Diagnostic Microbiology and Infectious Disease

BackgroundImmunocompromised (IC) individuals are at increased risk for persistent SARS-CoV-2 infections and can develop new viral mutations and lineages not seen in the community. In this case report, a persistent SARS-CoV-2 infection (330 days) in an IC patient is examined for viral mutations and mutations associated with cryptic lineages. Case PresentationThe patient was followed in a longitudinal study examining persistent SARS-CoV-2 in IC patients. The patient provided stool and nasal swab samples biweekly until 28 days post-enrollment, then monthly, and then quarterly after 12 month post enrollment until the participant was no longer positive for SARS-CoV-2. Staff performed RT-qPCR and viral sequencing on the samples. Viral mutations from the XBK lineage were already present in the initial sample. By the end of the infection period, there were 40 fixed consensus changes from XBK of which two mutations were typical for cryptic lineages. Mutations increased steadily over time, with most mutations fixed by day 253, including the cryptic typical mutations. ConclusionThis case demonstrates the potential for persistent SARS-CoV-2 infections to develop mutations and lineages in IC patients and highlights the need for continued SARS-CoV-2 monitoring and treatment in this vulnerable population.

Sickle cell disease (SCD) is the most common inherited hemoglobinopathy worldwide. Improving the quality of life of people with SCD requires prenatal and neonatal screening. Our primary objective was to demonstrate that prenatal diagnosis of SCD is possible even in situations of poverty. Secondarily, we described the socioeconomic profile of couples seeking molecular diagnosis of SCD in Kinshasa, Democratic Republic of Congo. Methods This was a cross-sectional study conducted in Kinshasa between January 2020 and December 2025. During this study period, 107 couples underwent prenatal diagnosis. Prenatal diagnosis was performed using amniocentesis with FTA Elute technology. This diagnosis was confirmed at birth using cord blood DNA extracted via the conventional salting-out technique. Results The mean age of the pregnant women was 28 {+/-} 4 years. Eighty-one couples (75.7%) were Christian, nine couples (8.4%) were Muslim, and seventeen couples (15.8%) were animist. Eighty-two couples (76.6%) were known heterozygous AS couples, eleven (10.2%) were heterozygous couples, and fourteen (13.0%) were couples composed of one homozygous SS and one heterozygous AS partner. All pregnancies were singleton. Socioeconomic status was upper middle class (39.2%). The AS genotype was found in 79% of the fetuses. One intrauterine fetal death was observed after amniocentesis. In terms of handling, the FTA Elute technology reduces DNA extraction time to 30 minutes. It is easy to use. Results are available in less than 24 hours. Conclusion The FTA Elute technology is a reliable, less expensive, and easy-to-use prenatal screening technique for sickle cell disease. Sample transport and storage conditions are better suited to resource-limited settings.

Severe combined immunodeficiency (SCID) is a heterogeneous, recessive disorder, associated with the onset of severe, recurrent infections in the first few months of life. SCID is fatal if left untreated, but outcomes can be significantly improved by prompt diagnosis and treatment, particularly prior to onset of infection. Consequently, SCID is already included in many newborn screening programmes around the world, as well as multiple international genomic newborn screening (gNBS) research programmes. However, there is a vital need to estimate penetrance of SCID variants in population cohorts, to mitigate the potential consequences of reporting low penetrance variants in a genotype-first gNBS setting. This study aimed to assess the penetrance and prevalence of these variants in the UK Biobank population cohort. Whole genome sequencing data from 490,640 individuals was used to interrogate 16 SCID genes for potentially causal variation. We identified 4206 carriers of single heterozygous pathogenic variants ([~]1% of cohort), but only 6 individuals double heterozygous, homozygous or hemizygous for relevant pathogenic variants. 3 individuals would be expected to require further testing had they been identified by gNBS, suggesting that fewer than 1 in 100,000 newborns might require follow-up testing due to SCID variants. Following detailed variant curation, we were able to identify only 2 unabected individuals likely to be harbouring biallelic pathogenic variants, potentially indicative of reduced penetrance. Nonetheless, SCID remains an excellent candidate for inclusion in gNBS studies, due its severity, clinical actionability and expected low false positive rate, although care should be taken when reporting hypomorphic variants.

BackgroundGenetic drift and host-associated adaptation in influenza A viruses threaten the long-term reliability of RT-qPCR-based diagnostics, particularly when nucleotide mismatches arise within primer and probe binding regions. Conventional assay evaluations often emphasize sequence conservation but rarely assess functional mismatch tolerance across divergent subtypes and hosts. MethodsWe performed an in silico evaluation of a matrix (M) gene-targeted RT-qPCR assay by aligning primer and probe binding regions against 22 H1N1 isolates and representative H3N2 and H5N1 reference strains, including recent zoonotic isolates from avian and bovine hosts. Nucleotide mismatches were identified, quantified, and mapped relative to assay components and oligonucleotide termini. Mismatch burden was summarized by subtype and assay region. ResultsH1N1 isolates exhibited complete conservation across primer and probe regions. In contrast, H3N2 and H5N1 strains demonstrated subtype-specific sequence variability, with a total of eleven mismatches identified across seven non-H1N1 isolates (mean mismatch per isolate = 2.43). Probe mismatches predominated (63.6%), occurring primarily at internal positions, while primer mismatches were infrequent and largely avoided 3' terminal nucleotides. Recent H5N1 isolates (2023-2024) shared conserved internal mismatches in the probe and forward primer, whereas a historical H5N1 isolate (2016) exhibited a distinct profile including a terminal probe mismatch. Despite this variability, mismatch patterns were consistent with preserved amplification potential. ConclusionThis study demonstrates that the evaluated influenza A M gene RT-qPCR assay exhibits inherent mismatch tolerance across human and zoonotic subtypes. By shifting diagnostic evaluation from strict sequence identity to functional resilience, our findings provide a framework for designing and maintaining robust molecular assays suitable for surveillance and pandemic preparedness amid ongoing viral evolution. Graphical AbstractIn silico evaluation of an influenza A matrix gene RT-qPCR assay demonstrates subtype-specific primer and probe mismatches across H3N2 and H5N1 strains, including recent zoonotic isolates. Despite observed variability, mismatches predominantly occur at internal positions and spare primer 3' termini, supporting inherent assay mismatch tolerance and suitability for surveillance applications. O_FIG O_LINKSMALLFIG WIDTH=150 HEIGHT=200 SRC="FIGDIR/small/707407v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@e48677org.highwire.dtl.DTLVardef@1380ddcorg.highwire.dtl.DTLVardef@11606f0org.highwire.dtl.DTLVardef@121b4ab_HPS_FORMAT_FIGEXP M_FIG C_FIG

Sequencing the respiratory tract transcriptome has the potential to provide insights into infectious pathogens and the hosts immune response. While DNA-based sequencing is more standard in clinical laboratories due to its stability, RNA assays offer unique advantages. RNA reflects dynamic physiological changes, and for RNA viruses, viral RNA particles directly represent copies of the viral genome, enabling greater diagnostic sensitivity. However, RNAs susceptibility to degradation remains a significant challenge, particularly in RNase-rich specimens like saliva. To address this, we conducted a systematic, combinatorial evaluation of 24 distinct mNGS workflows, crossing eight nucleic acid extraction methods with three RNA-Seq library preparation protocols. Remnant saliva samples (n = 6) were pooled and spiked with MS2 phage as a control. The SARS-CoV-2 virus was spiked into half of the samples, which were extracted using the eight different extraction methods (n = 3) and compared using RNA Integrity Number equivalent (RINe) scores and RNA concentration. The extracted RNA was then processed across the three library construction methods and subjected to short-read sequencing to assess all 24 combinations head-to-head. We compared methods based on viral read recovery and found that RINe and concentration did not correlate with viral detection. The Zymo Quick-RNA Magbead kit and the Tecan Revelo RNA-Seq High-Sensitivity RNA library kit were the extraction and library-preparation kits that yielded the most SARS-CoV-2 reads, respectively. Importantly, our combinatorial analysis revealed that any small variability attributable to different nucleic acid extraction methods was heavily overshadowed by differences in quality attributable to the RNA-Seq library preparation methods. These findings challenge the reliance on conventional RNA quality metrics for clinical metagenomics and underscore the need to redefine extraction quality standards for mNGS applications. IMPORTANCEmNGS is a powerful and unbiased approach towards pathogen detection that has mostly been applied to blood and cerebrospinal fluid samples. However mNGS has recently been applied to more areas including the respiratory pathogen detection space, with potential applications in both in-patient diagnostics and public health surveillance. Saliva samples are an ideal sample type for these use cases since they can be collected non-invasively. However, saliva is also a challenging sample type due to its high RNase activity and often yields low-quality nucleic acid. This study explores the feasibility of using saliva specimens in mNGS with contrived SARS-CoV-2 samples to optimize the combination of two factors: nucleic acid extraction and RNA-seq library preparation. Exploration in this area could enhance the sensitivity of saliva-based mNGS assays, with the goal of future expansion of this specimen type in clinical diagnostics and public health surveillance. Key PointsO_LIThe choice of RNA-Seq library preparation kit has a greater impact on pathogen detection than the nucleic acid extraction method. C_LIO_LIThe combination of Zymo Quick-RNA Magbead extraction kit and TECAN Revelo RNA-Seq High Sensitivity RNA library kit recovered the highest percentage of total SARS-CoV-2 reads. C_LIO_LIRNA quantity and RINe score do not correlate with viral read capture, indicating a need for an alternative metric to assess RNA quality for downstream mNGS clinical diagnostics. C_LI

This dual-center study evaluated the impact of artificial intelligence (AI) on urine culture turnaround times in Canadian diagnostic laboratories employing full microbiology laboratory automation. Data were collected before and after the implementation of PhenoMATRIX (PM), an AI-based software designed to support culture sorting and result interpretation. In both a low-volume tertiary care hospital and a high-volume community laboratory, PM reduced the time to final culture reporting, with decreases of approximately 1.5 hours and 3.9 hours, respectively. Implementation of PM+, which automatically releases defined results to patient charts, further improved turnaround time. These findings indicate that microbiology laboratories with full laboratory automation can achieve further improvements in turnaround time by integrating AI-culture assessment and results release.

iii.Background and ObjectivesThe "Pan-European Transfusion Research InfrAstructure" (PETRA) project was established to advance the use of donor, blood product, and patient datasets in Europe, aiming to benefit both patient and donor health. Here, the initial PETRA objective was to describe the landscape of existing donor and blood establishment (BE) databases. Materials and MethodsAn online survey was circulated to the European Blood Alliances BE members. The survey collected information on the feasibility of accessing donor data, and challenges and possibilities for linking these datasets with information on the associated blood products and transfusion recipients, and donors own health records. ResultsSeventeen BEs across 16 countries completed the survey. The majority could, in principle, link their donor data to product data (13 BEs (76%)) and recipient data (10 BEs (59%)), for research purposes. However, capabilities were limited and in only 29% of the BEs was the donor to recipients linkage an automated process. BEs reported significant challenges to achieve full vein-to-vein linkage, including legal constraints and lack of consent (11 BEs) and resources (10-14 BEs). IT and data issues as well as lack of knowledge and training were cited as obstacles by a minority of BEs. ConclusionWhilst the survey results suggest considerable interest in developing linkages between blood donors, their products, and recipients, many challenges remain due to a variety of obstacles. First steps in working towards a PETRA may be assistance to navigate legal frameworks as well as investing in resources and quality and harmonisation of data collections. iv. HighlightsO_LI17 blood establishments (BEs) in 16 countries responded to a survey on obstacles and opportunities for achieving vein-to-vein datasets. C_LIO_LIIn 59% of the BEs donor-to-recipient links can be established for research improving transfusion outcomes, but only in 29% this is an automated process. C_LIO_LIIn order to work towards a "Pan-European Transfusion Research InfrAstructure" (PETRA), legal frameworks, adequate donor consent and (financial and human) resources are the most common obstacles that require addressing. C_LI

ObjectiveThis study investigates the prevalence of human pegivirus (HPgV) in SARS-CoV-2-positive patients within the context of viral co-infections that may modulate COVID-19 outcomes and assesses whether HPgV co-infection is associated with COVID-19 severity. HPgV is a widely circulating but rarely monitored human virus with documented immunomodulatory effects in other viral infections, including HIV and Ebola. While HPgV prevalence is low in the general U.S. population (1-2%), it rises markedly in the setting of chronic viral co-infections, particularly HIV (15-40%). Given its immunologic effects and persistence, HPgV represents a biologically plausible but unexplored viral co-factor SARS-CoV-2 infection. MethodsWe analyzed four cohorts: SARS-CoV-2-positive individuals, ICU patients with respiratory symptoms but SARS-CoV-2-negative, HIV-positive individuals as a positive control for HPgV detection, and uninfected controls. ResultsHPgV prevalence in COVID-19 patients was low (2.1%) and comparable to population estimates. As expected, HPgV prevalence was substantially higher in the HIV cohort (34%), validating assay performance and cohort stratification. Among HPgV-positive COVID-19 cases, most experienced mild disease, with directional trends toward reduced severity despite high baseline risk factors. Healthcare workers in the control group showed unexpectedly elevated HPgV prevalence (9.6%). ConclusionsHPgV is an unmonitored but widely circulating viral co-infection in humans that may influence host responses to SARS-CoV-2. Although limited by small numbers, our findings support further investigation of HPgV and other immunomodulatory viral co-infections in COVID-19. This study suggests that HPgV co-infection may influence COVID-19 outcomes, warranting further investigation. HighlightsO_LISystematic screening of human pegivirus (HPgV), an unmonitored viral co-infection, in COVID-19 (n = 634). C_LIO_LIHPgV prevalence in COVID-19 mirrored population estimates but was markedly enriched in HIV (positive control). C_LIO_LIHPgV-positive COVID-19 cases showed trends toward milder clinical outcomes. C_LIO_LIFindings highlight the potential relevance of immunomodulatory viral co-infections in SARS-CoV-2 infection. C_LI Executive SummaryThis study evaluated the prevalence of human pegivirus (HPgV) co-infection among SARS-CoV-2-positive patients as part of a broader effort to understand how concurrent viral infections may influence COVID-19 severity. HPgV is a largely unmonitored, persistent human virus with well-described immunomodulatory effects in other viral infections, yet it has not been systematically evaluated in COVID-19. We therefore screened HPgV prevalence across COVID-19 cases, comparator cohorts, and an HIV-positive cohort as a positive control due to the well-established high prevalence of HPgV in HIV infection. Our findings indicate that HPgV prevalence in SARS-CoV-2-positive and -negative hospitalized individuals are consistent with the general U.S. population range (approximately 1-5%). Healthcare professionals exhibited a higher HPgV prevalence ([~]10%), suggesting that repeated occupational viral exposures may influence infection rates. While limited by small numbers, HPgV co-infection in COVID-19 cases was associated with directional trends toward reduced disease severity, warranting further longitudinal and mechanistic investigation. Editors summaryThis study identifies human pegivirus as a widely circulating, unmonitored viral co-infection in COVID-19 with potential relevance to disease severity.

PurposeWhile genomic testing is integral to pediatric inborn errors of immunity (IEI) care, few studies have examined strategies to support its optimal delivery. This study aimed to characterize a pediatric IEI cohort and assess the impact of implementing a mainstream model-of-care (MoC). Materials/MethodsComprehensive chart audit was conducted for patients ([&le;]18y) who received IEI genomic testing in Queensland, Australia, from 2017-2025. Descriptive analyses captured demographic and clinical characteristics, genomic testing and results, and management outcomes. Inferential analyses assessed changes in genomic practices pre-MoC (<2021) and post-MoC ([&ge;]2021). Results322 patients met eligibility criteria (n=481 genomic test). Diagnostic yield (27.6%) varied by testing indication, with the highest rate among phagocytic defects (n=4/4;100%) and severe combined immunodeficiency (n=8/10;80%). Very-early-onset inflammatory bowel disease had the lowest diagnostic yield (n=3/68;4.4%), prompting changes to testing criteria. Molecular diagnosis resulted in management changes for 90.5% patients. Genomic testing was widely used pre-MoC (n=251 genomic tests). All outcomes significantly improved pre-and post-MoC (p<0.05): duplicate testing decreased (13.9% to 0%); variants of uncertain significance reduced (37.7% to 7.1%); informed consent documentation increased (70.5% to 88.4%); and diagnostic yield increased (16.2% to 27.4%). ConclusionTargeted interventions are needed to support delivery of genomic testing and strengthen service effectiveness.

AimsTo evaluate the association between platelet indices and platelet count severity in patients with primary immune thrombocytopenia during routine post-treatment follow-up. MethodsThis retrospective observational study included patients with primary immune thrombocytopenia followed at a single tertiary care center between 2011 and 2025. Demographic and laboratory data were obtained from medical records. Platelet count severity was categorized as less than 30 x 10^9/L, 30 to 100 x 10^9/L, and greater than 100 x 10^9/L. Platelet indices, including mean platelet volume (MPV) and platelet distribution width (PDW), were analyzed using the most recent complete blood count obtained during routine follow-up after treatment initiation. Continuous variables were summarized as median and interquartile range. Comparisons across platelet count categories were performed using the Kruskal-Wallis test with post hoc Mann-Whitney U testing. Correlation analysis and simple linear regression were also conducted. ResultsA total of 243 patients were identified, of whom 232 met the inclusion criteria. Platelet distribution width differed significantly across platelet count severity categories (Kruskal-Wallis p < 0.001) and demonstrated a strong inverse association with platelet count. Mean platelet volume also showed a statistically significant difference across platelet count groups (Kruskal-Wallis p = 0.007), although the association was weaker and less consistent compared with PDW. Regression analysis confirmed a significant association between platelet count and PDW. ConclusionPlatelet distribution width is more closely associated with platelet count severity than mean platelet volume in patients with primary immune thrombocytopenia during routine post-treatment follow-up. PDW may represent a useful adjunctive laboratory parameter when interpreted alongside platelet count in routine clinical practice.

BackgroundNatural killer (NK) cell degranulation is a key immune defense mechanism where exposure to tumor or virus-infected cells triggers the fusion of cytoplasmic granules containing apoptotic proteins, perforin, and granzyme with the cell membrane. This process transiently expresses CD107a on the NK cell surface, and measuring CD107a is a standard method to assess NK cell activity. MethodsWe compared two stimulation protocols differing only in duration (6-hour vs. 18-hour) using K562 target cells to induce NK cell degranulation. Isolated PBMCs without stimulation served as controls to assess spontaneous degranulation. Anti-CD107a-PE antibody was present throughout stimulation in both test and control samples. After stimulation, cells were stained with anti-CD45, anti-CD3, and anti-CD56 and analyzed by flow cytometry. ResultsFor 6 of 7 healthy controls, results from both methods fell within 2 standard deviations. Notably, longer (18-hour) stimulation resulted in lower CD107a expression than the 6-hour assay. Interlaboratory comparisons of two samples showed no significant difference (p>0.05). In a suspected hemophagocytic lymphohistiocytosis (HLH) case, two labs reported similarly reduced CD107a expression (9% and 7%). Inter-day variability was observed in a donor across both time points. The 6-hour assay showed higher sensitivity and specificity than the 18-hour assay. A resting period before ex vivo PBMC assays was found necessary. ConclusionStimulation periods beyond 6 hours are unsuitable for clinical NK degranulation assays. Screening for HLH should include multiple stimulants to improve assay reliability.

Respiratory syncytial virus (RSV), an approximately 15.2 kb negative sense RNA virus, causes acute respiratory infections in infants and older adults. Its two subtypes, RSV/A and RSV/B, evolve rapidly, making ongoing monitoring of circulating strains essential. The Georgia Public Health Laboratory (GPHL) developed and evaluated an amplicon-based whole-genome sequencing (WGS) assay for RSV surveillance. A total of 214 deidentified remnant clinical specimens (102 RSV/A; 112 RSV/B) with RT PCR Ct values <31 were included. RSV genomes were amplified using ARTIC style and custom primer sets, with the ARTIC set showing superior performance. Libraries were prepared using a modified Illumina COVIDSeq protocol, sequenced on NextSeq 1000/2000 instruments, and analyzed using the GPHL-RSV-PIPE bioinformatics pipeline. Among genomes meeting validation criteria, sequencing depth was slightly higher for RSV/A (median 53,433x; mean 51,076x) than RSV/B (median 49,699x; mean 46,945x), whereas genomic coverage was slightly lower for RSV/A (median 97.5%; mean 96.6%) than RSV/B (median 98.3%; mean 97.6%). Predominant lineages were A.D.3.1 and A.D.5.2 for RSV/A and B.D.E.1 for RSV/B. For RSV/A, the assay showed 92.8% accuracy, 96.2% sensitivity, 87.2% specificity, 92.6% positive predictive value, and 93.2% negative predictive value. Intra and inter run precision assessed using 16 and 53-57 genomes, respectively, showed nearly 100% consensus genome identity with 0 to 5 nucleotide differences. Specificity testing of 31 non-RSV specimens produced no false-positive detections. These results demonstrate that the ARTIC-based RSV WGS assay enables near real time surveillance and strengthens data driven public health responses to future outbreaks.

BackgroundNeutralising antibody titres are widely used as key immunogenicity endpoints in Ebola virus (EBOV) vaccine and monoclonal antibody clinical trials. However, direct comparison of results across studies remains challenging due to the use of heterogeneous neutralisation platforms, ranging from pseudotyped viruses to live EBOV assays. These limitations restrict assay standardisation, validation, scalability, and compliance with good clinical laboratory practice (GCLP), particularly in outbreak-prone and resource-limited settings. There is an unmet need for neutralisation assays that combine biological authenticity with clinical-trial compatibility. MethodsWe developed and optimised a fluorescence-based microneutralisation assay using a biologically contained EBOV lacking the essential VP30 gene (EBOV{Delta}VP30), enabling multi-cycle viral replication under containment level 2 conditions. Using a defined panel of serum samples from Ebola virus disease survivors and EBOV-negative controls, we benchmarked EBOV{Delta}VP30 neutralisation titres against previously generated data obtained with wild-type EBOV and pseudotyped virus platforms. Assay performance was evaluated in terms of sensitivity, reproducibility, discrimination between positive and negative samples, and correlation with live virus neutralisation. Calibration was performed using the WHO International Standard for anti-EBOV immunoglobulin. FindingsThe EBOV{Delta}VP30 microneutralisation assay robustly distinguished EBOV survivor sera from negative controls (p < 0{middle dot}0001) and demonstrated a strong correlation with live EBOV neutralisation titres (Spearman {rho} = 0{middle dot}8725). This correlation exceeded that observed for HIV-1-based pseudotyped assays and for the vesicular stomatitis virus-based platforms. The fluorescence-based read-out showed comparable sensitivity to conventional immunostaining, supporting its suitability for high-throughput and standardised implementation. Importantly, assay conditions were compatible with BSL-2 laboratories and GCLP-aligned workflows. InterpretationBiologically contained EBOV{Delta}VP30 provides a clinically relevant and scalable alternative to existing neutralisation platforms, bridging the gap between pseudotyped assays and wild-type virus testing. By improving biological relevance while maintaining accessibility and standardisation, this assay has the potential to enhance comparability of immunogenicity data across EBOV vaccine and therapeutic antibody (pre-)clinical trials, aligning with global outbreak preparedness and trial harmonisation objectives. FundingStated in acknowledgement section of manuscript. Research in contextO_ST_ABSEvidence before the studyC_ST_ABSBefore starting this study, we reviewed published work on how neutralising antibodies against Ebola virus are measured in vaccine and monoclonal antibody research. We searched PubMed, Web of Science, and reference lists of key review papers for studies published up to mid-2025, without restricting by language. Search terms included "Ebola virus", "neutralising antibodies", "neutralisation assay", "pseudovirus", "live virus", and "clinical trials". We focused on studies describing neutralisation tests using wild-type Ebola virus as well as commonly used pseudotyped virus systems. From this body of evidence, neutralisation assays using wild-type Ebola virus are considered the most biologically relevant but can only be performed in biosafety level 4 laboratories. This limits their availability, scalability, and use in clinical trials. Pseudotyped virus assays can be performed under lower biosafety conditions and are widely used, but multiple studies have reported variable performance and inconsistent agreement with live virus results. Although biologically contained Ebola viruses have been developed and used in laboratory research, their application as neutralisation assays and their direct comparison with both live virus and pseudotyped systems using the same human serum samples had not been systematically studied. As a result, it remained unclear whether such systems could support reliable immunogenicity assessment in clinical trials. Added value of this studyThis study shows that a biologically contained Ebola virus lacking the VP30 gene can be used to measure neutralising antibodies in a robust and scalable way under biosafety level 2 conditions. By directly comparing this system with wild-type Ebola virus and widely used pseudotyped assays using the same set of human serum samples, we demonstrate that neutralisation results obtained with the biologically contained virus closely align with those of the wild-type virus reference assay. The assay reliably distinguishes samples from Ebola survivors and uninfected individuals and can be read using different detection methods, making it compatible with GCLP-aligned workflows and suitable for further qualification and validation in support of clinical development. This work provides clear evidence that biologically contained Ebola virus can combine biological relevance with practical usability. Implications of all the available evidenceTogether with existing evidence, our findings indicate that biologically contained Ebola virus offers a valuable new option for measuring neutralising antibodies in vaccine and monoclonal antibody clinical trials. By reducing reliance on high-containment laboratories while preserving key features of authentic virus infection, this approach can improve the consistency and comparability of immunogenicity data across studies and sites. Broader use of such assays could support better decision-making during clinical development and strengthen outbreak preparedness. More generally, this work highlights how biologically contained viruses can help advance research licensure of medical countermeasures for high-consequence pathogens in ways that are directly relevant to human health.

Introduction: Herpes simplex virus type 1 (HSV-1) is highly prevalent worldwide, making accurate serological testing essential for both clinical diagnosis and epidemiological surveillance. Automated chemiluminescent immunoassays (CLIAs) offer operational advantages over enzyme-linked immunosorbent assays (ELISAs); however, their diagnostic performance relative to Western blot (WB) confirmation in high-prevalence settings remains insufficiently characterized. Hypothesis/Gap Statement: The comparative diagnostic accuracy of CLIA- and ELISA-based assays for HSV-1 IgG detection, when benchmarked against a WB reference standard in endemic populations, remains unclear. Aim: This study aimed to evaluate HSV-1 IgG seroprevalence and diagnostic performance of one CLIA and two ELISA platforms using Western blot as the reference method. Methodology: Four hundred archived serum samples from adult male craft and manual workers in Qatar were tested using the Mindray CL-900i CLIA, HerpeSelect ELISA, NovaLisa ELISA, and Euroimmun Western blot. Seroprevalence, diagnostic accuracy, and interassay agreement were assessed using WB as the reference standard, with equivocal and indeterminate results excluded from analysis. Results: HSV-1 IgG seroprevalence estimates were comparable across assays: HerpeSelect 72.5%, Mindray 70.5%, NovaLisa 66.3%, and Western blot 66.5%, with no statistically significant differences (all p > 0.05). The Mindray CLIA demonstrated the highest diagnostic performance (sensitivity 95.7%, specificity 88.9%, accuracy 93.4%) and strong agreement with Western blot ({kappa} = 0.85). HerpeSelect showed substantial agreement ({kappa} = 0.81), while NovaLisa exhibited lower specificity. Conclusion: CLIA- and ELISA-based assays produced comparable HSV-1 seroprevalence estimates in this high-prevalence population; however, diagnostic accuracy varied across platforms. The CLIA platform demonstrated the strongest agreement with Western blot, supporting its use in high-throughput settings, while confirmatory testing remains important to minimize misclassification.

BACKGROUNDAutomated antimicrobial susceptibility testing (AST) systems are crucial for accurate, timely detection of drug-resistant microbial isolates. This meta-analysis assessed the performance of the BD Phoenix ("Phoenix", BD Diagnostic Solutions), Vitek(R) 2 ("Vitek 2", bioMerieux), and DxM MicroScan WalkAway ("MicroScan", Beckman Coulter, Inc.) AST systems relative to common reference methodology. METHODSA systematic literature search in Ovid (MEDLINE and Embase) yielded 275 unique (not duplicated) records, with 44 additional records retrieved from handsearching; 39 studies met inclusion criteria. Categorical agreement (CA), essential agreement (EA), very major errors (VMEs), and major errors (MEs) for the three instruments were compared to a common reference method. Ratios of proportions were analyzed using random-effect meta-regression. RESULTSThe instruments did not differ significantly in CA, EA, or ME. Vitek 2 showed a higher overall VME rate than Phoenix ([~]44% higher; Vitek 2-to-Phoenix ratio = 1.44; p=0.062 [approaching significance]) and MicroScan (74% higher; ratio = 1.74; p=0.045). No appreciable difference was observed for VME between Phoenix and MicroScan. Subgroup analyses should be interpreted cautiously due to limited overall significance indicating varying performance across systems. Vitek 2 generally had higher relative VMEs for gram-negative organisms and lower relative VMEs for gram-positive organisms, whereas Phoenix showed the opposite pattern. MicroScan had relatively low VMEs when stratified by Clinical and Laboratory Standards Institute (CLSI) criteria; no differences in VMEs were observed using European Committee on Antimicrobial Susceptibility Testing (EUCAST) criteria. CONCLUSIONAlthough some VME differences were noted, overall performance of the three systems was comparable. Organism- and drug-specific VME patterns--and updates to CLSI criteria over time--highlight the importance of continued monitoring of current breakpoints for all three instruments.

A multiplex diagnostic test is evaluated for self-reported long COVID associated persistent symptoms and a poor recovery from a SARS-CoV-2 infection. A mass-standardised concentration of total antibodies (AC), high-quality (HQ) antibodies and percentage of HQ antibodies (HQ%) is assessed against a spectrum of spike proteins to the SARS-CoV-2 variants: Wuhan, , {delta}, and the Omicron variants BA.1, BA.2, BA.2.12.1, BA.2.75, BA.5, CH.1.1, BQ.1.1 and XBB.1.5 in three cohorts. A cohort of control patients (n = 46) recovered (CC) and a cohort of self-declared long COVID patients (n = 113) (LCC). A nested Receiver Operating Characteristic (ROC) analysis, performed for the variant with lowest HQ concentration in the spectrum, produced an area under the curve and AUC = 0.61 (0.53-0.70) for the CC vs LCC cohorts. For the LCC cohort, the cut-off thresholds for AC = 0.8 mg/L, HQ = 1.5 mg/L and HQ% of 34% were determined, leading to a 71% sensitivity and 66% specificity derived by the Youden metric. The cohorts may be fully classified based on ROC and outlier analysis to give an incidence of persistent virus 62% (95% CI 52% - 71%), hyperimmune 12% (95% CI 7% - 20%) and unclassified, 26% (95% CI 18% - 35%). The overall diagnostic accuracy for both the hyper and hypo immune is 69%. All clinical interventions can now be tailored for the heterogenous long COVID patient cohort.

Background: Mucopolysaccharidosis type IIIA (MPS IIIA; Sanfilippo syndrome) is a fatal neurodegenerative lysosomal storage disorder caused by impaired degradation of heparan sulfate (HS). Despite rapid advances in gene and enzyme therapies, there remains a critical need for an analytically validated, quantitative biomarker that accurately reflects central nervous system (CNS) substrate burden. Such biomarker would be a valuable tool in assessing disease progression and monitoring therapeutic efficacy. Objective: This study describes the method development, fit for purpose validation, and preliminary clinical application of a quantitative liquid chromatography-mass spectrometry (LC-MS/MS) assay for the HS-derived disaccharide N-sulfoglucosamine-glucuronic acid (GlcNS-GlcUA) in human cerebrospinal fluid (CSF), a critical biomarker for diagnosis, disease monitoring, and regulatory evaluation of emerging MPS IIIA therapies. Methods: A structurally defined GlcNS-GlcUA reference standard and its [13C6]-labeled internal standard were used in a derivatization and detection workflow employing 1-phenyl-3-methyl-5-pyrazolone labeling, and LC-MS/MS. Results: The method exhibited acceptable linearity across 0.005-0.500 nmol/mL (r[&ge;]0.9976), with intra- and inter-assay imprecision [&le;]3.5%CV and accuracy within 95%-110% of nominal concentrations. No matrix or hemolysis interference or carryover was observed, and the analyte remained stable during freeze-thaw storage conditions. Application of the method to 12 CSF samples from patients with MPS IIIA demonstrated quantifiable GlcNS-GlcUA levels ranging from 0.0054 to 0.106 nmol/mL, confirming suitability for clinical and regulatory use. Comparison of the MPS IIIA sample results between the development laboratory and the contract research organization laboratory support robust inter-lab assay transfer. Conclusions: This validated LC-MS/MS method establishes a regulatory-grade quantitative assay for measurement of CSF HS in MPS IIIA. Its high analytical sensitivity and reproducibility enable reliable assessment of CNS substrate reduction and pharmacodynamic response, supporting biomarker-driven therapeutic development and accelerated approval pathways for neuronopathic mucopolysaccharidoses.

ObjectiveThe rapid availability of phenotypic antimicrobial susceptibility results is crucial for the timely detection of multidrug-resistant Gram-negative organisms and for guiding optimized treatment strategies. Recently, novel methods have been introduced that enable direct antimicrobial susceptibility testing (AST) from positive blood cultures. However, their performance has not yet been systematically compared in head-to-head evaluations. This study aimed to assess the analytical performance of two rapid AST approaches--the agar diffusion-based EUCAST rapid AST (RAST) method and the automated QuickMIC system--using a challenging collection of highly resistant Gram-negative organisms. MethodsA total of 101 Gram-negative bacteria (Escherichia coli, n = 24; Klebsiella pneumoniae, n = 22; Acinetobacter baumannii, n = 30; Pseudomonas aeruginosa, n = 25) were spiked into blood cultures and processed according to the respective AST workflows. Broth microdilution (BMD) was performed from pure cultures as the reference method. Time to result (TTR), categorical agreement (CA), and essential agreement (EA) with BMD were evaluated. Boruta analysis was applied to identify genetic determinants associated with AST errors. ResultsOverall TTR for QuickMIC was 3 h 44 min with a CA of 86.2%, an EA of 92.3 % for Enterobacteriaceae and 97.0 % for non-fermenters. Overall CA of RAST ranged from 90.7%-93.7% across reading time points. Overall, very major discrepancy rates were low (QuickMIC n=0.7%, RAST n=0.1%). Presence of NDM-5 and KPC was most frequently associated with errors for QuickMIC and EUCAST RAST, respectively. ConclusionsBoth rapid AST approaches yielded robust results in this diverse and highly resistant bacterial study population, directly from positive blood cultures, with a short turnaround time. These findings underscore the potential of rapid AST methods to facilitate timely optimization of antimicrobial therapy in bloodstream infections, even in the context of extensively drug-resistant pathogens. ImportanceAccurate antimicrobial susceptibility testing (AST) is essential for stewardship and effective therapy, especially as rising antimicrobial resistance increases the risk of empiric treatment failure. Traditional AST methods are limited by slow turnaround times, creating a need for rapid alternatives. This study evaluated the diagnostic accuracy of two rapid AST methods--EUCAST RAST and QuickMIC--using 101 genetically characterized, carbapenem-resistant Enterobacterales, Pseudomonas aeruginosa, and Acinetobacter baumannii tested directly from positive blood cultures. Broth microdilution served as the reference. Both rapid assays provided results within 3.5-6 hours and demonstrated high categorical and essential agreement with few very major discrepancies. Incorrect results were more common in isolates harboring NDM-5 and KPC carbapenemases. Overall, the findings support EUCAST RAST and QuickMIC as reliable tools for challenging resistant pathogens and highlight their potential to enable earlier detection of carbapenem-resistant phenotypes and more timely initiation of appropriate, last-resort antimicrobial therapy.

Highly pathogenic avian influenza (HPAI) viruses of H5N1 clade 2.3.4.4b, are spreading worldwide, posing a threat to wildlife, domestic animals, and humans. In 2025, a multidisciplinary collaboration for HPAI H5N1 surveillance among birds within Galveston County, Texas, was initiated. Between November and December 2025, oropharyngeal and cloacal swabs were collected from wild and domestic birds reported as dead or dying by Galveston County residents. Specimens were studied with molecular assays, Sanger sequencing, virus isolation, and next-generation sequencing. Molecular evidence of HPAI H5N1 was detected in 7 of 10 (70%) birds, and the virus was successfully cultured in MDCK cells. Next-generation sequencing analysis of eight influenza A genome segments demonstrated a 4:4 gene segment reassortant constellation within clade 2.3.4.4b, consistent with genotype D1.1. Community members exposed to HPAI were offered antiviral prophylaxis. No human infections were identified. This surveillance demonstrates that community involvement combined with cross-sectoral collaboration can ensure rapid detection and characterization of circulating avian influenza viruses. Sustained local surveillance is essential for early warning, risk assessment, and prevention of virus spread to poultry, mammals, and humans.

BackgroundCefiderocol is a siderophore-conjugated cephalosporin antibiotic used to treat multi drug resistant Gram negative infections, including metallo-beta-lactamase producing Enterobacterales. Antimicrobial useage is guided by antimicrobial susceptibility testing (AST) which is hampered by differences between EUCAST and CLSI breakpoints, methodological challenges of AST, and lack of information on clinical outcome related to AST. ObjectivesThis study assessed the agreement between AST methods under EUCAST and CLSI breakpoints in a collection of 57 blaNDM producing Enterobacterales isolated from a UK hospital network. MethodsAll isolates, including Klebsiella pneumoniae, Enterobacter hormaechei, Escherichia coli and Citrobacter freundii, were whole-genome sequenced and tested with disk diffusion and MIC gradient test strip, and broth microdilution MICs were determined for a subset. Categorical agreement between methods was calculated using both EUCAST and CLSI breakpoints. Mutations and acquired resistance genes associated with cefiderocol resistance were identified and compared with AST results. ResultsThe disk diffusion method, based on EUCAST interpretation, classified 94.7% of isolates as cefiderocol resistant and 5.3% as susceptible, with 22.8% within the Area of Technical Uncertainty. The CLSI breakpoint classified one isolate as resistant (1.8%) and 5.26% intermediate. Category agreement of broth microdilution and disk diffusion for E. coli using EUCAST guidelines was 38.5%. Mutations associated with cefiderocol resistance were highly prevalent and varied between species. ConclusionsThe discordant EUCAST and CLSI breakpoint values provided have large impacts on the classification of isolates susceptibility to cefiderocol, which will impact global cefiderocol usage and surveillance of resistance, further complicated by poor agreement between AST methods.