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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Scanning the RBD-ACE2 molecular interactions in Omicron variant

The emergence of new SARS-CoV-2 variants poses a threat to the human population where it is difficult to assess the severity of a particular variant of the virus. Spike protein and specifically its receptor binding domain (RBD) which makes direct interaction with the ACE2 receptor of the human has shown prominent amino acid substitutions in most of the Variants of Concern. Here, in this work, by using all-atom molecular dynamics simulations we compare the interaction of Wild-type RBD/ACE2 receptor complex with that of the latest Omicron variant of the virus. We observed a very interesting diversification of the charge, dynamics and energetics of the protein complex formed upon mutations. These results would help us in understanding the molecular basis of binding of the Omicron variant with that of SARS-CoV-2 Wild-type.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Rare, convergent antibodies targeting the stem helix broadly neutralize diverse betacoronaviruses

Humanity has faced three recent outbreaks of novel betacoronaviruses, emphasizing the need to develop approaches that broadly target coronaviruses. Here, we identify 55 monoclonal antibodies from COVID-19 convalescent donors that bind diverse betacoronavirus spike proteins. Most antibodies targeted an S2 epitope that included the K814 residue and were non-neutralizing. However, 11 antibodies targeting the stem helix neutralized betacoronaviruses from different lineages. Eight antibodies in this group, including the six broadest and most potent neutralizers, were encoded by IGHV1-46 and IGKV3-20. Crystal structures of three antibodies of this class at 1.5–1.75-Å resolution revealed a conserved mode of binding. COV89-22 neutralized SARS-CoV-2 variants of concern including Omicron BA.4/5 and limited disease in Syrian hamsters. Collectively, these findings identify a class of IGHV1-46/IGKV3-20 antibodies that broadly neutralize betacoronaviruses by targeting the stem helix but indicate these antibodies constitute a small fraction of the broadly reactive antibody response to betacoronaviruses after SARS-CoV-2 infection.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Multi-omics of NET formation and correlations with CNDP1, PSPB, and L-cystine levels in severe and mild COVID-19 infections

We report that we performed a multi-omics analysis of an immunologically naïve SARS-CoV-2 clinical cohort to characterize overall changes in plasma among control (uninfected), mild, and severe infections. A comparison of healthy controls and patient samples showed activation of neutrophil degranulation pathways. Consistent with this observation, we characterized neutrophil extracellular trap (NET) complexes that were partially initiated in a subset of the mild infections (showing partially formed NETs) and fully-formed NETs in a subset of severe infections (containing multiple NET proteins in individual patient samples). As a potential mechanism to suppress NET formation, multiple redox enzymes were elevated in the mild and severe population. Analysis of metabolites from the same cohort showed a 24 and 60-fold elevation in plasma L-cystine, the oxidized form of cysteine and substrate of the powerful antioxidant glutathione in mild and severe patients, respectively. Unique to patients with mild infections, the carnosine dipeptidase modifying enzyme (CNDP1) was up-regulated. The strong protein and metabolite oxidation signatures suggest multiple compensatory pathways working to suppress both free radical and NET formation in SARS-CoV-2 infections.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Neutralizing monoclonal antibodies elicited by mosaic RBD nanoparticles bind conserved sarbecovirus epitopes

Increased immune evasion by SARS-CoV-2 variants of concern highlights the need for new therapeutic neutralizing antibodies. Immunization with nanoparticles co-displaying spike receptor-binding domains (RBDs) from eight sarbecoviruses (mosaic-8 RBD-nanoparticles) efficiently elicits cross-reactive polyclonal antibodies against conserved sarbecovirus RBD epitopes. Here, we identified monoclonal antibodies (mAbs) capable of cross-reactive binding and neutralization of animal sarbecoviruses and SARS-CoV-2 variants by screening single mouse B cells secreting IgGs that bind two or more sarbecovirus RBDs. Single-particle cryo-EM structures of antibody-spike complexes, including a Fab-Omicron complex, mapped neutralizing mAbs to conserved class 1/4 RBD epitopes. Structural analyses revealed neutralization mechanisms, potentials for intra-spike trimer cross-linking by IgGs, and induced changes in trimer upon Fab binding. In addition, we identified a mAb-resembling Bebtelovimab, an EUA-approved human class 3 anti-RBD mAb. These results support using mosaic RBD-nanoparticle vaccination to generate and identify therapeutic pan-sarbecovirus and pan-variant mAbs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Dynamic Profiling of β-Coronavirus 3CL Mpro Protease Ligand-Binding Sites

β-coronavirus (CoVs) alone has been responsible for three major global outbreaks in the 21st century. The current crisis has led to an urgent requirement to develop therapeutics. Even though a number of vaccines are available, alternative strategies targeting essential viral components are required as a backup against the emergence of lethal viral variants. One such target is the main protease (Mpro) that plays an indispensable role in viral replication. The availability of over 270 Mpro X-ray structures in complex with inhibitors provides unique insights into ligand–protein interactions. Herein, we provide a comprehensive comparison of all nonredundant ligand-binding sites available for SARS-CoV2, SARS-CoV, and MERS-CoV Mpro. Extensive adaptive sampling has been used to investigate structural conservation of ligand-binding sites using Markov state models (MSMs) and compare conformational dynamics employing convolutional variational auto-encoder-based deep learning. Our results indicate that not all ligand-binding sites are dynamically conserved despite high sequence and structural conservation across β-CoV homologs. This highlights the complexity in targeting all three Mpro enzymes with a single pan inhibitor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Light-Induced Transformation of Virus-Like Particles on TiO 2

Titanium dioxide (TiO 2 ) shows significant potential as a self-cleaning material to inactivate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and prevent virus transmission. This study provides insights into the impact of UV-A light on the photocatalytic inactivation of adsorbed SARS-CoV-2 virus-like particles (VLPs) on a TiO 2 surface at the molecular and atomic levels. X-ray photoelectron spectroscopy, combined with density functional theory calculations, reveals that spike proteins can adsorb on TiO 2 predominantly via their amine and amide functional groups in their amino acids blocks. We employ atomic force microscopy and grazing-incidence small-angle X-ray scattering (GISAXS) to investigate the molecular-scale morphological changes during the inactivation of VLPs on TiO 2 under light irradiation. Notably, in situ measurements reveal photoinduced morphological changes of VLPs, resulting in increased particle diameters. These results suggest that the denaturation of structural proteins induced by UV irradiation and oxidation of the virus structure through photocatalytic reactions can take place on the TiO 2 surface. The in situ GISAXS measurements under an N 2 atmosphere reveal that the virus morphology remains intact under UV light. This provides evidence that the presence of both oxygen and UV light is necessary to initiate photocatalytic reactions on the surface and subsequently inactivate the adsorbed viruses. The chemical insights into the virus inactivation process obtained in this study contribute significantly to the development of solid materials for the inactivation of enveloped viruses.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Self-Assembly Interactions in Magnetite-Coated Cellulose Nanocrystals: Implications for Magnetic Hyperthermia Applications

Magnetic cellulose nanocrystal (MCNC) nanocomposites are promising sustainable and biocompatible platforms for magnetic hyperthermia; however, the molecular mechanisms governing Fe 3 O 4 adsorption and deposition onto CNCs remain poorly understood. Here, sulfated (S-CNC) and TEMPO-oxidized CNCs (T-CNC) were used to prepare nanocomposites at 1:2 and 1:4 CNC:Fe 3 O 4 mass ratios, enabling a systematic evaluation of how surface chemistry and nanoparticle loading dictate interfacial interactions and magneto-colloidal behavior. Bare magnetite nanoparticles were 21 ± 5 nm by TEM but grew to 144 ± 18 in the DLS measurement at pH 7. The S-CNC nanocomposites had hydrodynamic sizes between 144 and 210 nm, not much larger than the 140 nm long CNC rods, suggesting an enhanced dispersion stability compared to Fe3O4 alone. X-ray photoelectron spectroscopy combined with density functional theory revealed that −OH and −COOH groups drive electrostatic adsorption with charge transfer from Fe 3 O 4 to the CNC surface, while T-CNCs showed more favorable adsorption energies and evidence of covalent Fe−O bonding. Vibrating sample magnetometry demonstrated superparamagnetic behavior for all samples, with S-CNC/Fe 3 O 4 1:4 and 1:2 displaying saturation magnetizations of 78 and 77 emu/g-Fe 3 O 4 , close to the 83 emu/g of bare magnetite. The T-CNC composites showed lower (60 and 66 emu/g-Fe3O4) saturation magnetizations. Zero-field-cooled/field-cooled measurements resulted in a blocking temperature of 112 K for all samples, except T-CNC/Fe 3 O 4 1:2 (100 K). Magnetic hyperthermia studies revealed that specific absorption rate (SAR) increased with field strength and Fe 3 O 4 content; however, S-CNC/Fe 3 O 4 (1:2) achieved the highest intrinsic SAR per gram of Fe 3 O 4 (649 W/g-Fe 3 O 4 ) likely due to its anisotropy and fast magnetic relaxation. Cytotoxicity assays confirmed that all nanocomposites were nontoxic toward mammalian cells. These results establish quantitative structure−property relationships between CNC surface chemistry, interfacial bonding mechanisms, and magnetic heating performance, providing a foundation for rational design of biocompatible magnetic nanocomposites for hyperthermia and related applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

S -Adenosylhomocysteine Analogs Selectively Suppress Pan-Coronavirus Replication by Inhibition of nsp14 Methyltransferase

To address the ongoing threat of SARS-CoV-2 and potential emergence of novel coronaviruses, we employed a comprehensive strategy to identify and synthesize inhibitors of coronavirus methyltransferases with chemical analogs of S-adenosylhomocysteine (SAH). Two analogs, designated 4h and 4p, inhibit both mouse hepatitis virus and SARS-CoV-2 replication. Compound 4p was the most potent with half-maximal inhibition of biochemical activity at 0.2 μM and antiviral activity at ∼20 μM. This compound also has low cytotoxicity and preferentially inhibits nsp14 over nsp16 and human methyltransferases. Furthermore, molecular docking based on a newly determined crystal structure of the apo nsp16−nsp10 complex predicts that 4p occupies both the Sadenosylmethione and Gppp binding pockets of nsp14 and nsp16. Selectivity of 4p for nsp14 is likely due to the enhanced structural stability of the nsp14 binding pocket relative to nsp16. These findings highlight SAH analogs as scaffolds for pan-coronavirus therapeutics and underscore the value of structure-guided design in antiviral drug discovery.

Coronavirus↗
DOE OSTI2023

Fully synthetic platform to rapidly generate tetravalent bispecific nanobody–based immunoglobulins

Nanobodies bind a target antigen with a kinetic profile similar to a conventional antibody, but exist as a single heavy chain domain that can be readily multimerized to engage antigen via multiple interactions. Presently, most nanobodies are produced by immunizing camelids; however, platforms for animal-free production are growing in popularity. Here, we describe the development of a fully synthetic nanobody library based on an engineered human V H 3-23 variable gene and a multispecific antibody-like format designed for biparatopic target engagement. To validate our library, we selected nanobodies against the SARS-CoV-2 receptor–binding domain and employed an on-yeast epitope binning strategy to rapidly map the specificities of the selected nanobodies. We then generated antibody-like molecules by replacing the V H and V L domains of a conventional antibody with two different nanobodies, designed as a molecular clamp to engage the receptor-binding domain biparatopically. The resulting bispecific tetra-nanobody immunoglobulins neutralized diverse SARS-CoV-2 variants with potencies similar to antibodies isolated from convalescent donors. Subsequent biochemical analyses confirmed the accuracy of the on-yeast epitope binning and structures of both individual nanobodies, and a tetra-nanobody immunoglobulin revealed that the intended mode of interaction had been achieved. This overall workflow is applicable to nearly any protein target and provides a blueprint for a modular workflow for the development of multispecific molecules.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Comparing multi-source urban flood indicators: satellite, simulation, and citizen-reported data

Urban flooding arises from complex mechanisms, making it challenging to capture accurately with a single detection method. This study evaluates three complementary approaches to detect flooding across three Chicago neighborhoods: (i) Sentinel-1 synthetic aperture radar (SAR), offering weather-independent, high-resolution (10 m) imagery of surface inundation; (ii) the storm water management model (SWMM), simulating combined sewer overflow and drainage performance; and (iii) citizen-generated 311 service requests, capturing observed flooding impacts. By analyzing six storms ranging from severe to mild, we examine how each source uniquely contributes to identifying urban flood events. SAR imagery effectively identifies standing water but can miss brief flooding due to satellite revisit constraints. SWMM provides detailed insights into system-wide drainage behavior yet may underestimate localized street-level flooding. Meanwhile, 311 calls reflect real-world flooding impacts but are vulnerable to underreporting. Statistical overlap analysis highlights chronic flood hotspots repeatedly identified across multiple detection methods, indicating persistent infrastructure and topographic vulnerabilities. Temporal analysis further reveals that while SWMM flooding aligns closely with rainfall peaks, 311 calls typically precede or persist beyond these peaks. Our findings emphasize the value of using satellite observations, hydrological modeling, and resident-reported data in a complementary manner to better interpret patterns in flood timing, severity, and spatial distribution—providing insights that can inform targeted infrastructure improvements and contribute to urban flood resilience planning.

311↗
DOE OSTI2021

Viral Load Kinetics of Severe Acute Respiratory Syndrome Coronavirus 2 in Hospitalized Individuals With Coronavirus Disease 2019

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) kinetics remain understudied, including the impact of remdesivir. In hospitalized individuals, peak sputum viral load occurred in week 2 of symptoms, whereas viremia peaked within 1 week of symptom-onset, suggesting early systemic seeding of SARS-CoV-2. Remdesivir treatment was associated with faster viral decay.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Dysregulation of lung epithelial cell homeostasis and immunity contributes to Middle East respiratory syndrome coronavirus disease severity

Coronaviruses (CoV) emerge suddenly from animal reservoirs to cause novel diseases in new hosts. Discovered in 2012, the Middle East respiratory syndrome coronavirus (MERS-CoV) is endemic in camels in the Middle East and is continually causing local outbreaks and epidemics. While all three newly emerging human CoVs from the past 20 years (SARS-CoV, SARS-CoV-2, and MERS-CoV) cause respiratory disease, each CoV has unique host interactions that drive differential pathogeneses. To better understand the virus and host interactions driving lethal MERS-CoV infection, we performed a longitudinal multi-omics analysis of sublethal and lethal MERS-CoV infection in mice. Significant differences were observed in body weight loss, virus titers, and acute lung injury among lethal and sub-lethal virus doses. Virus-induced apoptosis of type I and II alveolar epithelial cells suggests that loss or dysregulation of these key cell populations was a major driver of severe disease. Omics analysis suggested differential pathogenesis was multi-factorial with clear differences among innate and adaptive immune pathways as well as those that regulate lung epithelial homeostasis. Infection of mice lacking functional T and B cells showed that adaptive immunity was important in controlling viral replication but also increased pathogenesis. In summary, we provide a high-resolution host response atlas for MERS-CoV infection and disease severity. Multi-omics studies of viral pathogenesis offer a unique opportunity to not only better understand the molecular mechanisms of disease but also to identify genes and pathways that can be exploited for therapeutic intervention all of which is important for our future pandemic preparedness.

MERS-CoV↗
DOE OSTI2021

Detection of significant antiviral drug effects on COVID-19 with reasonable sample sizes in randomized controlled trials: A modeling study

Development of an effective antiviral drug for Coronavirus Disease 2019 (COVID-19) is a global health priority. Although several candidate drugs have been identified through in vitro and in vivo models, consistent and compelling evidence from clinical studies is limited. The lack of evidence from clinical trials may stem in part from the imperfect design of the trials. We investigated how clinical trials for antivirals need to be designed, especially focusing on the sample size in randomized controlled trials. A modeling study was conducted to help understand the reasons behind inconsistent clinical trial findings and to design better clinical trials. We first analyzed longitudinal viral load data for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) without antiviral treatment by use of a within-host virus dynamics model. The fitted viral load was categorized into 3 different groups by a clustering approach. Comparison of the estimated parameters showed that the 3 distinct groups were characterized by different virus decay rates (p-value < 0.001). The mean decay rates were 1.17 d -1 (95% CI: 1.06 to 1.27 d -1 ), 0.777 d -1 (0.716 to 0.838 d -1 ), and 0.450 d -1 (0.378 to 0.522 d -1 ) for the 3 groups, respectively. Such heterogeneity in virus dynamics could be a confounding variable if it is associated with treatment allocation in compassionate use programs (i.e., observational studies). Subsequently, we mimicked randomized controlled trials of antivirals by simulation. An antiviral effect causing a 95% to 99% reduction in viral replication was added to the model. To be realistic, we assumed that randomization and treatment are initiated with some time lag after symptom onset. Using the duration of virus shedding as an outcome, the sample size to detect a statistically significant mean difference between the treatment and placebo groups (1:1 allocation) was 13,603 and 11,670 (when the antiviral effect was 95% and 99%, respectively) per group if all patients are enrolled regardless of timing of randomization. The sample size was reduced to 584 and 458 (when the antiviral effect was 95% and 99%, respectively) if only patients who are treated within 1 day of symptom onset are enrolled. We confirmed the sample size was similarly reduced when using cumulative viral load in log scale as an outcome. We used a conventional virus dynamics model, which may not fully reflect the detailed mechanisms of viral dynamics of SARS-CoV-2. The model needs to be calibrated in terms of both parameter settings and model structure, which would yield more reliable sample size calculation. In this study, we found that estimated association in observational studies can be biased due to large heterogeneity in viral dynamics among infected individuals, and statistically significant effect in randomized controlled trials may be difficult to be detected due to small sample size. The sample size can be dramatically reduced by recruiting patients immediately after developing symptoms. We believe this is the first study investigated the study design of clinical trials for antiviral treatment using the viral dynamics model.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Using Deep Mutational Data and Machine Learning to Guide Outbreak and Pandemic Response

A significant fraction of pathogens known to infect humans originate in non-human (zoonotic) hosts (Taylor, Latham, and Woolhouse 2001), and new and emerging pathogens continue to spill over into the human population more frequently at an alarming rate (e.g., SARS, MERS, Cholera, etc.). The recent outbreaks of Ebola virus in West Africa and the ongoing SARS-CoV-2 pandemic demonstrate the need for rapid and reliable assessments of viral phenotype information to help inform scientists and policy makers how best to control the spread of disease. Further understanding of the virus pathogenic evolutionary space and potential trajectory could guide appropriate control measures to limit the spread of a new virus throughout the local and global human population.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Drugsniffer: An Open Source Workflow for Virtually Screening Billions of Molecules for Binding Affinity to Protein Targets

The SARS-CoV2 pandemic has highlighted the importance of efficient and effective methods for identification of therapeutic drugs, and in particular has laid bare the need for methods that allow exploration of the full diversity of synthesizable small molecules. While classical high-throughput screening methods may consider up to millions of molecules, virtual screening methods hold the promise of enabling appraisal of billions of candidate molecules, thus expanding the search space while concurrently reducing costs and speeding discovery. Here, we describe a new screening pipeline, called drugsniffer, that is capable of rapidly exploring drug candidates from a library of billions of molecules, and is designed to support distributed computation on cluster and cloud resources. As an example of performance, our pipeline required ~40,000 total compute hours to screen for potential drugs targeting three SARS-CoV2 proteins among a library of ~3.7 billion candidate molecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Antiviral Effect of Antimicrobial Peptoid TM9 and Murine Model of Respiratory Coronavirus Infection

New antiviral agents are essential to improving treatment and control of SARS-CoV-2 infections that can lead to the disease COVID-19. Antimicrobial peptoids are sequence-specific oligo-N-substituted glycine peptidomimetics that emulate the structure and function of natural antimicrobial peptides but are resistant to proteases. We demonstrate antiviral activity of a new peptoid (TM9) against the coronavirus, murine hepatitis virus (MHV), as a closely related model for the structure and antiviral susceptibility profile of SARS-CoV-2. This peptoid mimics the human cathelicidin LL-37, which has also been shown to have antimicrobial and antiviral activity. In this study, TM9 was effective against three murine coronavirus strains, demonstrating that the therapeutic window is large enough to allow the use of TM9 for treatment. All three isolates of MHV generated infection in mice after 15 min of exposure by aerosol using the Madison aerosol chamber, and all three viral strains could be isolated from the lungs throughout the 5-day observation period post-infection, with the peak titers on day 2. MHV-A59 and MHV-A59-GFP were also isolated from the liver, heart, spleen, olfactory bulbs, and brain. These data demonstrate that MHV serves as a valuable natural murine model of coronavirus pathogenesis in multiple organs, including the brain.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Protection against Chemical Warfare Agents and Biological Threats Using Metal–Organic Frameworks as Active Layers

The SARS-CoV-2 pandemic outbreak and the unfortunate misuse of toxic chemical warfare agents (CWAs) highlight the importance of developing functional materials to protect against these chemical and pathogen threats. Metal–organic frameworks (MOFs), which comprise a tunable class of crystalline porous materials built from inorganic nodes and organic linkers, have emerged as a class of heterogeneous catalysts capable of rapid detoxification of multiple classes of these harmful chemical or biological hazards. In particular, zirconium-based MOFs (Zr-MOFs) feature Lewis acidic nodes that serve as active sites for a wide range of catalytic reactions, including the hydrolysis of organophosphorus nerve agents within seconds in basic aqueous solutions. In addition, postsynthetic modification of Zr-MOFs enables the release of active species capable of reacting with and deactivating harmful pathogens. Despite this impressive performance, utilizing Zr- MOFs in powder form is not practical for application in masks or protective uniforms. To address this challenge, our team sought to develop MOF/fiber composite systems that could be adapted for use under realistic operating conditions to protect civilians, military personnel, and first responders from harmful pathogens and chemical warfare agents. Over the last several years, our group has designed and fabricated reactive and biocidal MOF/fiber composites that effectively capture and deactivate these toxic species. In this Account, we describe the evolution of these porous and reactive MOF/fiber composites and focus on key design challenges and considerations. First, we devised a scalable method for the integration of Zr-MOFs onto textile substrates using aqueous precursor solutions and without using pretreated textiles, highlighting the potential scalability of this method. Moving beyond standard textiles, we also developed a microbial synthesis strategy to prepare hierarchically porous MOF/bacterial cellulose nanofiber composite sponges that can both capture and detoxify nerve agents when exposed to contaminated gas flows. The mass loading of the MOF in the nanofibrous composite sponge is up to 90%, affording higher work capacities compared to those of textile-fiber-based composites with relatively lower MOF loadings. Next, we demonstrated that heterogeneous polymeric bases are suitable replacements for volatile liquid bases typically used in solution-phase reactions, and we showed that these composite systems are capable of effectively hydrolyzing nerve agents in the solid state by using only water that is present as humidity. Moreover, incorporating a reactive dye precursor into the composite affords a dual function sensing and detoxifying material that changes color from white to orange upon reaction with the byproduct following nerve agent hydrolysis, demonstrating the versatility of this platform for use in decontamination applications. We then created chlorine-loaded MOF/fiber composites that act as biocidal and reactive textiles that are capable of not only detoxifying sulfur-mustard-based chemical warfare agents and simulants but also deactivating both bacteria and the SARS-CoV-2 virus within minutes of exposure. Lastly, we synthesized a mixed-metal Ti/Zr-MOF coating on cotton fibers to afford a photoactive biocidal cloth that shows fast and broad-spectrum biocidal performance against viruses and Gram-positive and Gram-negative bacteria under visible light irradiation. Given the tunable, multifunctional nature of these MOF/fiber composites, we believe that this Account will offer new insights for the rational design and preparation of functional MOF/fiber composites and pave the way toward the development of next-generation reactive and protective textiles.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Evaluation of the Impact of Concentration and Extraction Methods on the Targeted Sequencing of Human Viruses from Wastewater

Sequencing human viruses in wastewater is challenging due to their low abundance compared to the total microbial background. This study compared the impact of four virus concentration/extraction methods (Innovaprep, Nanotrap, Promega, and Solids extraction) on probe-capture enrichment for human viruses followed by sequencing. Different concentration/extraction methods yielded distinct virus profiles. Innovaprep ultrafiltration (following solids removal) had the highest sequencing sensitivity and richness, resulting in the successful assembly of several near-complete human virus genomes. However, it was less sensitive in detecting SARS-CoV-2 by digital polymerase chain reaction (dPCR) compared to Promega and Nanotrap. Across all preparation methods, astroviruses and polyomaviruses were the most highly abundant human viruses, and SARS-CoV-2 was rare. These findings suggest that sequencing success can be increased using methods that reduce nontarget nucleic acids in the extract, though the absolute concentration of total extracted nucleic acid, as indicated by Qubit, and targeted viruses, as indicated by dPCR, may not be directly related to targeted sequencing performance. Further, using broadly targeted sequencing panels may capture viral diversity but risks losing signals for specific low-abundance viruses. Overall, this study highlights the importance of aligning wet lab and bioinformatic methods with specific goals when employing probe-capture enrichment for human virus sequencing from wastewater.

59 BASIC BIOLOGICAL SCIENCES↗