Symposium F.GI01—Special Symposium on Materials Approaches for Tackling COVID-19

COVID-19 has raised serious global public health concerns. The causative agent, SARS-CoV-2, has found to be environmentally persistent, and it can be transmitted through droplets or aerosols from an infected person and indirect contact via fomites. Nanotechnology has emerged as a promising tool for fighting against COVID-19, including but not limited to disease diagnosis, drug delivery, vaccine development, and pathogen detection and inactivation. In this talk, we will highlight recent progresses in controlling and inactivating pathogens in different environmental media, including SARS-CoV-2, by harnessing the power of nanotechnology. Specifically, electrospun nanofibrous membranes are developed to capture SARS-CoV-2-laden aerosols and they can be used for HVAC filters and masks/respirators. Photocatalysis that takes the advantage of environmental light can be implemented for effectively inactivating persistent pathogens on contact surfaces at an ambient condition.

Synthetic biology is bringing together engineers, physicists and biologists to model, design and construct biological circuits out of proteins, genes and other bits of DNA, and to use these circuits to rewire and reprogram organisms as well as create novel biomaterials. These biological circuits, living materials and re-engineered organisms are going to change our lives in the coming years, leading to cheaper drugs, rapid diagnostic tests, and synthetic probiotics to treat infections and a range of complex diseases. In this talk, we highlight recent efforts to create synthetic gene networks and programmable cells as new classes of diagnostics, therapeutics and vaccines for fighting pathogens, including SARS-CoV-2.

Facial masks are among the most important personal protection equipment to fight COVID-19. This talk covers our exciting progress related to facial masks including: 1) We utilized X-ray tomography and deep learning to perform 3D imaging and analysis of facial masks and the particle filtration to provide critical understanding how facial masks work. 2) We developed heating methods (dry and humid) as the most efficiency methods to disinfect N-95 level facial masks while maintaining their high filtration efficiency for over 20 times. 3) We studied a variety of household textiles and identify the most effective ones for homemade masks; 4) We propose that nanofiber filtration technology would afford the next generation high performance facial masks with high filtration efficiency and great breathability.

The disruption of the COVID-19 global pandemic has caused severe supply-chain disruption within several industries, to include food and medical devices. Due to supply shortages, focusing on medical devices, innovative solutions in additive manufacturing have been expedited through FDA approval, specifically in the arena of nasopharyngeal (NP) swabs, to increase testing rates of suspected COVID-19 patients. Further, there are other innovations, such as touchless door handles, allowing individuals to avoid hand contact with entry points if desired, leading to more hygienic interactions with public spaces. These provide strong examples that 3D printing can provide end-use products beyond prototyping. However, like many such manufacturing processes, additional processing techniques are required to produce the end-use products. The technology leading 3D printed NP swabs are SLA/DLP printers with acrylic based resins. This chemistry exhibits many drawbacks including both poor lubrication that leads to patient discomfort as well as less than desired wettability with specimens of patient sputum. This study investigated and screened biocompatible and hydrophilic coatings that may be applied to NP swabs in post-processing to increase lubrication and improve upon specimen collection quantity. Notably, the study was conducted during COVID lockdown which offers some additional supply chain learnings. To this end, a biocompatible modified poly(vinyl alcohol) (PVA) coating was applied to a 3D printed swab with a current marketed NP swab printing material already in use. The coating results showed an improvement in wettability as demonstrated by a 43.9% lowering of contact angle and a 39.3% improvement of specimen collection using synthetic saliva. This test case study was completed to help provide an additional solution to the manufacturing bottleneck for NP swabs. Additionally some further COVID case studies that are enabled by 3D printing will be briefly highlighted.

Electrospray deposition (ESD) is a well-established technique for the creation of thin films from the spray of highly-charged droplets loaded with the materials to be deposited. While a majority of ESD research has focused on droplet evolution in air, the dissipation of charge on arrival at the substrate is critical in determining the macro- and micro-scale morphology of the final spray. Recently, we have categorized various modes of ESD, including self-limiting electrospray deposition (SLED). In SLED, specific manipulation of the electrostatic repulsion, hydrodynamic forces, and evaporation kinetics can be employed to conformally cover 3D architectures with microcoatings. The generated coatings are hierarchical, possessing either nanoshell or nanoparticle microstructure. The initial demonstrations of SLED employed single glassy polymers as the solutes and simple cm-scale geometries as substrates. Here, I will discuss opportunities to create bioactive conformal coatings on medically-relevant architectures by employing blending, self-assembly, and complex geometries. Specifically, we explore coating transdermal microneedles with blends of DNA vaccines and rapid-dissolving matrices as a high-efficiency, scalable alternative to dip or inkjet coating. We demonstrate that we can deposit up to 70 wt% viable coatings of DNA in a sugar matrix that quickly dissolve upon insertion into the skin and show expression of GFP (pEGFP-N1). This method is compatible with rapid continuous manufacturing and is a route to shelf-stable, low-training vaccination administration for the current and future pandemic crises.

The personal protective equipment (PPE) may help reduce the risk of infection of the front-line healthcare workers of COVID-19 patients and others but the virus in aerosols, PPE and other materials’ surfaces may also cause infections^1,2. Studying the dynamics of the binding of SARS-CoV-2 spike glycoprotein (S-protein) to various substrates such as polylactic acid (PLA), the common material used in PPE, by in silico and in vitro experiments is essential. The S-protein, the key receptor for binding and promoting entry to host cells, is the main subject of our study that correlates in silico and in vitro data for validating the analysis of guidelines for improving PPE and other protection measures.
For in silico experiment, GROMACS is used for the MD simulations that are carried out at the reference room temperature (297K). The initial structure of the S-protein is obtained from the Protein Data Bank (PDB: 6VXX). CHARMM22/CMAP is used as the force field to perform MD for 200 ns for the structural relaxation of the S-protein in the NPT ensemble in the water system. PLA substrate is built with repeating optimized unit cells, where each unit cell is made of a set of lactic acid monomer which is generated using AVOGADRO and LigParGen. The structure of the PLA sheet is relaxed in a vacuum box in the NVT ensemble using OPLS-AA. To achieve the desired structure of the sheet, additional relaxation is performed in the NVT ensemble with CHARMM36. The well-relaxed S-protein and the PLA sheet are placed in a water box of size 21×27×21 nm³ and the initial distance between two species is set to 0.8 nm. CHARMM36 is adapted to this system and Van der Waals radii of the carbon atom are increased to 0.51 nm to prevent the H2O molecules from erroneously slipping into the PLA substrate. The substrate is restrained during the equilibriums. The NPT production run is carried and the RMSD of the S-protein and the system trajectory are monitored to ensure the stability of the system. For in vitro experiment, the H1N1 is used as an alternative to the SARS-CoV-2 due to the laboratory restrictions. The viruses are placed on a plate and the plate is left at room temperature (297K) for an arbitrary period.
The relaxed S-protein-PLA system allows us to do an analysis of binding by i) counting the number of the atomic contacts among S-protein and PLA atoms and quantify the binding intensity. ii) calculating the binding force as a function of time to extract the binding dynamics. The analysis of in vitro experiment is done by washing the virus adhered to the plate with water every arbitrary period. The number of remaining viruses on the plate is counted accordingly and the results are plotted over time. Finally, both in silico and in vitro data are correlated with statistical tools and both results are cross-validated.
The data we obtain from our in silico and in vitro experiments provide a vital understanding of the binding dynamics of the protein and the guidelines for the protection of the contagion. We will expand our research to a matrix of various environmental conditions including temperature, pH values, and salinities on various substrates including inorganic, organic, and living cells, beyond our current studies with only one temperature (297K) and one material (PLA). In addition to understanding the elusive virus-substrate properties for the S-protein, our methodology and the resulting platform can be extended to the study of other viruses and substrates at other conditions.

The project is supported by OVPR&IEDM COVID-19 Grant and SUNY-IBM Consortium Award.

¹ van Doremalen, Neeltje et al. “Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1.” The New England journal of medicine vol. 382,16 (2020): 1564-1567. doi:10.1056/NEJMc2004973
² Vasickova, P. et al. “Issues Concerning Survival of Viruses on Surfaces.” Food and Environmental Virology vol. 2,1 (2010): 24–34. doi:10.1007/s12560-010-9025-6

With the COVID-19 pandemic, we face a global health crisis not seen since the influenza pandemic of 1918. It is believed that the transmission of COVID-19 is thought to occur through respiratory droplets. As such, current CDC guidelines recommend using N95 masks for healthcare providers managing the care of patients infected with SARS-CoV-2 or persons under investigation (PUI) for COVID-19. The shortage of N95 style masks that could effectively protect health care professionals against harmful pathogens is of critical need in halting the current pandemic's trajectory and containing future outbreaks.

Using modified halloysite nanotubes (HNTs), we manufactured two products that work in conjunction with each other. We applied a simple, novel, and effective electrodeposition method for coating the surfaces of HNTs with metal nanoparticles (copper, silver, and zinc). Each metal is known to possess potent antiviral and antimicrobial properties. Metal-coated HNTs (mHNTs) were then added to polylactic acid and extruded to form a mHNT/PLA 3D printer filament. Furthermore, the halloysite's inner lumen was vacuum loaded with an additional antibacterial agent before the extrusion process.

Our antimicrobial/antiviral mHNT/polymer composite 3D printer filament was used to fabricate an N95-style mask with an interchangeable filter with surfaces that will deactivate a virus and reduce or eliminate adhesion, prevent bacterial growth, and reduce deadly infections. Antibacterial studies were conducted using methods that tested the efficacy of our design in a liquid medium and as a surface. Testing discs were 3D printed using the antimicrobial polymer composite. E. coli and S. aureus were the bacteria used in our experiments as they represent fast-growing gram-positive and gram-negative bacteria. The samples containing non-doped mHNTs showed a marked inhibition in the growth of both bacteria. However, the samples containing doped mHNTs showed an even greater ability to inhibit bacterial growth.

The filter respirator was made using the same ratio of PLA to mHNTs. Once dissolved in the solvent, the mixture was sprayed onto sterile gauze using a commercially available airbrush. Following the blow spraying of the gauze, the new filter was allowed to dry before another layer of treated gauze was added to the filter to make a three-layer sandwich consisting of gauze, blow spun antimicrobial fibers, and gauze. Simultaneously, the mask can be sanitized by alcohol or hydrogen peroxide solution, or UV light radiation and reused. The National Institute for Occupational Safety and Health (NIOSH) guidelines require that a mask must be able to protect people with different facial features. Our mask can be form-fitted to an individual's unique facial features due to our mask’s unique design. Merely placing the mask in warm water will momentarily make the mask moldable. Once cooled, the shape is preserved for a custom fit. Additionally, masks were manufactured in smaller sizes that could accommodate children and young adults.

The technology developed for the respirator has additional uses. Utilizing the airbrushing method to cover a filter material, air-conditioning filters can be coated with the antimicrobial coating. Using preexisting air conditioning filters as a building platform, this technology can be used to keep areas such as hospitals, clean rooms, and quarantine areas free of contaminants. Moreover, the air can be filtered on its way out using a different filtration system to keep harmful pathogens from exiting those closed-off areas.

Future studies will include antiviral studies. We are confident in our mask and filter system's ability to perform as designed and eliminate the viruses promptly. Fit testing to become NIOSH certified will also be conducted. A qualitative study will rate the degree of discomfort the wearer experiences while wearing the mask for long periods, ranging between 4, 8, and 10 hours.

Coronavirus disease 19 (Covid-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, is the worst global pandemic of the 21st century to date, and continues to infect and kill many individuals worldwide. SARS-CoV-2 remains intact and contagious in small droplets (<5µm) and can be suspended in the air for up to three hours. Therefore, airborne isolation, room ventilation, and appropriate application of disinfectant might restrict aerosolspread of the virus. However, the virus-laden droplets that are too heavy to remain in the air would rather fall on nearby floors or surfaces, creating fomites (or contaminated surfaces). Recent studies have evaluated the stability of SARS-CoV-2 on different surfaces, and it was found that the virus could survive from 24h on cardboard to 2 days on stainless steel and wood and even to 7 days on outside of surgical masks. This indicates that the fomites can represent a considerable mode of transmission mainly in closed areas.

Nowadays, most experiments to synthesize and test antimicrobial/antiviral materials are based on trial and error, and often it is not known how the inhibitors act on the microorganism. In this work we will showcase how artificial intelligence andmachine learning methods could be used to speed the design and optimization of antimicrobial/antiviral surfaces. Using computational methods, namely electronic structure calculations combined with data analytics and machine learning algorithms, we build a model able to estimate the activity of pathogen inhibitors. We focus our attention on photocatalytic systems that can be tailored to give a balanced production of Reactive Oxygen Species (ROS) upon illumination while taking into consideration the cost associated with a large-scale deployment of this solution. We built an artificial intelligence model that is able to predict the rates of ROS production while varying the composition and properties of the photocatalyticsystem. The proposed candidate materials, predicted from the computational modeling, may find application for high touch surfaces to avoid fomite viral and bacterial transmission, and also as coating for air conditioning and air cleaning filters to mitigate the viral transmission via aerosol.

Objectives: The SARS-CoV-2 engulfs the world from tropical countries like India [1] at 51°C to cold supply chains [2, 3]at 3-4°C.Our molecular dynamics (MD) analysis of the temperature-dependent structural changes of the virus’ spike glycoprotein (S-protein) [4-6] help bridge the data gaps from in vitro experiments to viral transmission assessment. Our thermolability studies of the protein immersing in H2O, differing from most protein binding simulations as the percentage of drug bound or unbound fraction [7, 8], complement the sparse and inconsistent in vitro experiments with high-infectious virus cultivation [9-12]. Correlating the in vitro and in silico experiments allows us to establish a deep nueral network model for relating the virus’s survival time or metamorphosis to the ambient temperatures.
Methods and Materials: Our in silico experiments of S-protein (PDB file 6VXX) involve immersing it in a H2O box of 21×21×21 nm³ using the CHARMM27 force field under NVT ensemble. We calculate the S-protein’s thermal inabilities based on RMSD of backbone, at eventful or purposeful temperatures: 3°C, 20°C, 37°C, 60°C, 80°C, 95°C, and 300°C. The in vitro experiments, where the infectivity is determined by a TCID50 assay, is reported [12, 13]. The curve of RMSD vs. temperatures of the in silico data is corroborated with that of the inactivation time vs. temperature of the in vitro. The in vitro and in silico data are applied to cluster the distributions of RMSD of both experiments to generate a rough grouping of the protein’s survival duration from weeks to milliseconds.
Results: The in vitro experiments and the in silica results can complement and verify each other:
Stable at low temperature: The average of RMSD at 3°C is 38% lower than it at 20°C with the small variance, agreeing with in vitro experiments that salmon-attached coronavirus at 4°C remain infectious for more than a week [3] and there was only around a 0.7 log-unit reduction of infectious titer on day 14 at 4°C[13].
Sensitive at 60°C~80°C: the distribution of RMSD at 20°C is similar to it at 37°C but different with it at 60°C. Two peaks in distribution at 60°C indicate the structure inability is shifting from a lower to higher level. The average of RMSD increases 30% with temperature from 60°C and 80°C, serving as a signal for the presence of a critical heat denaturation in that range. Those in silico results perfect agree with in vitro results that the inactivation time at 37°C, 56°C and 70°C change from 24h, 30min to 5min [12, 13].
3) The in vitro survival time vs. temperature [12] agrees with the curve of RMSD vs. temperatures in silico experiments, showing a zone of substantial structural variation, suggesting existence of a critical temperature.
4) Correlate with in vitro data [12, 13], the clustering distributions of RMSD roughly group the virus’ survival time at temperature ranges: 60°C-70°C, 80°C-95°C, and 300°C groups to week-, day-, hour-, minute- and microsecond-scales, respectively.
Discussions: Our millisecond-scale MD simulations help reveal the thermal properties of the S-protein. These in silico experiments corroborate well with the in vitro ones and, conversely, guide additional in vitro experiments, showing the benefits of “amalgamating” these two experiments. The 10-ms runs are expected to enhance the correlation and prediction accuracy. Our continued simulations at higher temperatures will likely capture the denaturation. This vital ground truth, coupled with in vitro experiments, will allow us to develop machine learning algorithms to predict the virus’ survival duration at a given temperature and make quicker and wider discovery of properties of the coronavirus and, potentially, other materials.
Acknowledgment: The project is supported by OVPR&IEDM COVID-19 Grant and SUNY-IBM Consortium Award.

Rigorous and widespread testing remains a critical component of strategies for containing the COVID-19 pandemic. The limited availability of molecular diagnostics, however, creates a gap between requirements for population level testing and the availability of tests, likely to persist for the foreseeable future. These circumstances motivate the development of complementary technologies for diagnosing and monitoring COVID-19 infections. Consumer-grade wearables may have some utility in this context, but intrinsic shortcomings prevent measurements of the key symptoms of the disease: fever (98%), cough (65%) and shortness of breath (55%). This talk describes the custom development of a soft, hybrid electronic device, originally designed to track patients with aphasia and dysphagia, that mounts on the suprasternal notch to track all of these symptoms, continuously and with clinical-grade accuracy. Uses range from detecting early signs of symptoms in high risk populations, to monitoring the progression of patients with the disease in the hospital and in the home. Deployments on more than 250 healthcare workers and COVID-19 patients across the medical complex in Chicago over the last 20 weeks demonstrate the power of this technology, particularly when paired with HIPAA-compliant cloud data services and advanced analytics. Current and future activities will be discussed.

The emergence of COVID-19 has underscored the importance of rapid, frequent, sensitive and specific diagnostics for tracking and containing an infectious disease. Current detection methods including polymerase chain reaction (PCR) and enzyme-linked immunosorbent assays (ELISA) are robust and sensitive, but generally either rapid and qualitative or quantitative and slow; they are also constrained to measuring one analyte, such as a gene sequence or antibody isotype, at a time, and cannot correlate viral load to antibody type and level. Here, we present a new photonic chip-based technology that uses optical characterization to rapidly and quantitatively measure gene sequences and antibodies, and determine the corresponding viral load from the same patient. Our platform relies on high-quality-factor (“high-Q”) nanostructured dielectric substrates, known as metasurfaces. These high Q metasurfaces produce a large amplification of the electromagnetic field intensity, increasing the response to minute refractive index changes from targeted binding of a nucleic acid sequence or antibody; simultaneously, the optical signal is beam-steered for multiplexed detection. We will present the design and development of this quantitative optical assay, as well as application to clinical nasal-pharangeal and serological samples from Stanford’s Clinical Virology Lab.

The widely recognized need for more personalized, patient-centered healthcare requires the development of cheap, easy-to-use, yet reliable biomedical devices that are capable of detecting specific diseases. The current COVID-19 pandemic has made this need abundantly clear and has shown that we are ill-prepared for this and future viral pandemics. Immunoassays form the cornerstone of today`s clinical biomolecular diagnosis. Their success is rooted in their modularity and the possibility to generate specific and high-affinity antibodies for almost any molecular target. However, translation of traditional heterogeneous immunoassays into point-of-care assays has proven challenging, because they require multiple incubation and washing steps, the addition of exogenous reagents, and external calibration. Laminar flow immune assays (LFIAs) have been introduced as cheap and relatively easy-to-use POC immunoassays, but they suffer from limited sensitivity and are primarily used as qualitative tests.
In recent years our group pioneered the development of bioluminescent sensor proteins that allow affinity-based detection of antibodies, proteins, small molecules, and DNA/RNA directly in blood plasma using the camera of a smart phone as the sole piece of equipment. Unlike fluorescence, whose dependence on external illumination gives rise to autofluorescence and scattering, bioluminescence is ideally suited to measure analytes directly in complex media such as blood with minimal sample handling. In my presentation I’ll focus on the development of a generic bioluminescent sandwich immunoassay platform that combines the analytical performance of a laboratory-based immunoassay such as ELISA with the speed and ease-of-use of laminar flow immunoassays. RAPPID (Ratiometric Plug-and-Play Immunodiagnostics) combines ratiometric bioluminescent detection with antibody-based target recognition into an easy-to-implement standardized workflow, and therefore represents an attractive, fast, and low-cost alternative to traditional immunoassays, both in an academic setting and in clinical laboratories for point-of-care applications. The modularity of the RAPPID workflow also enables rapid development of point of diagnostics for newly emerging analytes, as demonstrated here by development of RAPPID assays for SARS-CoV-2 spike proteins and anti-SARS-CoV-2 antibodies. To allow further development for point-of-care diagnostic applications, RAPPID can be integrated in cheap and simple paper- or thread-based analytical devices or integrated into microfluidic cartridges, and dedicated readers could be developed to further increase sensitivity.

The COVID-19 pandemic has suffered from a lack of rapid diagnostic tests, where the need far exceeds current supplies. Tests are required both for diagnosing infections as well those that can test for the presence of antibodies, which will aid in determining immunity. To meet what is expected to be an extreme demand for mass testing, there needs to be point of care tests that can be run by non-experts and go from sample to answer within minutes. Also, because the supply chain for reagents has been unable to meet the needs for testing, a diversified portfolio of biological reagents tests is also needed.

Paper based immunoassays are attractive for use as rapid diagnostics for COVID-19 and many other infectious diseases because they are low cost and can be administered at point of care and in field settings. Readout by eye is made possible by the gold nanoparticle-antibody conjugates, which have a strong absorption due to the nanoparticle surface plasmon resonance, thus providing sample-to-answer times of minutes. We describe the development of gold nanoparticle-antibody conjugates for use in COVID-19 tests, and how the physical properties of the nanoparticle can impact test performance and sensitivity.

In addition, preparation for the next emerging outbreak requires the ability to develop tests in a nimble manner. We describe a route for repurposing stockpiled antibodies to make immunoassays for new diseases for which antibodies have not yet been developed. We leverage cross reactive antibodies and the size- and material- dependent properties of gold nanoparticles, demonstrating it for
for multiplexed diagnostics for yellow fever, dengue, and zika viruses. By adapting immunoassays for selective sensing as opposed to specific sensing and using machine learning of the color test lines, we are able to construct an assay for yellow fever non structural protein 1(NS1) using cross-reactive antibodies raised for dengue and zika.

The global COVID-19 pandemic strains healthcare systems with a sharp increase in critical care demand coupled with a decrease in available staff as healthcare workers are more likely to fall ill as well. To prevent these strains from leading to collapse, it is essential to find new ways to quickly detect new infections and closely monitor disease progression. Quick detection would greatly assist in the process of contact tracing. As for monitoring, one critical point in the healthcare chain is to identify patients who are developing severe COVID-19 and to provide treatment before critical care becomes necessary in order to avoid oversaturation of ICUs (1). There is a common consensus that a hyper-inflammatory syndrome or a “cytokine storm” is responsible for poor outcomes in COVID-19. Thus, it is crucial to develop rapid point-of-care tests for cytokine detection so that patients with a poor prognosis can be detected early and eschew the need for critical care. At the same time, healthcare workers must be tested regularly to limit contagions. While this is currently done with RT-PCR, it would be desirable to find alternative ways to screen for new infections for hospital staff.

In this presentation I introduce a diagnostic platform for monitoring disease severity and new SARS-CoV-2 infections. It is based on modifying conventional filter paper with polymers so that it can store antibody-decorated gold nanoparticles (2). The polymer treatment also ensures a highly efficient transfer to other substrates such as cellulose or polypropylene, which is the basis for the diverse family of diagnostic tests presented here. For example, we have developed tests for detecting IL-6 at the point of care using cellulose as the substrate. IL-6 is a key player in the COVID-19 cytokine storm as well as a therapeutic target for immunomodulating drugs. Our tests can detect alarming levels of this biomarker in the blood of COVID-19 patients in less than 20 min. They can also detect IL-6 in respiratory samples (bronchial aspirate, sputum) of COVID-19 patients rapidly thanks to our method for sample liquefaction. This approach could greatly improve the evidence base for the coronavirus management by revealing fluctuations in local inflammatory biomarkers. We have also developed diagnostic tests based on the detection of viral proteins attached to a medical face mask. In this approach, biomarkers adsorbed to the propylene fibers inside the filter of the mask are detected by pressing our paper-based tests against them. This transfers antibody-decorated nanoparticles to the mask, which then generate a colored spot on it if the target proteins are present. This approach could be an inexpensive alternative to RT-PCR for COVID-19 screening. All our analytical platforms benefit from smartphone-based detection approaches developed in our lab, which makes them highly portable and easy to implement at the bedside. Because the assays are paper-based, they can be easily disposed of by incineration, therefore circumventing biosafety issues. These features, along with the versatile design for detecting antigens in different sample types, make our diagnostic tests excellent candidates for managing and screening COVID-19 at the point of care.
(1) ACS Sensors DOI: 10.1021/acssensors.0c00979
(2) ACS Sensors 2020, 5, 1, 147-153.

The proliferation of cases during the COVID-19 pandemic has increased the urgency for point-of-care (POC) diagnostic tests. A rapid, accurate, affordable, and accessible diagnostic system in the field is necessary to extensively monitor an affected population to suppress the spread of the epidemics effectively. In this study, an electrochemical diagnostic sensor was developed to be capable of detecting entire virions or virion-associated proteins, which can be applied for rapid POC detection of SARS-CoV-2. The molecular imprinting (MI) technique was utilized on the surface of a gold substrate with virions and hydroxyl-terminated alkanethiol chains to form a self-assembled-monolayer (SAM) crystallized to the specific shape of targeted analytes. The crystalline SAM behaved as a footprint by forming cavities on the surface, and it allows specificity can be attributed to the cavities formed in the thiol layer based upon the size, orientation, and hydrophilicity of the analytes. Real-time detection of the target virus was possible by measuring the potential difference through the re-adsorbing of the analyte with the imprinted pattern to generate a surface charge on the chip. The technique was previously shown to be comparable to Elisa in accuracy of CEA cancer marker detection in humans but with 1/100 of the test volume [1]. In a recent publication, we also demonstrated that the technique could detect ZIKV in saliva at sub infectious concentrations of less than 10 PFU/mL and accurately discriminate against DENV [2]. Here we show that the sensor could selectively detect the influenza A viruses H1N1 and H3N2, which are morphologically similar to SARS-CoV-2, as well as the four capsid SARS-COV-2 proteins, in phosphate-buffered saline and human saliva without any sample manipulation. Heat inactivated H1N1 and H3N2 will also be tested and compared to results from heat inactivated SARS-COV-2 virus. These results demonstrate that the molecular imprinting technique has the potential to become a POC detection system for rapid and accurate screening of SARS-CoV-2.
This work was performed in part at the Center for Functional Nanomaterials (CFN) of Brookhaven National Laboratory (BNL).

[1] Yingjie Yu, et al. “Quantitative real-time detection of carcinoembryonic antigen (CEA) from pancreatic cyst fluid using 3-D surface molecular imprinting.” Analyst, 2016, 141, 4424–4431
[2] Vincent Ricotta, et al. “A chip-based potentiometric sensor for a Zika virus diagnostic using 3D surface molecular imprinting.” Analyst, 2019, 144, 4266-4280

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread across the world and led to more than 924,000 deaths to date according to John Hopkins Coronavirus Resource Centre (September 14, 2020). Researchers and scientists around the world are actively working on developing therapeutics and vaccines for coronavirus disease 2019 (COVID-19). The rapid transmission from asymptomatic infected people has made COVID-19 such a widespread and deadly pandemic compared to SARS or MERS. Relying on “social-distancing” measures comes at enormous economic and social cost; this type of compliance is not a sustainable long-term solution. Rapid large population screening to determine the confirmed cases and contact tracing are vital for controlling the spread. The current essential technology for confirmation of SARS-CoV-2 infection is nucleic acid amplification. Nucleic acid amplification-based diagnostics are reliable and highly sensitive, however, the time required for sample transportation, preparation, and completion of the assay does not provide the high throughput capacity for quick and mass population screening. Hence, developing a rapid and accurate sensing platform for SARS-CoV-2 detection is still an urgent need.
In this work, we have developed a prototype point-of-care device for rapid SARS-CoV-2 subunit 1 (S1) spike protein detection using organic electrochemical transistor (OECT) based biosensors. These sensors are being developed to work with saliva samples. The OECTs were fabricated using Optomec Aerosol Jet 5X 3D printer on flexible polyimide substrate, with Au nanoparticle ink for source, drain and gate electrodes, PEDOT:PSS channel, and UV-curable PDMS as the insulator. The printed in-plane Au gate electrode was chemically modified and immobilized with a specific antibody against the SARS-CoV-2 S1 spike protein. A distinctive shift in the transfer characteristics of OECT before and after the chemical modification and the antibody immobilization. Spike test was performed with biasing the OECT at constant voltages and adding SARS-CoV-2 S1 spike protein with different concentrations. The biosensors being developed are single use disposable chips. In addition, a small measurement kit has been developed which will provide the readout result from the chip indicating a positive or negative test result. As the proposed biosensors are printed using aerosol jet 3D printer and they can economically be scaled while maintaining their quality. The sensor can be deployed quickly at workplaces, schools, hospitals, airports, etc. for immediate test results.

The development of a portable, rapid and efficient breath detector could potentially benefit the study of human respiration. This is of particular interest under the background of a global pandemic which could be spread through the respiratory system. Herein, we report an integrated, low-cost breath analyser that is composed of multi-layered, suspended PEDOT:PSS microfibre arrays, fabricated by original inflight fluidic fibre printing technique. Based on that the resistance of PEDOT:PSS is sensitive to the moisture change, this breath analyser offers a direct signal read-out. Thanks to the small diameter and large surface-to-volume ratio, the microfibres are much more responsive to the dynamics of moisture flow in air compared with planer or film based moisture sensor. Moreover, the ultrathin diameter and substrate-free feature enable the entire fibre array to be transparent and air permissive; thus, this sensor could be directly mounted in front of a camera, allowing visualisation at the same time. We demonstrate that this human breath analyser could be able to detect and distinguish the human breath level, when talking, breathing and coughing. In addition, we show that the breath sensor is also able to distinguish the human breath level change when wearing various face masks.

To rapidly respond to the COVID-19 pandemic and address the extreme shortage of proper sterilization methods for Personal Protective Equipment (PPE) and surfaces, we have urgently advanced safe, sustainable and high-efficiency corona discharge (CD) based sterilization technology. Filtering facepiece respirators (FFRs) like N95 masks and surgical masks are essential for reducing the spread of the virus. FFRs are primarily made of hydrophobic melt blown polypropylene layers. In addition to small pore sizes (<1μm), the filtration efficiency of N95 masks are also attributed to the electrostatic charges embedded in the fibers. These charges result in electrostatic attraction of small droplets carrying micro-organisms, effectively trapping them between the fibers. There are several attempts to decontaminate and reuse masks using existing sterilization techniques like heat, UV, etc. Although, these methods are effective in killing the virus, they negatively affect the filtration efficiency over time.
In this study, we use CD to effectively sterilize masks and renew their filtration efficiency to make masks reusable. A high voltage is applied to a sharp electrode leading to dielectric breakdown of air. Electron and ion pairs are generated due to the avalanche effect. The combination of high electric field, ion bombardment and reactive species leads to effective sterilization of FFRs. The ions also renew the electrostatic charges on the surface of the fibers, thus recovering the filtration efficiency of the masks. Sterilization effect and mechanisms are being tested against E. coli, spores and SARS-CoV-2 virus. The sterility assurance level (SAL) has reached 10^-3 with single spot electrode discharge, which is the requirement for safe mask reuse. Masks are also successfully recharged after CD treatment within seconds, sterilizing them simultaneously, making them safe to reuse. We are also developing portable devices for sterilization of FFRs and other kinds of surfaces.

SARS-CoV-2 is transmitted by respiratory droplets containing protein surfactants and NaCl, which relates to virus transmission when surfactants are in negligible amounts. These droplets land on surfaces and evaporate depending on environmental factors such as relative humidity, temperature, and contact surface causing NaCl concentration to increase as the droplet dries. We aim to examine the effect of electrostatic interactions on the conformation of the spike glycoprotein (S-protein), as has been done in vitro with other respiratory viruses, showing a decrease in viability [2] throughout evaporation. This is a leading investigation correlating the results of in silico modelling and in vitro droplet drying dynamic experiments to analyze the transmission of SARS-CoV-2.
Saline droplets of 1-2µl are pipetted onto paper, PLA, glass, and aluminum and left to evaporate at 297K, 1 atm, and 48% relative humidity. Concentration is extrapolated from droplet mass using a microbalance. The S-protein structure was retrieved from the Protein Data Bank (PDB: 6VXX), cleaned, and placed into a system using the AMBERsb14 force field with Joung and Cheatham ion parameters [1], placed 2.0nm from the box edge in 0M, 0.5M, 1M and 4.0nm from the box edge in 1.5M. The system was solvated with TIP3P water and ions were added by replacing water molecules. Equilibration steps were carried out with a timestep of 2.0fs. Energy minimization was performed for 50,000 steps followed by NVT equilibration for 100ps to heat the system to the temperature of in vitro experiments. NPT equilibration was employed for 100ps and the system was brought to 1 atm. The equilibrated structure is input to the production run using an NPT ensemble and Parrinello-Rahman pressure coupling. Density is monitored to ensure no system collapse or changes in concentration. Raw trajectories from the run are processed by re-centering the protein in the box and realigning with the first frame as the reference structure.
Benchtop experiments indicate that a 2µl droplet of saline reaches 1M in 45 minutes and fully desiccates over several hours with concentrations between 0.15M and 6M. The evaporation rate of saline on different surfaces is constant regardless of NaCl concentration. On non-metal substrates, the evaporation rate is negatively correlated to the water contact angle of the substrate and on metal substrates the evaporation rate remains lowest of all the substrates, although it has a higher water contact angle than glass. The in silico model is analyzed by calculating the RMSD of atomic positions for the S-protein backbone yielding that the 1.5M increases more rapidly.
Simulation of the S-protein in varied NaCl concentrations is consistent with droplet drying experiments and depicts how Na+ and Cl- ions interact with S-protein structure. We aim to correlate the volume and concentration from in vitro droplet drying experiments with the structural analysis from in silico experiments and to eventually utilize machine learning to predict the relationship between NaCl concentration and S-protein conformation over longer time, and to conduct further structural analysis on the S-protein. Simulation at higher salt concentrations (above 1.5M) has yet to be validated due to the need for a large number of monovalent ions, currently crashing our simulations. Future benchtop work will include plaque assays with the BSL-2 coronavirus OC-43 in drying saline droplets.

The project is supported by OVPR&IEDM COVID-19 Grant and SUNY-IBM Consortium Award.


[1] Joung, I. S., & Cheatham, T. E., 3rd. (2008). Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations. J Phys Chem B, 112(30), 9020-9041. doi:10.1021/jp8001614
[2] Yang, W., Elankumaran, S., & Marr, L. C. (2012). Relationship between humidity and influenza A viability in droplets and implications for influenza's seasonality. PLoS One, 7(10), e46789. doi:10.1371/journal.pone.0046789

SARS-CoV-2 (CoV) has sickened millions and killed hundreds of thousands since emerging less than a year ago. Aerosol transmission of CoV in respiratory droplets is well-established, but its capacity for fomite transmission is not well defined [1,2]. Fomite transmission of viruses are generally impacted by two factors: surface materials and droplet composition. However, both mechanisms are not well defined. For example, viral lifetimes may be affected by different surface-droplet interactions which influence the amount of water retained in a dried droplet residue, or through distribution patterns that create the localization of dried droplet solutes. Thus, this study aims to better characterize the expected lifetime of CoV by simulating various surface-droplet interactions frequent in real life.
Droplets of distilled water, saline, DMEM+10%FBS, lung fluid, and human saliva, with volumes ranging from 0.25 - 2.0 uL, were deposited onto paper, glass, polylactic acid (PLA), and aluminum. All samples were analyzed using contact angle goniometry and microbalance data; the changes in droplet volume over time were recorded, from which the evaporation rate and concentration of solutes were determined. Images of the drying pattern of each surface-droplet interaction were generated using confocal laser scanning. Plaque assays are now being performed at 10-minute time intervals to determine virus lifetimes.
Results indicate that the surface material greatly affects the drying rate. Significantly different evaporation rates were obtained when placing distilled water on aluminum, glass, and PLA. More importantly, fluids relevant to virus transmission, such as saliva and lung fluid, evaporated significantly slower on paper and faster on glass than they did on PLA and aluminum, with rabbit lung fluid evaporating at 0.164ul/min on glass and 0.051 ul/min on paper. Droplet composition also impacted the drying rates. Based on the contents of the droplets, two different drying mechanisms have been observed. Distilled water and human saliva dried at a linear rate, but in saline, DMEM+10%FBS and lung fluid, an initial linear decrease in volume followed by a slower asymptotic approach to the volume of the solutes was observed. Droplets with the asymptotic mechanism could keep viruses hydrated for a much longer time than previously predicted. Saline droplets retained 3.75% of their starting mass and porcine lung fluid retained 12.08% after 50 minutes, compared to 0.08% for water droplets after only 39 minutes. This contrast suggests increased hydration, and potentially lengthened virus lifetimes, for droplets that dry by the asymptotic mechanism. Images taken using confocal laser scanning show that both the surface and the composition of the liquid droplet affect the distribution of droplet solutes. On aluminum, glass, and PLA, droplets of saline and rabbit lung fluid showed a pinned contact line, leading to the buildup of solutes near the edge of the droplet, while saliva droplets created a buildup of solutes in the center of the droplet. The localization of solutes in saline, rabbit lung, and saliva droplets may also indicate an ability to hold water for a longer period of time.
Continued experiments using plaque assays of droplets and droplet residues containing H1N1 and the coronavirus OC43 deposited on different surfaces will reveal more directly the lifetime of CoV on different surfaces over time.

[1] Aboubakr HA, Sharafeldin TA, Goyal SM. Stability of SARS CoV 2 and other coronaviruses in the environment and on common touch surfaces and the influence of climatic conditions: A review. Transboundary and emerging diseases.
[2] Firquet, S., Beaujard, S., Lobert, P. E., Sané, F., Caloone, D., Izard, D., & Hober, D. (2015). Survival of Enveloped and Non-Enveloped Viruses on Inanimate Surfaces. Microbes and environments, 30(2), 140–144.

We gratefully acknowledge support from the Louis Morin Charitable Trust

In light of the global need for COVID-19 testing there is a need for much faster testing device and the exhaled breath present significant potential to be used for this purpose. SARS-CoV-2 19 attacks the upper respiratory tract (nose and throat) and progresses down to the lower respiratory tract (lungs). SARS-CoV-2 causes lung inflammation increasing the number of particles in an individual’s exhale. Pathogens present in respiratory fluid can be carried in aerosol particles. It is uncertain if SARS-CoV-2 stays viable in droplet nuclei particles; some studies that claim that droplet nuclei particles remain viable, presenting the threat of airborne transmission [1, 2]. Air samples tested positive in a Wuhan hospital confirming aerosol transmission [3]. SARS-CoV-2 microdroplets exhaled from infectious patients can be detected by specially developed breath analyzer. This analyzer is based on the biosensor to detect viral SARS-CoV-2 microdroplets from exhaled breath.
The aim of the present work is examining the characteristic of exhaled air samples from healthy individuals and finding suitable substrate that can be used for further development of SARS-CoV-2 biosensor. We are using three techniques to measure the quantity and composition of exhaled air samples such as Optical Particle Counter (OPC), Quartz Crystal Microbalance (QCM) and Quadrupole Mass Spectrometer (QMS). The LiNbO3 crystal was selected to the biosensor substrate and characterized with Low Energy Electron Diffraction (LEED) and Auger Electron Spectroscopy (AES) for the capturing of the microdroples from exhaled breath. In order to work as SARS-CoV-2 biosensor the LiNbO3 substrate has to be developed further to be functionalized with ACE2 receptor.
OPC tests confirm the possibility of significant exhale particle generation -356% of inhaled air. High concentration of background particles induce a greater difference in exhale to inhale than low particle concentration background. Low relative humidity (RH) influences the amount of particles added by the breath to be lower. This indicates that that the amount of exhaled particles produced increases when worse air quality is inhaled. QMS data confirm that less gaseous water is in exhale than in inhaled air suggesting exhaled microdroplets agglomeration. QCM data shows difficulties in adsorption and holding the microdroplets on the crystal sensor. A LiNbO3 crystal was selected for the biosensor suitable substrate because it is strongly hydrophilic and has a very stable surface crystalline structure even after exposure to ambient air, water, and alcohol as was confirmed with LEED and AES study.
References:
[1] N. M. Wilson, A. Norton, F. P. Young, and D. W. Collins, “Airborne transmission of severe acute respiratory syndrome coronavirus 2 to healthcare workers: a narrative review,” Anaesthesia, 2020.
[2] M. Yao, L. Zhang, J. Ma, and L. Zhou, “On airborne transmission and control of SARS-CoV-2,” Science of The Total Environment, vol. 731, p. 139178, 2020.
[3] Z.-D. Guo et al., “Aerosol and Surface Distribution of Severe Acute Respiratory Syndrome Coronavirus 2 in Hospital Wards, Wuhan, China, 2020,” Emerging Infectious Diseases, vol. 26, no. 7, 2020.

Given the severity of the COVID-19 pandemic caused by the novel SARS-CoV-2 coronavirus, it is essential to develop effective approaches for treatment and prevention. The improvement of personal protective equipment (PPE) for front-line healthcare workers also relies on comprehensive binding analysis of surface stability and binding intensity of the virus on certain substrates1. As the SARS-CoV-2 spike glycoprotein (S protein) is the key receptor for promoting entry to host cells and binding, we investigate its conformational transitions during binding using computer simulations to inform development and improvement of drugs and PPE to treat and prevent infection.
Our plan is to use Monte Carlo methods for our simulations. Two main methods for such computer simulations are molecular dynamics (MD) and MC. MD simulations are based on trajectories determined by Newton’s equations of motion and use small time steps typically on the order of femtoseconds. This makes the simulations computationally expensive. MC simulations generate random movements based on probability distributions at each step. This has often been found to be more computationally efficient. As such, we are motivated to employ MC methods to greatly increase the efficiency of the S protein simulations. Our first step is to simulate the S protein in an aerosol environment. Our next steps include simulating the binding of the S protein-aerosol system onto various substrates such as polylactic acid (PLA), the common material used in PPE. We plan to correlate the in silico results with in vitro experiments to better inform and improve PPE guidelines.
Our current step is simulating the closed state 6vxx S protein in its aerosol environment. The Cassandra and GOMC (GPU-optimized MC) softwares were employed. Using Cassandra, data files such as the molecular connectivity file (MCF) needed to be generated. However, due to the complex nature of the S protein creating difficulties in generating the MCF file and the fact that Cassandra is not specifically designed for such large systems, we concluded that Cassandra was not suited for our simulation studies. As such, we decided to employ GOMC. We overcame difficulties with generating the appropriate PDB and PSF files. However, we discovered that there were limitations with GOMC for this type of simulation that prevented us from successfully running the entire simulation, including the fact that it does not support simulations for proteins with multiple residues. We are currently working on adjusting the source code with the help of the GOMC developers to support this type of simulation. We made some progress, and we expect to complete the simulations within the next few months.
Ultimately, these simulations of the conformational changes of the S protein during binding will allow scientists to make more informed decisions on developments of drugs and PPE to treat and prevent infection. However, as time is of the essence, the need for efficient simulations using MC methods is vital to studying the S protein binding at a larger scale.

[1] Stewart CL, Thornblade LW, Diamond DJ, Fong Y, Melstrom LG. Personal Protective Equipment and COVID-19: A Review for Surgeons. Ann Surg.
[2] Walls AC, Park YJ, Tortorici MA, Wall A, McGuire AT, Veesler D. Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell. 2020;181(2):281-292.e6.
[3] Shah JK, Marin-Rimoldi E, Mullen RG, et al. Cassandra: An open source Monte Carlo package for molecular simulation. J Comput Chem. 2017;38(19):1727-1739.
[4] Nejahi Y, Barhaghi MS, Mick J, Jackman B, Rushaidat K, Li Y, Schwiebert L, Potoff J. GOMC: GPU Optimized Monte Carlo for the Simulation of Phase Equilibria and Physical Properties of Complex Fluids. SoftwareX 2019;9:20-27.

We gratefully acknowledge support from the Louis Morin Charitable Trust

An effective mass vaccination strategy against SARS-CoV-2 and future pandemics requires both an efficacious vaccine and a reliable delivery method. To this end, intradermal (ID) delivery offers significant advantages over intramuscular (IM) or subcutaneous (SC) routes for developing rapid, potent, and long-lasting immunity. However, current ID delivery methods are unreliable and inconsistent, particularly for replication-competent and/or live attenuated vaccines. An effective way to address this problem is to use microneedle arrays (MNAs) for safe, reliable, efficient, and clinically relevant intradermal delivery of vaccines into the skin. MNAs include hundreds of micro-scale needles in a patch form. Vaccination using MNAs facilitates reproducible delivery of a high concentration of antigen to skin microenvironments for efficient and effective presentation of antigens to the skin’s immune cells. In this talk, we will discuss the different type of MNA technologies, associated fabrication approaches for scalable manufacturing of MNAs, and their effectiveness in delivering surrogate vaccines to the human skin ex vivo and animal skin in vivo. One of those technologies include our new approach that uses Hybrid-MNAs, which combines advantages of other MNA technologies while addressing their drawbacks to realize significant advantages in regulation, manufacturing, application, and distribution aspects. Hybrid-MNAs will be inexpensive and patient friendly, will minimize cold-chain requirements and eliminate biohazardous sharps disposal. This would be transformational for global immunization programs.

The coronavirus disease 2019 (COVID-19) pandemic has focused attention on the need to develop effective therapies against the causative agent, SARS-CoV-2, and also against other pathogenic coronaviruses (CoV) that have yet to emerge. Focusing on steps in the CoV replication cycle, in particular the entry steps involving membrane fusion that are vulnerable to inhibition by broad-spectrum or specific antiviral agents, is an astute choice because of the conserved nature of the fusion machinery and mechanism across the CoV family. For coronavirus, entry into a host cell is mediated by a single glycoprotein protruding from its membrane envelope, called spike (S). Within S, the region that directly interacts with the membrane is called the fusion peptide, FP. It is the physico-chemical interactions of the FP with the host membrane that anchors it, thus enabling the necessary deformations of the membrane that lead to delivery of the viral genome into the cell when a fusion pore opens. Understanding of thermodynamics, kinetics, and intermolecular interactions are useful to describe FP interactions with the host membrane at the most fundamental molecular level. This knowledge in turn, can be used to facilitate the development of strategies to limit those interactions to stop the spread of infection. In this talk, I will describe our work on understanding the impact of calcium ions on CoV infection. Using cell infectivity, biophysical assays, and spectroscopic methods, we found that calcium ions serve to stabilize the fusion peptide structure during conformational change that then allows its insertion into the host membrane, resulting in increased lipid ordering in the membrane. This lipid ordering precedes membrane fusion and has been shown to correlate with increased fusion activity and higher levels of infection in the presence of calcium. As such, depletion of calcium ions leads to structure and activity changes in the fusion peptide that correlate well with in vitro experiments using calcium-chelating agents to block cell infection. In a final set of experiments, we used calcium channel blockers that are FDA approved for cardiac conditions to test their ability to block virus infection in lung cells. In some cases, these drugs eliminated infection, pointing to the possibility for re-purposing these drugs to treat COVID-19.

We are developing porous membranes containing affinity molecules to quantitatively capture antibodies and determine their concentration. Previously, we immobilized peptide mimotopes to bind therapeutic antibodies in serum. Flow through the membrane rapidly brings antibodies to binding sites to enable their capture with high efficiencies. In an effort to apply this to quantitation of COVID-19 antibodies, we are immobilizing COVID-19 proteins and capturing their antibodies. Subsequent binding of a fluorescently labelled secondary antibody provides a signal that we hope will be proportional to the quantity of polyclonal antibody. Moreover, because capture rates are high we will try to use a monoclonal antibody as a standard to estimate the absolute antibody concentration, whereas most analyses give a relative or qualitative value for antibody concentration. The presentation will present preliminary results and explain the method.

Due to the COVID-19 outbreak, many critical supplies for patient care and disease prevention are becoming increasingly scarce. One area that is increasingly in demand is ventilators. Ventilators are the mainstay treatment for COVID-19 patients that develop ARDS (Acute Respiratory Distress Syndrome), one of the primary causes of death of COVID-19. There exists an enormous gap between demand and supply. It is predicted that there is a global shortage of 880,000 ventilators. This is especially concerning in developing countries, where ventilators are already in short supply, and the hospitals may not have resources to meet those demands. Ventilator splitters are the most feasible option to increase capacity rapidly but face many challenges in inpatient care. The Society of Critical Care Medicine released a statement listing the challenges of splitting ventilators. Despite these challenges, ventilator splitting has already happened globally, including in New York City, as “the other option is death.” We have worked with anesthesiologists, clinicians, and ICU intensivists at Johns Hopkins Hospital to address pressing needs through materials research.

We will present our approaches to provide safe treatments for each patient by addressing the challenges associated with splitting ventilators. Due to the unstable supply chain, we have prototyped de novo ventilator splitters (“Vent-lock”) with flow restriction valve via 3D printing using biocompatible and easily sterilizable materials. Inspired by the shape and angles of the human bronchi, we designed the splitter to minimize turbulent airflow. We have used the ventilator splitter and flow restriction valve in a circuit containing filters, one-way valves, continuous monitoring, and positive end-expiratory pressure (PEEP) valves to safely allow clinicians to split ventilators for patients. Our 1+n(1) system is compatible with most ventilators and anesthesia machines.

We have tested our breathing circuits using a ventilator for two simulated patients with differing lung compliances, with continuous intrapulmonary data collection. We validated our airtight breathing circuit, and also produced one-way valves integrated into the ventilator splitter and filter drawers with replaceable filters to minimize aerosolization or cross-contamination of viruses. Our device was also validated for splitting anesthesia machines in in-vivo swine studies. Two swine were stably ventilated for five hours by one anesthesia gas machine, as confirmed by arterial blood gases, continuous airflow monitoring, and final lung histopathology. Our device is currently under review by the U.S. Food and Drug Administration for Emergency Use Authorization.

We envision that our study can contribute to increasing ventilator capacity safely to meet urgent ventilator shortages and provide another example that materials scientists and engineers contribute to addressing societal challenges such as COVID-19 by working with stakeholders from healthcare, government, and industry. Due to the multidisciplinary and collaborative nature of the materials research, the materials community is well-positioned to enable advances in medicine and public health.

Introduction: The coronavirus SARS-CoV-2 is postulated to infect cells by attaching its outer membrane S-protein (spike glycoprotein) [1] to the host cell targets such as ACE2, CD26, Ezrin, and cyclophilins [2]. Structurally altering the S-protein may mitigate or even block the infectivity of coronavirus. One way to alter the S-protein’s physicochemical properties including structures and function is to surgically change the protonation and deprotonation state of each ionizable group to control the pH value[3]. The pH values of the aerosol droplets environment are known to change the chemical form, distribution, and reactivity [4-6] of the protein. Performing such study, e.g., immersing the virus and especially the S-protein in a solution of given pH values, is dangerous and nebulous. Our all-atomic molecular dynamics simulations, with their own challenges of long computation, allow us to examine the conformational states of the S-protein at extreme pH values. This is what we report in this work.

Contributions: We have performed our MD simulations of S-protein for five pH values in 3, 4, 5, 7, 11 for longer than the microsecond scales. With the current rate of simulation progress, we expect to reach a record simulated time and obtain the states of the S-protein for the first time. As the first attempt to control the pH values during MD simulation by protonation and deprotonation state of the amino acid sidechain residues in the S-protein, we may corroborate the simulated conformational states with the properties obtained in the lab bench experiments. We examine the detailed conformational states change at different pH values of the entire S-protein as well as the individual residues of interest.

Methodologies: We use the Gromacs program [7] to perform the MD simulation on the IBM Power9-based AiMOS supercomputer. The S-protein structure data is taken from the protein data bank (6VXX.pdb) and the force field for the S-protein and water molecule is from the CHARMM27. The S-protein is 12×13×16 nm³ in size which is placed in the water box of size 21×21×21 nm³. Every simulation is controlled at the normal human body temperature of 37°C and a control group at this temperature and the neutral pH7 is run. Our MD simulations away from this neutral pH require the addition of the Na⁺ or Cl^- ions in the solvent to balance the charges and ensure the protonation state accuracy [8].

Results: The protein structure changes measured by RMSD for backbone and RMSF for individual residue were performed. Here is a list of brief observations: (1) The states of protein show significant RMSD increases for pH3 and pH11. We expect the protein to denature as we continue the simulation. (2) The conformational states for pH4 and pH5 appear to be quite similar to those of the pH7, at least for the simulated time we reached so far. (3) After 500ns, the protein at pH3 and pH11 showed obvious structural changes in specific residues. For pH3, ARG-466 and ASP-467 in Chain B are extremely active. Moreover, this is on the S1 domain, for binding the host cell [9]. For pH11, in both Chain A and Chain C, ASP-1146 and SER-1147 are more active than others. This part is on the S2 domain, which is for membrane fusion [9].

Conclusion and Future Work: The first studies of the effects of pH on S-protein at the microseconds scales provide us detailed pictures of the structural changes of whole S-protein and its individual residues. We continue the MD simulations to collect more data for various analyses of structures and functions of the S-protein and corroborate them with laboratory results.

The SARS-CoV-2 pandemic has quickly spread throughout the globe in 2020. As such, engineers have applied their knowledge in materials design to approach prevention of infection, testing to diagnose infections, and treatment after an individual has COVID-19. These advancements rely on an understanding of the basic biology of SARS-CoV-2 from virology to immunology. Here, we will focus on a general overview of what is known about SARS-CoV-2 biology, focusing on components that are critical for materials design in prevention, diagnostics, and treatments.

The widely recognized need for more personalized, patient-centered healthcare requires the development of cheap, easy-to-use, yet reliable biomedical devices that are capable of detecting specific diseases. The current COVID-19 pandemic has made this need abundantly clear and has shown that we are ill-prepared for this and future viral pandemics. Immunoassays form the cornerstone of today`s clinical biomolecular diagnosis. Their success is rooted in their modularity and the possibility to generate specific and high-affinity antibodies for almost any molecular target. However, translation of traditional heterogeneous immunoassays into point-of-care assays has proven challenging, because they require multiple incubation and washing steps, the addition of exogenous reagents, and external calibration. Laminar flow immune assays (LFIAs) have been introduced as cheap and relatively easy-to-use POC immunoassays, but they suffer from limited sensitivity and are primarily used as qualitative tests.
In recent years our group pioneered the development of bioluminescent sensor proteins that allow affinity-based detection of antibodies, proteins, small molecules, and DNA/RNA directly in blood plasma using the camera of a smart phone as the sole piece of equipment. Unlike fluorescence, whose dependence on external illumination gives rise to autofluorescence and scattering, bioluminescence is ideally suited to measure analytes directly in complex media such as blood with minimal sample handling. In my presentation I’ll focus on the development of a generic bioluminescent sandwich immunoassay platform that combines the analytical performance of a laboratory-based immunoassay such as ELISA with the speed and ease-of-use of laminar flow immunoassays. RAPPID (Ratiometric Plug-and-Play Immunodiagnostics) combines ratiometric bioluminescent detection with antibody-based target recognition into an easy-to-implement standardized workflow, and therefore represents an attractive, fast, and low-cost alternative to traditional immunoassays, both in an academic setting and in clinical laboratories for point-of-care applications. The modularity of the RAPPID workflow also enables rapid development of point of diagnostics for newly emerging analytes, as demonstrated here by development of RAPPID assays for SARS-CoV-2 spike proteins and anti-SARS-CoV-2 antibodies. To allow further development for point-of-care diagnostic applications, RAPPID can be integrated in cheap and simple paper- or thread-based analytical devices or integrated into microfluidic cartridges, and dedicated readers could be developed to further increase sensitivity.

Rigorous and widespread testing remains a critical component of strategies for containing the COVID-19 pandemic. The limited availability of molecular diagnostics, however, creates a gap between requirements for population level testing and the availability of tests, likely to persist for the foreseeable future. These circumstances motivate the development of complementary technologies for diagnosing and monitoring COVID-19 infections. Consumer-grade wearables may have some utility in this context, but intrinsic shortcomings prevent measurements of the key symptoms of the disease: fever (98%), cough (65%) and shortness of breath (55%). This talk describes the custom development of a soft, hybrid electronic device, originally designed to track patients with aphasia and dysphagia, that mounts on the suprasternal notch to track all of these symptoms, continuously and with clinical-grade accuracy. Uses range from detecting early signs of symptoms in high risk populations, to monitoring the progression of patients with the disease in the hospital and in the home. Deployments on more than 250 healthcare workers and COVID-19 patients across the medical complex in Chicago over the last 20 weeks demonstrate the power of this technology, particularly when paired with HIPAA-compliant cloud data services and advanced analytics. Current and future activities will be discussed.

The emergence of COVID-19 has underscored the importance of rapid, frequent, sensitive and specific diagnostics for tracking and containing an infectious disease. Current detection methods including polymerase chain reaction (PCR) and enzyme-linked immunosorbent assays (ELISA) are robust and sensitive, but generally either rapid and qualitative or quantitative and slow; they are also constrained to measuring one analyte, such as a gene sequence or antibody isotype, at a time, and cannot correlate viral load to antibody type and level. Here, we present a new photonic chip-based technology that uses optical characterization to rapidly and quantitatively measure gene sequences and antibodies, and determine the corresponding viral load from the same patient. Our platform relies on high-quality-factor (“high-Q”) nanostructured dielectric substrates, known as metasurfaces. These high Q metasurfaces produce a large amplification of the electromagnetic field intensity, increasing the response to minute refractive index changes from targeted binding of a nucleic acid sequence or antibody; simultaneously, the optical signal is beam-steered for multiplexed detection. We will present the design and development of this quantitative optical assay, as well as application to clinical nasal-pharangeal and serological samples from Stanford’s Clinical Virology Lab.

COVID-19 has raised serious global public health concerns. The causative agent, SARS-CoV-2, has found to be environmentally persistent, and it can be transmitted through droplets or aerosols from an infected person and indirect contact via fomites. Nanotechnology has emerged as a promising tool for fighting against COVID-19, including but not limited to disease diagnosis, drug delivery, vaccine development, and pathogen detection and inactivation. In this talk, we will highlight recent progresses in controlling and inactivating pathogens in different environmental media, including SARS-CoV-2, by harnessing the power of nanotechnology. Specifically, electrospun nanofibrous membranes are developed to capture SARS-CoV-2-laden aerosols and they can be used for HVAC filters and masks/respirators. Photocatalysis that takes the advantage of environmental light can be implemented for effectively inactivating persistent pathogens on contact surfaces at an ambient condition.

Synthetic biology is bringing together engineers, physicists and biologists to model, design and construct biological circuits out of proteins, genes and other bits of DNA, and to use these circuits to rewire and reprogram organisms as well as create novel biomaterials. These biological circuits, living materials and re-engineered organisms are going to change our lives in the coming years, leading to cheaper drugs, rapid diagnostic tests, and synthetic probiotics to treat infections and a range of complex diseases. In this talk, we highlight recent efforts to create synthetic gene networks and programmable cells as new classes of diagnostics, therapeutics and vaccines for fighting pathogens, including SARS-CoV-2.

Facial masks are among the most important personal protection equipment to fight COVID-19. This talk covers our exciting progress related to facial masks including: 1) We utilized X-ray tomography and deep learning to perform 3D imaging and analysis of facial masks and the particle filtration to provide critical understanding how facial masks work. 2) We developed heating methods (dry and humid) as the most efficiency methods to disinfect N-95 level facial masks while maintaining their high filtration efficiency for over 20 times. 3) We studied a variety of household textiles and identify the most effective ones for homemade masks; 4) We propose that nanofiber filtration technology would afford the next generation high performance facial masks with high filtration efficiency and great breathability.

An effective mass vaccination strategy against SARS-CoV-2 and future pandemics requires both an efficacious vaccine and a reliable delivery method. To this end, intradermal (ID) delivery offers significant advantages over intramuscular (IM) or subcutaneous (SC) routes for developing rapid, potent, and long-lasting immunity. However, current ID delivery methods are unreliable and inconsistent, particularly for replication-competent and/or live attenuated vaccines. An effective way to address this problem is to use microneedle arrays (MNAs) for safe, reliable, efficient, and clinically relevant intradermal delivery of vaccines into the skin. MNAs include hundreds of micro-scale needles in a patch form. Vaccination using MNAs facilitates reproducible delivery of a high concentration of antigen to skin microenvironments for efficient and effective presentation of antigens to the skin’s immune cells. In this talk, we will discuss the different type of MNA technologies, associated fabrication approaches for scalable manufacturing of MNAs, and their effectiveness in delivering surrogate vaccines to the human skin ex vivo and animal skin in vivo. One of those technologies include our new approach that uses Hybrid-MNAs, which combines advantages of other MNA technologies while addressing their drawbacks to realize significant advantages in regulation, manufacturing, application, and distribution aspects. Hybrid-MNAs will be inexpensive and patient friendly, will minimize cold-chain requirements and eliminate biohazardous sharps disposal. This would be transformational for global immunization programs.

The coronavirus disease 2019 (COVID-19) pandemic has focused attention on the need to develop effective therapies against the causative agent, SARS-CoV-2, and also against other pathogenic coronaviruses (CoV) that have yet to emerge. Focusing on steps in the CoV replication cycle, in particular the entry steps involving membrane fusion that are vulnerable to inhibition by broad-spectrum or specific antiviral agents, is an astute choice because of the conserved nature of the fusion machinery and mechanism across the CoV family. For coronavirus, entry into a host cell is mediated by a single glycoprotein protruding from its membrane envelope, called spike (S). Within S, the region that directly interacts with the membrane is called the fusion peptide, FP. It is the physico-chemical interactions of the FP with the host membrane that anchors it, thus enabling the necessary deformations of the membrane that lead to delivery of the viral genome into the cell when a fusion pore opens. Understanding of thermodynamics, kinetics, and intermolecular interactions are useful to describe FP interactions with the host membrane at the most fundamental molecular level. This knowledge in turn, can be used to facilitate the development of strategies to limit those interactions to stop the spread of infection. In this talk, I will describe our work on understanding the impact of calcium ions on CoV infection. Using cell infectivity, biophysical assays, and spectroscopic methods, we found that calcium ions serve to stabilize the fusion peptide structure during conformational change that then allows its insertion into the host membrane, resulting in increased lipid ordering in the membrane. This lipid ordering precedes membrane fusion and has been shown to correlate with increased fusion activity and higher levels of infection in the presence of calcium. As such, depletion of calcium ions leads to structure and activity changes in the fusion peptide that correlate well with in vitro experiments using calcium-chelating agents to block cell infection. In a final set of experiments, we used calcium channel blockers that are FDA approved for cardiac conditions to test their ability to block virus infection in lung cells. In some cases, these drugs eliminated infection, pointing to the possibility for re-purposing these drugs to treat COVID-19.

We are developing porous membranes containing affinity molecules to quantitatively capture antibodies and determine their concentration. Previously, we immobilized peptide mimotopes to bind therapeutic antibodies in serum. Flow through the membrane rapidly brings antibodies to binding sites to enable their capture with high efficiencies. In an effort to apply this to quantitation of COVID-19 antibodies, we are immobilizing COVID-19 proteins and capturing their antibodies. Subsequent binding of a fluorescently labelled secondary antibody provides a signal that we hope will be proportional to the quantity of polyclonal antibody. Moreover, because capture rates are high we will try to use a monoclonal antibody as a standard to estimate the absolute antibody concentration, whereas most analyses give a relative or qualitative value for antibody concentration. The presentation will present preliminary results and explain the method.