Synthesis of Heterostructured TiO2 Nanopores/Nanotubes by Anodizing at High Voltages.

This paper reports on the coating of heterostructured TiO2 nanopores/nanotubes on Ti substrates by anodizing at high voltages to design surfaces for biomedical implants. As the anodized voltage from 50 V to 350 V was applied, the microstructure of the coating shifted from regular TiO2 nanotubes to heterostructured TiO2 nanopores/nanotubes. In addition, the dimension of the heterostructured TiO2 nanopores/nanotubes was a function of voltage. The electrochemical characteristics of TiO2 nanotubes and heterostructured TiO2 nanopores/nanotubes were evaluated in simulated body fluid (SBF) solution. The creation of heterostructured TiO2 nanopores/nanotubes on Ti substrates resulted in a significant increase in BHK cell attachment compared to that of the Ti substrates and the TiO2 nanotubes.

Synthesis of Up-Conversion CaTiO3: Er3+ Films on Titanium by Anodization and Hydrothermal Method for Biomedical Applications.

The present study investigates the effects of Er3+ doping content on the microstructure and up-conversion emission properties of CaTiO3: Er3+ phosphors as a potential material in biomedical applications. The CaTiO3: x%Er3+ (x = 0.5, 1.0, 1.5, 2.0, 2.5, and 3.0%) films were synthesized on Ti substrates by a hydrothermal reaction at 200 °C for 24 h. The SEM image showed the formation of cubic nanorod CaTiO3: Er3+ films with a mean edge size value of (1-5) µm. When excited with 980 nm light, the CaTiO3: Er3+ films emitted a strong green band and a weak red band of Er3+ ions located at 543, 661, and 740 nm. The CaTiO3: Er3+ film exhibited excellent surface hydrophilicity with a contact angle of ~zero and good biocompatibility against baby hamster kidney (BHK) cells. CaTiO3: Er3+ films emerge as promising materials for different applications in the biomedical field.

LocoBox: Modular Hardware and Open-Source Software for Circadian Entrainment and Behavioral Monitoring in Home Cages.

Day-night locomotor activities are the most readily observed outputs of the circadian (~24-h period) clock in many animals. Temporal patterns of the light-dark schedule serve as input to the clock. While circadian activity patterns under various lighting conditions have been observed and documented, the full extent of circadian locomotor activities by genotype and entrainment remains uncharacterized. To facilitate large-scale, parallel cataloging of circadian input-output patterns, we created the LocoBox, an easy-to-construct and easy-to-operate system that can control environmental light with flexible entrainment scenarios combined with the T-cycle and measure locomotor activities in individual home cages. The LocoBox is made using economical, common components, and normal breeding cages can be used for long-term recording. We provide details of the components and blueprints, along with software programs for Arduino and a Python-based graphical user interface (GUI), so that the system can be easily replicated in other laboratories.

High-efficiency energy transfer in the strong orange-red-emitting phosphor CeO2:Sm3+, Eu3.

High-efficiency energy transfer (ET) from Sm3+ to Eu3+ leads to dominant red emission in Sm3+, Eu3+ co-doped single-phase cubic CeO2 phosphors. In this work, a series of Sm3+ singly and Sm3+/Eu3+ co-doped CeO2 cubic phosphors was successfully synthesized by solution combustion followed by heat treatment at 800 °C in air. The crystal structure, morphology, chemical element composition, and luminescence properties of the obtained phosphors were investigated using X-ray diffraction, scanning electron microscopy, energy-dispersive X-ray spectroscopy, and photoluminescence analysis. Under 360 nm excitation, the Sm3+ singly doped CeO2 phosphor emitted strong yellow-red light at 573 nm (4G5/2-6H5/2) and 615 nm (4G5/2-6H7/2). Meanwhile, the CeO2:Sm3+, Eu3+ phosphors showed the emission characteristic of both Sm3+ and Eu3+, with the highest emission intensity at 631 nm. The emission intensity of Sm3+ decreased with increasing Eu3+ content, suggesting the ET from Sm3+ to Eu3+ in the CeO2:Sm3+, Eu3+ phosphors. The decay kinetics of the 4G5/2-6H5/2 transition of Sm3+ in the CeO2:Sm3+, Eu3+ phosphors were investigated, confirming the high-efficiency ET from Sm3+ to Eu3+ (reached 84%). The critical distance of energy transfer (RC = 13.7 Å) and the Dexter theory analysis confirmed the ET mechanism corresponding to the quadrupole-quadrupole interaction. These results indicate that the high-efficiency ET from Sm3+ to Eu3+ in CeO2:Sm3+, Eu3+ phosphors is an excellent strategy to improve the emission efficiency of Eu3+.

Expanding the Design Space of Constraints in Auxiliary-Field Quantum Monte Carlo.

We formulate and characterize a new constraint for auxiliary-field quantum Monte Carlo (AFQMC) applicable for general fermionic systems, which allows for the accumulation of phase in the random walk but disallows walkers with a magnitude of phase greater than π with respect to the trial wave function. For short imaginary times, before walkers accumulate sizable phase values, this approach is equivalent to exact free projection, allowing one to observe the accumulation of bias associated with the constraint and thus estimate its magnitude a priori. We demonstrate the stability of this constraint over arbitrary imaginary times and system sizes, highlighting the removal of noise due to the fermionic sign problem. Benchmark total energies for a variety of weakly and strongly correlated molecular systems reveal a distinct bias with respect to standard phaseless AFQMC, with a comparative increase in accuracy given sufficient quality of the trial wave function for the set of studied cases. We then take this constraint, termed linecut AFQMC (lc-AFQMC), and systematically release it (lcR-AFQMC), providing a route to obtain a smooth bridge between constrained AFQMC and the exact free projection results.

Toward Benchmark-Quality Ab Initio Predictions for 3d Transition Metal Electrocatalysts: A Comparison of CCSD(T) and ph-AFQMC.

Generating accurate ab initio ionization energies for transition metal complexes is an important step toward the accurate computational description of their electrocatalytic reactions. Benchmark-quality data is required for testing existing theoretical methods and developing new ones but is complicated to obtain for many transition metal compounds due to the potential presence of both strong dynamical and static electron correlation. In this regime, it is questionable whether the so-called gold standard, coupled cluster with singles, doubles, and perturbative triples (CCSD(T)), provides the desired level of accuracy─roughly 1-3 kcal/mol. In this work, we compiled a test set of 28 3d metal-containing molecules relevant to homogeneous electrocatalysis (termed 3dTMV) and computed their vertical ionization energies (ionization potentials) with CCSD(T) and phaseless auxiliary-field quantum Monte Carlo (ph-AFQMC) in the def2-SVP basis set. A substantial effort has been made to converge away the phaseless bias in the ph-AFQMC reference values. We assess a wide variety of multireference diagnostics and find that spin-symmetry breaking of the CCSD wave function and the PBE0 density functional correlate well with our analysis of multiconfigurational wave functions. We propose quantitative criteria based on symmetry breaking to delineate correlation regimes inside of which appropriately performed CCSD(T) can produce mean absolute deviations from the ph-AFQMC reference values of roughly 2 kcal/mol or less and outside of which CCSD(T) is expected to fail. We also present a preliminary assessment of density functional theory (DFT) functionals on the 3dTMV set.

Firing-Associated Recycling of Coal-Fired Power Plant Fly Ash.

Coal-fired power plant fly ash is a global environmental concern due to its small particle size, heavy metal content, and increased emissions. Although widely used in concrete, geopolymer, and fly ash brick production, a large amount of fly ash remains in storage sites or is used in landfills due to inadequate raw material quality, resulting in a waste of a recoverable resource. Therefore, the ongoing need is to develop new methods for recycling fly ash. The present review differentiates the physiochemical properties of fly ash from two coal combustion processes: fluidized bed combustion and pulverized coal combustion. It then discusses applications that can consume fly ash without strict chemical requirements, focusing on firing-associated methods. Finally, the challenges and opportunities of fly ash recycling are discussed.

Sequential Organ Failure Assessment (SOFA) Score for predicting mortality in patients with sepsis in Vietnamese intensive care units: a multicentre, cross-sectional study.

OBJECTIVES: To compare the accuracy of the Sequential Organ Failure Assessment (SOFA) and Acute Physiology and Chronic Health Evaluation II (APACHE II) Scores in predicting mortality among intensive care unit (ICU) patients with sepsis in a low-income and middle-income country. DESIGN: A multicentre, cross-sectional study. SETTING: A total of 15 adult ICUs throughout Vietnam. PARTICIPANTS: We included all patients aged ≥18 years who were admitted to ICUs for sepsis and who were still in ICUs from 00:00 to 23:59 of the specified study days (ie, 9 January, 3 April, 3 July and 9 October of the year 2019). PRIMARY AND SECONDARY OUTCOME MEASURES: The primary outcome was hospital all-cause mortality (hospital mortality). We also defined the secondary outcome as all-cause deaths in the ICU (ICU mortality). RESULTS: Of 252 patients, 40.1% died in hospitals, and 33.3% died in ICUs. SOFA Score (areas under the receiver operating characteristic curve (AUROC): 0.688 (95% CI 0.618 to 0.758); cut-off value≥7.5; PAUROC<0.001) and APACHE II Score (AUROC: 0.689 (95% CI 0.622 to 0.756); cut-off value ≥20.5; PAUROC<0.001) both had a poor discriminatory ability for predicting hospital mortality. However, the discriminatory ability for predicting ICU mortality of SOFA (AUROC: 0.713 (95% CI 0.643 to 0.783); cut-off value≥9.5; PAUROC<0.001) was fair and was better than that of APACHE II Score (AUROC: 0.672 (95% CI 0.603 to 0.742); cut-off value≥18.5; PAUROC<0.001). A SOFA Score≥8 (adjusted OR (AOR): 2.717; 95% CI 1.371 to 5.382) and an APACHE II Score≥21 (AOR: 2.668; 95% CI 1.338 to 5.321) were independently associated with an increased risk of hospital mortality. Additionally, a SOFA Score≥10 (AOR: 2.194; 95% CI 1.017 to 4.735) was an independent predictor of ICU mortality, in contrast to an APACHE II Score≥19, for which this role did not. CONCLUSIONS: In this study, SOFA and APACHE II Scores were worthwhile in predicting mortality among ICU patients with sepsis. However, due to better discrimination for predicting ICU mortality, the SOFA Score was preferable to the APACHE II Score in predicting mortality.Clinical trials registry - India: CTRI/2019/01/016898.

Predictive validity of the quick Sequential Organ Failure Assessment (qSOFA) score for the mortality in patients with sepsis in Vietnamese intensive care units.

BACKGROUND: The simple scoring systems for predicting the outcome of sepsis in intensive care units (ICUs) are few, especially for limited-resource settings. Therefore, this study aimed to evaluate the accuracy of the quick Sequential (Sepsis-Related) Organ Failure Assessment (qSOFA) score in predicting the mortality of ICU patients with sepsis in Vietnam. METHODS: We did a multicenter cross-sectional study of patients with sepsis (≥18 years old) presenting to 15 adult ICUs throughout Vietnam on the specified days (i.e., 9th January, 3rd April, 3rd July, and 9th October) representing the different seasons of 2019. The primary and secondary outcomes were the hospital and ICU all-cause mortalities, respectively. The area under the receiver operating characteristic curve (AUROC) was calculated to determine the discriminatory ability of the qSOFA score for deaths in the hospital and ICU. The cut-off value of the qSOFA scores was determined by the receiver operating characteristic curve analysis. Upon ICU admission, factors associated with the hospital and ICU mortalities were assessed in univariable and multivariable logistic models. RESULTS: Of 252 patients, 40.1% died in the hospital, and 33.3% died in the ICU. The qSOFA score had a poor discriminatory ability for both the hospital (AUROC: 0.610 [95% CI: 0.538 to 0.681]; cut-off value: ≥2.5; sensitivity: 34.7%; specificity: 84.1%; PAUROC = 0.003) and ICU (AUROC: 0.619 [95% CI: 0.544 to 0.694]; cutoff value: ≥2.5; sensitivity: 36.9%; specificity: 83.3%; PAUROC = 0.002) mortalities. However, multivariable logistic regression analyses show that the qSOFA score of 3 was independently associated with the increased risk of deaths in both the hospital (adjusted odds ratio, AOR: 3.358; 95% confidence interval, CI: 1.756 to 6.422) and the ICU (AOR: 3.060; 95% CI: 1.651 to 5.671). CONCLUSION: In our study, despite having a poor discriminatory value, the qSOFA score seems worthwhile in predicting mortality in ICU patients with sepsis in limited-resource settings. CLINICAL TRIAL REGISTRATION: Clinical trials registry-India: CTRI/2019/01/016898.

A Localized-Orbital Energy Evaluation for Auxiliary-Field Quantum Monte Carlo.

Phaseless auxiliary-field quantum Monte Carlo (ph-AFQMC) has recently emerged as a promising method for the production of benchmark-level simulations of medium- to large-sized molecules because of its accuracy and favorable polynomial scaling with system size. Unfortunately, the memory footprints of standard energy evaluation algorithms are nontrivial, which can significantly impact timings on graphical processing units (GPUs) where memory is limited. Previous attempts to reduce scaling by taking advantage of the low-rank structure of the Coulombic integrals have been successful but exhibit high prefactors, making their utility limited to very large systems. Here we present a complementary cubic-scaling route to reduce memory and computational scaling based on the low rank of the Coulombic interactions between localized orbitals, focusing on the application to ph-AFQMC. We show that the error due to this approximation, which we term localized-orbital AFQMC (LO-AFQMC), is systematic and controllable via a single variable and that the method is computationally favorable even for small systems. We present results demonstrating robust retention of accuracy versus both experiment and full ph-AFQMC for a variety of test cases chosen for their potential difficulty for localized-orbital-based methods, including the singlet-triplet gaps of the polyacenes benzene through pentacene, the heats of formation for a set of Platonic hydrocarbon cages, and the total energy of ferrocene, Fe(Cp)2. Finally, we reproduce our previous result for the gas-phase ionization energy of Ni(Cp)2, agreeing with full ph-AFQMC to within statistical error while using less than 1/15th of the computer time.

The Translational Landscape of SARS-CoV-2-infected Cells Reveals Suppression of Innate Immune Genes.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes a number of strategies to modulate viral and host mRNA translation. Here, we used ribosome profiling in SARS-CoV-2-infected model cell lines and primary airway cells grown at an air-liquid interface to gain a deeper understanding of the translationally regulated events in response to virus replication. We found that SARS-CoV-2 mRNAs dominate the cellular mRNA pool but are not more efficiently translated than cellular mRNAs. SARS-CoV-2 utilized a highly efficient ribosomal frameshifting strategy despite notable accumulation of ribosomes within the slippery sequence on the frameshifting element. In a highly permissive cell line model, although SARS-CoV-2 infection induced the transcriptional upregulation of numerous chemokine, cytokine, and interferon-stimulated genes, many of these mRNAs were not translated efficiently. The impact of SARS-CoV-2 on host mRNA translation was more subtle in primary cells, with marked transcriptional and translational upregulation of inflammatory and innate immune responses and downregulation of processes involved in ciliated cell function. Together, these data reveal the key role of mRNA translation in SARS-CoV-2 replication and highlight unique mechanisms for therapeutic development. IMPORTANCE SARS-CoV-2 utilizes a number of strategies to modulate host responses to ensure efficient propagation. Here, we used ribosome profiling in SARS-CoV-2-infected cells to gain a deeper understanding of the translationally regulated events in infected cells. We found that although viral mRNAs are abundantly expressed, they are not more efficiently translated than cellular mRNAs. SARS-CoV-2 utilized a highly efficient ribosomal frameshifting strategy and alternative translation initiation sites that help increase the coding potential of its RNAs. In permissive cells, SARS-CoV-2 infection induced the translational repression of numerous innate immune mediators. Though the impact of SARS-CoV-2 on host mRNA translation was more subtle in primary airway cell cultures, we noted marked transcriptional and translational upregulation of inflammatory and innate immune responses and downregulation of processes involved in ciliated cell function. Together, these data provide new insight into how SARS-CoV-2 modulates innate host responses and highlight unique mechanisms for therapeutic intervention.

Characterization of structural and optical properties of Mn2+ -doped Zn2 GeO4 nanorods as an efficient green phosphor for solid-state lighting.

A series of Mn2+ -doped zinc germinate ZGO:xMn2+ (x = 0-0.05) nanorods was synthesized successfully using a hydrothermal method. XRD revealed that crystal phases of the ZGO:xMn2+ were rhombohedral and in the R-3 space group. The Williamson-Hall equation was also used to explain the strain, nanocrystalline size, and stacking fault. Green LEDs were successfully fabricated by coating ZGO:Mn2+ nanorods onto UV-LED chips. For high color purity, CIE of the fabricated green LEDs were (0.2404, 0.5428), which made this material a promising candidate for fabrication of UV-based green LEDs.

Factors relating to mortality in septic patients in Vietnamese intensive care units from a subgroup analysis of MOSAICS II study.

Sepsis is the most common cause of in-hospital deaths, especially from low-income and lower-middle-income countries (LMICs). This study aimed to investigate the mortality rate and associated factors from sepsis in intensive care units (ICUs) in an LMIC. We did a multicenter cross-sectional study of septic patients presenting to 15 adult ICUs throughout Vietnam on the 4 days representing the different seasons of 2019. Of 252 patients, 40.1% died in hospital and 33.3% died in ICU. ICUs with accredited training programs (odds ratio, OR: 0.309; 95% confidence interval, CI 0.122-0.783) and completion of the 3-h sepsis bundle (OR: 0.294; 95% CI 0.083-1.048) were associated with decreased hospital mortality. ICUs with intensivist-to-patient ratio of 1:6 to 8 (OR: 4.533; 95% CI 1.621-12.677), mechanical ventilation (OR: 3.890; 95% CI 1.445-10.474) and renal replacement therapy (OR: 2.816; 95% CI 1.318-6.016) were associated with increased ICU mortality, in contrast to non-surgical source control (OR: 0.292; 95% CI 0.126-0.678) which was associated with decreased ICU mortality. Improvements are needed in the management of sepsis in Vietnam such as increasing resources in critical care settings, making accredited training programs more available, improving compliance with sepsis bundles of care, and treating underlying illness and shock optimally in septic patients.

Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) variants govern transmissibility, responsiveness to vaccination, and disease severity. In a screen for new models of SARS-CoV-2 infection, we identify human H522 lung adenocarcinoma cells as naturally permissive to SARS-CoV-2 infection despite complete absence of angiotensin-converting enzyme 2 (ACE2) expression. Remarkably, H522 infection requires the E484D S variant; viruses expressing wild-type S are not infectious. Anti-S monoclonal antibodies differentially neutralize SARS-CoV-2 E484D S in H522 cells as compared to ACE2-expressing cells. Sera from vaccinated individuals block this alternative entry mechanism, whereas convalescent sera are less effective. Although the H522 receptor remains unknown, depletion of surface heparan sulfates block H522 infection. Temporally resolved transcriptomic and proteomic profiling reveal alterations in cell cycle and the antiviral host cell response, including MDA5-dependent activation of type I interferon signaling. These findings establish an alternative SARS-CoV-2 host cell receptor for the E484D SARS-CoV-2 variant, which may impact tropism of SARS-CoV-2 and consequently human disease pathogenesis.

Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell.

Established in vitro models for SARS-CoV-2 infection are limited and include cell lines of non-human origin and those engineered to overexpress ACE2, the cognate host cell receptor. We identified human H522 lung adenocarcinoma cells as naturally permissive to SARS-CoV-2 infection despite complete absence of ACE2. Infection of H522 cells required the SARS-CoV-2 spike protein, though in contrast to ACE2-dependent models, spike alone was not sufficient for H522 infection. Temporally resolved transcriptomic and proteomic profiling revealed alterations in cell cycle and the antiviral host cell response, including MDA5-dependent activation of type-I interferon signaling. Focused chemical screens point to important roles for clathrin-mediated endocytosis and endosomal cathepsins in SARS-CoV-2 infection of H522 cells. These findings imply the utilization of an alternative SARS-CoV-2 host cell receptor which may impact tropism of SARS-CoV-2 and consequently human disease pathogenesis.

Network-Forming Liquids from Metal-Bis(acetamide) Frameworks with Low Melting Temperatures.

Molten phases of metal-organic networks offer exciting opportunities for using coordination chemistry principles to access liquids and glasses with unique and tunable structures and properties. Here, we discuss general thermodynamic strategies to provide an increased enthalpic and entropic driving force for reversible, low-temperature melting transitions in extended coordination solids and illustrate this approach through a systematic study of a series of bis(acetamide)-based networks with record-low melting temperatures. The low melting temperatures of these compounds are the result of weak coordination bonds, conformationally flexible bridging ligands, and weak electrostatic interactions between spatially separated cations and anions, which collectively reduce the enthalpy and increase the entropy of fusion. Through a combination of crystallography, spectroscopy, and calorimetry, enthalpic trends are found to be dictated by the strength of coordination bonds and hydrogen bonds within each compound, while entropic trends are strongly influenced by the degree to which residual motion and positional disorder are restricted in the crystalline state. Extended X-ray absorption fine structure (EXAFS) and pair distribution function (PDF) analysis of Co(bba)3[CoCl4] [bba = N,N'-1,4-butylenebis(acetamide)], which features a record-low melting temperature for a three-dimensional metal-organic network of 124 °C, provide direct evidence of metal-ligand coordination in the liquid phase, as well as intermediate- and extended-range order that support its network-forming nature. In addition, rheological measurements are used to rationalize differences in glass-forming ability and relaxation dynamics. These results provide new insights into the structural and chemical factors that influence the thermodynamics of melting transitions of extended coordination solids, as well as the structure and properties of coordination network-forming liquids.

A cloud platform for atomic pair distribution function analysis: PDFitc.

A cloud web platform for analysis and interpretation of atomic pair distribution function (PDF) data (PDFitc) is described. The platform is able to host applications for PDF analysis to help researchers study the local and nanoscale structure of nanostructured materials. The applications are designed to be powerful and easy to use and can, and will, be extended over time through community adoption and development. The currently available PDF analysis applications, structureMining, spacegroupMining and similarityMapping, are described. In the first and second the user uploads a single PDF and the application returns a list of best-fit candidate structures, and the most likely space group of the underlying structure, respectively. In the third, the user can upload a set of measured or calculated PDFs and the application returns a matrix of Pearson correlations, allowing assessment of the similarity between different data sets. structureMining is presented here as an example to show the easy-to-use workflow on PDFitc. In the future, as well as using the PDFitc applications for data analysis, it is hoped that the community will contribute their own codes and software to the platform.

The translational landscape of SARS-CoV-2 and infected cells.

SARS-CoV-2 utilizes a number of strategies to modulate viral and host mRNA translation. Here, we used ribosome profiling in SARS-CoV-2 infected model cell lines and primary airway cells grown at the air-liquid interface to gain a deeper understanding of the translationally regulated events in response to virus replication. We find that SARS-CoV-2 mRNAs dominate the cellular mRNA pool but are not more efficiently translated than cellular mRNAs. SARS-CoV-2 utilized a highly efficient ribosomal frameshifting strategy in comparison to HIV-1, suggesting utilization of distinct structural elements. In the highly permissive cell models, although SARS-CoV-2 infection induced the transcriptional upregulation of numerous chemokines, cytokines and interferon stimulated genes, many of these mRNAs were not translated efficiently. Impact of SARS-CoV-2 on host mRNA translation was more subtle in primary cells, with marked transcriptional and translational upregulation of inflammatory and innate immune responses and downregulation of processes involved in ciliated cell function. Together, these data reveal the key role of mRNA translation in SARS-CoV-2 replication and highlight unique mechanisms for therapeutic development.

A Simplified Quantitative Real-Time PCR Assay for Monitoring SARS-CoV-2 Growth in Cell Culture.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected millions within just a few months, causing severe respiratory disease and mortality. Assays to monitor SARS-CoV-2 growth in vitro depend on time-consuming and costly RNA extraction steps, hampering progress in basic research and drug development efforts. Here, we developed a simplified quantitative real-time PCR assay that bypasses viral RNA extraction steps and can monitor SARS-CoV-2 growth from a small amount of cell culture supernatants. In addition, we show that this approach is easily adaptable to numerous other RNA and DNA viruses. Using this assay, we screened the activities of a number of compounds that were predicted to alter SARS-CoV-2 entry and replication as well as HIV-1-specific drugs in a proof-of-concept study. We found that E64D (inhibitor of endosomal proteases cathepsin B and L) and apilimod (endosomal trafficking inhibitor) potently decreased the amount of SARS-CoV-2 RNA in cell culture supernatants with minimal cytotoxicity. Surprisingly, we found that the macropinocytosis inhibitor ethylisopropylamiloride (EIPA) similarly decreased SARS-CoV-2 RNA levels in supernatants, suggesting that entry may additionally be mediated by an alternative pathway. HIV-1-specific inhibitors nevirapine (a nonnucleoside reverse transcriptase inhibitor [NNRTI]), amprenavir (a protease inhibitor), and allosteric integrase inhibitor 2 (ALLINI-2) modestly inhibited SARS-CoV-2 replication, albeit the 50% inhibitory concentration (IC50) values were much higher than that required for HIV-1. Taking the data together, this simplified assay will expedite basic SARS-CoV-2 research, be amenable to mid-throughput screening assays (i.e., drug, CRISPR, small interfering RNA [siRNA], etc.), and be applicable to a broad number of RNA and DNA viruses.IMPORTANCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of the coronavirus disease 2019 (COVID-19) pandemic, is continuing to cause immense respiratory disease and social and economic disruptions. Conventional assays that monitor SARS-CoV-2 growth in cell culture rely on costly and time-consuming RNA extraction procedures, hampering progress in basic SARS-CoV-2 research and development of effective therapeutics. Here, we developed a simple quantitative real-time PCR assay to monitor SARS-CoV-2 growth in cell culture supernatants that does not necessitate RNA extraction and that is as accurate and sensitive as existing methods. In a proof-of-concept screen, we found that E64D, apilimod, EIPA, and remdesivir can substantially impede SARS-Cov-2 replication, providing novel insight into viral entry and replication mechanisms. In addition, we show that this approach is easily adaptable to numerous other RNA and DNA viruses. This simplified assay will undoubtedly expedite basic SARS-CoV-2 and virology research and be amenable to use in drug screening platforms to identify therapeutics against SARS-CoV-2.

A facile Q-RT-PCR assay for monitoring SARS-CoV-2 growth in cell culture.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of the ongoing COVID-19 pandemic, has infected millions within just a few months and is continuing to spread around the globe causing immense respiratory disease and mortality. Assays to monitor SARS-CoV-2 growth depend on time-consuming and costly RNA extraction steps, hampering progress in basic research and drug development efforts. Here we developed a facile Q-RT-PCR assay that bypasses viral RNA extraction steps and can monitor SARS-CoV-2 replication kinetics from a small amount of cell culture supernatants. Using this assay, we screened the activities of a number of entry, SARS-CoV-2- and HIV-1-specific inhibitors in a proof of concept study. In line with previous studies which has shown that processing of the viral Spike protein by cellular proteases and endosomal fusion are required for entry, we found that E64D and apilimod potently decreased the amount of SARS-CoV-2 RNA in cell culture supernatants with minimal cytotoxicity. Surprisingly, we found that macropinocytosis inhibitor EIPA similarly decreased viral RNA in supernatants suggesting that entry may additionally be mediated by an alternative pathway. HIV-1-specific inhibitors nevirapine (an NNRTI), amprenavir (a protease inhibitor), and ALLINI-2 (an allosteric integrase inhibitor) modestly inhibited SARS-CoV-2 replication, albeit the IC 50 values were much higher than that required for HIV-1. Taken together, this facile assay will undoubtedly expedite basic SARS-CoV-2 research, be amenable to mid-throughput screens to identify chemical inhibitors of SARS-CoV-2, and be applicable to a broad number of RNA and DNA viruses.