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Brains of 42 COVID-19 decedents and 107 non-COVID-19 controls were studied. RT-PCR screening of 16 regions from 20 COVID-19 autopsies found SARS-CoV-2 E gene viral sequences in 7 regions (2.5% of 320 samples), concentrated in 4/20 subjects (20%). Additional screening of olfactory bulb (OB), amygdala (AMY) and entorhinal area for E, N1, N2, RNA-dependent RNA polymerase, and S gene sequences detected one or more of these in OB in 8/21 subjects (38%). It is uncertain whether these RNA sequences represent viable virus. Significant histopathology was limited to 2/42 cases (4.8%), one with a large acute cerebral infarct and one with hemorrhagic encephalitis. Case-control RNAseq in OB and AMY found more than 5000 and 700 differentially expressed genes, respectively, unrelated to RT-PCR results; these involved immune response, neuronal constituents, and olfactory/taste receptor genes. Olfactory marker protein-1 reduction indicated COVID-19-related loss of OB olfactory mucosa afferents. Iba-1-immunoreactive microglia had reduced area fractions in cerebellar cortex and AMY, and cytokine arrays showed generalized downregulation in AMY and upregulation in blood serum in COVID-19 cases. Although OB is a major brain portal for SARS-CoV-2, COVID-19 brain changes are more likely due to blood-borne immune mediators and trans-synaptic gene expression changes arising from OB deafferentation.

Here, we use Raman spectroscopy to investigate temperature-dependent changes in the atomic-scale structure of the zeolitic imidazolate framework ZIF-7 in a CO2atmosphere and uncover the mechanism of maximal CO2adsorption at 206 K. At 301 K, the Raman spectra of ZIF-7 at various CO2gas pressures reveal a narrow-pore (np) to large-pore (lp) phase transition commencing at 0.1 bar as a result of adsorption of CO2, as evident in the appearance of Fermi resonance bands of CO2at 1272 and 1376 cm–1. Moreover, the Raman inactive bending mode of CO2becomes active due to geometrical distortion of adsorbed CO2. It further splits into two peaks due to hydrogen bonding interactions between CO2and the benzene ring of the benzimidazole linker ZIF-7, as supported by our computational studies. In addition, the interaction between CO2molecules plays a key role. Upon reducing the temperature at 1 bar CO2gas pressure, ZIF-7 exhibits softening of the imidazole puckering mode and the Fermi resonance CO2band due to interactions between CO2and the framework through hydrogen bonding. At 206 K, substantial modification in the lattice mode and disappearance of the Raman inactive CO2bending mode confirm the changes in the size of the pore cavity through structural rearrangements of CO2.

The integration of iron (Fe) into a cobalt metal–organic framework (Co-MOF) tunes the electronic structure of the parent MOF as well as enhances their electrocatalytic characteristics. By using pyrazine and hydrofluoric acid, we have synthesized three-dimensional Co-MOF [CoFC4H4N2(SO4)0.5], (1), and Fe-MOF [FeFC4H4N2(SO4)0.5], (2), through a single-step solvothermal method. Further, a series of bimetallic (having both Co and Fe metal centers) MOFs [Co1–xFexFC4H4N2(SO4)0.5] were synthesized with variable concentrations of Fe, and their electrocatalytic performances were analyzed. The optimized amount of Fe significantly impacted the electrocatalytic behavior of the bimetallic MOF toward water oxidation. Particularly, the Co0.75Fe0.25-MOF needs only 239 and 257 mV of overpotential to deliver 10 and 50 mA/cm2current density, respectively, in alkaline electrolytic conditions. The Co0.75Fe0.25-MOF shows a lower Tafel slope (42 mV/dec.) among other bimetallic MOFs and even the commercial RuO2, and it has excellent durability (with ∼8 mV increases in overpotential after 18 h of electrolysis) and 97.05% Faradaic efficiency, which further evident its catalytic excellency. These findings explore the intrinsic properties of MOF-based electrocatalysts and prospect the suitability for future water electrolysis.

The development of an active and efficient electrocatalyst for the oxygen evolution reaction remains indispensable for the smooth running of an electrolyzer. Herein, we have synthesized two cobalt metal–organic frameworks (Co-MOFs) with the formulas [C6H6CoN2O4] (compound 1) and [C12H10CoN2O4] (compound 2) using pyrazine and 4,4′-bipyridine as linkers in dimethylformamide medium by a solvothermal method. Both Co-MOFs shows strong antiferromagnetic interactions with Θp= −70 and −61 K for compounds 1and 2, respectively. The in situ transformation of both compounds catalyzes the OER efficiently in alkaline medium, affording a current density of 10 mA/cm2at overpotentials of 276 ± 3 and 302 ± 3 mV by compounds 1and 2, respectively. Moreover, compound 1shows a very high turnover frequency (15.087 s–1), lower Tafel slope (56 mV/dec), and greater Faradaic efficiency of 95.42% in comparison to compound 2. The transformations of the Co-MOFs have been accessed by employing powder X-ray diffraction (PXRD), high-resolution transmission electron microscopic (HRTEM) analysis, and X-ray photoelectron spectroscopy, which reveal the formation of uniform hexagonal Co(OH)2plates. Therefore, the as-developed Co-MOF is found to be an efficient pre-electrocatalyst for the OER in alkaline medium. These results not only reveal the preparation of OER electrocatalysts from a Co-MOF but also establish a method to derive a potentially active electrocatalyst to substitute for the traditional noble-metal-based materials.

Mesoporous reduced graphene oxide nanoparticles (RGO NPs) have been synthesized by using different templates. Three types of RGO NPs, namely mesoporous RGO1 NPs, RGO2 NPs and RGO3 NPs, have been synthesized by using cetyltrimethylammonium bromide (CTAB), polyethylene glycol (PEG) and polyethylene glycol–polypropylene glycol–polyethylene glycol (Pluronic P123), respectively. In the present study, CTAB, PEG and P123 are used as both template and capping agent for the formation of mesoporous RGO NPs. N2sorption, XRD, XPS and Raman spectra have proved the mesoporous and NPs nature of the RGO samples. It has been observed that mesoporous RGO NPs samples have high adsorption of dyes molecules like as methylene blue, malachite green and rhodamine 6G. Among them, mesoporous RGO1 NPs exhibited the highest dye adsorption capacity.

Genotypic antiretroviral drug resistance testing is a critical component of the global efforts to control the HIV-1 epidemic. This study investigates the semiautomated, next-generation sequencing (NGS)-based Vela Diagnostics Sentosa SQ HIV-1 Genotyping Assay in a prospective cohort of HIV-1–infected patients. Two-hundred sixty-nine samples were successfully sequenced by both NGS and Sanger sequencing. Among the 261 protease/reverse transcriptase (PR/RT) sequences, a mean of 0.37 drug resistance mutations were identified by both Sanger and NGS, 0.08 by NGS alone, and 0.03 by Sanger alone. Among the 50 integrase sequences, a mean of 0.3 drug resistance mutations were detected by both Sanger and NGS, and 0.08 by NGS alone. NGS estimated higher levels of drug resistance to one or more antiretroviral drugs for 6.5% of PR/RT sequences and 4.0% of integrase sequences, whereas Sanger estimated higher levels of drug resistance for 3.8% of PR/RT sequences. Although the samples successfully sequenced by the Sentosa SQ HIV Genotyping Assay demonstrated similar predicted resistance compared with Sanger, 44% of Sentosa runs failed quality control requiring 17 additional runs. This semi-automated NGS-based assay may aid in HIV-1 genotypic drug resistance testing, though numerous quality control issues were observed when this platform was used in a clinical laboratory setting. With additional refinement, the Sentosa SQ HIV-1 Genotyping Assay may contribute to the global efforts to control HIV-1.

A three-dimensional (3D) Ni-MOF of the formula [Ni(C4H4N2)(CHO2)2]n,has been reported, which shows a capacitance of 2150 F/g at a current density of 1A/g in a three-electrode setup (5.0 M KOH). Post-mortem analysis of the sample after three-electrode measurements revealed the bias-induced transformation of Ni-MOF to Ni(OH)2, which has organic constituents intercalated within the sample exhibiting better storage performance than bulk Ni(OH)2. Afterward, the synthesized MOF and reduced graphene (rGO) were used as the anode and cathode electrode material, respectively, and a two-electrode asymmetric supercapacitor device (ASC) setup was designed that exhibited a capacitance of 125 F/g (at 0.2 A/g) with a high energy density of 50.17 Wh/kg at a power density of 335.1 W/kg. The ASC further has a very high reversibility (97.9% Coulombic efficiency) and cyclic stability (94%) after 5000 constant charge–discharge cycles. Its applicability was also demonstrated by running a digital watch. Using sophisticated density functional theory simulations, the electronic properties, diffusion energy barrier for the electrolytic ions (K+), and quantum capacitance for the Ni(OH)2electrode have been reported. The lower diffusion energy barrier (0.275 eV) and higher quantum capacitance (1150 μF/cm2) are attributed to the higher charge storage performance of the Ni-MOF-transformed Ni(OH)2electrode as observed in the experiment.

A point-of-care HIV-1 genotypic resistance assay that could be performed during a clinic visit would enable care providers to make informed treatment decisions for patients starting therapy or experiencing virologic failure on therapy. The main challenge for such an assay is the genetic variability at and surrounding each drug-resistance mutation (DRM). We analyzed a database of diverse global HIV sequences and used thermodynamic simulations to design an array of surface-bound oligonucleotide probe sets with each set sharing distinct 5′ and 3′ flanking sequences but having different centrally located nucleotides complementary to six codons at HIV-1 DRM reverse transcriptase position 103: AAA, AAC, AAG, AAT, AGA, and AGC. We then performed in vitroexperiments using 80-mer oligonucleotides and PCR-amplified DNA from clinical plasma HIV-1 samples and culture supernatants that contained subtype A, B, C, D, CRF01_AE, and CRF02_AG viruses. Multiplexed solid-phase melt curve analysis discriminated perfectly among each of the six reported reverse transcriptase position 103 codons in both 80-mers and clinical samples. The sensitivity and specificity for detecting targets that contained AAC mixed with targets that contained AAA were >98% when AAC was present at a proportion of ≥10%. Multiplexed solid-phase melt curve analysis is a promising approach for developing point-of-care assays to distinguish between different codons in genetically variable regions such as those surrounding HIV-1 DRMs.

BackgroundToxoplasma gondiiis the most common infectious cause of posterior uveitis worldwide. Two multicopy targets (B1 and Rep529) are commonly used in T. gondiiPCR assays, but studies evaluating these targets in ocular fluid samples are limited. Herein, we determine the analytical characteristics of a single-reaction, internally controlled, dual-target, real-time T. gondiiPCR and evaluate the clinical performance of this assay in intraocular fluid samples obtained at a reference ophthalmologic centre in the USA.MethodsLower limits of detection for the B1 and Rep529 components of the dual-target assay were determined using serial dilutions of cultured T. gondiistrain Z185. The dual-target assay was then used to test 148 archived intraocular samples (132 vitreous,16 aqueous humour) collected at the Francis I. Proctor Foundation between January 2010 and December 2015 for testing by a nested, conventional PCR targeting the B1 gene.ResultsThe 95% lower limits of detection for the dual-target assay was determined to be 1.05 tachyzoites/mL for B1 and 0.83 tachyzoites/mL for Rep529. Using archived clinical intraocular specimens, the dual-target assay demonstrated 97.2% positive per cent agreement (n=35/36; 95% CI 83.7% to 99.9%) and 99.1% negative per cent agreement (n=111/112; 95% CI 94.4% to 100%) compared with the nested, conventional B1 PCR.ConclusionThis single-reaction, internally controlled, dual-target (B1, Rep529) real-time PCR for the detection of T. gondiiDNA in intraocular specimens demonstrated excellent agreement with nested, conventional, B1 PCR. The dual-target design may ensure T. gondiidetection when variation is present in one of two target regions.

Quantitation of human herpesvirus-6 (HHV-6) DNA in clinical specimens is important for the diagnosis and management of HHV-6-associated infection and reactivation in immunocompromised patients, particularly transplant recipients.

ABSTRACTOral poliovirus vaccine can mutate to regain neurovirulence. To date, evaluation of these mutations has been performed primarily on culture-enriched isolates by using conventional Sanger sequencing. We therefore developed a culture-independent, deep-sequencing method targeting the 5' untranslated region (UTR) and P1 genomic region to characterize vaccine-related poliovirus variants. Error analysis of the deep-sequencing method demonstrated reliable detection of poliovirus mutations at levels of <1%, depending on read depth. Sequencing of viral nucleic acids from the stool of vaccinated, asymptomatic children and their close contacts collected during a prospective cohort study in Veracruz, Mexico, revealed no vaccine-derived polioviruses. This was expected given that the longest duration between sequenced sample collection and the end of the most recent national immunization week was 66 days. However, we identified many low-level variants (<5%) distributed across the 5' UTR and P1 genomic region in all three Sabin serotypes, as well as vaccine-related viruses with multiple canonical mutations associated with phenotypic reversion present at high levels (>90%). These results suggest that monitoring emerging vaccine-related poliovirus variants by deep sequencing may aid in the poliovirus endgame and efforts to ensure global polio eradication.

ABSTRACTSignificant interassay variability in the quantification of BK virus (BKV) DNA precludes establishing broadly applicable thresholds for the management of BKV infection in transplantation. The 1st WHO International Standard for BKV (primary standard) was introduced in 2016 as a common calibrator for improving the harmonization of BKV nucleic acid amplification testing (NAAT) and enabling comparisons of biological measurements worldwide. Here, we evaluated the Altona RealStar BKV assay (Altona) and calibrated the results to the international unit (IU) using the Exact Diagnostics BKV verification panel, a secondary standard traceable to the primary standard. The primary and secondary standards on Altona had nearly identical linear regression equations (primary standard, Y = 1.05X - 0.28, R2= 0.99; secondary standard, Y = 1.04X - 0.26, R2= 0.99) and conversion factors (primary standard, 1.11 IU/copy; secondary standard, 1.09 IU/copy). A comparison of Altona with a laboratory-developed BKV NAAT assay in IU/ml versus copies/ml using Passing-Bablok regression revealed similar regression lines, no proportional bias, and improvement in the systematic bias (95% confidence interval of intercepts: copies/ml, -0.52 to -1.01; IU/ml, 0.07 to -0.36). Additionally, Bland-Altman analyses revealed a clinically significant reduction of bias when results were reported in IU/ml (IU/ml, -0.10 log10; copies/ml, -0.70 log10). These results indicate that the use of a common calibrator improved the agreement between the two assays. As clinical laboratories worldwide use calibrators traceable to the primary standard to harmonize BKV NAAT results, we anticipate improved interassay comparisons with a potential for establishing broadly applicable quantitative BKV DNA load cutoffs for clinical practice.

Plasma Epstein-Barr Virus (EBV) DNA is an established biomarker for endemic nasopharyngeal carcinoma (NPC). However, existing real-time PCR (qPCR) assays are limited by poor inter-laboratory reproducibility. This is a barrier to biomarker integration into staging systems and management.

ABSTRACTHIV-1 RNA quantitation in plasma, or virus load testing, is the primary method by which the response to antiretroviral therapy is monitored. Here we describe evaluation of the Aptima HIV-1 Quant Dx assay (Aptima) performed on the automated Panther system. The clinical performance of Aptima was compared to that of the Cobas AmpliPrep/Cobas TaqMan HIV-1 Test v2.0 (CAP/CTM) using 162 EDTA plasma samples collected from patients undergoing HIV-1 monitoring. Overall agreement was 84.0% (136/162), with a kappa statistic of 0.723 (standard error, 0.047; 95% confidence interval [CI], 0.630 to 0.815), indicating substantial agreement. Using the 86 clinical samples quantifiable by both methods, Passing-Bablok regression revealed a regression line of Y= (1.069 × X) - 0.346 (95% CI of the slope [1.003 to 1.139] and intercept [-0.666 to -0.074]), and Bland-Altman analysis demonstrated a mean difference (Aptima-CAP/CTM) of -0.075 log10copies/ml (95% limits of agreement of -0.624 to 0.475), consistent with negative bias. Comparison of Aptima results for paired dried blood spot (DBS) and plasma specimens archived from participants in the Peninsula AIDS Research Cohort Study (PARC) demonstrated an overall agreement of 94.7% (90/95) when 1,000 copies/ml was used as the threshold. In conclusion, the Aptima HIV-1 Quant Dx assay provides a suitable alternative for HIV-1 monitoring in plasma and DBS.

ABSTRACTBK virus (BKV) infection causing end-organ disease remains a formidable challenge to the hematopoietic cell transplant (HCT) and kidney transplant fields. As BKV-specific treatments are limited, immunologic-based therapies may be a promising and novel therapeutic option for transplant recipients with persistent BKV infection. Here, we describe a whole-genome, deep-sequencing methodology and bioinformatics pipeline that identify BKV variants across the genome and at BKV-specific HLA-A2-, HLA-B0702-, and HLA-B08-restricted CD8 T-cell epitopes. BKV whole genomes were amplified using long-range PCR with four inverse primer sets, and fragmentation libraries were sequenced on the Ion Torrent Personal Genome Machine (PGM). An error model and variant-calling algorithm were developed to accurately identify rare variants. A total of 65 samples from 18 pediatric HCT and kidney recipients with quantifiable BKV DNAemia underwent whole-genome sequencing. Limited genetic variation was observed. The median number of amino acid variants identified per sample was 8 (range, 2 to 37; interquartile range, 10), with the majority of variants (77%) detected at a frequency of <5%. When normalized for length, there was no statistical difference in the median number of variants across all genes. Similarly, the predominant virus population within samples harbored T-cell epitopes similar to the reference BKV strain that was matched for the BKV genotype. Despite the conservation of epitopes, low-level variants in T-cell epitopes were detected in 77.7% (14/18) of patients. Understanding epitope variation across the whole genome provides insight into the virus-immune interface and may help guide the development of protocols for novel immunologic-based therapies.

We developed a multiplexed assay on a plasmonic-gold platform for measuring IgG and IgA antibodies and IgG avidity against both Zika virus (ZIKV) and dengue virus (DENV) infections. In contrast to IgM cross-reactivity, IgG and IgA antibodies against ZIKV nonstructural protein 1 (NS1) antigen were specific to ZIKV infection, and IgG avidity revealed recent ZIKV infection and past DENV-2 infection in patients in dengue-endemic regions. This assay could enable specific diagnosis of ZIKV infection over other flaviviral infections.

ABSTRACTDengue, leptospirosis, and malaria are among the most common etiologies of systemic undifferentiated febrile illness (UFI) among travelers to the developing world, and these pathogens all have the potential to cause life-threatening illness in returned travelers. The current study describes the development of an internally controlled multiplex nucleic acid amplification test for the detection of dengue virus (DENV) and Leptospiraand Plasmodiumspecies, with a specific callout for Plasmodium falciparum(referred to as the UFI assay). During analytical evaluation, the UFI assay displayed a wide dynamic range and a sensitive limit of detection for each target, including all four DENV serotypes. In a clinical evaluation including 210 previously tested samples, the sensitivities of the UFI assay were 98% for DENV (58/59 samples detected) and 100% for Leptospiraand malaria (65/65 and 20/20 samples, respectively). Malaria samples included all five Plasmodiumspecies known to cause human disease. The specificity of the UFI assay was 100% when evaluated with a panel of 66 negative clinical samples. Furthermore, no amplification was observed when extracted nucleic acids from related pathogens were tested. Compared with whole-blood samples, the UFI assay remained positive for Plasmodiumin 11 plasma samples from patients with malaria (parasitemia levels of 0.0037 to 3.4%). The syndrome-based design of the UFI assay, combined with the sensitivities of the component tests, represents a significant improvement over the individual diagnostic tests available for these pathogens.

ABSTRACTIn immunosuppressed hosts, the development of multidrug resistance complicates the treatment of cytomegalovirus (CMV) infection. Improved genotypic detection of impending drug resistance may follow from recent technical advances. A severely T-cell-depleted patient with chronic lymphocytic leukemia developed CMV pneumonia and high plasma viral loads that were poorly responsive to antiviral therapy. Serial plasma specimens were analyzed for mutant viral populations by conventional and high-throughput deep-sequencing methods. Uncharacterized mutations were phenotyped for drug resistance using recombinant viruses. Conventional genotyping detected viruses with the UL97 kinase substitution C607Y after ganciclovir treatment, a transient subpopulation of UL54 polymerase L773V mutants first detected 8 weeks after foscarnet was started, and a subpopulation of a mutant with deletion of UL54 codons 981 and 982 2 months after the addition of cidofovir. Deep sequencing of the same serial specimens revealed the same UL54 mutants sooner, along with a more complex evolution of known and newly recognized mutant subpopulations missed by conventional sequencing. The UL54 exonuclease substitutions D413N, K513R, and C539G were newly shown to confer ganciclovir-cidofovir resistance, while L773V was shown to confer foscarnet resistance and add to the ganciclovir resistance conferred by UL97 C607Y. Increased sequencing depth provided a more timely and detailed diagnosis of mutant viral subpopulations that evolved with changing anti-CMV therapy.

ABSTRACTBK polyomavirus (BKV) is an emerging pathogen in immunocompromised individuals. BKV subtype III is rarely identified and has not previously been associated with disease. Here we provide the whole-genome sequence of a subtype III BKV from a pediatric kidney transplant patient with polyomavirus-associated nephropathy.

ABSTRACTAntiviral therapy for cytomegalovirus (CMV) plays an important role in the clinical management of solid organ and hematopoietic stem cell transplant recipients. However, CMV antiviral therapy can be complicated by drug resistance associated with mutations in the phosphotransferase UL97 and the DNA polymerase UL54. We have developed an amplicon-based high-throughput sequencing strategy for detecting CMV drug resistance mutations in clinical plasma specimens using a microfluidics PCR platform for multiplexed library preparation and a benchtop next-generation sequencing instrument. Plasmid clones of the UL97 and UL54 genes were used to demonstrate the low overall empirical error rate of the assay (0.189%) and to develop a statistical algorithm for identifying authentic low-abundance variants. The ability of the assay to detect resistance mutations was tested with mixes of wild-type and mutant plasmids, as well as clinical CMV isolates and plasma samples that were known to contain mutations that confer resistance. Finally, 48 clinical plasma specimens with a range of viral loads (394 to 2,191,011 copies/ml plasma) were sequenced using multiplexing of up to 24 specimens per run. This led to the identification of seven resistance mutations, three of which were present in <20% of the sequenced population. Thus, this assay offers more sensitive detection of minor variants and a higher multiplexing capacity than current methods for the genotypic detection of CMV drug resistance mutations.

Metal oxides have been used as supports and promoters to enhance the electrocatalytic activity of Pt/C for methanol oxidation reaction (MOR). In this work, Gd2O3prepared by simple precipitation method (Gd2O3(PC)) and polymer-assisted method (Gd2O3(PL)) is examined as support for Pt/C. The Gd2O3samples are characterized by FTIR, HR-SEM, and PXRD. The ease of surface oxygen exchange and formation of surface –OH groups are better in the case of Gd2O3(PC) for MOR activity. The microwave-assisted polyol reflux method is used to prepare Pt-Gd2O3(PC)/C and Pt-Gd2O3(PL)/C) electrocatalysts. Electrocatalysts are characterized by XPS, ICP, TEM, PXRD, and examined by cyclic voltammetry (CV), CO stripping experiments, chronopotentiometry (CP), and chronoamperometry (CA) in acidic media. The MOR activity of Pt-Gd2O3(PC)/C is found to be 2.8 times higher than commercial Pt/C with good anti-poisoning activity. This result is further corroborated by the first principle calculations which show that there is significant electron transfer from Pt/Gd2O3to adsorbed CO. This electron transfer reduces the Gibbs free energy for CO adsorption and decreases the CO poisoning. The overall benefit of Gd2O3is to increase the performance of Pt electrocatalyst for methanol oxidation.

ABSTRACTA number of diagnostic tests are available for dengue virus (DENV) detection, including a variety of nucleic acid amplification tests (NAATs). However, reports describing a direct comparison of different NAATs have been limited. In this study, we report the design of an internally controlled real-time reverse transcriptase PCR (rRT-PCR) that detects all four DENV serotypes but does not distinguish between them (the pan-DENV assay). Two hundred clinical samples were then tested using four different DENV RT-PCR assays: the pan-DENV assay, a commercially produced, internally controlled DENV rRT-PCR (the Altona assay), a widely used heminested RT-PCR, and a serotype-specific multiplex rRT-PCR assay. The pan-DENV assay had a linear range extending from 1.0 to 7.0 log10cDNA equivalents/µl and a lower limit of 95% detection ranging from 1.7 to 7.6 cDNA equivalents/µl, depending on the serotype. When measured against a composite reference standard, the pan-DENV assay proved to be more clinically sensitive than either the Altona or heminested assays, with a sensitivity of 98.0% compared to 72.3% and 78.8%, respectively (P= 0.0001 for both comparisons). The pan-DENV assay detected DENV in significantly more samples collected on or after day 5 of illness and in a subgroup of patients with detectable anti-DENV IgM at presentation. No significant difference in sensitivity was observed between the pan-DENV assay and the multiplex rRT-PCR, despite the presence of an internal control in the former. The detection of DENV RNA late in the course of clinical illness should serve to lengthen the period during which a confirmed molecular diagnosis of DENV infection can be provided.

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with concerning phenotypic mutations is of public health interest. Genomic surveillance is an important tool for a pandemic response, but many laboratories do not have the resources to support population-level sequencing.

ABSTRACTThe commutability of international reference standards is critical for ensuring quantitative agreement across different viral load assays. Here, we demonstrate the commutability of the Epstein-Barr virus (EBV) WHO international standard for the BamHI-W and artus EBV assays.

ABSTRACTFebrile travelers from countries with unique endemic pathogens pose a significant diagnostic challenge. In this report, we describe the case of a Tongan man presenting with fever, rash, and altered mental status. The diagnosis of Chikungunya encephalitis was made using a laboratory-developed real-time RT-PCR and serologic testing.

ABSTRACTDengue virus (DENV) is the agent of the most common vector-borne disease worldwide. Using 199 clinical samples collected from Nicaragua and Sri Lanka, a laboratory-developed DENV multiplex real-time reverse transcription-PCR (rRT-PCR) proved more clinically sensitive than the FDA-approved CDC assay for DENV serotypes 1 to 4 when measured against a composite reference standard, with sensitivities of 97.4% versus 87.1%, respectively.

Several point-of-care (POC) molecular tests have received emergency use authorization (EUA) from the Food and Drug Administration (FDA) for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The test performance characteristics of the Accula (Mesa Biotech) SARS-CoV-2 POC test need to be evaluated to inform its optimal use. The aim of this study was to assess the test performance of the Accula SARS-CoV-2 test. The performance of the Accula test was assessed by comparing results of 100 nasopharyngeal swab samples previously characterized by the Stanford Health Care EUA laboratory-developed test (SHC-LDT), targeting the envelope (E) gene.

Infections with DNA viruses are frequent causes of morbidity and mortality in transplant recipients.

Ohgami: Agilent technologies: Other: received support/funding.

Angioimmunoblastic T-cell lymphoma is a uniquely aggressive mature T-cell neoplasm. In recent years, recurrent genetic mutations in RHOA, TET2, DNMT3Aand IDH2have been identified which characterize this disease. However, a deep molecular study assessing both DNA mutations and RNA expression profile, combined with digital image analysis is lacking.

Pathogen cell-free DNA (pcfDNA) in blood and urine is an attractive biomarker; however, the impact of preanalytical factors is not well understood. Blood and urine samples from healthy donors spiked with cfDNA from Mycobacterium tuberculosis, Salmonella enterica, Aspergillus fumigatus, and Epstein-Barr virus (EBV) and samples from tuberculosis patients were used to evaluate the impact of blood collection tube, urine preservative, processing delay, processing method, freezing and thawing, and sample volume on pcfDNA.

Hepatitis C virus (HCV) RNA quantitation is the primary method by which active HCV infections are identified and the response to direct-acting antiviral therapy is monitored. This study describes the evaluation of the Aptima HCV Quant Dx assay (Aptima HCV) performed on the Panther system.