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1. Inactivation of Coronaviruses and Phage Phi6 from Irradiation across UVC Wavelengths

   https://doi.org/10.1021/acs.estlett.1c00178  

   Ma, Ben ; Linden, Yarrow S. ; Gundy, Patricia M. ; Gerba, Charles P. ; Sobsey, Mark D. ; Linden, Karl G. ( March 2021 , Environmental Science & Technology Letters)

   null (Ed.)

   Ultraviolet (UV) devices emitting UVC irradiation (200− 280 nm) have proven to be effective for virus disinfection, especially on surfaces and in air, due to their rapid effectiveness and limited to no material corrosion. Numerous studies of UV-induced inactivation focused on nonenveloped viruses. Little is known about UVC action on enveloped viruses across UVC wavelengths. In this study, we determined inactivation efficiencies of two coronaviruses (ssRNA) and an enveloped dsRNA bacteriophage surrogate in buffered aqueous solution (pH 7.4) using five commonly available UVC devices that uniquely emit light at different wavelengths spanning 222 nm emitting krypton chloride (KrCl*) excimers to 282 nm emitting UVC LEDs. Our results show that enveloped viruses can be effectively inactivated using UVC devices, among which the KrCl* excimer had the best disinfection performance (i.e., highest inactivation rate) for all three enveloped viruses. The coronaviruses exhibited similar sensitivities to UV irradiation across the UVC range, whereas the bacteriophage surrogate was much more resistant and exhibited significantly higher sensitivity to the Far UVC (<230 nm) irradiation. This study provides necessary information and guidance for using UVC devices for enveloped virus disinfection, which may help control virus transmission in public spaces during the ongoing COVID-19 pandemic and beyond. 

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2. Direct detection of human adenovirus or SARS-CoV-2 with ability to inform infectivity using DNA aptamer-nanopore sensors

   https://doi.org/10.1126/sciadv.abh2848  

   Peinetti, Ana S. ; Lake, Ryan J. ; Cong, Wen ; Cooper, Laura ; Wu, Yuting ; Ma, Yuan ; Pawel, Gregory T. ; Toimil-Molares, María Eugenia ; Trautmann, Christina ; Rong, Lijun ; et al ( September 2021 , Science Advances)

   Viral infections are a major global health issue, but no current method allows rapid, direct, and ultrasensitive quantification of intact viruses with the ability to inform infectivity, causing misdiagnoses and spread of the viruses. Here, we report a method for direct detection and differentiation of infectious from noninfectious human adenovirus and SARS-CoV-2, as well as from other virus types, without any sample pretreatment. DNA aptamers are selected from a DNA library to bind intact infectious, but not noninfectious, virus and then incorporated into a solid-state nanopore, which allows strong confinement of the virus to enhance sensitivity down to 1 pfu/ml for human adenovirus and 1 × 10 4 copies/ml for SARS-CoV-2. Applications of the aptamer-nanopore sensors in different types of water samples, saliva, and serum are demonstrated for both enveloped and nonenveloped viruses, making the sensor generally applicable for detecting these and other emerging viruses of environmental and public health concern. 

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3. Accurate virus identification with interpretable Raman signatures by machine learning

   https://doi.org/10.1073/pnas.2118836119  

   Ye, Jiarong ; Yeh, Yin-Ting ; Xue, Yuan ; Wang, Ziyang ; Zhang, Na ; Liu, He ; Zhang, Kunyan ; Ricker, RyeAnne ; Yu, Zhuohang ; Roder, Allison ; et al ( June 2022 , Proceedings of the National Academy of Sciences)

   Rapid identification of newly emerging or circulating viruses is an important first step toward managing the public health response to potential outbreaks. A portable virus capture device, coupled with label-free Raman spectroscopy, holds the promise of fast detection by rapidly obtaining the Raman signature of a virus followed by a machine learning (ML) approach applied to recognize the virus based on its Raman spectrum, which is used as a fingerprint. We present such an ML approach for analyzing Raman spectra of human and avian viruses. A convolutional neural network (CNN) classifier specifically designed for spectral data achieves very high accuracy for a variety of virus type or subtype identification tasks. In particular, it achieves 99% accuracy for classifying influenza virus type A versus type B, 96% accuracy for classifying four subtypes of influenza A, 95% accuracy for differentiating enveloped and nonenveloped viruses, and 99% accuracy for differentiating avian coronavirus (infectious bronchitis virus [IBV]) from other avian viruses. Furthermore, interpretation of neural net responses in the trained CNN model using a full-gradient algorithm highlights Raman spectral ranges that are most important to virus identification. By correlating ML-selected salient Raman ranges with the signature ranges of known biomolecules and chemical functional groups—for example, amide, amino acid, and carboxylic acid—we verify that our ML model effectively recognizes the Raman signatures of proteins, lipids, and other vital functional groups present in different viruses and uses a weighted combination of these signatures to identify viruses. 

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4. Novel viruses of the family Partitiviridae discovered in Saccharomyces cerevisiae

   https://doi.org/10.1371/journal.ppat.1011418  

   Taggart, Nathan T. ; Crabtree, Angela M. ; Creagh, Jack W. ; Bizarria, Rodolfo ; Li, Shunji ; de la Higuera, Ignacio ; Barnes, Jonathan E. ; Shipley, Mason A. ; Boyer, Josephine M. ; Stedman, Kenneth M. ; et al ( June 2023 , PLOS Pathogens)

   Wang, Aiming (Ed.)

   It has been 49 years since the last discovery of a new virus family in the model yeastSaccharomyces cerevisiae. A large-scale screen to determine the diversity of double-stranded RNA (dsRNA) viruses inS.cerevisiaehas identified multiple novel viruses from the familyPartitiviridaethat have been previously shown to infect plants, fungi, protozoans, and insects. MostS.cerevisiaepartitiviruses (ScPVs) are associated with strains of yeasts isolated from coffee and cacao beans. The presence of partitiviruses was confirmed by sequencing the viral dsRNAs and purifying and visualizing isometric, non-enveloped viral particles. ScPVs have a typical bipartite genome encoding an RNA-dependent RNA polymerase (RdRP) and a coat protein (CP). Phylogenetic analysis of ScPVs identified three species of ScPV, which are most closely related to viruses of the genusCryspovirusfrom the mammalian pathogenic protozoanCryptosporidium parvum. Molecular modeling of the ScPV RdRP revealed a conserved tertiary structure and catalytic site organization when compared to the RdRPs of thePicornaviridae. The ScPV CP is the smallest so far identified in thePartitiviridaeand has structural homology with the CP of other partitiviruses but likely lacks a protrusion domain that is a conspicuous feature of other partitivirus particles. ScPVs were stably maintained during laboratory growth and were successfully transferred to haploid progeny after sporulation, which provides future opportunities to study partitivirus-host interactions using the powerful genetic tools available for the model organismS.cerevisiae.

    

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5. A generalized purification step for viral particles using mannitol flocculation

   https://doi.org/10.1002/btpr.2651  

   Heldt, Caryn L. ; Saksule, Ashish ; Joshi, Pratik U. ; Ghafarian, Majid ( January 2018 , Biotechnology Progress)

   Vaccine manufacturing has conventionally been performed by the developed world using traditional unit operations like filtration and chromatography. There is currently a shift in the manufacturing of vaccines to the less developed world, requiring unit operations that reduce costs, increase recovery, and are amenable to continuous manufacturing. This work demonstrates that mannitol can be used as a flocculant for an enveloped and nonenveloped virus and can purify the virus from protein contaminants after microfiltration. The recovery of the virus ranges from 58 to 96% depending on virus, the filter pore size, and the starting concentration of the virus. Protein removal of 80% was achieved for the small nonenveloped virus using a 0.1 µm filter because proteins were not flocculated with the virus and flowed through the filter. It is hypothesized that mannitol dehydrates the viral surface by controlling the water structure surrounding the virus. Without the ability to become compact, as occurs with proteins, the virus aggregates in the presence of osmolytes and proteins do not. Osmolyte flocculation is a scalable process using high flux microfilters. It has been applied to both an enveloped and nonenveloped virus, making this process friendly to a variety of vaccine and gene therapy products. 

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