Global and cell type-specific immunological hallmarks of severe dengue progression identified via a systems immunology approach.

Severe dengue (SD) is a major cause of morbidity and mortality. To define dengue virus (DENV) target cells and immunological hallmarks of SD progression in children's blood, we integrated two single-cell approaches capturing cellular and viral elements: virus-inclusive single-cell RNA sequencing (viscRNA-Seq 2) and targeted proteomics with secretome analysis and functional assays. Beyond myeloid cells, in natural infection, B cells harbor replicating DENV capable of infecting permissive cells. Alterations in cell type abundance, gene and protein expression and secretion as well as cell-cell communications point towards increased immune cell migration and inflammation in SD progressors. Concurrently, antigen-presenting cells from SD progressors demonstrate intact uptake yet impaired interferon response and antigen processing and presentation signatures, which are partly modulated by DENV. Increased activation, regulation and exhaustion of effector responses and expansion of HLA-DR-expressing adaptive-like NK cells also characterize SD progressors. These findings reveal DENV target cells in human blood and provide insight into SD pathogenesis beyond antibody-mediated enhancement.

Multiplex Dual-Target Reverse Transcription PCR for Subtyping Avian Influenza A(H5) Virus.

An increased risk for human infection with avian influenza A(H5N1) viruses is of concern. We developed an internally controlled, dual-target reverse transcription PCR for influenza A(H5) subtyping. This test could be used to detect influenza A(H5) in clinical samples.

Three-Dimensional Ni-MOF as a High-Performance Supercapacitor Anode Material; Experimental and Theoretical Insight.

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)2 electrode 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)2 electrode as observed in the experiment.

Retrospective Screening of Clinical Samples for Monkeypox Virus DNA, California, USA, 2022.

We retrospectively screened oropharyngeal and rectal swab samples originally collected in California, USA, for Chlamydia trachomatis and Neisseria gonorrhoeae testing for the presence of monkeypox virus DNA. Among 206 patients screened, 17 (8%) had samples with detectable viral DNA. Monkeypox virus testing from mucosal sites should be considered for at-risk patients.

Human immunodeficiency virus 1 5'-leader mutations in plasma viruses before and after the development of reverse transcriptase inhibitor-resistance mutations.

Human immunodeficiency virus 1 (HIV-1) reverse transcriptase (RT) initiation depends on interaction between viral 5'-leader RNA, RT and host tRNA3Lys. Therefore, we sought to identify co-evolutionary changes between the 5'-leader and RT in viruses developing RT-inhibitor resistance mutations. We sequenced 5'-leader positions 37-356 of paired plasma virus samples from 29 individuals developing the nucleoside RT inhibitor (NRTI)-resistance mutation M184V, 19 developing a non-nucleoside RT inhibitor (NNRTI)-resistance mutation and 32 untreated controls. 5'-Leader variants were defined as positions where ≥20 % of next-generation sequencing (NGS) reads differed from the HXB2 sequence. Emergent mutations were defined as nucleotides undergoing a ≥4-fold change in proportion between baseline and follow-up. Mixtures were defined as positions containing ≥2 nucleotides each present in ≥20 % of NGS reads. Among 80 baseline sequences, 87 positions (27.2 %) contained a variant; 52 contained a mixture. Position 201 was the only position more likely to develop a mutation in the M184V (9/29 vs 0/32; P=0.0006) or NNRTI-resistance (4/19 vs 0/32; P=0.02; Fisher's exact test) groups than the control group. Mixtures at positions 200 and 201 occurred in 45.0 and 28.8 %, respectively, of baseline samples. Because of the high proportion of mixtures at these positions, we analysed 5'-leader mixture frequencies in two additional datasets: five publications reporting 294 dideoxyterminator clonal GenBank sequences from 42 individuals and six National Center for Biotechnology Information (NCBI) BioProjects reporting NGS datasets from 295 individuals. These analyses demonstrated position 200 and 201 mixtures at proportions similar to those in our samples and at frequencies several times higher than at all other 5'-leader positions. Although we did not convincingly document co-evolutionary changes between RT and 5'-leader sequences, we identified a novel phenomenon, wherein positions 200 and 201 immediately downstream of the HIV-1 primer binding site exhibited an extraordinarily high likelihood of containing a nucleotide mixture. Possible explanations for the high mixture rates are that these positions are particularly error-prone or provide a viral fitness advantage.

Hepatitis E virus seropositivity in an ethnically diverse community blood donor population.

BACKGROUND AND OBJECTIVES: Hepatitis E virus (HEV) is an underrecognized and emerging infectious disease that may threaten the safety of donor blood supply in many parts of the world. We sought to elucidate whether our local community blood supply is at increased susceptibility for transmission of transfusion-associated HEV infections. MATERIALS AND METHODS: We screened 10,002 randomly selected donations over an 8-month period between 2017 and 2018 at the Stanford Blood Center for markers of HEV infection using commercial IgM/IgG serological tests and reverse transcriptase quantitative polymerase chain reaction assays (RT-qPCR). Donor demographic information, including gender, age, self-identified ethnicity, location of residence and recent travel, were obtained from the donor database and used to generate multivariate binary logistic regressions for risk factors of IgG seropositivity. RESULTS: A total of 10,002 blood donations from 7507 unique donors were screened, and there was no detectable HEV RNA by RT-qPCR. The overall seropositivity rate was 12.1% for IgG and 0.56% for IgM. Multivariate analysis of unique donors revealed a significantly higher risk of IgG seropositivity with increasing age, White/Asian ethnicities and residence in certain local counties. CONCLUSION: Although HEV IgG seroprevalence in the San Francisco Bay Area is consistent with ongoing infection, the screening of a large donor population did not identify any viraemic blood donors. While HEV is an underrecognized and emerging infection in other regions, there is no evidence to support routine blood screening for HEV in our local blood supply currently; however, periodic monitoring may still be required to assess the ongoing risk.

Insight into the structure and transport properties of pyrrolidinium-based geminal dicationic-organic ionic crystals: unravelling the role of alkyl-chain length.

The present study has been undertaken with an aim to design and develop safer and more efficient all solid-state electrolytes, so that the issues associated with the use of conventional room temperature ionic liquid-based electrolytes can be tackled. To fulfil this objective, a series of geminal di-cationic Organic Ionic Crystals (OICs), based on C3-, C6-, C8- and C9-alkylbridged bis-(methylpyrrolidinium)bromide are synthesized, and the structural features, thermal properties and phase behaviours of these as synthesized OICs have been investigated. Additionally, a number of electro-analytical techniques have been employed to assess their suitability as an efficient electrolyte composite (OIC:I2:TBAI) for all solid-state dye sensitised solar cells (DSSCs). The structural analysis has revealed that along with excellent thermal stability and well-defined surface morphology, all thsese OICs exhibit a well-ordered three-dimensional network of cations and anions that can serve as a conducting channel for the diffusion of iodide ions. Electrochemical investigations have shown that OICs with an intermediate length of alkyl bridge (C6- and C8-alkyl bridged) show better electrolytic performance than those that are based on OICs with a relatively shorter (C3-) or longer (C9-) alkyl-bridge chain. A careful analysis of the above data has essentially demonstrated that the length of the alkyl bridge chain plays a significant role in determining the structural organisation, morphology and eventually the ionic conductivity of OICs. Overall, the comprehensive knowledge on OICs that has been extracted from the current study is expected to be helpful to explore further new types of OIC-based all solid-state electrolytes with improved electrolytic performance for targeted applications.

Identification and confirmation via in situ hybridization of Merkel cell polyomavirus in rare cases of posttransplant cutaneous T-cell lymphoma.

BACKGROUND: Viral infection is an oncogenic factor in many hematolymphoid malignancies. We sought to determine the diagnostic yield of aligning off-target reads incidentally obtained during targeted hematolymphoid next-generation sequencing to a large database of viral genomes to screen for viral sequences within tumor specimens. METHODS: Alignment of off-target reads to viral genomes was performed using magicBLAST. Localization of Merkel cell polyomavirus (MCPyV) RNA was confirmed by RNAScope in situ hybridization. Integration analysis was performed using Virus-Clip. RESULTS: Four cases of post-cardiac-transplant folliculotropic mycosis fungoides (fMF) and one case of peripheral T-cell lymphoma (PTCL) were positive in off-target reads for MCPyV DNA. Two of the four cases of posttransplant fMF and the case of PTCL showed localization of MCPyV RNA to malignant lymphocytes, whereas the remaining two cases of posttransplant fMF showed MCPyV RNA in keratinocytes. CONCLUSIONS: Our findings raise the question of whether MCPyV may play a role in rare cases of T-lymphoproliferative disorders, particularly in the skin and in the heavily immunosuppressed posttransplant setting.

Electric field-driven microfluidics for rapid CRISPR-based diagnostics and its application to detection of SARS-CoV-2.

The rapid spread of COVID-19 across the world has revealed major gaps in our ability to respond to new virulent pathogens. Rapid, accurate, and easily configurable molecular diagnostic tests are imperative to prevent global spread of new diseases. CRISPR-based diagnostic approaches are proving to be useful as field-deployable solutions. In one basic form of this assay, the CRISPR-Cas12 enzyme complexes with a synthetic guide RNA (gRNA). This complex becomes activated only when it specifically binds to target DNA and cleaves it. The activated complex thereafter nonspecifically cleaves single-stranded DNA reporter probes labeled with a fluorophore-quencher pair. We discovered that electric field gradients can be used to control and accelerate this CRISPR assay by cofocusing Cas12-gRNA, reporters, and target within a microfluidic chip. We achieve an appropriate electric field gradient using a selective ionic focusing technique known as isotachophoresis (ITP) implemented on a microfluidic chip. Unlike previous CRISPR diagnostic assays, we also use ITP for automated purification of target RNA from raw nasopharyngeal swab samples. We here combine this ITP purification with loop-mediated isothermal amplification and the ITP-enhanced CRISPR assay to achieve detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA (from raw sample to result) in about 35 min for both contrived and clinical nasopharyngeal swab samples. This electric field control enables an alternate modality for a suite of microfluidic CRISPR-based diagnostic assays.

Multiplex Epstein-Barr virus BALF2 genotyping detects high-risk variants in plasma for population screening of nasopharyngeal carcinoma.

BACKGROUND: Epstein-Barr Virus (EBV)-associated nasopharyngeal carcinoma (NPC) exhibits unusual geographic restriction despite ubiquitous lifelong infection. Screening programs can detect most NPC cases at an early stage, but existing EBV diagnostics are limited by false positives and low positive predictive value (PPV), leading to excess screening endoscopies, MRIs, and repeated testing. Recent EBV genome-wide association studies (GWAS) suggest that EBV BALF2 variants account for more than 80% of attributable NPC risk. We therefore hypothesized that high-risk BALF2 variants could be readily detected in plasma for once-lifetime screening triage. METHODS: We designed and validated a multiplex genotyping assay to detect EBV BALF2 polymorphisms in human plasma. Targeted next-generation sequencing was used to validate this assay, conduct association studies with clinical phenotype, and longitudinally genotype plasma to assess within-host haplotype stability. We examined the association between NPC and BALF2 haplotypes in a large non-endemic population and three prior EBV GWAS. Finally, we estimated NPC mortality reduction, resource utilization, and cost-effectiveness of BALF2 variant-informed screening using a previously-validated cohort model. RESULTS: Following analytical validation, the BALF2 genotyping assay had 99.3% concordance with sequencing in a cohort of 24 NPC cases and 155 non-NPC controls. BALF2 haplotype was highly associated with NPC in this non-endemic population (I613V: odds ratio [OR] 7.9; V317M: OR 178.8). No other candidate BALF2 polymorphisms were significantly associated with NPC or hematologic disorders. Longitudinal genotyping revealed 97.8% within-host haplotype concordance, indicative of lifelong latent infection. In a meta-analysis of 755 NPC cases and 981 non-NPC controls, BALF2 I613V and V317M were significantly associated with NPC in both endemic and non-endemic populations. Modeled variant-informed screening strategies achieved a 46% relative increase in PPV with 7% decrease in effective screening sensitivity, thereby averting nearly half of screening endoscopies/MRIs among endemic populations in east/southeast Asia. CONCLUSIONS: EBV BALF2 haplotypes are temporally stable within hosts and can be readily detected in plasma via an inexpensive multiplex genotyping assay that offers near-perfect sequencing concordance. In endemic and non-endemic populations, I613V and V317M were highly associated with NPC and could be leveraged to develop variant-informed screening programs that mitigate false positives with small reductions in screening sensitivity.

Human Monkeypox without Viral Prodrome or Sexual Exposure, California, USA, 2022.

We report human monkeypox in a man who returned to the United States from the United Kingdom and reported no sexual contact. He had vesicular and pustular skin lesions but no anogenital involvement. The potential modes of transmission may have implications for the risk of spread and for epidemic control.

Vaccine-Associated Measles Encephalitis in Immunocompromised Child, California, USA.

We report a fatal case of vaccine-associated measles encephalitis in an immunocompromised child in California, USA. The infection was confirmed by whole-genome RNA sequencing of measles virus from brain tissue. We observed biased matrix-gene hypermutation consistent with persistent measles virus central nervous system infection.

Evaluation of a Rapid and Accessible Reverse Transcription-Quantitative PCR Approach for SARS-CoV-2 Variant of Concern Identification.

The ability to distinguish between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) is of ongoing interest due to differences in transmissibility, responses to vaccination, clinical prognosis, and therapy. Although detailed genetic characterization requires whole-genome sequencing (WGS), targeted nucleic acid amplification tests can serve a complementary role in clinical settings, as they are more rapid and accessible than sequencing in most laboratories. We designed and analytically validated a two-reaction multiplex reverse transcription-quantitative PCR (RT-qPCR) assay targeting spike protein mutations L452R, E484K, and N501Y in reaction 1 and del69-70, K417N, and T478K in reaction 2. This assay had 95 to 100% agreement with WGS for 502 upper respiratory tract swab samples collected between 26 April 2021 and 1 August 2021, consisting of 43 Alpha, 2 Beta, 20 Gamma, 378 Delta, and 59 non-VOC infections. Validation in a separate group of 230 WGS-confirmed Omicron variant samples collected in December 2021 and January 2022 demonstrated 100% agreement. This RT-qPCR-based approach can be implemented in clinical laboratories already performing SARS-CoV-2 nucleic acid amplification tests to assist in local epidemiological surveillance and clinical decision-making.

Impact of Iron in Three-Dimensional Co-MOF for Electrocatalytic Water Oxidation.

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/cm2 current 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.

Unusual CO2 Adsorption in ZIF-7: Insight from Raman Spectroscopy and Computational Studies.

Here, we use Raman spectroscopy to investigate temperature-dependent changes in the atomic-scale structure of the zeolitic imidazolate framework ZIF-7 in a CO2 atmosphere and uncover the mechanism of maximal CO2 adsorption at 206 K. At 301 K, the Raman spectra of ZIF-7 at various CO2 gas 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 CO2 at 1272 and 1376 cm-1. Moreover, the Raman inactive bending mode of CO2 becomes active due to geometrical distortion of adsorbed CO2. It further splits into two peaks due to hydrogen bonding interactions between CO2 and the benzene ring of the benzimidazole linker ZIF-7, as supported by our computational studies. In addition, the interaction between CO2 molecules plays a key role. Upon reducing the temperature at 1 bar CO2 gas pressure, ZIF-7 exhibits softening of the imidazole puckering mode and the Fermi resonance CO2 band due to interactions between CO2 and the framework through hydrogen bonding. At 206 K, substantial modification in the lattice mode and disappearance of the Raman inactive CO2 bending mode confirm the changes in the size of the pore cavity through structural rearrangements of CO2.

Design of ZIF-67 nanoflake derived NiCo-LDH/rGO hybrid nanostructures for aqueous symmetric supercapattery application under alkaline condition.

Well-defined polyhedral ZIF-67 metal-organic frameworks (MOFs) are usually synthesized using methanol as solvent. In this work, methanol is replaced with deionized water as a solvent to synthesize ZIF-67 MOFs with unique nanoflake morphology. The ZIF-67 nanoflakes are synthesized directly byin situmethod on reduced graphene oxide (rGO) to obtain ZIF-67/rGO-xprecursors which are further transformed into NiCo-layered double hydroxide nanocomposites (NiCo-LDH/rGO-x,x = 10, 30, 50 and 90 mg of rGO). The NiCo-LDH/rGO-xnanostructured composites are found to be excellent materials for battery type supercapacitor (supercapattery) applications. Among these samples, the NiCo-LDH/rGO-30 composite gives maximum specific capacity of 829 C g-1(1658 F g-1) at a current density of 1 A g-1and high rate capability. The as fabricated 2-electrode symmetric Swagelok deviceNiCo-LDH/rGO-30NiCo-LDH/rGO-30delivered a high energy density of 49.2 Wh kg-1and a power density of 4511 W kg-1, and enabled us to glow red, blue and white LED bulbs using three coin cells. The device can show good capacity retention even after 3000 continuous charge-discharge cycles. The NiCo-LDH/rGO-30 composite,in situderived from ZIF-67 MOF in combination with optimal amount of rGO, is an excellent material to deliver both high energy density and high power density in supercapattery devices.

Ultra-sensitive Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Antigen Detection for the Diagnosis of Coronavirus Disease 2019 (COVID-19) in Upper Respiratory Samples.

An ultra-sensitive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid antigen assay (S-PLEX, MesoScale Diagnostics) was evaluated in 250 retrospective and 200 prospective upper respiratory specimens. In samples with cycle threshold <35, there was 95%-98% positive and 93%-96% negative percent agreement with reverse transcription-polymerase chain reaction. S-PLEX may provide a high-throughput alternative to nucleic acid-based testing for coronavirus disease 2019 (COVID-19) diagnosis.

High Frequency of SARS-CoV-2 RNAemia and Association With Severe Disease.

BACKGROUND: Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in blood, also known as RNAemia, has been reported, but its prognostic implications are poorly understood. This study aimed to determine the frequency of SARS-CoV-2 RNA in plasma and its association with coronavirus disease 2019 (COVID-19) clinical severity. METHODS: An analytical cross-sectional study was performed in a single-center tertiary care institution and included consecutive inpatients and outpatients with confirmed COVID-19. The prevalence of SARS CoV-2 RNAemia and the strength of its association with clinical severity variables were examined and included intensive care unit (ICU) admission, invasive mechanical ventilation, and 30-day all-cause mortality. RESULTS: Paired nasopharyngeal and plasma samples were included from 85 patients. The median age was 55 years, and individuals with RNAemia were older than those with undetectable SARS-CoV-2 RNA in plasma (63 vs 50 years; P = .04). Comorbidities were frequent including obesity (37.6%), hypertension (30.6%), and diabetes mellitus (22.4%). RNAemia was detected in 28/85 (32.9%) of patients, including 22/28 (78.6%) who required hospitalization. In models adjusted for age, RNAemia was detected more frequently in individuals who developed severe disease including ICU admission (32.1 vs 14.0%; P = .04) and invasive mechanical ventilation (21.4% vs 3.5%; P = .02). All 4 deaths occurred in individuals with detectable RNAemia. An additional 121 plasma samples from 28 individuals with RNAemia were assessed longitudinally, and RNA was detected for a maximum duration of 10 days. CONCLUSIONS: This study demonstrated a high proportion of SARS-CoV-2 RNAemia, and an association between RNAemia and clinical severity suggesting the potential utility of plasma viral testing as a prognostic indicator for COVID-19.

Strand-Specific Reverse Transcription PCR for Detection of Replicating SARS-CoV-2.

We developed an assay that detects minus-strand RNA as a surrogate for actively replicating severe acute respiratory syndrome coronavirus 2. We detected minus-strand RNA in 41 persons with coronavirus disease up to 30 days after symptom onset. This assay might inform clinical decision-making about patient infectiousness.

Performance of Nucleic Acid Amplification Tests for Detection of Severe Acute Respiratory Syndrome Coronavirus 2 in Prospectively Pooled Specimens.

Pooled nucleic acid amplification tests for severe acute respiratory syndrome coronavirus 2 could increase availability of testing at decreased cost. However, the effect of dilution on analytical sensitivity through sample pooling has not been well characterized. We tested 1,648 prospectively pooled specimens by using 3 nucleic acid amplification tests for severe acute respiratory syndrome coronavirus 2: a laboratory-developed real-time reverse transcription PCR targeting the envelope gene, and 2 commercially available Panther System assays targeting open reading frame 1ab. Positive percent agreement (PPA) of pooled versus individual testing ranged from 71.7% to 82.6% for pools of 8 and from 82.9% to 100.0% for pools of 4. We developed and validated an independent stochastic simulation model to estimate effects of dilution on PPA and efficiency of a 2-stage pooled real-time reverse transcription PCR testing algorithm. PPA was dependent on the proportion of tests with positive results, cycle threshold distribution, and assay limit of detection.