The NVBL Viral Fate and Transport Team includes researchers from eleven DOE national laboratories and is utilizing unique experimental facilities combined with physics-based and data-driven modeling and simulation to study the transmission, transport, and fate of SARSCoV-2. The team was focused on understanding and ultimately predicting SARS-CoV-2 viability in varied environments with the goal of rapidly informing strategies that guide the nation’s resumption of normal activities. The primary goals of this project include prioritizing administrative and engineering controls that reduce the risk of SARS-CoV-2 transmission within an enclosed environment; identifying the chemical and physical properties that influence binding of SARS-CoV-2 to common surfaces; and understanding the contribution of environmental reservoirs and conditions on transmission and resurgence of SARS-CoV-2.
A preliminary investigation of the use of supercritical carbon dioxide for treating of 3M 1860 N95 masks was undertaken to evaluate a potential route to low-cost, scalable, sterilization of personal protective equipment for multiple reuse in hospital settings. Upon entering the supercritical regime, the normally distinct liquid and gaseous phases of CO2 merge into a single homogeneous phase that has density, short-range order, and solvation capacity of a liquid, but the volume-filling and permeation properties that of a gas. This enables supercritical CO2 to function as a vehicle for delivery of biocidal agents such peracetic acid into microporous structures. The potentially adverse effect of a liquid-to-gas phase transition on mask filter media is avoided by conducting cleaning operations above 31 C, the critical temperature for carbon dioxide. A sample of fifteen 3M 1860 N95 masks was subjected to ten consecutive cycles of supercritical CO2 cleaning to determine its effect on mask performance. These 15 masks, along with 5 control samples then underwent a battery of standardized tests at the CDC NIOSH NPPTL research facility in Pittsburgh, PA. The data from these tests strongly suggest (but do not prove) that supercritical carbon dioxide do not damage 3M 1860 N95 masks. Additional tests conducted during this project confirmed the compatibility of supercritical CO2 with ventilator tubing that, like N95 masks, has been in short supply during portions of the COVID-19 pandemic and cannot be sterilized by conventional means. Finally, a control experiment was also conducted to examine the effect of supercritical CO2 on a BSL-2 surrogate virus, vesicular stomatitis virus (VSV), Indiana serotype strain. In the absence of biocidal additives, supercritical CO2 exhibited no measurable lethality against VSV. This surrogate virus experiment suggests that a biocidal additive such as peracetic acid will be necessary to achieve required sterilization metrics.
Strutt, Steven C.; Torrez, Rachel M.; Kaya, Emine; Negrete, Oscar N.; Doudna, Jennifer A.
Double-stranded DNA (dsDNA) binding and cleavage by Cas9 is a hallmark of type II CRISPR-Cas bacterial adaptive immunity. All known Cas9 enzymes are thought to recognize DNA exclusively as a natural substrate, providing protection against DNA phage and plasmids. Here, we show that Cas9 enzymes from both subtypes II-A and II-C can recognize and cleave single-stranded RNA (ssRNA) by an RNA-guided mechanism that is independent of a protospacer-adjacent motif (PAM) sequence in the target RNA. RNA-guided RNA cleavage is programmable and site-specific, and we find that this activity can be exploited to reduce infection by single-stranded RNA phage in vivo. We also demonstrate that Cas9 can direct PAM-independent repression of gene expression in bacteria. These results indicate that a subset of Cas9 enzymes have the ability to act on both DNA and RNA target sequences, and suggest the potential for use in programmable RNA targeting applications.
Current multiplexed diagnostics for Zika, dengue, and chikungunya viruses are situated outside the intersection of affordability, high performance, and suitability for use at the point-of-care in resource-limited settings. Consequently, insufficient diagnostic capabilities are a key limitation facing current Zika outbreak management strategies. Here we demonstrate highly sensitive and specific detection of Zika, chikungunya, and dengue viruses by coupling reverse-transcription loop-mediated isothermal amplification (RT-LAMP) with our recently developed quenching of unincorporated amplification signal reporters (QUASR) technique. We conduct reactions in a simple, inexpensive and portable "LAMP box" supplemented with a consumer class smartphone. The entire assembly can be powered by a 5 V USB source such as a USB power bank or solar panel. Our smartphone employs a novel algorithm utilizing chromaticity to analyze fluorescence signals, which improves the discrimination of positive/negative signals by 5-fold when compared to detection with traditional RGB intensity sensors or the naked eye. The ability to detect ZIKV directly from crude human sample matrices (blood, urine, and saliva) demonstrates our device's utility for widespread clinical deployment. Together, these advances enable our system to host the key components necessary to expand the use of nucleic acid amplification-based detection assays towards point-of-care settings where they are needed most.
The emergence of Zika virus (ZIKV) infections in Latin America and Southeast Asia has created an urgent need for new, simple, yet sensitive, diagnostic tests. We highlight recent work using paper-based sensors coupled with CRISPR/Cas9 to detect ZIKV RNA as a new approach to achieve rapid development and deployment of field-ready diagnostics for emerging infectious diseases.
Pathogenic viruses are a primary threat to our national security and to the health and economy of our world. Effective defense strategies to combat viral infection and spread require the development of understanding of the mechanisms that these pathogens use to invade the host cell. We present in this report results of our research into viral particle recognition and fusion to cell membranes and the role that protein affinity and confinement in lipid domains plays in membrane curvature in cellular fusion and fission events. Herein, we describe 1) the assembly of the G attachment protein of Nipah virus using point mutation studies to define its role in viral particle fusion to the cell membrane, 2) how lateral pressure of membrane bound proteins induce curvature in model membrane systems, and 3) the role of membrane curvature in the selective partitioning of molecular receptors and specific affinity of associated proteins.
In the response to and recovery from a critical homeland security event involving deliberate or accidental release of biological agents, initial decontamination efforts are necessarily followed by tests for the presence of residual live virus or bacteria. Such 'clearance sampling' should be rapid and accurate, to inform decision makers as they take appropriate action to ensure the safety of the public and of operational personnel. However, the current protocol for clearance sampling is extremely time-intensive and costly, and requires significant amounts of laboratory space and capacity. Detection of residual live virus is particularly problematic and time-consuming, as it requires evaluation of replication potential within a eukaryotic host such as chicken embryos. The intention of this project was to develop a new method for clearance sampling, by leveraging Sandia's expertise in the biological and material sciences in order to create a C. elegans-based foam that could be applied directly to the entire contaminated area for quick and accurate detection of any and all residual live virus by means of a fluorescent signal. Such a novel technology for rapid, on-site detection of live virus would greatly interest the DHS, DoD, and EPA, and hold broad commercial potential, especially with regard to the transportation industry.
A microfluidic RNA interference screening device was designed to study which genes are involved in Rift Valley Fever Virus (RVFV) infection. Spots of small interfering RNA (siRNA) are manually spotted onto a glass microscope slide, and aligned to a screening device designed to accommodate cell seeding, siRNA transfection, cell culture, virus infection and imaging analysis. This portable and disposable PDMS-based microfluidic device for RNAi screening was designed for a 96-well library of transfection against variety of gene targets. Current results show transfection of GFP-22 siRNA within the device, as compared to controls, which inhibit the expression of GFP produced by recombinant RVFV. This technique can be applied to host-pathogen interactions for highly dangerous systems in BSL-3/4 laboratories, where bulky robotic equipment is not ideal.
This report provides a detailed overview of the work performed for project number 130781, 'A Systems Biology Approach to Understanding Viral Hemorrhagic Fever Pathogenesis.' We report progress in five key areas: single cell isolation devices and control systems, fluorescent cytokine and transcription factor reporters, on-chip viral infection assays, molecular virology analysis of Arenavirus nucleoprotein structure-function, and development of computational tools to predict virus-host protein interactions. Although a great deal of work remains from that begun here, we have developed several novel single cell analysis tools and knowledge of Arenavirus biology that will facilitate and inform future publications and funding proposals.
Understanding and defending against pathogenic viruses is an important public health and biodefense challenge. The focus of our LDRD project has been to uncover the mechanisms enveloped viruses use to identify and invade host cells. We have constructed interfaces between viral particles and synthetic lipid bilayers. This approach provides a minimal setting for investigating the initial events of host-virus interaction - (i) recognition of, and (ii) entry into the host via membrane fusion. This understanding could enable rational design of therapeutics that block viral entry as well as future construction of synthetic, non-proliferating sensors that detect live virus in the environment. We have observed fusion between synthetic lipid vesicles and Vesicular Stomatitis virus particles, and we have observed interactions between Nipah virus-like particles and supported lipid bilayers and giant unilamellar vesicles.