Comparative analysis of triplex nucleic acid test assays in United States blood donors

Ultrasensitive PCR system for HBV DNA detection: Risk stratification for occult hepatitis B virus infection in English blood donors

Occult hepatitis B (HBV) infection (OBI), characterized by low viral loads, accounts for much of the risk of HBV transfusion-transmitted infection. With anticore antibodies (anti-HBc) screening introduced in England, the imperative to identify OBI donors has increased. We aimed to develop an ultra-sensitive PCR system and investigate risk factors for HBV DNA presence in blood donations. Seven extraction methods and three PCR assays were compared. The optimal system was sought to determine HBV DNA presence in anti-HBc-positive donations. Predictors of DNA positivity were subsequently investigated. Extraction from 5 mL of plasma increased sample representation and resulted in HBV DNA detection in low viral load samples (~0.5 IU/mL). Screening of 487 763 donations in 2022 identified two OBI donors and 2042 anti-HBc-positive donors, 412 of the latter with anti-HBs < 100 mIU/mL. Testing of 134 anti-HBc-positive donations utilizing the 5 mL extraction method identified two further HBV DNA-positive donations. Higher anti-HBc titer and anti-HBs negativity were significant predictors of DNA detectability in anti-HBc-positive donations. An ultrasensitive PCR assay identified potentially infectious donations increasing HBV DNA detection in anti-HBc-positive donors from 0.5% to 1.9%. Anti-HBc titers may further complement the risk stratification for DNA positivity in anti-HBc screening and minimize unnecessary donor deferral.

Estimating the prevalence of two or more diseases using outcomes from multiplex group testing

When screening a population for infectious diseases, pooling individual specimens (e.g., blood, swabs, urine, etc.) can provide enormous cost savings when compared to testing specimens individually. In the biostatistics literature, testing pools of specimens is commonly known as group testing or pooled testing. Although estimating a population-level prevalence with group testing data has received a large amount of attention, most of this work has focused on applications involving a single disease, such as human immunodeficiency virus. Modern methods of screening now involve testing pools and individuals for multiple diseases simultaneously through the use of multiplex assays. Hou et al. (2017, Biometrics, 73, 656-665) and Hou et al. (2020, Biostatistics, 21, 417-431) recently proposed group testing protocols for multiplex assays and derived relevant case identification characteristics, including the expected number of tests and those which quantify classification accuracy. In this article, we describe Bayesian methods to estimate population-level disease probabilities from implementing these protocols or any other multiplex group testing protocol which might be carried out in practice. Our estimation methods can be used with multiplex assays for two or more diseases while incorporating the possibility of test misclassification for each disease. We use chlamydia and gonorrhea testing data collected at the State Hygienic Laboratory at the University of Iowa to illustrate our work. We also provide an online R resource practitioners can use to implement the methods in this article.

Varying-coefficient regression analysis for pooled biomonitoring

Human biomonitoring involves measuring the accumulation of contaminants in biological specimens (such as blood or urine) to assess individuals' exposure to environmental contamination. Due to the expensive cost of a single assay, the method of pooling has become increasingly common in environmental studies. The implementation of pooling starts by physically mixing specimens into pools, and then measures pooled specimens for the concentration of contaminants. An important task is to reconstruct individual-level statistical characteristics based on pooled measurements. In this article, we propose to use the varying-coefficient regression model for individual-level biomonitoring and provide methods to estimate the varying coefficients based on different types of pooled data. Asymptotic properties of the estimators are presented. We illustrate our methodology via simulation and with application to pooled biomonitoring of a brominated flame retardant provided by the National Health and Nutrition Examination Survey (NHANES).

Re-Entry Evaluation of Chinese Blood Donors with Unconfirmed Hepatitis B Screening Results

The hepatitis B virus (HBV) remains a high priority for Chinese blood banks due to the high prevalence of infection. HBV blood safety has been significantly improved by the implementation of highly sensitive and specific serological and molecular HBV screening assays. The multiplication of viral markers tested and the ever-increasing analytical sensitivity of the tests can make the interpretation of the results difficult. False-positive or indeterminate results may lead to permanent donor deferrals and conflicts between donors and blood banks. To avoid blood shortages, blood services aim to limit unnecessary donor losses by developing procedures for the re-entry of donors temporarily deferred due to an unconfirmed HBV reactivity. The development of such procedures based on donor follow-up and HBV confirmation remains limited. A review of the scarce data available revealed considerable heterogeneity in testing methods and re-entry algorithms, limited validation studies, and a lack of accurate assessment of the residual infectious risk potentially associated with donor re-entry. In conclusion, systematic and widely validated confirmatory testing and prolonged follow-up are essential for safe re-entry of temporary deferred donors. Standardization of HBV testing methods and the establishment of dedicated expert laboratories are needed because of the complexity of HBV infection in blood donors.

Genotype Distribution and Demographic Characteristics of Hepatitis C Virus NAT Yield Cases among US Blood Donors

BACKGROUND

HCV infection rates among U.S. blood donors have been well characterized; however, few studies evaluate HCV genotypes among blood donors. Monitoring trends in disease and demographic patterns contribute to understanding the safety of the blood supply. Here we examined the demographic characteristics and the distribution of HCV genotypes/subgenotypes for nearly a 16-year period among blood donors confirmed positive for HCV RNA but antibody negative (defined as NAT yield).

METHODS

A retrospective assessment of demographic characteristics and testing data was used to determine temporal trends and geographical distribution of HCV genotypes/subgenotypes among American Red Cross blood donors confirmed positive as HCV-NAT yield.

RESULTS

From 2003-2018, 343 donors (0.38 per 100,000 donations; 95% CI, 0.35-0.43) confirmed positive as HCV-NAT-yield cases. Temporal analysis revealed a significant increase in HCV-NAT-yield cases of 54.1% between 2009-2014 (p=0.014), followed by a significant decline of 31.4% between 2015-2018 (p=0.002). Significantly more HCV-NAT-yield cases were detected among first-time donors, non-Hispanic Whites, donors aged 20-29 years, equally likely to be males as females, with the highest frequency in the South (0.52/100,000 donations). Subgenotype 1a (49.6%) was most frequent, followed by 3a (18.7%), 2b (12.5%), 1b (8.5%) and 2a (1.7%).

CONCLUSION

Voluntary non-remunerated blood donors are at low risk for HCV infection. Since 2015, the frequency of HCV-NAT-yield cases decreased despite an increase of acute HCV infection in the general population. HCV subgenotypes 1a and 3a continue to remain predominant among U.S. blood donors with recent HCV infection.

Droplet digital PCR of viral ‎DNA/RNA, current progress, challenges, and future perspectives

High-throughput droplet-based digital PCR (ddPCR) is a refinement of the conventional polymerase chain reaction (PCR)‎ methods. In ddPCR, DNA/RNA is encapsulated stochastically inside the microdroplets as reaction chambers. A small percentage of the reaction chamber contains one or fewer copies of the DNA or RNA. After PCR amplification, concentrations are determined based on the proportion of nonfluorescent partitions through the Poisson distribution. Some of the main features of ddPCR include high sensitivity and specificity, absolute quantification without a standard curve, high reproducibility, good tolerance to PCR inhibitor, and high efficacy compared to conventional molecular methods. These advantages make ddPCR a valuable addition to the virologist's toolbox. The following review outlines the recent technological advances in ddPCR methods and their applications in viral identification.

Array testing for multiplex assays

Group testing involves pooling individual specimens (e.g., blood, urine, swabs, etc.) and testing the pools for the presence of disease. When the proportion of diseased individuals is small, group testing can greatly reduce the number of tests needed to screen a population. Statistical research in group testing has traditionally focused on applications for a single disease. However, blood service organizations and large-scale disease surveillance programs are increasingly moving towards the use of multiplex assays, which measure multiple disease biomarkers at once. Tebbs and others (2013, Two-stage hierarchical group testing for multiple infections with application to the Infertility Prevention Project. Biometrics69, 1064-1073) and Hou and others (2017, Hierarchical group testing for multiple infections. Biometrics73, 656-665) were the first to examine hierarchical group testing case identification procedures for multiple diseases. In this article, we propose new non-hierarchical procedures which utilize two-dimensional arrays. We derive closed-form expressions for the expected number of tests per individual and classification accuracy probabilities and show that array testing can be more efficient than hierarchical procedures when screening individuals for multiple diseases at once. We illustrate the potential of using array testing in the detection of chlamydia and gonorrhea for a statewide screening program in Iowa. Finally, we describe an R/Shiny application that will help practitioners identify the best multiple-disease case identification algorithm.

Multiply spliced HIV RNA is a predictive measure of virus production ex vivo and in vivo following reversal of HIV latency

BACKGROUND

One strategy being pursued to clear latently infected cells that persist in people living with HIV (PLWH) on antiretroviral therapy (ART) is to activate latent HIV infection with a latency reversing agent (LRA). Surrogate markers that accurately measure virus production following an LRA are needed.

METHODS

We quantified cell-associated unspliced (US), multiply spliced (MS) and supernatant (SN) HIV RNA by qPCR from total and resting CD4+ T cells isolated from seven PLWH on ART before and after treatment ex vivo with different LRAs, including histone deacetylase inhibitors (HDACi). MS and plasma HIV RNA were also quantified from PLWH on ART (n-11) who received the HDACi panobinostat.

FINDINGS

In total and resting CD4+ T cells from PLWH on ART, detection of US RNA was common while detection of MS RNA was infrequent. Primers used to detect MS RNA, in contrast to US RNA, bound sites of the viral genome that are commonly mutated or deleted in PLWH on ART. Following ex vivo stimulation with LRAs, we identified a strong correlation between the fold change increase in SN and MS RNA, but not the fold change increase in SN and US RNA. In PLWH on ART who received panobinostat, MS RNA was significantly higher in samples with detectable compared to non0detectable plasma HIV RNA.

INTERPRETATION

Following administration of an LRA, quantification of MS RNA is more likely to reflect an increase in virion production and is therefore a better indicator of meaningful latency reversal.

FUNDING

NHMRC, NIH DARE collaboratory.

Comprehensive analysis of hepatitis B virus infections in blood donors in southern China that are surface antigen positive but nucleic acid testing negative

BACKGROUND

Hepatitis B virus (HBV) infection is one of the major concerns for the safety of blood transfusion in high-prevalent countries such as in China. Prior studies outside of China have shown hepatitis B surface antigen (HBsAg) false-reactive rate of 0.02% to 0.04%. Similarly, false-negative HBsAg and HBV DNA results may occur in infected donors. Our study analyzed HBsAg enzyme-linked immunosorbent assay (ELISA)-reactive but NAT-negative donations in Shenzhen Blood Center, China.

STUDY DESIGN AND METHODS

HBsAg ELISA-positive/NAT-negative plasma samples identified from screening 101,025 donations during 2017-2018 were analyzed by molecular and serologic tests including neutralization, chemiluminescence immunoassays, and various HBV DNA amplification assays. Molecular characterizations of HBsAg-positive/NAT-negative samples were determined by quantitative polymerase chain reaction (qPCR) and nested PCR amplification of the basic core and precore promotor regions (295 base pairs) and HBsAg (S) region (496 base pairs).

RESULTS

Screening of 101,025 eligible blood donations identified 157 (0.16%, 95% confidence interval, 0.13%-0.18%) HBsAg ELISA-positive/NAT-negative plasma samples; of those, 71 (45.2%) were HBsAg confirmed positive by further HBsAg testing and DNA positive by molecular tests with increased sensitivity. Of the 71, all but one was antibody to hepatitis B core antigen reactive without antibody to hepatitis B surface antigen, yielding one recent (window-period) HBV infection. Of the remaining donations, 80 (51%) were not considered as HBV-infected donors, and 6 (3.8%) were interpreted as indeterminate since HBsAg results were discordant with unconfirmed HBV DNA results. In the 71 confirmed positives, HBsAg levels ranged from 0.05 to 400 IU/mL and HBV DNA from 6 to 2654 IU/mL; however, the correlation between the two was weak (R² = 0.24).

CONCLUSION

Fewer than half of HBsAg ELISA-positive/NAT-negative samples were confirmed as HBsAg positive. Our study demonstrates that in highly HBV-endemic countries, assays with high sensitivity and specificity may be required.

Menace of Hepatitis C virus among multitransfused thalassemia patients in Balasore district of Odisha state in India

CONTEXT

Hepatitis C virus (HCV) is a potential cause of morbidity and mortality worldwide. It is most commonly transmitted through injecting drug use; the reuse or inadequate sterilization of medical equipment and the transfusion of unscreened blood products. Management of thalassemia requires long-term blood transfusion. Though it improves the overall survival, it carries a definite risk of infection which is expected to be higher in resource limited settings.

AIMS

To find the percentage of transfusion-transmitted infections (TTIs) in multitransfused patients of thalassemia in Eastern India.

SETTINGS AND DESIGN

The study was conducted to assess blood safety in rural population in India by measuring the percentage of TTIs including HCV in multitransfused thalassemia patients.

METHODS AND MATERIALS

One hundred and twenty three patients with major beta-thalassemia were enrolled in this study. The blood samples were tested using ELISA technique for all TTIs. HIV fourth generation kits, HbsAg, HCV third generation kits, malaria and syphilis, parbovirus IgM and parbovirus IgG kits, HEV Antigen and IgM antibody were used.

STATISTICAL ANALYSIS USED

Proportions and means were calculated for categorical and continuous variables, respectively. Chi-square test was applied and P value of <0.05 was taken as significant.

RESULTS

The mean age of patients was 9.5 years ± 5.2 years. Among various TTIs, Hepatitis C and HIV was prevalent among 59.3% and 4.1% of the study participants, respectively.

CONCLUSIONS

The causes of high prevalence of HCV may be due to donors being usually asymptomatic in early stages, despite being screened for HCV possibly due to missing early window period infections. The screening methodology of TTIs particularly HCV at the district and village level and consequent increased prevalence of HCV in multitransfused rustic population of India shows the extent of blood safety.

A methodology for deriving the sensitivity of pooled testing, based on viral load progression and pooling dilution

BACKGROUND

Pooled testing, in which biological specimens from multiple subjects are combined into a testing pool and tested via a single test, is a common testing method for both surveillance and screening activities. The sensitivity of pooled testing for various pool sizes is an essential input for surveillance and screening optimization, including testing pool design. However, clinical data on test sensitivity values for different pool sizes are limited, and do not provide a functional relationship between test sensitivity and pool size. We develop a novel methodology to accurately compute the sensitivity of pooled testing, while accounting for viral load progression and pooling dilution. We demonstrate our methodology on the nucleic acid amplification testing (NAT) technology for the human immunodeficiency virus (HIV).

METHODS

Our methodology integrates mathematical models of viral load progression and pooling dilution to derive test sensitivity values for various pool sizes. This methodology derives the conditional test sensitivity, conditioned on the number of infected specimens in a pool, and uses the law of total probability, along with higher dimensional integrals, to derive pooled test sensitivity values. We also develop a highly accurate and easy-to-compute approximation function for pooled test sensitivity of the HIV ULTRIO Plus NAT Assay. We calibrate model parameters using published efficacy data for the HIV ULTRIO Plus NAT Assay, and clinical data on viral RNA load progression in HIV-infected patients, and use this methodology to derive and validate the sensitivity of the HIV ULTRIO Plus Assay for various pool sizes.

RESULTS

We demonstrate the value of this methodology through optimal testing pool design for HIV prevalence estimation in Sub-Saharan Africa. This case study indicates that the optimal testing pool design is highly efficient, and outperforms a benchmark pool design.

CONCLUSIONS

The proposed methodology accounts for both viral load progression and pooling dilution, and is computationally tractable. We calibrate this model for the HIV ULTRIO Plus NAT Assay, show that it provides highly accurate sensitivity estimates for various pool sizes, and, thus, yields efficient testing pool design for HIV prevalence estimation. Our model is generic, and can be calibrated for other infections.

Regression analysis and variable selection for two-stage multiple-infection group testing data

Group testing, as a cost-effective strategy, has been widely used to perform large-scale screening for rare infections. Recently, the use of multiplex assays has transformed the goal of group testing from detecting a single disease to diagnosing multiple infections simultaneously. Existing research on multiple-infection group testing data either exclude individual covariate information or ignore possible retests on suspicious individuals. To incorporate both, we propose a new regression model. This new model allows us to perform a regression analysis for each infection using multiple-infection group testing data. Furthermore, we introduce an efficient variable selection method to reveal truly relevant risk factors for each disease. Our methodology also allows for the estimation of the assay sensitivity and specificity when they are unknown. We examine the finite sample performance of our method through extensive simulation studies and apply it to a chlamydia and gonorrhea screening data set to illustrate its practical usefulness.

New Approaches and Trials in Pediatric Transfusion Medicine

Blood transfusions are frequently lifesaving, but there is growing awareness of their associated infectious and noninfectious adverse events. Patient blood management advocates for judicious use of transfusions and considerations of alternatives to correct anemia or achieve hemostasis. Several transfusion practices, either already implemented or under investigation, aim to further improve the safety of transfusions. An enduring challenge in pediatric and neonatal transfusion practice is that studies typically focus on adults, and findings are extrapolated to younger patients. This article aims to summarize some of the newer developments in transfusion medicine with a focus on the neonatal and pediatric population.

Recent and occult hepatitis B virus infections among blood donors in the United States

BACKGROUND

Characteristics of US blood donors with recent (RBI) or occult (OBI) hepatitis B virus (HBV) infection are not well defined.

METHODS

Donors with RBI and OBI were identified by nucleic acid and serologic testing among 34.4 million donations during 2009-2015. Consenting donors were interviewed and their HBV S-gene sequenced.

RESULTS

The overall rate of HBV-infected donors was 7.95 per 100,000; of these, 0.35 per 100,000 and 1.70 per 100,000 were RBI and OBI, respectively. RBI (n = 120) and OBI (n = 583) donors constituted 26% of all HBV-infected (n = 2735) donors. Detection of HBV DNA in 92% of OBI donors required individual donation nucleic acid testing. Donors with OBI compared to RBI were older (mean age, 48 vs 39 years; p < 0.0001) with lower median viral loads (9 vs. 529 IU/mL; p < 0.0001). A higher proportion of OBI than RBI donors were born or resided in an endemic country (39% vs. 5%; p = 0.0078). Seventy-seven percent of all RBI and OBI donors had multiple sex partners, an HBV-risk factor. Of 40 RBI and 10 OBI donors whose S gene was sequenced, 33 (83%) and 6 (60%), respectively, carried HBV subgenotype A2; 18 (55%) and 2 (33%), respectively, shared an identical sequence. Infection with 1 or more putative HBV-immune-escape mutants was identified in 5 (50%) of OBI but no RBI donors.

CONCLUSION

RBI and OBI continue to be identified at low rates, confirming the importance of comprehensive HBV DNA screening of US blood donations. HBV-infected donors require referral for care and evaluation and contact tracing; their HBV strains may provide important information on emergent genotypes.

Blood donor testing for hepatitis B virus in the United States: is there a case for continuation of hepatitis B surface antigen detection?

BACKGROUND

In the United States, blood donor testing for hepatitis B surface antigen (HBsAg) was initiated in the early 1970s. More recently, testing for antibody to hepatitis B core antigen (anti-HBc) and hepatitis B virus (HBV) DNA have been added. The incidence of hepatitis B has been declining. This study reviews the current status of testing and questions the need for continuation of HBsAg testing.

STUDY DESIGN AND METHODS

From July 2011 to June 2015, a total of 22.4 million donations were serologically tested for HBsAg and anti-HBc and for HBV-DNA by nucleic acid testing (NAT). All reactive results were evaluated and a subset of donations that were either potential NAT yield (seronegative) or serologically positive but nonreactive by HBV NAT in minipools (MPs) of 16 were further evaluated by individual donation (ID)-NAT. Samples with detectable HBV DNA were defined as actively infected and considered potentially infectious.

RESULTS

Routine testing plus supplemental ID-NAT identified 2035 samples representing active infection including 1965 with anti-HBc, 1602 with HBsAg, and 1453 with HBV DNA by MP-NAT, for respective rates per hundred-thousand donations of 9.10, 8.78, 7.16, and 6.50, continuing the downward trend previously observed. There were 29 HBV DNA-yield samples (1:771,389), 35 HBsAg-yield samples (anti-HBc nonreactive), and 404 with occult hepatitis B infection. There were six samples with HBsAg and HBV DNA detectable only by ID-NAT in the absence of anti-HBc; additional testing was consistent with extremely low or negligible levels of DNA.

CONCLUSIONS

Point estimates of HBV infection rates among blood donors continue to decline, as do those for incidence and residual risk. Elimination of HBsAg screening would have negligible impact, with a risk less than 1 per 4 million donations.

An ultra-sensitive Abbott ARCHITECT® assay for the detection of hepatitis B virus surface antigen (HBsAg)

BACKGROUND

Critical to the identification of HBV infection and the prevention of transfusion transmitted disease is the sensitive and accurate detection of Hepatitis B virus surface antigen (HBsAg). Improvements in HBsAg assay sensitivity approaching the performance of nucleic acid testing (NAT) are essential to further reduce the detection window for acute HBV infection in regions where NAT is not widely available.

OBJECTIVES AND STUDY DESIGN

An improved HBsAg assay on the fully-automated Abbott ARCHITECT^® platform was developed to improve sensitivity, mutant and genotype detection.

RESULTS

The analytical sensitivity of the improved prototype assay is 5.2 mIU/ml, which is 3.86- to 14.54-fold more sensitive than comparator assays based on the WHO International Reference Standard. The enhanced sensitivity was also demonstrated with 27 HBV seroconversion panels, detecting more panel members (191 of 364) vs. the ARCHITECT^® Qual I (144), Qual II (160) and PRISM^® (148) HBsAg assays. Further, the assay detected 7 of 12 HBV DNA positive/HBsAg negative samples, and detected all evaluated mutants and genotypes with higher sensitivity than the comparator assays. The improvement in sensitivity did not diminish assay specificity, attaining 100% (95% CI, 99.97-100%) on 10,633 blood donors.

CONCLUSIONS

An Abbott ARCHITECT^® HBsAg assay with clinical performance approaching that of mini-pool NAT (approximately 100 copies/ml was developed. The assay has superior HBsAg mutant and genotype detection and specificity, all of which are important for the diagnosis and management of HBV infection.

Sequential prevalence estimation with pooling and continuous test outcomes

Prevalence estimation is crucial for controlling the spread of infections and diseases and for planning of health care services. Prevalence estimation is typically conducted via pooled, or group, testing due to limited testing budgets. We study a sequential estimation procedure that uses continuous pool readings and considers the dilution effect of pooling so as to efficiently estimate an unknown prevalence rate. Embedded into the sequential estimation procedure is an optimization model that determines the optimal pooling design (number of pools and pool sizes) under a limited testing budget, considering the trade-off between testing cost and estimation accuracy. Our numerical study indicates that the proposed sequential estimation procedure outperforms single-stage procedures, or procedures that use binary test outcomes. Further, the sequential procedure provides robust prevalence estimates in cases where the initial estimate of the unknown prevalence rate is poor, or the assumed distribution of the biomarker load in infected subjects is inaccurate. Thus, when limited and unreliable information is available about the current status of, or biomarker dynamics related to, an infection, the sequential procedure becomes an attractive estimation strategy, due to its ability to mitigate the initial bias.

Hepatitis B Virus Blood Screening: Need for Reappraisal of Blood Safety Measures?

Over the past decades, the risk of HBV transfusion–transmission has been steadily reduced through the recruitment of volunteer donors, the selection of donors based on risk-behavior evaluation, the development of increasingly more sensitive hepatitis B antigen (HBsAg) assays, the use of hepatitis B core antibody (anti-HBc) screening in some low-endemic countries, and the recent implementation of HBV nucleic acid testing (NAT). Despite this accumulation of blood safety measures, the desirable zero risk goal has yet to be achieved. The residual risk of HBV transfusion–transmission appears associated with the preseroconversion window period and occult HBV infection characterized by the absence of detectable HBsAg and extremely low levels of HBV DNA. Infected donations tested false-negative with serology and/or NAT still persist and derived blood components were shown to transmit the virus, although rarely. Questions regarding the apparent redundancy of some safety measures prompted debates on how to reduce the cost of HBV blood screening. In particular, accumulating data strongly suggests that HBsAg testing may add little, if any HBV risk reduction value when HBV NAT and anti-HBc screening also apply. Absence or minimal acceptable infectious risk needs to be assessed before considering discontinuing HBsAg. Nevertheless, HBsAg remains essential in high-endemic settings where anti-HBc testing cannot be implemented without compromising blood availability. HBV screening strategy should be decided according to local epidemiology, estimate of the infectious risk, and resources.

Group testing case identification with biomarker information

Screening procedures for infectious diseases, such as HIV, often involve pooling individual specimens together and testing the pools. For diseases with low prevalence, group testing (or pooled testing) can be used to classify individuals as diseased or not while providing considerable cost savings when compared to testing specimens individually. The pooling literature is replete with group testing case identification algorithms including Dorfman testing, higher-stage hierarchical procedures, and array testing. Although these algorithms are usually evaluated on the basis of the expected number of tests and classification accuracy, most evaluations in the literature do not account for the continuous nature of the testing responses and thus invoke potentially restrictive assumptions to characterize an algorithm's performance. Commonly used case identification algorithms in group testing are considered and are evaluated by taking a different approach. Instead of treating testing responses as binary random variables (i.e., diseased/not), evaluations are made by exploiting an assay's underlying continuous biomarker distributions for positive and negative individuals. In doing so, a general framework to describe the operating characteristics of group testing case identification algorithms is provided when these distributions are known. The methodology is illustrated using two HIV testing examples taken from the pooling literature.

Sensitivity and specificity of a new automated system for the detection of hepatitis B virus, hepatitis C virus, and human immunodeficiency virus nucleic acid in blood and plasma donations

BACKGROUND

Use of nucleic acid testing (NAT) in donor infectious disease screening improves transfusion safety. Advances in NAT technology include improvements in assay sensitivity and system automation, and real-time viral target discrimination in multiplex assays. This article describes the sensitivity and specificity of cobas MPX, a multiplex assay for detection of human immunodeficiency virus (HIV)-1 Group M, HIV-2 and HIV-1 Group O RNA, HCV RNA, and HBV DNA, for use on the cobas 6800/8800 Systems.

STUDY DESIGN AND METHODS

The specificity of cobas MPX was evaluated in samples from donors of blood and source plasma in the United States. Analytic sensitivity was determined with reference standards. Infectious window periods (WPs) before NAT detectability were calculated for current donor screening assays.

RESULTS

The specificity of cobas MPX was 99.946% (99.883%-99.980%) in 11,203 blood donor samples tested individually (IDT), 100% (99.994%-100%) in 63,012 donor samples tested in pools of 6, and 99.994% (99.988%-99.998%) in 108,306 source plasma donations tested in pools of 96. Seven HCV NAT-yield donations and one seronegative occult HBV infection were detected. Ninety-five percent and 50% detection limits in plasma (IU/mL) were 25.7 and 3.8 for HIV-1M, 7.0 and 1.3 for HCV, and 1.4 and 0.3 for HBV. The HBV WP was 1 to 4 days shorter than other donor screening assays by IDT.

CONCLUSION

cobas MPX demonstrated high specificity in blood and source plasma donations tested individually and in pools. High sensitivity, in particular for HBV, shortens the WP and may enhance detection of occult HBV.

The Alphabet Soup of HIV Reservoir Markers

PURPOSE OF REVIEW

Despite the success of antiretroviral therapy in suppressing HIV, life-long therapy is required to avoid HIV reactivation from long-lived viral reservoirs. Currently, there is intense interest in searching for therapeutic interventions that can purge the viral reservoir to achieve complete remission in HIV patients off antiretroviral therapy. The evaluation of such interventions relies on our ability to accurately and precisely measure the true size of the viral reservoir. In this review, we assess the most commonly used HIV reservoir assays, as a clear understanding of the strengths and weaknesses of each is vital for the accurate interpretation of results and for the development of improved assays.

RECENT FINDINGS

The quantification of intracellular or plasma HIV RNA or DNA levels remains the most commonly used tests for the characterization of the viral reservoir. While cost-effective and high-throughput, these assays are not able to differentiate between replication-competent or defective fractions or quantify the number of infected cells. Viral outgrowth assays provide a lower bound for the fraction of cells that can produce infectious virus, but these assays are laborious, expensive and substantially underestimate the potential reservoir of replication-competent provirus. Newer assays are now available that seek to overcome some of these problems, including full-length proviral sequencing, inducible HIV RNA assays, ultrasensitive p24 assays and murine adoptive transfer techniques. The development and evaluation of strategies for HIV remission rely upon our ability to accurately and precisely quantify the size of the remaining viral reservoir. At this time, all current HIV reservoir assays have drawbacks such that combinations of assays are generally needed to gain a more comprehensive view of the viral reservoir. The development of novel, rapid, high-throughput assays that can sensitively quantify the levels of the replication-competent HIV reservoir is still needed.

A general framework for the regression analysis of pooled biomarker assessments

As a cost-efficient data collection mechanism, the process of assaying pooled biospecimens is becoming increasingly common in epidemiological research; for example, pooling has been proposed for the purpose of evaluating the diagnostic efficacy of biological markers (biomarkers). To this end, several authors have proposed techniques that allow for the analysis of continuous pooled biomarker assessments. Regretfully, most of these techniques proceed under restrictive assumptions, are unable to account for the effects of measurement error, and fail to control for confounding variables. These limitations are understandably attributable to the complex structure that is inherent to measurements taken on pooled specimens. Consequently, in order to provide practitioners with the tools necessary to accurately and efficiently analyze pooled biomarker assessments, herein, a general Monte Carlo maximum likelihood-based procedure is presented. The proposed approach allows for the regression analysis of pooled data under practically all parametric models and can be used to directly account for the effects of measurement error. Through simulation, it is shown that the proposed approach can accurately and efficiently estimate all unknown parameters and is more computational efficient than existing techniques. This new methodology is further illustrated using monocyte chemotactic protein-1 data collected by the Collaborative Perinatal Project in an effort to assess the relationship between this chemokine and the risk of miscarriage. Copyright © 2017 John Wiley & Sons, Ltd.

APASL consensus statements and recommendations for hepatitis C prevention, epidemiology, and laboratory testing

The Asian Pacific Association for the Study of the Liver (APASL) convened an international working party on "APASL consensus statements and recommendations for management of hepatitis C" in March 2015 to revise the "APASL consensus statements and management algorithms for hepatitis C virus infection" (Hepatol Int 6:409-435, 2012). The working party consisted of expert hepatologists from the Asian-Pacific region gathered at the Istanbul Congress Center, Istanbul, Turkey on 13 March 2015. New data were presented, discussed, and debated during the course of drafting a revision. Participants of the consensus meeting assessed the quality of the cited studies. The finalized recommendations for hepatitis C prevention, epidemiology, and laboratory testing are presented in this review.

Residual risk and waste in donated blood with pooled nucleic acid testing

An accurate estimation of the residual risk of transfusion-transmittable infections (TTIs), which includes the human immunodeficiency virus (HIV), hepatitis B and C viruses (HBV, HCV), among others, is essential, as it provides the basis for blood screening assay selection. While the highly sensitive nucleic acid testing (NAT) technology has recently become available, it is highly costly. As a result, in most countries, including the United States, the current practice for human immunodeficiency virus, hepatitis B virus, hepatitis C virus screening in donated blood is to use pooled NAT. Pooling substantially reduces the number of tests required, especially for TTIs with low prevalence rates. However, pooling also reduces the test's sensitivity, because the viral load of an infected sample might be diluted by the other samples in the pool to the point that it is not detectable by NAT, leading to potential TTIs. Infection-free blood may also be falsely discarded, resulting in wasted blood. We derive expressions for the residual risk, expected number of tests, and expected amount of blood wasted for various two-stage pooled testing schemes, including Dorfman-type and array-based testing, considering infection progression, infectivity of the blood unit, and imperfect tests under the dilution effect and measurement errors. We then calibrate our model using published data and perform a case study. Our study offers key insights on how pooled NAT, used within different testing schemes, contributes to the safety and cost of blood. Copyright © 2016 John Wiley & Sons, Ltd.

Multiplex qPCR for serodetection and serotyping of hepatitis viruses: A brief review

The present review describes the current status of multiplex quantitative real time polymerase chain reaction (qPCR) assays developed and used globally for detection and subtyping of hepatitis viruses in body fluids. Several studies have reported the use of multiplex qPCR for the detection of hepatitis viruses, including hepatitis A virus (HAV), hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis D virus (HDV), and hepatitis E virus (HEV). In addition, multiplex qPCR has also been developed for genotyping HBV, HCV, and HEV subtypes. Although a single step multiplex qPCR assay for all six hepatitis viruses, i.e., A to G viruses, is not yet reported, it may be available in the near future as the technologies continue to advance. All studies use a conserved region of the viral genome as the basis of amplification and hydrolysis probes as the preferred chemistries for improved detection. Based on a standard plot prepared using varying concentrations of template and the observed threshold cycle value, it is possible to determine the linear dynamic range and to calculate an exact copy number of virus in the specimen. Advantages of multiplex qPCR assay over singleplex or other molecular techniques in samples from patients with co-infection include fast results, low cost, and a single step investigation process.

Current concepts in the prevention of pathogen transmission via blood/plasma-derived products for bleeding disorders

The pathogen safety of blood/plasma-derived products has historically been a subject of significant concern to the medical community. Measures such as donor selection and blood screening have contributed to increase the safety of these products, but pathogen transmission does still occur. Reasons for this include lack of sensitivity/specificity of current screening methods, lack of reliable screening tests for some pathogens (e.g. prions) and the fact that many potentially harmful infectious agents are not routinely screened for. Methods for the purification/inactivation of blood/plasma-derived products have been developed in order to further reduce the residual risk, but low concentrations of pathogens do not necessarily imply a low level of risk for the patient and so the overall challenge of minimising risk remains. This review aims to discuss the variable level of pathogenic risk and describes the current screening methods used to prevent/detect the presence of pathogens in blood/plasma-derived products.

The Depsipeptide Romidepsin Reverses HIV-1 Latency In Vivo

Pharmacologically-induced activation of replication competent proviruses from latency in the presence of antiretroviral treatment (ART) has been proposed as a step towards curing HIV-1 infection. However, until now, approaches to reverse HIV-1 latency in humans have yielded mixed results. Here, we report a proof-of-concept phase Ib/IIa trial where 6 aviremic HIV-1 infected adults received intravenous 5 mg/m² romidepsin (Celgene) once weekly for 3 weeks while maintaining ART. Lymphocyte histone H3 acetylation, a cellular measure of the pharmacodynamic response to romidepsin, increased rapidly (maximum fold range: 3.7–7.7 relative to baseline) within the first hours following each romidepsin administration. Concurrently, HIV-1 transcription quantified as copies of cell-associated un-spliced HIV-1 RNA increased significantly from baseline during treatment (range of fold-increase: 2.4–5.0; p = 0.03). Plasma HIV-1 RNA increased from <20 copies/mL at baseline to readily quantifiable levels at multiple post-infusion time-points in 5 of 6 patients (range 46–103 copies/mL following the second infusion, p = 0.04). Importantly, romidepsin did not decrease the number of HIV-specific T cells or inhibit T cell cytokine production. Adverse events (all grade 1–2) were consistent with the known side effects of romidepsin. In conclusion, romidepsin safely induced HIV-1 transcription resulting in plasma HIV-1 RNA that was readily detected with standard commercial assays demonstrating that significant reversal of HIV-1 latency in vivo is possible without blunting T cell-mediated immune responses. These finding have major implications for future trials aiming to eradicate the HIV-1 reservoir.

One proposed way of curing HIV is to activate virus transcription and kill latently infected cells while the presence of antiretroviral therapy prevents spreading the infection. Induction of global T cell activation by mitogenic or other potent activators effectively reverses HIV-1 from latency ex vivo, but such compounds are generally too toxic for clinical use. Therefore, investigating the capacity of small molecule latency reversing agents to induce production of virus without causing global T cell activation has been a top research priority for scientists in recent years. In the present clinical trial, we demonstrate that significant viral reactivation can be safely induced using the depsipeptide romidepsin (HDAC inhibitor) in long-term suppressed HIV-1 individuals on antiretroviral therapy. Following each romidepsin infusion, we observed clear increases in lymphocyte H3 acetylation, HIV-1 transcription, and plasma HIV-1 RNA. Importantly, this reversal of HIV-1 latency could be measured using standard clinical assays for detection of plasma HIV-1 RNA. Furthermore, romidepsin did not alter the proportion of HIV-specific T cells or inhibit T cell cytokine production which is critically important for future trials combining HDAC inhibitors with interventions (e.g. therapeutic HIV-1 vaccination) designed to enhance killing of latently infected cells.

Evaluation of an individual-donation nucleic acid amplification testing algorithm for detecting hepatitis B virus infection in Chinese blood donors

BACKGROUND

This multicenter study was performed to evaluate the efficiency of a multiplex individual-donation nucleic acid amplification technology (ID-NAT) and discriminatory testing algorithm for detecting hepatitis B virus (HBV) infection in Chinese blood donors.

STUDY DESIGN AND METHODS

A total of 1,205,796 hepatitis B surface antigen (HBsAg)-nonreactive donations from 10 blood centers were tested by ID-NAT using the Ultrio assay. Multiplex Ultrio-reactive donations were tested in the discriminatory tests as well as in quantitative polymerase chain reaction (qPCR) and in supplemental electrochemiluminescence immunoassays for HBsAg, hepatitis B surface antibody (anti-HBs), hepatitis B e antigen, and antibody to hepatitis B core antigen (anti-HBc). Meanwhile, a control group of 4317 Ultrio-nonreactive donations was tested for anti-HBc and anti-HBs.

RESULTS

Of all donations, 2033 (0.17%) were reactive in the multiplex Ultrio assay. Among 1776 further tested samples, 548 (30.9%) were HBV discriminatory assay (dHBV)-reactive, while 1214 (68.4%) were nonreactive. Of 472 Ultrio+ and dHBV+ samples 86.2% were qPCR positive compared to 15.0% in 1046 Ultrio+ and dHBV- samples. The proportion of anti-HBc+ and anti-HBs- (potentially infectious) donations was higher in 409 Ultrio+ and dHBV+ than in 1028 Ultrio+ and dHBV- samples (51.3% vs. 31.1%, p < 0.001). The yield rate of Ultrio+, dHBV+, and qPCR+ donations was estimated at 1 in 2500, but at 1 in 1100 when all supplemental tests were taken into account assuming that 44% of detected donations by Ultrio were false reactive.

CONCLUSIONS

A quarter of HBsAg-negative Ultrio+ and dHBV- donations in China are likely given by potentially infectious low-viral-load occult carriers. Although this has no implication for blood safety, the testing algorithm needs to be redesigned to more efficiently discriminate between true and false NAT reactivity.

A general regression framework for group testing data, which incorporates pool dilution effects

Group testing, through the use of pooling, has been widely implemented as a more efficient means to screen individuals for infectious diseases. Typically, in these settings, practitioners are tasked with the complimentary goals of both case identification and estimation. For these purposes, many group testing strategies have been proposed, which address issues such as preserving anonymity in estimation studies, quality control, and classification. In general, these strategies require that a significant number of the individuals be retested, either in pools or individually. In order to provide practitioners with a general methodology that can be used to accurately and precisely analyze data of this form, herein, we propose a binary regression framework that can incorporate data arising from any group testing strategy. Further, we relax previously made assumptions regarding testing error rates by relating the diagnostic testing results to the latent biological marker levels of the individuals being tested. We investigate the finite sample performance of our proposed methodology through simulation and by applying our techniques to hepatitis B data collected as part of a study involving Irish prisoners.

Comparison of Rapid Point-of-Care Tests for Detection of Antibodies to Hepatitis C Virus

OraSure had the highest sensitivity at 92.7% followed closely by Chembio's three blood tests. False results were associated with HIV, and hepatitis B core antibody. The OraSure and Chembio blood tests have good performance characteristics.

Background. Hepatitis C is one of the most prevalent blood-borne diseases in the United States. Despite the benefits of early screening, among 3.2 million Americans who are infected with hepatitis C virus (HCV), 50%–70% are unaware of their infection status.

Methods. Data were collected between 2011 and 2014, from 1048 clients who were in the following groups: (1) injection drug users, (2) women at sexual risk, (3) gay and bisexual men, and (4) transgender individuals. The sensitivity and specificity of point-of-care tests included (1) the MedMira rapid human immunodeficiency virus (HIV)/HCV antibody test, (2) MedMira hepatitis B (HBV)/HIV/HCV antibody test, (3) Chembio HCV Screen Assay used with both whole blood and (4) oral specimens, (5) Chembio HIV-HCV Assay also used with both whole blood and (6) oral specimens, (7) Chembio HIV-HCV-Syphilis Assay, and (8) OraSure HCV Rapid Antibody Test used with whole blood. The gold standard for the HCV tests were HCV enzyme immunoassay (EIA) 2.0.

Results. OraSure had the highest sensitivity at 92.7% (95% confidence interval [CI] = 88.8%–96.5%) followed closely by Chembio's 3 blood tests at 92.1% (95% CI = 87.7%–96.4%), 91.5% (95% CI = 87.2%–95.7%), and 92.3% (95% CI = 88.4%–96.2%). The sensitivities of MedMira HIV/HCV and MedMira HIV/HCV/HBV tests were the lowest, at 79.1% (95% CI = 72.6%–85.5%), and 81.5% (95% CI = 75.2%–87.8%), respectively. Specificity for the OraSure was 99.8% (95% CI = 99.4%–100%); specificity for the Chembio blood tests was 99.2% (95% CI = 98.6%–99.9%), 99.4% (95% CI = 98.8%–99.9%), and 99.3% (95% CI = 98.8%–99.9%); and specificity for the MedMira was100% and 100%. False-negative results were associated with HIV and hepatitis B core antibody serostatus.

Conclusions. The OraSure and Chembio blood tests (including those multiplexed with HIV and syphilis) appear to good performance characteristics. This study has identified potential limitations of rapid testing in those testing positive for HIV and HBcAb. There should be discussion of updates to the 2013 CDC guidance.

Inclusion of human immunodeficiency virus Type 2 (HIV-2) in a multiplex transcription-mediated amplification assay does not affect detection of HIV-1 and hepatitis B and C virus genotypes: a multicenter performance evaluation study

BACKGROUND

The Ultrio Elite assay (Hologic/Grifols) runs on the Panther blood screening system and is comparable to the Ultrio Plus assay apart from the addition of oligonucleotides for human immunodeficiency virus Type 2 (HIV-2) detection. In this multicenter evaluation study the analytical sensitivity and genotype detection efficiency of the two assay versions were compared.

STUDY DESIGN AND METHODS

The analytical sensitivity and genotype detection efficiency were analyzed by replicate (18-303) testing of 27 hepatitis B virus (HBV), hepatitis C virus (HCV), HIV-1, and HIV-2 standard dilution panels calibrated in international units (IUs) and copies/mL. A wider range of subgenotypes was tested at 25 copies/mL. Specificity was evaluated in 30,756 donor samples.

RESULTS

The 95% lower limits of detection (LODs) in Ultrio Elite assay on WHO standards were 4.6, 7.3, 23.5, and 23.3 IU/mL for HBV, HCV, HIV-1, and HIV-2, respectively, and ranged from 13 to 44, 7 to 23, 6 to 15, and 9 copies/mL on genotype panels of the respective viruses. Comparable LODs had been previously found on the same panels with the Ultrio Plus assay. The specificity was 99.95% on initial test and 100% in the repeat test algorithm.

CONCLUSION

The change in the oligonucleotide design of the Ultrio Elite assay to enable HIV-2 detection has not affected the analytical sensitivity for the other viruses regardless of the genotype. Genotype reference panels are instrumental to compare the sensitivity of nucleic acid test assay versions and could serve as an alternative to seroconversion panels.

Activation of latent human immunodeficiency virus by the histone deacetylase inhibitor panobinostat: a pilot study to assess effects on the central nervous system

In a substudy of a clinical trial, we assessed whether activation of latent human immunodeficiency virus (HIV) by the histone deacetylase inhibitor panobinostat had detrimental effects on the central nervous system (CNS). Adults infected with HIV received oral panobinostat 20 mg 3 times per week every other week for 8 weeks. In cerebrospinal fluid (CSF), we assayed panobinostat concentration, HIV RNA, and the level of neuroinflammatory or degenerative biomarkers in 11 individuals before and during study therapy. Neither panobinostat nor HIV RNA was detected in CSF. In addition, there was no change from baseline in CSF biomarkers. Thus, panobinostat administration was not associated with CNS adverse effects as assessed by CSF biomarkers.

Panobinostat, a histone deacetylase inhibitor, for latent-virus reactivation in HIV-infected patients on suppressive antiretroviral therapy: a phase 1/2, single group, clinical trial

BACKGROUND

Activating the expression of latent virus is an approach that might form part of an HIV cure. We assessed the ability of the histone deacetylase inhibitor panobinostat to disrupt HIV-1 latency and the safety of this strategy.

METHODS

In this phase 1/2 clinical trial, we included aviraemic adults with HIV treated at Aarhus University Hospital, Denmark. Participants received oral panobinostat (20 mg) three times per week every other week for 8 weeks while maintaining combination antiretroviral therapy. The primary outcome was change from baseline of cell-associated unspliced HIV RNA. Secondary endpoints were safety, plasma HIV RNA, total and integrated HIV DNA, infectious units per million CD4 T cells, and time to viral rebound during an optional analytical treatment interruption of antiretroviral therapy. This trial is registered with ClinicalTrial.gov, number NCT01680094.

FINDINGS

We enrolled 15 patients. The level of cell-associated unspliced HIV RNA increased significantly at all timepoints when patients were taking panobinostat (p < 0·0001). The median maximum increase in cell-associated unspliced HIV RNA during panobinostat treatment was 3·5-fold (range 2·1-14·4). Panobinostat induced plasma viraemia with an odds ratio of 10·5 (95% CI 2·2-50·3; p = 0·0002) compared with baseline. We recorded a transient decrease in total HIV DNA, but no cohort-wide reduction in total HIV DNA, integrated HIV DNA, or infectious units per million. Nine patients participated in the analytical treatment interruption, median time to viral rebound was 17 days (range 14-56). Panobinostat was well tolerated. 45 adverse events were reported, but only 16 (all grade 1) were presumed related to panobinostat.

INTERPRETATION

Panobinostat effectively disrupts HIV latency in vivo and is a promising candidate for future combination clinical trials aimed at HIV eradication. However, panobinostat did not reduce the number of latently infected cells and this approach may need to be combined with others to significantly affect the latent HIV reservoir.

FUNDING

The Danish Council for Strategic Research and Aarhus University.

Detection and identification of occult HBV in blood donors in Taiwan using a commercial, multiplex, multi-dye nucleic acid amplification technology screening test

BACKGROUND

The ability of a new generation commercial, multiplex, multi-dye test from Roche, the cobas TaqScreen MPX test, version 2.0, to detect and identify occult HBV infections was evaluated using routine donor samples from Kaohsiung Blood Bank, Taiwan.

STUDY DESIGN AND METHODS

A total of 5973 samples were tested by nucleic acid amplification technology (NAT); 5898 in pools of six, 66 in pools of less than six and nine samples individually. NAT-reactive samples were retested with alternative NAT tests, and follow-up samples from the donors were tested individually by NAT and for all the HBV serological markers.

RESULTS

Eight NAT-only-reactive donors were identified, and follow-up samples were obtained from six of the donors. The results indicated that all eight donors had an occult HBV infection with viral loads <12 IU/ml.

CONCLUSION

The cobas(®) TaqScreen MPX test, version 2.0, has an advantage over the current Roche blood screening test, the cobas TaqScreen MPX test, for screening donations in countries with a high prevalence of occult HBV infections since the uncertainty associated with identifying samples with very low viremia is removed by the ability of the test to identify the viral target in samples that are reactive with the cobas TaqScreen MPX test, version 2.0.