How safe is safe: new human immunodeficiency virus Type 1 variants missed by nucleic acid testing

Multispecies Cocirculation of Adenoviruses Identified by Next-Generation Sequencing During an Acute Gastroenteritis Outbreak in Coastal Kenya in 2023

Background

Although 7 human adenovirus (HAdV) species are known to exist, only F (types 40 and 41) and G are identified as diarrheal disease agents. The role of other HAdV species in diarrheal disease remains unclear, and data on their prevalence are limited. We describe HAdV species and types in hospitalized children with diarrhea in coastal Kenya.

Methods

Three hundred twenty-nine stool samples collected between June 2022 and August 2023 from children aged <13 years were screened for HAdV using quantitative polymerase chain reaction (qPCR). Positive HAdV cases were genotyped by adenovirus primers from the RespiCoV panel by amplification, next-generation sequencing, and phylogenetic analysis.

Results

Sixty-five samples (20%) tested HadV positive, of which 5 HAdV species were identified. Other than HAdV F, other species included A, B, C, and D; these were detected as either mono-detections or coinfections. Six HAdV F identified by NGS had been missed by our qPCR typing method. This appeared to be as a result of a 133-nucleotide deletion in the long fiber protein, which abrogated a primer and probe binding site. Based on grading of diarrheal disease severity using VESIKARI scores, 93% of the HAdV cases presented with severe disease. One child with an HAdV F infection died.

Conclusions

Our study shows the enormous diversity and clinical characteristics of HAdV species in children with diarrhea in coastal Kenya. These data offer an opportunity to improve current diagnostic assays and increase knowledge of HAdV in Africa for control of outbreaks in the future.

Spotlights on the trends in performance assessment of qualitative in vitro diagnostic medical devices in transfusion medicine

For reliable clinical decisions in transfusion medicine, assessing the performance of qualitative tests performed in medical laboratories is critical. When false results are reported, these can lead to an adverse reaction to blood components. Good performance assessment practices are essential for this kind of scenario, and they still remain as one of the many unmet high-priority challenges in this area. This paper aims to provide an overview of the current trends in this field. A review of the IFCC-IUPC. qualitative vocabulary was carried out, and a particular focus was given to the evaluation protocols CLSI EP12-A3 and Eurachem AQA, such as the European Union Regulation for class D in vitro diagnostic medical devices. There is a consistency between the current protocols and recognized performance assessment principles, which are mandatory in transfusion service labs. We believe that a revised imprecision interval approach and models based on emerging qualitative test types may prove beneficial in the long run. It is also important to emphasize the uncertainty of proportions to mitigate the risk of misclassification.

Fucose Binding Cancels out Mechanical Differences between Distinct Human Noroviruses

The majority of nonbacterial gastroenteritis in humans and livestock is caused by noroviruses. Like most RNA viruses, frequent mutations result in various norovirus variants. The strain-dependent binding profiles of noroviruses to fucose are supposed to facilitate norovirus infection. It remains unclear, however, what the molecular mechanism behind strain-dependent functioning is. In this study, by applying atomic force microscopy (AFM) nanoindentation technology, we studied norovirus-like particles (noroVLPs) of three distinct human norovirus variants. We found differences in viral mechanical properties even between the norovirus variants from the same genogroup. The noroVLPs were then subjected to fucose treatment. Surprisingly, after fucose treatment, the previously found considerable differences in viral mechanical properties among these variants were diminished. We attribute a dynamic switch of the norovirus P domain upon fucose binding to the reduced differences in viral mechanical properties across the tested norovirus variants. These findings shed light on the mechanisms used by norovirus capsids to adapt to environmental changes and, possibly, increase cell infection. Hereby, a new step towards connecting viral mechanical properties to viral prevalence is taken.

Modeling the Risk of HIV Transfusion Transmission

BACKGROUND

Blood donations are routinely screened for HIV to prevent an infectious unit from being released to the blood supply. Despite improvements to blood screening assays, donations from infected donors remain undetectable during the window period (WP), when the virus has not yet replicated above the lower limit of detection (LOD) of a screening assay. To aid in the quantitative risk assessments of WP donations, a dose-response model describing the probability of transfusion-transmission of HIV over a range of viral RNA copies was developed.

METHODS

An exponential model was chosen based on data fit and parsimony. A data set from a HIV challenge study using a nonhuman primate model and another data set from reported human blood transfusions associated with HIV infected donors were separately fit to the model to generate parameter estimates. A Bayesian framework using No-U-Turn Sampling (NUTS) and Monte Carlo simulations was performed to generate posterior distributions quantifying uncertainty in parameter estimation and model predictions.

RESULTS

The parameters of the exponential model for both nonhuman primate and human data were estimated with a mean (95% credible intervals) of 2.70 × 10 -2 (7.74 × 10 -3 , 6.06 × 10 -2 ) and 7.56 × 10 -4 (3.68 × 10 -4 , 1.31 × 10 -3 ), respectively. The predicted ID 50 for the animal and human models was 26 (12, 90) and 918 (529, 1886) RNA copies transfused, respectively.

CONCLUSION

This dose-response model can be used in a quantitative framework to estimate the probability of transfusion-transmission of HIV through WP donations. These models can be especially informative when assessing risk from blood components with low viral load.

Evaluation of a Trio Toscana Virus Real-Time RT-PCR Assay Targeting Three Genomic Regions within Nucleoprotein Gene

Toscana virus (TOSV) can cause central nervous system infections in both residents of and travelers to Mediterranean countries. Data mining identified three real-time RT-qPCR assays for detecting TOSV RNA targeting non-overlapping regions in the nucleoprotein gene. Here, they were combined to create a multi-region assay named Trio TOSV RT-qPCR consisting of six primers and three probes. In this study, (i) we evaluated in silico the three RT-qPCR assays available in the literature for TOSV detection, (ii) we combined the three systems to create the Trio TOSV RT-qPCR, (iii) we assessed the specificity and sensitivity of the three monoplex assays versus the Trio TOSV RT-qPCR assay, and (iv) we compared the performance of the Trio TOSV RT-qPCR assay with one of the reference monoplex assays on clinical samples. In conclusion, the Trio TOSV RT-qPCR assay performs equally or better than the three monoplex assays; therefore, it provides a robust assay that can be used for both research and diagnostic purposes.

Reliability of CE-marked NATs for HIV-1 subtype C detection and quantitation

We compared seven CE-marked HIV-1 RNA nucleic acid amplification technology (NAT) based assays for their detection efficiency and quantitation concordance in regard to HIV-1 subtype C. We used 398 plasma samples from South African repeat blood donors identified as HIV positive at occasion of routine screening NAT performed mainly during the years 2010-2013, with most plasma samples reflecting recent HIV-1 infections. All HIV-1 subtype C specimens were detected, independent of mono- or dual-target assay design. In the same time period new variants of HIV-1 subtype B had been identified which were missed by some mono-target assays, a finding which was not corroborated for subtype C in our study. A high level of concordance of HIV-1 subtype C quantitation was determined for the HIV-1 NATs, showing successful standardization in this diagnostic field.

Development and Evaluation of a Duo Chikungunya Virus Real-Time RT-PCR Assay Targeting Two Regions within the Genome

Chikungunya virus (CHIKV) re-emerged as a globalized health threat fifteen years ago. There are dozens of RT-PCR assays published. An inventory of the latter was made, and after in silico analysis, two assays were selected for their ability to detect strains belonging to the five CHIKV genetic lineages. They were combined in order to provide a robust assay not affected by genetic point mutations and the resulting Duo CHIKV real-time RT-PCR assay was compared to the two parental single-plex tests against five strains belonging to the five genetic lineages. The Duo CHIKV assay performed equally, or better, in terms of sensitivity, specificity, linearity and signal intensity. Dual-target assays are better suited for viruses having the propensity to evolve into new variants via point mutations or major sequence deletions/insertions. Here, we demonstrated that combining two single systems into a dual-target assay did not impair sensitivity and specificity, and proved a potent diagnostic tool to face a potential emergence of CHIKV variants by newly evolving mutations.

Nucleic acid testing and molecular characterization of HIV infections

Significant advances have been made in the molecular assays used for the detection of human immunodeficiency virus (HIV), which are crucial in preventing HIV transmission and monitoring disease progression. Molecular assays for HIV diagnosis have now reached a high degree of specificity, sensitivity and reproducibility, and have less operator involvement to minimize risk of contamination. Furthermore, analyses have been developed for the characterization of host gene polymorphisms and host responses to better identify and monitor HIV-1 infections in the clinic. Currently, molecular technologies including HIV quantitative and qualitative assays are mainly based on the polymerase chain reaction (PCR), transcription-mediated amplification (TMA), nucleic acid sequence-based amplification (NASBA), and branched chain (b) DNA methods and widely used for HIV detection and characterization, such as blood screening, point-of-care testing (POCT), pediatric diagnosis, acute HIV infection (AHI), HIV drug resistance testing, antiretroviral (AR) susceptibility testing, host genome polymorphism testing, and host response analysis. This review summarizes the development and the potential utility of molecular assays used to detect and characterize HIV infections.

Transfusion of HIV-infected blood products despite highly sensitive nucleic acid testing

BACKGROUND

In France, the risk of HIV transmission by transfusion was reduced by implementing pooled nucleic acid testing (NAT) in 2001 and individual NAT in 2010. We report here the first case in France of transfusion of human immunodeficiency virus (HIV)-infected blood donated during HIV pre-ramp-up phase that tested individual NAT negative.

METHODS

Blood donations are screened for HIV antibodies and HIV RNA (ProcleixUltrio, Grifols; limit of detection at 95%, 23 copies/mL). When a repeat donor tests positive for HIV, a repository sample from the previous donation is tested with the Cobas Taqman HIV-1 test (CTM, Roche; limit of detection at 95%, 17 copies/mL).

RESULTS

In August 2017, a 57-year-old male repeat donor was screened positive for HIV antibodies and RNA (plasma viral load, 11,599 copies/mL). The previous donation had tested negative with Ultrio in March 2017 but was positive with an unquantifiable plasma viral load when tested with CTM. Sequencing showed no mismatch between Ultrio primers/probes and the target sequence. HIV transmission was excluded by lookback studies in the recipient of platelets, which had been pathogen reduced, but not in the recipient of RBCs due to premature death.

CONCLUSION

This case demonstrates that the risk of contaminated donations due to the early HIV infection phase going undetected by highly sensitive NAT is real but exceptional. The absence of transmission to the platelets recipient could be due to the very low viral inoculum and/or to the efficacy of the viral inactivation. This case also highlights the additional value of a systematic donation archiving and the importance of donor education and predonation selection.

Genetic Characterization of a Panel of Diverse HIV-1 Isolates at Seven International Sites

HIV-1 subtypes and drug resistance are routinely tested by many international surveillance groups. However, results from different sites often vary. A systematic comparison of results from multiple sites is needed to determine whether a standardized protocol is required for consistent and accurate data analysis. A panel of well-characterized HIV-1 isolates (N = 50) from the External Quality Assurance Program Oversight Laboratory (EQAPOL) was assembled for evaluation at seven international sites. This virus panel included seven subtypes, six circulating recombinant forms (CRFs), nine unique recombinant forms (URFs) and three group O viruses. Seven viruses contained 10 major drug resistance mutations (DRMs). HIV-1 isolates were prepared at a concentration of 107 copies/ml and compiled into blinded panels. Subtypes and DRMs were determined with partial or full pol gene sequences by conventional Sanger sequencing and/or Next Generation Sequencing (NGS). Subtype and DRM results were reported and decoded for comparison with full-length genome sequences generated by EQAPOL. The partial pol gene was amplified by RT-PCR and sequenced for 89.4%-100% of group M viruses at six sites. Subtyping results of majority of the viruses (83%-97.9%) were correctly determined for the partial pol sequences. All 10 major DRMs in seven isolates were detected at these six sites. The complete pol gene sequence was also obtained by NGS at one site. However, this method missed six group M viruses and sequences contained host chromosome fragments. Three group O viruses were only characterized with additional group O-specific RT-PCR primers employed by one site. These results indicate that PCR protocols and subtyping tools should be standardized to efficiently amplify diverse viruses and more consistently assign virus genotypes, which is critical for accurate global subtype and drug resistance surveillance. Targeted NGS analysis of partial pol sequences can serve as an alternative approach, especially for detection of low-abundance DRMs.

Implementation of an HIV-1 Triple-Target NAT Assay in the Routine Screening at Three German Red Cross Blood Centres

BACKGROUND

Blood product safety was significantly improved by the introduction of NAT testing in the late 1990s, resulting in a strong decrease of transfusion-transmitted infections (TTIs). Due to the occurrence of HIV-1 NAT test failures as a consequence of mismatch mutations in the amplicon regions of mono-target NAT assays, the Paul Ehrlich Institute mandated the implementation of multi-target NAT assays for HIV-1 in 2014. Commercial suppliers mostly developed dual-target NAT assays, with only one implementing a triple-target NAT assay.

METHODS

The HIV-1 triple-target NAT assay v3 (GFE Blut) was tested on mutated specimens and synthetic DNA bearing mutations that resulted in sample underquantification or false-negative test results. In addition, data from 2 years routine testing at three German Red Cross Blood centres were analysed.

RESULTS

The HIV-1 triple-target PCR could compensate for all mutations tested and could compensate the loss of one amplicon without a significant loss of sensitivity. Data from 2 years routine testing showed a solid performance.

CONCLUSION

The HIV-1 triple-target v3 assay (GFE Blut) can compensate mutations in target sequences better than a dual-target assay and is applicable to high-throughput screening, thus increasing blood product safety.

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.

High sensitivity detection of HIV-1 using two genomic targets compared with single target PCR

The genetic diversity of Human Immunodeficiency Virus type-1(HIV-1) has been shown to affect the performance of Nucleic Acid Testing (NAT) of Human Immunodeficiency Virus type-1. Although, majority NAT assays were designed to detect the conserved regions of HIV-1 mutations at the primer or probe binding regions may lead to false negatives. In this study, we evaluated the feasibility of detecting two genomic targets for enhanced sensitivity. A total of 180 tests using HIV-1 VQA RNA quantitation standard, 240 tests using EQAPOL HIV-1 viral diversity subtype panel, and 30 clinical plasma samples from Cameroon were evaluated. The analysis was based on probit and hit rate. The genomic targets LOD estimated by PROBIT for the gag target was 118 cps/ml (95%CI 64 cps/ml lower bound), Pol or POL/LTR was at 40 cps/ml (95%CI 17, 16 cps/ml), LTR 45 cps/ml (95%CI 20 cps/ml lower bound), and Gag/LTR at 67.8 cps/ml (95%CI 32 cps/ml lower bound). For HIV-1 subtypes the overall reactivity was 55-100% when tested at 100 and 1000 cps/ml and combination of genomic targets detection increased the reactivity to 100%. The plasma samples evaluation showed LTR or pol/LTR combination yielded higher sensitivity for patients with lower viral load (<40 cps/ml). We conclude that detection of two HIV-1 genomic targets improved sensitivity for detection of genetically diverse HIV-1 strains.

Pharmacokinetics, phenotype and product choice in haemophilia B: how to strike a balance?

At the 7th Annual Congress of the European Association for Haemophilia and Allied Disorders (EAHAD) held in Brussels, Belgium, in February 2014, Pfizer sponsored a satellite symposium entitled: "Pharmacokinetics, phenotype and product choice in haemophilia B: How to strike a balance?" Co-chaired by Cedric Hermans (Cliniques Universitaires Saint Luc, Brussels, Belgium) and Mike Laffan (Imperial College, London, UK), the symposium provided an opportunity to debate whether pharmacokinetic (PK) parameters are good surrogates for clinical efficacy for haemophilia B in clinical practice, consider the perceptions and evidence of disease severity, and examine how these considerations can inform approaches to balancing the potential risks and benefits of the currently available treatment options for haemophilia B. PK parameters are routinely measured in clinical practice and are a requirement of regulatory bodies to demonstrate the clinical efficacy of products; however, the relationship between measured PK parameters and clinical efficacy is yet to be determined, an issue that was debated by Gerry Dolan (University Hospital, Queen's Medical Centre, Nottingham, UK) and Erik Berntorp (Lund University, Malmö Centre for Thrombosis and Haemostasis, Malmö, Sweden). Elena Santagostino (Universita degli Studi di Milano, Milano, Italy) reviewed how differing perceptions on the severity of haemophilia B compared with haemophilia A may have an impact on clinical decision-making. Finally, Andreas Tiede (Hannover Medical School, Hannover, Germany), examined the considerations for balancing the potential risks and benefits of the currently available treatment options for haemophilia B. Although the pathophysiology of haemophilia B has been widely studied and is largely understood, continued investigation and discussion around the optimal management course and appropriate therapeutic choice is warranted.

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.

Head-to-head comparison between two screening systems for HBsAG, anti-HBc, anti-HCV and HIV combination immunoassays in an international, multicentre evaluation study

BACKGROUND

Mandatory screening of blood donations for hepatitis B and hepatitis C viruses and human immunodeficiency viruses 1 and 2 requires assays with exceptional sensitivity and specificity. This study reports the results from a direct head-to-head comparison of the Elecsys HBsAG II, Elecsys Anti-HBc, Elecsys Anti-HCV II and Elecsys HIV combi PT immunoassays with the respective ABBOTT PRISM/Architect instrument immunoassays in a multicentre blood bank evaluation study.

STUDY DESIGN AND METHODS

Assay validation was performed in the blood screening laboratories of four blood bank centres in Austria, Germany, Spain and Thailand, where both first-time donor samples (approximately 6000 donors) and repeat donor samples (approximately 14,000 donors) were screened.

RESULTS

Of all screened donor samples, 93 (0.46%) were confirmed to be positive using assays from both manufacturers. The specificity of all immunoassays was >99.5% and was comparable between first-time and multiple-time donors. A direct comparison between the assays from Roche and ABBOTT according to Bland and Altman analysis demonstrated equivalent quality.

CONCLUSIONS

These results suggest that the Elecsys immunoassays for HBV, HCV and HIV infection, with a comparative sensitivity of 100% and a specificity exceeding the common technical specification threshold of >99.5%, meet the stringent performance criteria stipulated for blood donor screening for these infectious agents. Significant differences in the specificity between first-time and repeat donors were not detectable.

Scheme for the selection of measurement uncertainty models in blood establishments' screening immunoassays

Blood establishments routinely perform screening immunoassays to assess safety of the blood components. As with any other screening test, results have an inherent uncertainty. In blood establishments the major concern is the chance of false negatives, due to its possible impact on patients' health. This article briefly reviews GUM and diagnostic accuracy models for screening immunoassays, recommending a scheme to support the screening laboratories' staffs on the selection of a model considering the intended use of the screening results (i.e., post-transfusion safety). The discussion is grounded on a "risk-based thinking", risk being considered from the blood donor selection to the screening immunoassays. A combination of GUM and diagnostic accuracy models to evaluate measurement uncertainty in blood establishments is recommended.

Risk Minimization Measures for Blood Screening HIV-1 Nucleic Acid Amplification Technique Assays in Germany

BACKGROUND

Several publications describe HIV-1 RNA false-negative results or viral load underquantitation associated with Communauté Européenne(CE)-marked qualitative or quantitative nucleic acid amplification technique (NAT) assays. 6 cases occurred during blood screening in Germany, with 2 of them causing HIV-1 transmissions to recipients of blood components. The implicated NAT assays were mono-target assays amplifying in different viral genome regions (gag or long terminal repeat).

METHODS

Specimens characterized by HIV-1 NAT underquantitation or false-negative NAT results were comparatively investigated in CE-marked HIV-1 NAT systems of different design to identify potential reasons. The target regions of the viral nucleic acids were sequenced and these sequences compared to primers and probes of the assays. Potential risk minimization measures were considered for quantitative and blood-screening HIV-1 NAT systems.

RESULTS

Nucleotide sequencing of the viral target region in cases of HIV-1 RNA underquantitation or false-negative test results revealed new HIV-1 variants that were mismatched with primers and probes used in some mono-target assays. So far, dualtarget NAT assays have not been associated with mismatch-based false-negative test results. From 2015, the Paul Ehrlich Institute will request HIV-1 NAT assays of dual-target design or an analogous solution for further reducing the risk in blood screening.

CONCLUSION

HIV differs from other blood-borne viruses with regard to its fast evolution of new viral variants. The evolution of new sequences is hardly predictable; therefore, NAT assays with only 1 target region appear to be more vulnerable to sequence variations than dual-target assays. The associated risk may be higher for HIV-1 NAT assays used for blood screening compared to quantitative assays used for monitoring HIV-1-infected patients. In HIV-1 screening NAT assays of dual-target design may adequately address the risk imposed by new HIV-1 variants.