. We also test the utility of ddPCR and RT-qPCR for the reliable quantification of SARS-CoV-2 RNA from stool. We identify that the Zymo DNA/RNA preservative and the QiaAMP extraction kit yield more detectable RNA than the others, using both ddPCR and RT-qPCR. Taken together, we recommend a comprehensive methodology for preservation, extraction and detection of RNA from SARS-CoV-2 and other coronaviruses in stool.

The Comparison of Honeybee Viral Loads for Six Honeybee Viruses (ABPV, BQCV, CBPV, DWV, LSV3 and SBV) in Healthy and Clinically Affected Honeybees with TaqMan Quantitative Real-Time RT-PCR Assays

The viral loads of acute bee paralysis virus (ABPV), black queen cell virus (BQCV), chronic bee paralysis virus (CBPV), deformed wing virus (DWV), Lake Sinai virus 3 (LSV3), and sacbrood bee virus (SBV) were determined in samples with the use of quantitative TaqMan real-time reverse transcription and polymerase chain reaction (RT-qPCR). A total of 108 samples of healthy adult honeybees from four differently located apiaries and samples of honeybees showing different clinical signs of viral infections from 89 apiaries were collected throughout Slovenia. The aim of this study was to discover correlations between viral loads and clinical signs in adult honeybees and confirm previously set threshold viral load levels between healthy and clinically affected honeybees. Within this study, two new RT-qPCR assays for quantification of LSV3 and SBV were developed. Statistically significant differences in viral loads of positive samples were identified between healthy and clinically affected honeybees for ABPV, CBPV, DWV, and SBV, while for BQCV and LSV3, no statistical differences were observed between both groups. Despite high detected LSV3 prevalence and viral loads around 6.00 log₁₀ viral copies/bee, this lineage probably has a limited impact on the health status of honeybee colonies. The determined viral loads between 3.94 log₁₀ and 13.17 log₁₀ in positive samples for six viruses, collected over 10 consecutive months, including winter, present additional information of high viral load variations in healthy honeybee colonies.

Real-world application of the Xpert® HBV viral load assay on serum and dried blood spots

As we strive towards the WHO goal of elimination of viral hepatitis as a public health threat by 2030, implementation of reliable, accurate diagnostic assays is crucial to identify those at risk of disease progression and those at risk of transmission. Ironically those at greatest risk of chronic hepatitis B are often in resource-poor regions with limited access to testing, collection, storage, and/or transportation of peripheral blood. The Xpert® HBV Viral Load assay provides an easy to use, convenient means of measuring load on GeneXpert platforms. In this study, the Xpert assay is evaluated against four commercially available high-throughput assays for Hepatitis B virus (HBV) loads. In addition application of dried blood spots (DBS) for estimation of viral load is assessed on real-world samples collected from a remote Pacific Island, Kiribati. A total of 107 serum/plasma samples were tested in the Xpert HBV load assay and compared with the Abbott m2000, Alinity m, and Roche Cobas CAP/CTM and 6800. Fifty-three DBS were tested in the Xpert assay and compared with matching serum samples. Overall 82% serum/plasma samples demonstrated good correlation between the Xpert and Roche and Abbott assays, to within 0.5 log10 IU/ml. The greatest discrepancies were seen at the limits of quantification of all assays. About 85.4% DBS gave estimable viral loads to within 1 log10 IU/ml of the serum load. The Xpert HBV viral load assay is recommended for all settings but particularly useful for resource-poor settings. Utility of DBS with the Xpert assay provides a simple means for testing in remote settings.

Accurate dried blood spots collection in the community using non-medically trained personnel could support scaling up routine viral load testing in resource limited settings

Regular plasma HIV-RNA testing for persons living with HIV on antiretroviral therapy (ART) is now the global standard, but as many as 60% of persons in Africa today on ART do not have access to standard laboratory HIV-RNA assays. As a result, patients in Zambia often receive treatment without any means of determining true virologic failure, which poses a risk of premature switch of ART regimens and widespread HIV drug resistance. Dry blood spots (DBS) on the other hand require unskilled personnel and less complex storage supply chain so are ideal to capture viral-load results from HIV patients outside clinic settings. We assess collection of DBS in the community using non-medically trained personnel (NMP) and documented challenges. We trained 23 NMP to collect DBS from lost to follow-up (LTFU) patients in 4 rural and urban Zambian districts. We developed a phlebotomy box to transport DBS without contamination at ambient temperature and concomitant training and standard operating procedures. We evaluated this through field observations, bi-weekly meetings, reports, and staff meetings. The laboratory assessed DBS quality for testing validity. We attempted to collect DBS from 357 participants in the community. Though individual reasons for refusal from the remaining 37% were not collected, NMPs reported privacy concerns, awkward box-size which drew attention in the community and fears of undisclosed uses of samples related to witchcraft and circulating narratives about past research. Successful DBS collection was not associated with patient gender, age, time on ART, enrolment CD4, facility. DBS viral-load collection by NMP is feasible in Zambia. Our training approach and assessments of NMP not part of the health system can be extended to patients by giving them more responsibility to manage their own differentiated care groups. Concerted efforts that compare collection of DBS by NMP to those collected by skilled-medical personnel are needed.

Reassessment of hepatitis B virus window periods for two transcription-mediated amplification assays using screening data of South African blood donors

BACKGROUND

Transcription-mediated amplification assays for HBV DNA detection have transitioned from the Ultrio to the Ultrio Plus assay, which features increased analytic sensitivity due to inclusion of a target enhancer reagent. The impact on HBV detection for different categories of HBV infection has not been fully evaluated.

STUDY DESIGN AND METHODS

Hepatitis B virus (HBV) DNA and hepatitis B surface antigen (HBsAg) detection rates as well as viral load (VL) distributions in HBV nucleic acid test (NAT)-yield samples were compared during 1 year of screening of South African blood donors with the Ultrio assay and the subsequent year by the Ultrio Plus version. HBV-DNA concentration at the HBsAg seroconversion point was established by regression analysis using a set of antibody to hepatitis B core antigen-negative acute viremic samples.

RESULTS

Ultrio Plus detected twofold more window-period (WP) NAT yield donations and 1.7-fold more occult HBV infections than Ultrio. The VL distribution data indicated that Ultrio not only missed samples of less than 100 copies/mL, but also a substantial number higher than this level. The VL at the HBsAg seroconversion point was estimated at 916 copies/mL, whereas the VL at the NAT-conversion points was calculated at 63 and 4.1 copies/mL for Ultrio and Ultrio Plus. This reduced the infectious WP (compared to HBsAg testing) by 10.3 and 20.4 days, respectively.

CONCLUSION

The higher-than-expected increase in HBV-NAT yields after introduction of the Ultrio Plus assay is likely attributable to variable sensitivity of the former Ultrio assay for different HBV samples. Therefore, previously published HBV WP reduction and residual risk estimates based on analytical sensitivity of the Ultrio assay need to be revised.

[Analysis of the results of the HIV-1, HCV and HBV viral load of SEIMC External Quality Control Program. Year 2014]

Human immunodeficiency virus type 1 (HIV-1), hepatitis B virus (HBV) and hepatitis C virus (HCV) viral load determinations are among the most relevant markers for the follow up of patients infected with these viruses. External quality control tools are crucial to ensure the accuracy of results obtained by microbiology laboratories. This article summarizes the results obtained from the 2014 SEIMC (Spanish Society of Infectious Diseases and Clinical Microbiology) External Quality Control Programme for HIV-1, HCV, and HBV viral loads. In the HIV-1 program, a total of 5 standards were sent. One standard consisted in seronegative human plasma, while the remaining 4 contained plasma from 3 different viremic patients, in the range of 2-5 log10 copies/mL; 2 of these standards were identical aiming to determine repeatability. A significant proportion of the laboratories (30.8% on average) obtained values out of the accepted range (mean ± 0.25 log10 copies/mL), depending on the standard and on the method used for quantification. Repeatability was excellent, with up to 95.8% of laboratories reporting results within the limits (Δ < 0.5 log10 copies/mL). The HBV and HCV program consisted of 2 standards with different viral load contents. Most of the participants, 83.7% in the case of HCV and 87.9% in the HBV, obtained all the results within the accepted range (mean ± 1.96 standard deviations log10 IU/mL). Data from this analysis reinforce the utility of proficiency programmes to ensure the quality of the results obtained by a particular laboratory, as well as the importance of the post-analytical phase on the overall quality. Due to the remarkable interlaboratory variability, it is advisable to use the same method and the same laboratory for patient follow up.

Routine CD4 monitoring in HIV patients with viral suppression: Is it really necessary? A Portuguese cohort

PURPOSE

CD4 cell-count has been regarded as the key surrogate marker for prognostic staging and therapeutic monitoring of HIV-infected individuals. Our purpose was to assess the probability of maintaining a CD4 count >200 cells/μL in patients with continuous viral suppression and CD4 cell counts >200 cells/μL.

METHODS

Retrospective cohort study of HIV-infected patients, treatment naïve, who started antiretroviral therapy between 2007 and 2011. We estimated the probability of maintaining CD4 counts >200 cells/μL during continuous viral suppression using the Kaplan-Meier method. The hazard ratios of a CD4 count <200 cells/μL were estimated and compared using Cox proportional hazards regression.

RESULTS

401 patients were included: 70.1% men; median age 37 years; 98.8% HIV-1 infected. The median duration of continuous viral suppression with CD4 counts >200 cells/μL was 40.5 months. Ninety-three percent of patients maintained CD4 counts ≥200 cells/μL during the period of continuous viral suppression. Compared with those with an initial CD4 count ≥350 cells/μL, patients with initial CD4 count <300 cells/μL had a significantly higher risk of a CD4 count <200 cells/μL. Patients with viral suppression and CD4 counts ≥350 cells/μL had a 97.1% probability of maintaining CD4 cell counts ≥200 cells/μL for 48 months.

CONCLUSIONS

The probability of a CD4 count <200 cells/μL in an HIV-infected patient with viral suppression and CD4 ≥350 cells/μL was very low. These data suggests less frequent monitoring of CD4 counts in these patients.

Validation of RPS13 as a reference gene for absolute quantification of SIV RNA in tissue of rhesus macaques

Persistent HIV reservoirs and the absolute quantification of viral RNA copies in tissues have become a prominent focus of multiple areas ofHIV/SIV research. Absolute quantification of viral RNA via reverse transcription, quantitative PCR (RT-qPCR) necessitates the use of an appropriate RNA reference gene whose expression is unaffected by both experimental and confounding conditions. In this study, we demonstrate the utility of ribosomal protein S13 mRNA (RPS13) as a stable, medium abundance reference gene for RT-qPCR normalization of HIV/SIV RNA copy number. We developed a RPS13 RNA standard assay utilizing an in vitro RNA transcript for normalization of absolute SIV RNA quantities in tissues reservoirs. The RT-qPCR assay showed a high degree of repeatability and reproducibility across RNA levels appropriate for absolute SIV quantification. In assessing the utility of RPS13 as a reference gene, limited variation in the absolute, inter-tissue quantities of RPS13 mRNA was observed within multiple tissue samples obtained from rhesus macaques (average CV=2.86%). We demonstrate rhesus macaque RPS13 mRNA expression is not affected by alcohol administration, SIV infection, or antiviral therapy (PMPA/FTC). Additionally, assay functionality was validated for normalization of SIV copy number using cellular RNA prepared from samples of variable RNA integrity. RPS13 is a suitable reference gene for normalization of absolute SIV RNA quantities in tissues and is most appropriate for intra-tissue or similar tissue type comparisons of SIV copy number.

Quantification of HEV RNA by Droplet Digital PCR

The sensitivity of real-time PCR for hepatitis E virus (HEV) RNA quantification differs greatly among techniques. Standardized tools that measure the real quantity of virus are needed. We assessed the performance of a reverse transcription droplet digital PCR (RT-ddPCR) assay that gives absolute quantities of HEV RNA. Analytical and clinical validation was done on HEV genotypes 1, 3 and 4, and was based on open reading frame (ORF)3 amplification. The within-run and between-run reproducibilities were very good, the analytical sensitivity was 80 HEV RNA international units (IU)/mL and linearities of HEV genotype 1, 3 and 4 were very similar. Clinical validation based on 45 samples of genotype 1, 3 or 4 gave results that correlated well with a validated reverse transcription quantitative PCR (RT-qPCR) assay (Spearman rs = 0.89, p < 0.0001). The RT-ddPCR assay is a sensitive method and could be a promising tool for standardizing HEV RNA quantification in various sample types.

Scale-up of Routine Viral Load Testing in Resource-Poor Settings: Current and Future Implementation Challenges

Despite immense progress in antiretroviral therapy (ART) scale-up, many people still lack access to basic standards of care, with our ability to meet the Joint United Nations Programme on HIV/AIDS 90-90-90 treatment targets for HIV/AIDS dependent on dramatic improvements in diagnostics. The World Health Organization recommends routine monitoring of ART effectiveness using viral load (VL) testing at 6 months and every 12 months, to monitor treatment adherence and minimize failure, and will publish its VL toolkit later this year. However, the cost and complexity of VL is preventing scale-up beyond developed countries and there is a lack of awareness among clinicians as to the long-term patient benefits and its role in prolonging the longevity of treatment programs. With developments in this diagnostic field rapidly evolving-including the recent improvements for accurately using dried blood spots and the imminent appearance to the market of point-of-care technologies offering decentralized diagnosis-we describe current barriers to VL testing in resource-limited settings. Effective scale-up can be achieved through health system and laboratory system strengthening and test price reductions, as well as tackling multiple programmatic and funding challenges.

Relevance of a full-length genomic RNA standard and a thermal-shock step for optimal hepatitis delta virus quantification

Hepatitis D virus (HDV) is a defective RNA virus that requires the surface antigens of hepatitis B virus (HBV) (HBsAg) for viral assembly and replication. Several commercial and in-house techniques have been described for HDV RNA quantification, but the methodologies differ widely, making a comparison of the results between studies difficult. In this study, a full-length genomic RNA standard was developed and used for HDV quantification by two different real-time PCR approaches (fluorescence resonance energy transfer [FRET] and TaqMan probes). Three experiments were performed. First, the stability of the standard was determined by analyzing the effect of thawing and freezing. Second, because of the strong internal base pairing of the HDV genome, which leads to a rod-like structure, the effect of intense thermal shock (95°C for 10 min and immediate cooling to -80°C) was tested to confirm the importance of this treatment in the reverse transcription step. Lastly, to investigate the differences between the DNA and RNA standards, the two types were quantified in parallel with the following results: the full-length genomic RNA standard was stable and reliably mimicked the behavior of HDV-RNA-positive samples, thermal shock enhanced the sensitivity of HDV RNA quantification, and the DNA standard underquantified the HDV RNA standard. These findings indicate the importance of using complete full-length genomic RNA and a strong thermal-shock step for optimal HDV RNA quantification.

A one step real-time RT-PCR assay for the quantitation of Wheat yellow mosaic virus (WYMV)

BACKGROUND

Wheat yellow mosaic virus (WYMV) is an important pathogen in China and other countries. It is the member of the genus Bymovirus and transmitted primarily by Polymyxa graminis. The incidence of wheat infections in endemic areas has risen in recent years. Prompt and dependable identification of WYMV is a critical component of response to suspect cases.

METHODS

In this study, a one step real-time RT-PCR, followed by standard curve analysis for the detection and identification of WYMV, was developed. Two reference genes, 18s RNA and β-actin were selected in order to adjust the veracity of the real-time RT-PCR assay.

RESULTS

We developed a one-step Taqman-based real-time quantitative RT-PCR (RT-qPCR) assay targeting the conserved region of the 879 bp long full-length WYMV coat protein gene. The accuracy of normalized data was analyzed along with appropriate internal control genes: β-actin and 18s rRNA which were included in detecting of WYMV-infected wheat leaf tissues. The detectable end point sensitivity in RT-qPCR assay was reaching the minimum limit of the quantitative assay and the measurable copy numbers were about 30 at 10⁶-fold dilution of total RNA. This value was close to 10⁴-fold more sensitive than that of indirect enzyme-linked immunosorbent assay. More positive samples were detected by RT-qPCR assay than gel-based RT-PCR when detecting the suspected samples collected from 8 regions of China. Based on presented results, RT-qPCR will provide a valuable method for the quantitative detection of WYMV.

CONCLUSIONS

The Taqman-based RT-qPCR assay is a faster, simpler, more sensitive and less expensive procedure for detection and quantification of WYMV than other currently used methods.

Technical and regulatory shortcomings of the TaqMan version 1 HIV viral load assay

Background

The lower limit of detection of the original Roche Amplicor HIV plasma viral load (pVL) assay (50 copies/mL) has defined HIV treatment success. The Amplicor assay, however, has been replaced by the Roche TaqMan assay(s). Changes to the limits of detection and calibration have not been validated for clinical utility. Sudden increases in the number of patients with detectable pVL have been reported following the introduction of the TaqMan version 1 assay.

Methods

Between October 2009 and April 2010 all routine pVL samples from British Columbia, Canada, with 40–250 copies/mL by TaqMan were re-tested by Amplicor (N = 1198). Subsequent short-term virological and resistance outcomes were followed in patients with unchanged therapy (N = 279; median 3.2 months follow-up).

Results

TaqMan and Amplicor values correlated poorly at low pVL values. Low-level pVL by TaqMan was not associated with impending short-term virological failure; only 17% of patients with 40–250 copies/mL by TaqMan had detectable pVL by Amplicor at follow-up. During the follow-up period only 20% of patients had an increase in pVL by TaqMan (median [IQR]: 80 [36–283] copies/mL). In addition, in ∼2.4% of samples pVL was dramatically underestimated by TaqMan due to poor binding of the proprietary TaqMan primers.

Conclusions

The replacement of Amplicor with the TaqMan assay has altered the previously accepted definition of HIV treatment failure without any evidence to support the clinical relevance of the new definition. Given the systematic differences in measurement in the low pVL range the British Columbia HIV treatment guidelines now use a threshold of >250 copies/mL by TaqMan to define treatment failure.

Low-cost assays for monitoring HIV infected individuals in resource-limited settings

Use of a combination of CD4 counts and HIV viral load testing in the management of antiretroviral therapy (ART) provides higher prognostic estimation of the risk of disease progression than does the use of either test alone. The standard methods to monitor HIV infection are flow cytometry based for CD4+ T cell count and molecular assays to quantify plasma viral load of HIV. Commercial assays have been routinely used in developed countries to monitor ART. However, these assays require expensive equipment and reagents, well trained operators, and established laboratory infrastructure. These requirements restrict their use in resource-limited settings where people are most afflicted with the HIV-1 epidemic. With the advent of low-cost and/or low-tech alternatives, the possibility of implementing CD4 count and viral load testing in the management of ART in resource-limited settings is increasing. However, an appropriate validation should have been done before putting them to use for patient testing.

Viral load testing in a resource-limited setting: quality control is critical

BACKGROUND

World Health Organization guidelines now recommend routine use of viral load testing, where available, for patients receiving antiretroviral treatment (ART). However, its use has not been routinely implemented in many resource-limited settings due to cost, availability and accessibility. Viral load testing is complex, making its application in resource-limited settings challenging. We describe the issues encountered by Médecins Sans Frontières (MSF) when using routine viral load testing in a large HIV programme in sub-Saharan Africa.

METHODS

Between October 2005 and August 2006, more than 1200 patients on ART had viral load tests at baseline and at three-month intervals performed by a local reference laboratory that was quality assured by an experienced international institution. Concerns with reliability of results halted testing. The quality control measures instituted with a second laboratory and outcomes of these were documented.

RESULTS

In 2005 and 2006, only 178 of 334 (53%) previously ART-naïve patients tested after six to 12 months of treatment had viral loads of less than 1000 copies/mL. Similar MSF programmes elsewhere demonstrated virological suppression rates of more than 85%, and duplicate testing showed unacceptable discordance. Laboratory problems encountered included: disregarded quality control; time delays; requirement for retesting; and duplicate sample variations. Potentially harmful clinical outcomes of inaccurate viral load results include: unnecessary ART regimen changes; unnecessary enhanced adherence counselling after "false failures"; and undetected virological failure.

CONCLUSIONS

Viral load testing performed without rigorous quality control carries the risk of erroneous and potentially damaging results. Viral load testing should be utilized only if robust quality assurance has been implemented. Our experience in this and other settings led to the development of a guide for assessing the suitability of a laboratory for viral load testing that can be used to help achieve reliable results.

Quantitative HIV-1 proviral DNA detection: a multicentre analysis

Despite the widespread use of molecular biology techniques, standardized methods for the measurement of HIV-1 proviral DNA are currently lacking and several discordant results are still present in different studies. To assess the clinical meaning of the proviral DNA load, a study group comprising seven different laboratories was set up to standardize a HIV-1 proviral DNA quantification method able to assess the DNA proviral load of the most relevant circulating HIV-1 subtypes. Reference samples (24 cellular samples infected with HIV-1 clade B, and 40 samples of peripheral blood mononuclear cells containing different concentrations of plasmids expressing different HIV-1 clades) were distributed and tested blindly. All laboratories employed hTERT gene as housekeeping gene and primers within the gag gene to quantify different HIV-1 clades. Inter-laboratory results did not differ statistically but showed only minor variations concerning HIV-1 DNA amounts and different HIV clades, with a good agreement among the laboratories participating in the study. Since test standardization represents a key step for future application in clinical practice, further studies of the patients' samples are in progress to establish the real meaning and utility of the proviral DNA load for clinical management of HIV-1 infected patients.

Physical activity and immunity in HIV-infected individuals

The purpose of this study was to determine what relationship exists among physical activity levels and viral load and CD4+ cell count in HIV-infected individuals. Increased viral load is associated with disease progression and symptom severity. A convenience sample of 66 male and female subjects between the ages of 18 and 64 years of age (mean 39 +/- 8) was recruited from a hospital-based HIV/AIDS clinic. Components of PA were assessed for three continuous days using a mini-motion logger wrist actigraph. These components included mean PA level, and PA index and acceleration index. Pearson's correlational analysis was used to test the strength of association between PA components and viral load or CD4+ cell count. A significant inverse relationship was found between mean PA level and viral load (p=0.047). An inverse relationship was also observed between PA index and viral load (p=0.0061). Neither mean PA nor PA index scores correlated with CD4+ cell counts. Acceleration index, a measure of PA intensity, showed no correlation to viral load or CD4+ cell counts. These findings suggest that increasing levels of physical activity might have beneficial effects on viral load in HIV-infected individuals.

[Analysis of the results of the SEIMC External Quality Control Program for HIV-1 and HCV viral loads, 2007]

BACKGROUND

Human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) viral load determinations are among the most important tasks performed in the molecular microbiology laboratory, due to their importance in patient follow-up. Quality control tools are crucial in these laboratories to ensure the accuracy of the results. This article presents the analysis of the results obtained in 2007 from the SEIMC External Quality Control Program for HIV-1 and HCV viral loads.

METHODS AND RESULTS

In the HIV-1 program, a total of five standards were sent. One standard consisted of seronegative human plasma, while the remaining four contained plasma from three different viremic patients, in a range of 2-5 log(10) copies/mL; to analyze repeatability, two of these standards were identical. The specificity was good for all the methods used by the participants, and only two out of 75 results were considered to be false positive results. A substantial proportion of the laboratories (20% on average) obtained values outside the accepted range (mean +/-0.2 log(10) copies/mL), depending on the standard and on the method used for quantification. A few errors were due to the transcription of the analytical result. Repeatability was also acceptable but approximately 15% of laboratories failed this evaluation. The HCV program consisted of two standards with different viral load contents. Most of the participants (94.6%) obtained results within the accepted range (mean +/-1.96 SD log(10) UI/mL), and interlaboratory variability was <0.5 log units for both standards and all techniques.

CONCLUSIONS

Data from this analysis reinforce the utility of proficiency programs to ensure the quality of the results obtained by a particular laboratory, as well as the importance of the post-analytical phase in overall quality. Due to wide interlaboratory variability, the use of the same method and the same laboratory for patient follow-up is advisable.

Evaluation of real-time PCR laboratory-developed tests using analyte-specific reagents for cytomegalovirus quantification

Viral load testing for cytomegalovirus (CMV) has become the standard for the diagnosis of infection and monitoring of therapy at many transplant centers. However, no viral load test has been approved by the FDA. Therefore, many laboratories rely on laboratory-developed assays. This study evaluated the performance characteristics of two real-time PCR tests developed using the artus CMV analyte-specific reagents (ASRs). One version is distributed by Abbott Molecular and the other by QIAGEN. For plasma specimens, the Abbott test had a limit of detection of 2.3 log10 copies/ml and a linear range up to at least 6.0 log10 copies/ml. Comparison of plasma viral loads using the Abbott test and the Roche Amplicor Monitor test showed a mean difference of -0.012 log10 copies/ml. In addition, the Abbott test viral loads correlated with the Digene Hybrid Capture assay ratios. Viral loads obtained from plasma specimens tested by the Abbott and QIAGEN tests were in very close agreement (mean difference, 0.144 log10 copies/ml). When the QIAGEN test was evaluated with the QIAGEN, MagNA Pure, and easyMAG extraction methods, the viral loads for all three methods were within 0.370 log10 copies/ml. Thus, there is good agreement between viral loads obtained by the different tests using the same extraction method or by the same test using different extraction methods. The availability of real-time PCR ASRs provides additional reagents that can be used for CMV viral load testing.

Rates of and reasons for failure of commercial human immunodeficiency virus type 1 viral load assays in Brazil

We examined failures of commercial human immunodeficiency virus type 1 (HIV-1) viral load assays of 1,195 plasma samples from Brazilian patients. Assay failure was assumed for samples in which the virus was undetectable by commercial assay but which tested positive by real-time reverse transcription-PCR of the HIV-1 long terminal repeat (LTR) region or if the viral load differed by >2 log10 from that determined by LTR assay. Failure rates for Bayer Versant bDNA 3.0, Roche Amplicor Monitor v1.5, and bioMerieux NucliSens QT were 0.68, 0.47, and 4.33%, respectively. NucliSens may be inadequate for use in Brazil.

Cerebrospinal and peripheral human immunodeficiency virus type 1 load in a multisite, randomized, double-blind, placebo-controlled trial of D-Ala1-peptide T-amide for HIV-1-associated cognitive-motor impairment

D-Ala1-peptide T-amide (DAPTA) has shown neuroprotection in vitro against gp120-induced loss of dendritic arborization and is promulgated as a CCR5 antagonist. A multisite, randomized, double-blind clinical trial of DAPTA versus placebo prior to combination antiretroviral therapy conducted with human immunodeficiency virus (HIV)-1 seropositive participants having cognitive impairment showed no overall cognitive effect, though subgroups with greater impairment and CD4 cell counts of 201 to 500 cells/mm3 at baseline showed significant improvement. The objective of this study was to examine whether intranasal administration of DAPTA at a dose of 2 mg three times per day (tid) was associated with a reduction of cerebrospinal fluid (CSF) and peripheral (plasma and serum) viral load among a subgroup of participants completing 6 months of treatment. Baseline and 6-month CSF (n = 92) and peripheral (plasma n = 33; serum n = 24) viral load were measured by the Roche Ultrasensitive assay, version 1.5, with reflexive use of the AMPLICOR assay and preservation of the blind. A DAPTA treatment indicator variable was tested using generalized linear models on change in viral load. Peripheral load (combined plasma and serum) was significantly reduced in the DAPTA-treated group. No group differences in CSF viral load were found. This retrospective study on a limited subgroup of the original trial sample indicated that DAPTA treatment may reduce peripheral viral load without concomitant CSF effects. Future studies should be undertaken to confirm the existence of this result and the CSF-periphery dissociation observed with respect to HIV-1-associated cognitive-motor impairment.

Failure of HIV-2 viral load assay in a severely immunodeficient patient: clinical and therapeutic management issues

We report the case of an HIV-2-infected patient with severe immunosupression despite undetectable plasma HIV-2 RNA. This immunovirological discordance was due to failure of the viral load assay and infection by an unknown HIV-2 subtype. Treatment was probably suboptimal, leading to the selection of several resistance mutations and treatment failure.

Validation of clinical application of cytomegalovirus plasma DNA load measurement and definition of treatment criteria by analysis of correlation to antigen detection

Successful preemptive cytomegalovirus (CMV) therapy in transplant patients depends on the availability of sensitive, specific, and timely diagnostic tests for CMV infections. The pp65 antigenemia assay has been used for this purpose with considerable success. Quantification of CMV DNA is currently regarded to be an alternative diagnostic approach. The precise relationship between these two methods has still to be defined, but is essential to compare diagnostic results. This study compared the results of both assays with a large series of transplant recipients in different categories. An internally controlled quantitative real-time CMV DNA PCR was used to test 409 plasma samples from solid organ transplant (SOT) and stem cell transplant (SCT) patients. Levels of CMV DNA in plasma correlated well with classified outcomes of the pp65 antigenemia test. Despite this correlation, the quantitative CMV PCR values in a class of antigen test results were within a wide range, and the definition of an optimal cutoff value for initiating treatment required further analysis by a receiver-operating characteristic curve analysis. This is essential for reactivating infections in particular. For the SCT patients the optimal cutoff value of CMV DNA load defining relevant viral reactivation (in this assay, 10,000 copies/ml) was slightly higher than that for the SOT patients (6,300 copies/ml). Based on a comparison with the established pp65 antigenemia assay, quantification of CMV DNA in plasma appeared to be capable of guiding the clinical management of transplant recipients. This approach may have important advantages, which include a superior reproducibility and sensitivity, allowing the inclusion of kinetic criteria in clinical guidelines.

Molecular-based methods for quantifying HIV viral load

Viral load quantitation has become the major prognostic marker for disease prognosis and outcome of antiretroviral therapy in the treatment of HIV-infected individuals. The three major methodologies for viral load quantitation: the reverse transcriptase-polymerase chain reaction (RT-PCR; Amplicor HIV-1 Monitor Test, Roche Diagnostic Systems, Pleasanton, CA), the nucleic acid sequence-based amplification (NASBA; NucliSens HIV-1 QT Test, Organon Teknika, Bostel, The Netherlands); and a signal amplification methodology termed branchedchain DNA (bDNA) technique (Quantiplex HIV-1 RNA test, Bayer Diagnostics, Emeryville, CA) are briefly reviewed here.

Human herpesvirus 8 load in matched serum and plasma samples of patients with AIDS-associated Kaposi's sarcoma

Human herpesvirus 8 (HHV-8) (or Kaposi's sarcoma [KS]-associated herpesvirus) is associated with all forms of KS. HHV-8 DNA load in peripheral blood mononuclear cells (PBMCs) of KS patients has been shown to correlate with the clinical stage of the disease. Studies have been done to assess the HHV-8 viral load in different sample types from KS patients and its clinical relevance. This paper describes the design and evaluation of a quantitative real-time (TaqMan) PCR assay for routine diagnosis of HHV-8 infection. The linear dynamic range was 5 to 5 x 10(6) copies of HHV-8 DNA (r(2) > 0.99). The assay is very sensitive, specific, and easily reproducible (less than 2% variability) and can be used for different clinical samples, such as serum, plasma, and PBMCs. The question of which clinical sample, serum or plasma, is preferable for HHV8 DNA testing was addressed, using this newly developed real-time PCR assay. From 85 patients with diagnosed AIDS-KS, matched plasma and serum samples were collected. Of the 85 patients tested, 35 were positive for HHV-8 DNA in both plasma and serum (41%), 8 were positive in serum but not plasma, and 7 had detectable HHV-8 DNA only in plasma. The HHV-8 load was similar in both plasma and serum, and no significant difference was found. However, more inhibition was seen in the plasma samples with the use of a system quality control, seal herpesvirus type 1. Therefore, our results suggest that serum is the preferred material for HHV-8 load testing, since there is less possible hindrance in the amplification than with plasma.

Multiplex PCR using real time DNA amplification for the rapid detection and quantitation of HTLV I or II

A multiplex 'real-time' polymerase chain reaction (PCR) has been established as a general technique for the quantitation of proviral human T-lymphotrophic virus types 1 and 2 (HTLV-I/II). The technology utilizes fluorescence to measure amplification products from the tax gene of Human T-cell lymphotropic virus type 1 or the 5' long terminal repeat of Human T-cell lymphotropic virus type 2. The quantitative amplification of the standard was linear across four orders of magnitude with nearly identical amplification efficiencies for monoplex or the biplex format from 1.4 copes/assay (60 copies proviral DNA/0.5 micrograms human DNA) to 6000 copies/assay (240000 proviral copies/0.5 micrograms human DNA). The human beta-globin gene was used to normalize for human DNA input to determine the proviral DNA load. Three hundred fifty-six specimens received by Specialty Laboratories for HTLV I/II detection provided identical results in the detection of HTLV I/II proviral DNA. No additional positive specimens were identified with the biplex assay format. The coefficient of variation for the proviral DNA load was less than 30% for HTLV I or II quantitation (n=5). For spiked specimens, two groups of five separate 0.25 ml blood specimens (20 total) were spiked, respectively, with 0, 9.6, 48, 240 and 1200 copies of HTLV I or HTLV II DNA standards. The specimens were amplified with the HTLV I/II multiplex format. Twenty of twenty expected negative HTLV I or HTLV II specimens were negative (100% specificity) and 14/16 specimens spiked with 48 copies or more HTLV I were detected (87.5% sensitivity). Thirteen of sixteen HTLV II spiked specimens (>48 copies of HTLV II standard per 10 assays) were detected (81.2%). The real-time detection provides accurate and reliable results in a single amplification for both HTLV (I or II) targets with a more rapid turnaround time and a decrease in material required for results.

Stochastic processes defining sensitivity and variability of internally calibrated quantitative NASBA-based viral load assays

For quantitative assessment of virus particles in patient plasma samples various assays are commercially available. Typical performance characteristics for such assays are sensitivity, precision and the range of linearity. In order to assess these properties it is common practice to divide the range of inputs into subranges in order to apply different statistical models to evaluate these properties separately. We developed a general statistical model for internally calibrated amplification based viral load assays that combines these statistical properties in one powerful analysis. Based on the model an unambiguous definition of the lower limit of the linear range can be given. The proposed method of analysis was illustrated by a successful application to data generated by the NucliSens EasyQ HIV-1 assay.

Overestimation of the hepatitis C virus RNA content of reference preparations by the AMPLICOR HCV monitor test, version 2.0

An evaluation of the AMPLICOR hepatitis C virus (HCV) monitor test, version 2.0 (Roche Diagnostics), was carried out to investigate whether this test overestimates the HCV RNA content of reference preparations. Satisfactory accuracy was observed when the World Health Organization HCV international standard was included in the assay and a modified formula was used to calculate the viral content.

High-titer screening PCR: a successful strategy for reducing the parvovirus B19 load in plasma pools for fractionation

BACKGROUND

Human parvovirus B19 (B19) is regarded as a potential risk factor for certain patient populations receiving plasma components.

STUDY DESIGN AND METHODS

The prevalence of B19 was determined in a limited plasma donor population. Conditions for high-titer screening PCR were designed to allow the removal of plasma donations in the acute phase of infection with virus loads >or=10(7) genome equivalents per milliliter before manufacturing. Antithrombin III lots originating from screened plasma were compared to lots originating from untested plasma with respect to their B19 DNA load by a sensitive PCR assay.

RESULTS

B19 was shown to have a prevalence of about 1 per 800 plasma donations. Only a minority (1/8000) of occurrences were in the acute phase of infection. Removing plasma units with high virus load as determined by high-titer screening PCR significantly decreased peak virus loads of plasma pools for fractionation. Together with a virus-removal capacity of 10.4 log(10) of the manufacturing process, this screening resulted in a final antithrombin III product that was nonreactive for B19 on PCR.

CONCLUSION

Combining the strategy of high-titer screening PCR with the virus reduction capacity of the manufacturing process considerably increased the margin of B19 virus safety of antithrombin III. This strategy should have positive impact on other plasma components as well.

Centers for Disease Control and Prevention. Guidelines for laboratory test result reporting of human immunodeficiency virus type 1 ribonucleic acid determination. Recommendations from a CDC working group. Centers for Disease Control

Monitoring human immunodeficiency virus type 1 (HIV-1) ribonucleic acid levels (also known as HIV viral load) has become the standard of care for monitoring response to therapy in HIV-infected patients. In 1999, CDC published updated surveillance case definitions for HIV infection and acquired immunodeficiency syndrome (AIDS) reporting, including positive results of HIV-1 viral detection tests (CDC. Guidelines for national human immunodeficiency virus case surveillance, including monitoring for human immunodeficiency virus infection and acquired immunodeficiency syndrome. MMWR 1999;48[No. RR-131:1-28). Since 1996, an increased number of public and private laboratories have begun performing viral load tests. Results obtained with available test methods are variable, and laboratories present these results in different ways, indicating that guidelines to promote standard practice in reporting of test results are warranted. This report provides guidelines for standardized reporting of viral load test results by licensed laboratories to health-care providers and facilities for public health case reporting of HIV infection and AIDS. Recommended standards were developed through data review, input involving a working group of physicians and laboratorians experienced in viral load testing, and an assessment of laboratory practices. These guidelines were discussed, refined, and endorsed at the annual Human Retrovirus and Hepatitis C Laboratory Testing Conference, held March 6-9, 2000, in Charlotte, North Carolina, with participation of representatives from public health, hospital, independent, and blood-collection-facility laboratories. Adoption of these guidelines by all public and private laboratories that perform HIV viral load testing will improve the quality and usefulness of viral load test results for the physician ordering the test and for reporting to public health departments.

Toward standardization of Epstein-Barr virus DNA load monitoring: unfractionated whole blood as preferred clinical specimen

Epstein-Barr virus (EBV) DNA load monitoring in peripheral blood has been shown to be a useful tool for the diagnosis of aberrant EBV infections. In the present study we compared the relative diagnostic values of EBV DNA load monitoring in unfractionated whole blood and simultaneously obtained serum or plasma samples from Burkitt's lymphoma (BL) patients, transplant recipients, human immunodeficiency virus (HIV)-infected individuals, and infectious mononucleosis (IM) patients by a quantitative competitive PCR (Q-PCR). The EBV DNA load in BL patients was mainly situated in the cellular blood compartment (up to 4.5 x 10(6) copies/ml). EBV DNA loads in unfractionated whole blood and parallel serum samples showed no correlation. In transplant recipients, IM patients, and HIV-infected patients, the EBV burden in the circulation was almost exclusively restricted to the cellular blood compartment, because serum or plasma samples from these patients yielded negative results by Q-PCR, despite high viral loads in corresponding whole-blood samples. A 10-fold more sensitive but qualitative BamHI-W-repeat PCR occasionally revealed the presence of EBV at <2,000 copies of EBV DNA per ml of serum. Spiking of 100 copies of EBV DNA in samples with negative Q-PCR results excluded the presence of inhibitory factors in serum or plasma that influenced the Q-PCR result. Serum samples from all populations were often positive for beta-globin DNA, indicating cell damage in vivo or during serum preparation. We conclude that serum is an undesirable clinical specimen for EBV DNA load monitoring because it omits the presence of cell-associated virus and uncontrolled cell lysis may give irreproducible results or overestimation of the DNA load. Unfractionated whole blood is strongly preferred since it combines all blood compartments that may harbor EBV and it best reflects the absolute viral burden in the patient's circulation.

Frequent monitoring of Epstein-Barr virus DNA load in unfractionated whole blood is essential for early detection of posttransplant lymphoproliferative disease in high-risk patients

Posttransplant lymphoproliferative disease (PTLD) is a frequent and severe Epstein-Barr virus (EBV)-associated complication in transplantation recipients that is caused by iatrogenic suppression of T-cell function. The diagnostic value of weekly EBV DNA load monitoring was investigated in prospectively collected unfractionated whole blood and serum samples of lung transplantation (LTx) recipients with and without PTLD. In PTLD patients, 78% of tested whole blood samples were above the cut-off value of quantitative competitive polymerase chain reaction (Q-PCR) (greater than 2000 EBV DNA copies per mL blood), with the majority of patients having high viral loads before and at PTLD diagnosis. Especially in a primary EBV-infected patient and in patients with conversion of immunosuppressive treatment, rapid increases in peripheral blood EBV DNA load diagnosed and predicted PTLD. In non-PTLD transplantation recipients, only 3.4% of the whole blood samples was above the cut-off value (P <.0001) despite heavy immune suppression and cytomegalovirus (CMV)-related disease. These findings illustrate the clinical importance of frequent EBV DNA load monitoring in LTx recipients. The increased EBV DNA loads in PTLD patients were restricted to the cellular blood compartment, as parallel serum samples were all below cut-off value, which indicates absence of lytic viral replication. EBV(+) cells in PTLD patients have a very short doubling time, which can be as low as 56 hours, thereby creating the need for high screening frequency in high-risk patients. Furthermore, it is shown that EBV and CMV can reactivate independently in LTx recipients and that EBV DNA load monitoring may be useful in discriminating PTLD from rejection.

Predictors of operative outcome in patients with human immunodeficiency virus infection and acquired immunodeficiency syndrome

BACKGROUND

Plasma viral load has recently been associated with clinical outcome in patients with human immunodeficiency virus (HIV) infection and acquired immunodeficiency syndrome (AIDS). We hypothetized that, in addition to CD4 lymphocytes, plasma HIV-1 RNA counts are predictive of postoperative outcome.

METHODS

HIV-infected and AIDS patients admitted to a major teaching hospital requiring invasive or surgical procedures were retrospectively analyzed for postoperative outcome. Preoperative and postoperative immune cell counts including plasma HIV-1 RNA counts were recorded. Chi-square analysis, Fisher's exact test, and multivariate regression were performed with statistical significance P </=0.05.

RESULTS

Fifty-five consecutive patients between 14 and 62 years of age were admitted in a 1-year period and underwent 64 diagnostic and therapeutic procedures. Fourteen (22%) postoperative infections and 18 (28%) complications other than infection, with an overall mortality of 11%, were documented. Total preoperative white blood cell count ([WBC] P <0.01), preoperative percent lymphocyte count (P <0.01), absolute postoperative CD4 lymphocyte count (P <0.01), and postoperative plasma viral load (P <0.0001) are associated with mortality. Multivariate regression indicated that postoperative percent CD4 lymphocyte count is an independent predictor of both postoperative infection and other complications (P <0.05, R = 0.848, power = 0.9911), while the decrement in percent CD4 lymphocyte count is an independent predictor of postoperative complications other than infection (P <0.05, R = 0.596, power = 0.7838).

CONCLUSIONS

In accordance with the medical literature for clinical outcome in HIV-infected and AIDS patients, both immune cell counts and HIV-1 RNA counts were found to associate with postoperative mortality. However, the postoperative and decrement in percent CD4 lymphocyte proved to be the independent predictors of postoperative complications.

Predictive value of the ultrasensitive HIV viral load assay in clinical practice

The aim of this study was to determine whether an HIV viral load of <50 copies/ml (c/ml), in the first available plasma sample to have shown a viral load of <400 c/ml, in patients on antiretroviral therapy, is correlated with longer term suppression of viral load (at <400 c/ml) compared to a viral load of 50-399 c/ml, and secondly, to compare the results obtained by ultrasensitive and standard viral load assays carried out on the same sample. A total of 98 HIV-positive patients on antiretroviral therapy with a viral load of <400 c/ml and at least one subsequent viral load measurement, were selected. For each patient, the first available specimen showing a viral load of <400 c/ml was tested using the Roche Amplicor ultrasensitive viral load assay, and patients were followed up subsequently for a median period of 52 weeks. Whether patients achieved an ultrasensitive viral load (USVL) of <50 c/ml or not made very little difference to the proportion of patients in each group showing continued response to treatment (52% vs. 45% respectively). The only variable that was shown to significantly predict longevity of response was the number of antiretroviral drugs used. Secondly, a standard viral load of <400 c/ml but with a detectable signal above background levels, was strongly predictive of a USVL of >50 c/ml. Overall, the findings suggest that the advantage in predictive value of the ultrasensitive over the standard HIV viral load assay, shown previously in clinical trials, may be limited in clinical practice.

Real-time polymerase chain reaction for quantification of HTLV-1 proviral load: application for analyzing aberrant integration of the proviral DNA in adult T-cell leukemia

We describe the establishment of a real-time polymerase chain reaction (PCR) assay for the quantitative estimation of human T-cell leukemia virus type 1 (HTLV-1) proviral load using a LightCycler Technology (Roche Diagnostics, Mannheim, Germany) instrument. Proviral DNA level represents a measure of the integrated viral genome in host cells, so we applied this technique to evaluate the tumor burden in adult T-cell leukemia (ATL) patients with aberrant integration patterns of HTLV-1 detected by standard Southern blot hybridization (SBH) analysis. In 14 of our 15 ATL cases with 2 or more bands detected by SBH analysis, the ATL cells were shown to harbor multiple copies of the provirus within 1 ATL cell. This result suggests the usefulness of real-time PCR quantification for the study of the relationship between ATL pathology and HTLV-1-induced pathogenesis.

Group sequential analyses for the mean function of a repeated measure process

In many clinical trials, treatment efficacy is based upon response to a biological marker that is measured repeatedly during the course of follow-up. However, in some of these trials it is not clear, a priori, how treatment effects on the marker may manifest themselves or what kinds of effects are clinically meaningful and/or acceptable. It is, therefore, desirable to allow flexibility in design and monitoring process by not prespecifying a stopping rule or even the parameter on which inferences will be based. Using the more general results in Hu and Lagakos, this paper extends the idea of the repeated confidence intervals for a parameter (Jennison and Turnbull) to repeated confidence bands for the mean function of a repeated measure process. We illustrate the approach and some considerations in its application with the results of a recent AIDS clinical trial.

Efficacy of viral clearance methods used in the manufacture of activated prothrombin complex concentrates: focus on AUTOPLEX T

Various methods are described for the elimination of infectious viruses from activated prothrombin complex concentrates (aPCCs) and for the analysis of the final products (AUTOPLEX T and FEIBA VH). Viruses of concern in human plasma-derived products are enveloped (hepatitis B and C, cytomegalovirus, Epstein-Barr virus, and human immunodeficiency virus [HIV]) and nonenveloped (hepatitis A and parvovirus B19). Donated blood used for AUTOPLEX T is screened for antihepatitis C, HBsAg, anti-HIV types 1 and 2, and p24 antigen. Plasma pools utilized for raw materials are also tested by PCR for HIV and hepatitis C virus. Partial virus inactivation and partitioning are achieved by purification of the aPCC. Further reduction of virus infectivity is accomplished by lyophilization and dry-heat treatment. Each step undergoes virus elimination validation studies in which a relevant sample is 'spiked' with the appropriate virus or model virus. The total reduction in virus from raw material to final product can then be calculated. For AUTOPLEX T the cumulative log10 reduction factors for several viruses vary from 4.2 to 14.3. This ensures an exceptionally high margin of safety. Definitive evidence for product safety was obtained by clinical observation of treated patients. The viral inactivation process of AUTOPLEX T involves a four-tier viral safety program, including Cohn alcohol fractionation and dry-heat treatment, in place of the two-stage vapour-heating process for FEIBA.

Relationship between human immunodeficiency virus-associated dementia and viral load in cerebrospinal fluid and brain

Cerebrospinal fluid (CSF) human immunodeficiency virus (HIV) RNA levels were measured with the Nucleic Acid Sequence-Based Amplification (NASBA) assay to determine the relationship with neurological status; 37 subjects with HIV dementia (HIV-D) were compared with 77 with HIV with minor neurological signs (HIV-MCMD) and 93 neurologically normal HIV-seropositive individuals (HIV-NML). The NASBA assay had a lower limit of detection of 100 copies per milliliter. Mean CSF log HIV RNA levels were significantly higher in those with dementia after adjusting for CD4 count and were correlated with dementia severity. Plasma levels did not distinguish comparably immunosuppressed subjects with or without dementia. CSF and plasma RNA levels were significantly intercorrelated for subjects with CD4 counts <200/mm3 and also correlated inversely with CSF beta2-microglobulin. CSF RNA levels were independent of CSF pleocytosis or antiretroviral exposure. Brain RNA levels were consistently higher than CSF but correlated with CSF values for dementia subjects. The NASBA assay can be used reliably to determine HIV RNA levels in CSF, brain, and plasma samples. CSF HIV RNA may be a surrogate marker for brain infection, based on the observed correlation with brain levels. The association between plasma HIV RNA and CSF levels of HIV and beta2-microglobulin suggests that both viral load and CNS immune activation are important determinants of neurological disease.