Early prediction of hepatitis C virus (HCV) infection relapse in nonresponders to primary interferon therapy by means of HCV RNA whole-blood analysis

Development of a direct reverse-transcription quantitative PCR (dirRT-qPCR) assay for clinical Zika diagnosis

OBJECTIVE

The nucleic acid-based polymerase chain reaction (PCR) assay is commonly applied to detect infection with Zika virus (ZIKV). However, the time- and labor-intensive sample pretreatment required to remove inhibitors that cause false-negative results in clinical samples is impractical for use in resource-limited areas. The aim was to develop a direct reverse-transcription quantitative PCR (dirRT-qPCR) assay for ZIKV diagnosis directly from clinical samples.

METHODS

The combination of inhibitor-tolerant polymerases, polymerase enhancers, and dirRT-qPCR conditions was optimized for various clinical samples including blood and serum. Sensitivity was evaluated with standard DNA spiked in simulated samples. Specificity was evaluated using clinical specimens of other infections such as dengue virus and chikungunya virus.

RESULTS

High specificity and sensitivity were achieved, and the limit of detection (LOD) of the assay was 9.5×10¹ ZIKV RNA copies/reaction. The on-site clinical diagnosis of ZIKV required a 5μl sample and the diagnosis could be completed within 2h.

CONCLUSIONS

This robust dirRT-qPCR assay shows a high potential for point-of-care diagnosis, and the primer-probe combinations can also be extended for other viral detection. It realizes the goal of large-scale on-site screening for viral infections and could be used for early diagnosis and the prevention and control of viral outbreaks.

Direct DNA and RNA detection from large volumes of whole human blood

PCR inhibitors in clinical specimens negatively affect the sensitivity of diagnostic PCR and RT-PCR or may even cause false-negative results. To overcome PCR inhibition, increase the sensitivity of the assays and simplify the detection protocols, simple methods based on quantitative nested real-time PCR and RT-PCR were developed to detect exogenous DNA and RNA directly from large volumes of whole human blood (WHB). Thermus thermophilus (Tth) polymerase is resistant to several common PCR inhibitors and exhibits reverse transcriptase activity in the presence of manganese ions. In combination with optimized concentrations of magnesium ions and manganese ions, Tth polymerase enabled efficient detection of DNA and RNA from large volumes of WHB treated with various anticoagulants. The applicability of these methods was further demonstrated by examining WHB specimens collected from different healthy individuals and those stored under a variety of conditions. The detection limit of these methods was determined by detecting exogenous DNA, RNA, and bacteria spiked in WHB. To the best of our knowledge, direct RNA detection from large volumes of WHB has not been reported. The results of the developed methods can be obtained within 4 hours, making them possible for rapid and accurate detection of disease-causing agents from WHB.

Hepatitis C virus infection of a thyroid cell line: implications for pathogenesis of hepatitis C virus and thyroiditis

BACKGROUND

Autoimmune and non-autoimmune thyroiditis frequently occur in persons with hepatitis C virus (HCV) infection. Treatment with interferon alpha (IFNα) is also associated with significant risk for the development of thyroiditis. To explore HCV-thyroid interactions at a cellular level, we evaluated whether a human thyroid cell line (ML1) could be infected productively with HCV in vitro.

METHODS AND RESULTS

ML1 cells showed robust surface expression of the major HCV receptor CD81. Using a highly sensitive, strand-specific reverse transcription polymerase chain reaction assay, positive-sense and negative-sense HCV RNA were detected in ML1 cell lysates at days 3, 7, and 14 postinfection with HCV. HCV core protein was expressed at high levels in ML1 supernatants at days 1, 3, 5, 7, and 14 postinfection. The nonstructural protein NS5A was also detected in ML1 cell lysates by Western blotting. HCV entry into ML1 cells was shown to be dependent on the HCV entry factors CD81 and SR-B1/CLA1, while IFNα inhibited HCV replication in ML1 cells in a dose-dependent manner. Supernatants from HCV-infected ML1 cells were able to infect fresh ML1 cells productively, suggesting that infectious virions could be transferred from infected to naïve thyroid cells in vivo. Additionally, HCV infection of ML1 cells led to increased expression of the pro-inflammatory cytokine IL-8.

CONCLUSIONS

For the first time, we have demonstrated that HCV can infect human thyroid cells in vitro. These findings strongly suggest that HCV infection of thyrocytes may play a role in the association between chronic HCV infection and thyroid autoimmunity. Furthermore, the thyroid may serve as an extrahepatic reservoir for HCV viral replication, thus contributing to the persistence of viral infection and to the development of thyroid autoimmunity.

Presence of plus-strand HCV RNA in serum and PBMCs as an indicator for relapse and resistance to IFN therapy in patients infected by HCV

Aim: The aim of our study was to investigate the correlation between the presence of plus-/minus-strand HCV RNA in peripheral blood mononuclear cells (PBMCs) and serum following pegylated IFN/ribavirin therapy with response to therapy in HCV-infected patients. Methods: Forty-three HCV-infected patients who completed 48 weeks of IFN/ribavirin therapy, including 25 sustained virologic responders, 12 resistants and six relapsers, comprised the study population. Plus-/minus-strand HCV RNA was detected by reverse transcription PCR in serum and PBMCs. Results: The frequency of plus-strand HCV RNA was significantly higher in PBMC and serum samples of relapsers and resistants, and this might have important implications in clinical practice and patient management. There was no correlation between presence of plus- and minus-strand HCV RNA and genotypes, except the fact that most of the patients who had plus-strand HCV RNA in PBMCs (60%) and in serum (61.53%) belonged to genotype 1a. Conclusion: Presence of plus-strand HCV RNA in PBMCs and serum after termination of therapy is associated with viral relapse and resistance to IFN/ribavirin treatment in HCV-infected patients.

Direct DNA amplification from crude clinical samples using a PCR enhancer cocktail and novel mutants of Taq

PCR-based clinical and forensic tests often have low sensitivity or even false-negative results caused by potent PCR inhibitors found in blood and soil. It is widely accepted that purification of target DNA before PCR is necessary for successful amplification. In an attempt to overcome PCR inhibition, enhance PCR amplification, and simplify the PCR protocol, we demonstrate improved PCR-enhancing cocktails containing nonionic detergent, l-carnitine, d-(+)-trehalose, and heparin. These cocktails, in combination with two inhibitor-resistant Taq mutants, OmniTaq and Omni Klentaq, enabled efficient amplification of exogenous, endogenous, and high-GC content DNA targets directly from crude samples containing human plasma, serum, and whole blood without DNA purification. In the presence of these enhancer cocktails, the mutant enzymes were able to tolerate at least 25% plasma, serum, or whole blood and as high as 80% GC content templates in PCR reactions. These enhancer cocktails also improved the performance of the novel Taq mutants in real-time PCR amplification using crude samples, both in SYBR Green fluorescence detection and TaqMan assays. The novel enhancer mixes also facilitated DNA amplification from crude samples with various commercial Taq DNA polymerases.

Multi-target spectral moment: QSAR for antiviral drugs vs. different viral species

The antiviral QSAR models have an important limitation today. They predict the biological activity of drugs against only one viral species. This is determined by the fact that most of the current reported molecular descriptors encode only information about the molecular structure. As a result, predicting the probability with which a drug is active against different viral species with a single unifying model is a goal of major importance. In this work, we use Markov Chain theory to calculate new multi-target spectral moments to fit a QSAR model for drugs active against 40 viral species. The model is based on 500 drugs (including active and non-active compounds) tested as antiviral agents in the recent literature; not all drugs were predicted against all viruses, but only those with experimental values. The database also contains 207 well-known compounds (not as recent as the previous ones) reported in the Merck Index with other activities that do not include antiviral action against any virus species. We used Linear Discriminant Analysis (LDA) to classify all these drugs into two classes as active or non-active against the different viral species tested, whose data we processed. The model correctly classifies 5129 out of 5594 non-active compounds (91.69%) and 412 out of 422 active compounds (97.63%). Overall training predictability was 92.34%. The validation of the model was carried out by means of external predicting series, the model classifying, thus, 2568 out of 2779 non-active compounds and 224 out of 229 active compounds. Overall training predictability was 92.82%. The present work reports the first attempts to calculate within a unified framework the probabilities of antiviral drugs against different virus species based on a spectral moment analysis.

Hepatitis C virus RNA quantitation in venous and capillary small-volume whole-blood samples

Quantitation of hepatitis C virus (HCV) RNA in plasma and serum samples is a costly procedure in both time and reagents. Additionally, cell-associated viral RNA may not be detected. This study evaluated the accuracy of HCV RNA quantitation in small-volume whole-blood (WB) samples, which would be appropriate for point-of-care diagnostic devices. HCV RNA was extracted from 222 clinical plasma and WB samples of 82 patients with chronic hepatitis C by a specific locked nucleic acid-mediated capture method and quantified by real-time reverse transcription-PCR. The results were compared to the reference plasma viral load determined with the COBAS AmpliPrep/TaqMan (CAP/CTM) HCV test. This assay had an analytical sensitivity of 9 IU per 10-microl sample (95% limit of detection [95% LOD]), a linearity range of 500 to 5 x 10(6) IU/ml, and was accurate in testing 10 HCV subtypes (<0.22 log10 unit) in plasma. The assay was matrix equivalent for plasma and WB samples (coefficient of determination [R2] of 0.943) and had a specificity of 100% (n = 20) in WB samples. The HCV RNA concentration in clinical WB samples exceeded the estimated hematocrit-corrected plasma viral loads by 0.22 log10 unit, but absolute quantitation results in plasma and WB samples were identical (95% confidence interval, -0.06 to 0.04 log10 unit). The sensitivity in WB samples was 100% (n = 141) for plasma concentrations above the 95% LOD. Quantitation results in 10-microl WB samples correlated linearly with the CAP/CTM HCV plasma test results (R2 = 0.919; n = 140) and did not differ between capillary and venous samples (R2 = 0.960; n = 40). This study shows that HCV RNA quantitation in 10-microl WB samples is appropriate for monitoring viral loads of >900 IU/ml, although the use of WB does not increase the diagnostic sensitivity.

Whole blood as an alternative to plasma for detection of hepatitis C virus RNA

Peripheral blood mononuclear cells are reported to be one of the extrahepatic replication sites contributing to the persistence of hepatitis C virus (HCV) infection. Whole-blood and plasma samples from 61 individuals were compared as sources for the detection of HCV RNA. Forty-four of the individuals were receiving antiviral therapy, while 17 were treatment naïve. The quantitation of HCV RNA was done by a sensitive in-house real-time reverse transcription-PCR. When the viral loads in the two types of samples were compared, a correlation coefficient of 0.858 (P < 0.001) was found, indicating that plasma and whole blood are equally acceptable sources for testing for HCV RNA.

Hepatitis C viral kinetics in plasma and peripheral blood mononuclear cells during pegylated interferon-alpha2a/ribavirin therapy

BACKGROUND/AIMS

Analysis of hepatitis C virus (HCV) RNA kinetics in compartments other than plasma may help in understanding HCV replication and identifying clinically significant patterns of treatment response.

METHODS

After 6 weeks of pegylated interferon-alpha2a/ribavirin therapy, 74 chronic hepatitis C patients were randomized to individualized or standard treatments for another 42 weeks. HCV RNA was quantified in peripheral blood mononuclear cells (PBMCs) by TaqMan-based real-time PCR and compared to plasma HCV RNA.

RESULTS

HCV RNA declines in PBMCs and plasma were comparable during the initial 12 weeks of therapy (Spearman's rank correlation range over different time points, 0.73-0.97). However, a delay of HCV RNA decay in PBMCs, expected if kinetics in PBMCs only reflected kinetics in plasma, was rarely observed. For many patients, HCV RNA decline in PBMCs started as early as in plasma and for some of them the kinetics strongly differed in the two compartments, hinting at a compartment-specific HCV replication and treatment effect. Fast viral decay in PBMCs was associated with sustained virological response, but viral kinetics in PBMCs added only minor predictive information compared with kinetics in plasma.

CONCLUSIONS

Future kinetics studies of HCV RNA during therapy with new antivirals should take into account their compartment-specific effect.

Hepatitis C virus lymphotropism: lessons from a decade of studies

The possibility that HCV infects lymphoid cells has been widely discussed. Evidence in favor of HCV tropism for lymphoid cells derives from a series of data including: (1) the higher sensitivity of testing HCVRNA in PBMC than in serum or plasma samples, with possible detection of HCV RNA-positive PBMC in the absence of HCV viremia; (2) short-term cultures of PBMC which yield a significant increase in the amount of viral RNA on stimulation by mitogens; (3) results of "in situ" methods (i.e. in situ hybridization, immunofluorescence); (4) efficient infection of lymphoid cell lines or PBMC from normal individuals; (5) the persistence of HCV RNA in PBMC obtained from HCV-positive subjects and injected into SCID mice; (6) the long-term persistence of HCV RNA in PBMC in spite of HCV RNA negativity of serum and liver in sustained responder patients after therapy. The principal criticisms concerning effective HCV infection of lymphoid cells arise from technical difficulty in identifying HCV RNA replicative intermediate in these elements. Conflicting data may also result from differences in PBMC infection by different genotypes, samples taken at different stages in the disease process and differences in the sensitivity of detection methods, as well as low replication levels and/or proportion of infected PBMC. Interesting available data about HCV lymphotropism, which is possibly important in influencing the natural history of infection, include: (1) possible preferential viral tropism for specific PBMC subsets; (2) different lymphotropism of different viral strains; (3) selection of distinctive viral strains; (4) identification of putative HCV cell receptors; (5) association between determination of HCV lymphatic infection and t(14; 18) translocation. The clinical correlates of HCV lymphotropism are potentially very numerous, including, first, its role in determining HCV-related lymphoproliferative disorders.

Sustained virological response in the antiviral therapy of chronic hepatitis C: is there a predictive value of interferon-induced depression?

BACKGROUND

The study objective was to determine the contribution of cytokine-induced depression to a predictive model of sustained virological response (SVR) in chronic hepatitis C.

METHODS

One hundred and one therapy-naïve hepatitis C virus (HCV) outpatients received treatment with peginterferon alfa-2b and ribavirin. Neuropsychiatric side effects were monitored prospectively (Hospital Anxiety and Depression Scale, DSM-IV criteria for major depression). SVR was defined as a failure to detect HCV by PCR 24 weeks after therapy.

RESULTS

SVR rate was 72.3% (73 of 101 patients). Classification data and the extent of interferon-induced depression were not significantly linked to SVR. Virus genotype (p = 0.045) and gender (p = 0.016) contributed significantly to a logistic regression model. Mean (p = 0.811) and maximum (p = 0.744) depression increases were no significant predictors of SVR. Major depression rates (DSM-IV criteria) were 12.3% (9 of 73 patients) in the subgroup with SVR and 10.7% (3 of 28) in patients without SVR.

CONCLUSIONS

We found no significant association between depression and the efficacy of antiviral treatment in chronic hepatitis C. Interferon-induced depressive symptoms are important to be monitored and treated if necessary; however, they cannot be used to predict therapy success.

Compartmentalization of hepatitis C virus (HCV) during HCV/HIV coinfection

Extrahepatic replication has important implications for the transmission and treatment of hepatitis C virus (HCV). We analyzed longitudinal HCV diversity in peripheral-blood mononuclear cells (PBMCs) and serum during HCV monoinfection and HCV/HIV coinfection to determine whether distinct amino acid signatures characterized HCV replicating within PBMCs. Analysis of E1-HVR1 sequences demonstrated higher serum genetic distances among HCV/human immunodeficiency virus (HIV)-coinfected persons. Moreover, consensus PBMC sequences were rarely identical to those in the corresponding serum, suggesting divergence in these 2 compartments. Three of 5 HCV/HIV-coinfected participants showed evidence of HCV compartmentalization in PBMCs. Additionally, signature sequence analysis identified PBMC-specific amino acids in all HCV/HIV-coinfected persons. To our knowledge, this is the first study to identify specific amino acids that may distinguish HCV variants replicating in PBMCs. It is provocative to speculate that extrahepatic HCV diversity may be an important determinant of treatment response and thus warrants additional study, particularly during HCV/HIV coinfection.

Prediction of the efficacy of antiviral therapy for hepatitis C virus infection by an ultrasensitive RT-PCR assay

The efficacy of interferon therapy for hepatitis C virus (HCV) infection improved remarkably. However, virologic relapse occurs in a substantial proportion of patients with virologic response (defined as an HCV RNA level below 50 IU/ml at the end-of-treatment). A highly sensitive RT-nested PCR assay capable of detecting almost a single copy of HCV RNA and a real-time RT-PCR assay to quantify HCV RNA down to 120 copies per ml were developed. The RT-nested PCR assay showed that 1 IU of HCV RNA is equivalent to 12.2 copies. For 28 patients with virologic response (12 relapsers and 16 sustained virologic responders), week-4 and end-of-treatment plasma samples were retested. At week 4, HCV RNA was detected by the RT-nested PCR and qualitative COBAS Amplicor HCV version 2.0 in 8/9 (89%) and 6/9 (67%) samples from relapsers, and in 4/16 (25%) and 2/16 (13%) samples from sustained virologic responders, respectively. End-of-treatment samples with HCV-negative by the qualitative COBAS Amplicor were positive by the present assay in 4/12 (25%) of relapsing patients and 0/16 (0%) of sustained virologic responders. The viral levels detected by the present assay in the Amplicor-negative samples were 3.5-17.3 copies/ml, which is below the detection limit of COBAS Amplicor. In conclusion, the highly sensitive RT-nested PCR assay can predict sustained virologic response at week 4 and virologic relapse at the end-of-treatment more accurately than COBAS Amplicor, suggesting its usefulness in monitoring antiviral therapy for HCV infection.

Extrahepatic replication of HCV: insights into clinical manifestations and biological consequences

An estimated 170 million persons are infected with the hepatitis C virus (HCV) worldwide. While hepatocytes are the major site of infection, a broad clinical spectrum of extrahepatic complications and diseases are associated with chronic HCV infection, highlighting the involvement of HCV in a variety of non-hepatic pathogenic processes. There is a growing body of evidence to suggest that HCV can replicate efficiently in extrahepatic tissues and cell types, including peripheral blood mononuclear cells. Nonetheless, laboratory confirmation of HCV replication in extrahepatic sites is fraught with technical challenges, and in vitro systems to investigate extrahepatic replication of HCV are severely limited. Thus, future studies of extrahepatic replication should combine innovative in vitro assays with a prospective cohort design to maximize our understanding of this important phenomenon to the pathogenesis and treatment response rates of HCV.

Integration of nucleic acid amplification test results into hepatitis C virus supplemental serologic testing algorithms: implications for donor counseling and revision of existing algorithms

BACKGROUND

The routine use of hepatitis C virus (HCV) nucleic acid amplification testing (NAT) donor screening assays has provided an opportunity for revision of the current HCV supplemental testing algorithm, which requires that recombinant immunoblot assay (RIBA) be performed on every HCV enzyme immunoassay (EIA)-repeat-reactive donation. The FDA has approved variance requests to use a new algorithm that eliminates the need to perform RIBA when HCV NAT results are reactive. Data are provided in support of this new algorithm.

STUDY DESIGN AND METHODS

HCV EIA (including signal-to-cutoff optical density ratio), RIBA, and NAT data were compiled from 33.2 million donations screened over an approximately 4-year period by the American Red Cross and Blood Systems Laboratories. Further, donations having specific combinations of HCV EIA, RIBA, and minipool (MP) NAT results were evaluated, with more sensitive individual-donation (ID) NAT, to construct improved counseling messages for donors.

RESULTS

Of 47,041 EIA-repeat-reactive donations, 49.3 percent were RIBA-positive, 17.1 percent RIBA-indeterminate, and 33.5 percent RIBA-negative. NAT-reactive rates were 79.2, 2.5, and 0.18 percent for RIBA-positive, -indeterminate, and -negative donations, respectively. The new algorithm classified an additional 1 percent of donations as HCV-infected while at the same time detecting all infections classified as HCV-infected under the current algorithm. An additional 2.4 percent of RIBA-positive, MP NAT-nonreactive donations were reactive when a frozen-thawed aliquot was retested by ID NAT.

CONCLUSION

Integrating HCV NAT results with RIBA results for purposes of donor notification allows more appropriate counseling messages to be given to EIA-repeat-reactive donors. The new HCV supplemental algorithm is an acceptable alternative to the current algorithm because it provides equivalent or superior accuracy in formulating donor counseling messages and may also result in reduced costs and more timely notification of infected donors.

The Clinical Utility of Using Catrimox-14-Treated Whole Blood in Detecting Hepatitis C Virus RNA

Background

Measuring hepatitis C virus (HCV) RNA in serum or plasma may underestimate the true HCV burden. Extracting viral RNA from whole blood (WB) with a cationic surfactant (Catrimox-14) has resulted in HCV RNA concentrations up to 1000-fold higher than from serum or plasma in some studies, but not others. We compared the Catrimox-14 WB assay with a standard serum assay.

Methods

Seventy-two chronic HCV patients received 48 weeks of standard or pegylated interferon alpha-2b and ribavirin therapy. Catrimox-14-treated WB and corresponding serum samples were obtained at baseline and weeks 12, 24, 48 and 72. HCV RNA concentrations from WB and serum were quantified by a previously validated RT-PCR assay.

Results

Overall mean (±SD) baseline serum log10 HCV RNA concentration was 6.5 ((±0.58) copies/ml. Out of 72 patients, 33 had no detectable virus at 72 weeks. Neither assay detected virus in these patients at 12 weeks and neither WB nor serum assays detected virus at end-of-treatment in the 10 patients who subsequently relapsed at 72 weeks. HCV RNA concentrations from WB and serum assays were linearly correlated (R2=0.73; P<0.001), although mean serum HCV RNA concentrations were 0.5 log10 copies/ml higher in serum than in WB [6.0 (±0.82) vs 5.5 ((±0.84), respectively, P=0.12].

Conclusions

Catrimox-14-treated WB assays detect changes in HCV RNA, but do not offer clinical advantage over a conventional serum RT-PCR based assay.