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The evolution of analytical techniques has opened the possibilities of accurate analyte detection through a straightforward method and short acquisition time, leading towards their applicability to identify medical conditions. Surface-enhanced Raman spectroscopy (SERS) has long been proven effective for rapid detection and relies on SERS spectra that are unique to each specific analyte. However, the complexity of viruses poses challenges to SERS and hinders further progress in its practical applications. The principle of SERS revolves around the interaction among substrate, analyte, and Raman laser, but most studies only emphasize the substrate, especially label-free methods, and the synergy among these factors is often ignored. Therefore, issues related to reproducibility and consistency of results, which are crucial for medical diagnosis and are the main highlights of this review, can be understood and largely addressed when considering these interactions. Viruses are composed of multiple surface components and can be detected by label-free SERS, but the presence of non-target molecules in clinical samples interferes with the detection process. Appropriate spectral data processing workflow also plays an important role in the interpretation of results. Furthermore, integrating machine learning into data processing can account for changes brought about by the presence of non-target molecules when analyzing spectral features to accurately group the data, for example, whether the sample corresponds to a positive or negative patient, and whether a virus variant or multiple viruses are present in the sample. Subsequently, advances in interdisciplinary fields can bring SERS closer to practical applications., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Jiunn-Der Liao reports financial support was provided by National Science Council. Jiunn-Der Liao reports a relationship with National Cheng Kung University that includes: employment., (Copyright © 2024 Elsevier B.V. All rights reserved.)

The advent of cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET), coupled with computational modeling, has enabled the creation of integrative 3D models of viruses, bacteria, and cellular organelles. These models, composed of thousands of macromolecules and billions of atoms, have historically posed significant challenges for manipulation and visualization without specialized molecular graphics tools and hardware. With the recent advancements in GPU rendering power and web browser capabilities, it is now feasible to render interactively large molecular scenes directly on the web. In this work, we introduce Mesoscale Explorer, a web application built using the Mol* framework, dedicated to the visualization of large-scale molecular models ranging from viruses to cell organelles. Mesoscale Explorer provides unprecedented access and insight into the molecular fabric of life, enhancing perception, streamlining exploration, and simplifying visualization of diverse data types, showcasing the intricate details of these models with unparalleled clarity., (© 2024 The Author(s). Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.)

Chirality is ubiquitous in nature across all length scales, with major implications spanning fields from biology, chemistry and physics to materials science. How chirality propagates from nanoscale building blocks to meso- and macroscopic helical structures remains an open issue. Here, working with a canonical system of filamentous viruses, we demonstrate that their self-assembly into chiral liquid crystal phases quantitatively results from the interplay between two main mechanisms of chirality transfer: electrostatic interactions from the helical charge patterns on the virus surface, and fluctuation-based helical deformations leading to viral backbone helicity. Our experimental and theoretical approach provides a comprehensive framework for deciphering how chirality is hierarchically and quantitatively propagated across spatial scales. Our work highlights the ways in which supramolecular helicity may arise from subtle chiral contributions of opposite handedness that act either cooperatively or competitively, thus accounting for the multiplicity of chiral behaviours observed for nearly identical molecular systems., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Various diseases caused by harmful microorganisms and viruses have caused serious harm and huge economic losses to society. Thus, rapid detection of harmful microorganisms and viruses is necessary for disease prevention and treatment. Nanomaterials have unique properties that other materials do not possess, such as a small size effect and quantum size effect. Introducing nanomaterials into biosensors improves the performance of biosensors for faster and more accurate detection of microorganisms and viruses. This review aims to introduce the different kinds of biosensors and the latest advances in the application of nanomaterials in biosensors. In particular, this review focuses on describing the physicochemical properties of zero-, one-, two-, and three-dimensional nanostructures as well as nanoenzymes. Finally, this review discusses the applications of nanobiosensors in the detection of microorganisms and viruses and the future directions of nanobiosensors.

Membrane fouling by monoclonal antibodies (mAbs) is one of the main challenges in virus-filtration processes. Previous publications attributed membrane fouling to the presence of mAb aggregates in the solution, which block the membrane pores. This fouling mechanism can be solved by a prefilter; however, it was shown that there are mAbs that severely foul the membranes (reduce permeability by 90% and more) even after prefiltering the aggregates, while other mAbs foul the membrane weakly (reduce permeability by ~10% and less). Unfortunately, the differences between the fouling- and the nonfouling mAbs have never been convincingly explained. To get a deeper insight on these differences, we measured the fouling of chemically modified Isoprene-Styrene-4-vinylpyridine (ISV) membranes (TeraPore Technologies) by 8 mAbs exhibiting different hydrophobicity and charge. The results show that mAb solutions with low concentration of aggregates foul ISV membranes via an adsorptive mechanism, and the adsorption is driven mainly by hydrophobic forces between the mAb and the membrane. The charge of the mAbs plays a secondary role in fouling. We want to emphasize that the conclusions pertain to ISV membranes; the insights presented in this paper can potentially be used to engineer new surface chemistries to mitigate fouling of other virus-filtration and/or ultrafiltration membranes., (© 2023 Wiley Periodicals LLC.)

We develop a microscopic model of antibiotic diffusion in virus suspensions in a liquid crystalline state. We then approximate this with an effective homogenised model that is more amenable to analytical investigation, to understand the effect of charge on the antibiotic tolerance. We show that liquid crystalline virus suspensions slow down antibiotics significantly, and that electric charge strongly contributes to this by influencing the effective diameter and adsorptive capacity of the liquid crystalline viruses so that charged antibiotics diffuse much slower than neutral ones; this can be directly and efficiently derived from the homogenised model and is in good agreement with experiments in microbiology. Charge is also found to affect the relationship between antibiotic diffusion and viral packing density in a nontrivial way. The results elucidate the effect of charge on antibiotic tolerance in liquid crystalline biofilms in a manner that is straightforwardly extendable to other soft matter systems.

Monoclonal antibodies (mAbs) are an essential class of biotherapeutics. A platform process is used for mAb development to ensure clinically safe and stable molecules. Regulatory authorities ensure that mAb production processes include sufficient viral clearance steps to achieve less than one virus particle per million doses of product. Virus filtration is used for size-based removal of enveloped and nonenveloped viruses during downstream processing of mAbs. Process development in mAb purification relies on empirical approaches and often includes adsorptive prefiltration to mitigate virus filter fouling. Opportunities for molecular-level prediction of mAb filterability are needed to plug the existing knowledge gap in downstream processing. A molecular-level approach to understanding the factors influencing mAb filterability may reduce process development time, material loss, and processing costs due to oversized virus filters. In this work, pH step gradient fractionation was applied on polished bulk mAb feed to obtain concentrated pools of fractionated mAb variants. Biophysical properties and quality attributes of fractionated pools, including oligomeric state (size), isoelectric point profile, diffusion interaction parameters, and glycoform profile, were determined using bioanalytical methods. Filterability (loading and throughput) of fractionated pools were evaluated. Statistical methods were used to obtain correlations between quality attributes of mAb fractions and filterability on the Viresolve Pro virus filter., (© 2024 EMD Millipore Corporation. Biotechnology Progress published by Wiley Periodicals LLC on behalf of American Institute of Chemical Engineers.)

For numerous viruses, their capsid assembly is composed of two steps. The first step is that virus structural protein monomers are polymerized to building blocks. Then, these building blocks are cumulative and efficiently assembled to virus capsid shell. These building block polymerization reactions in the first step are fundamental for virus assembly, and some drug targets were found in this step. In this work, we focused on the first step. Often, virus building blocks consisted of less than six monomers. That is, dimer, trimer, tetramer, pentamer, and hexamer. We presented mathematical models for polymerization chemical reactions of these five building blocks, respectively. Then, we proved the existence and uniqueness of the positive equilibrium solution for these mathematical models one by one. Subsequently, we also analyzed the stability of the equilibrium states, respectively. These results may provide further insight into property of virus building block polymerization chemical reactions in vivo .

X-ray crystallography and cryo-electron microscopy have enabled the determination of structures of numerous viruses at high resolution and have greatly advanced the field of structural virology. These structures represent only a subset of snapshot end-state conformations, without describing all conformational transitions that virus particles undergo. Allostery plays a critical role in relaying the effects of varied perturbations both on the surface through environmental changes and protein (receptor/antibody) interactions into the genomic core of the virus. Correspondingly, allostery carries implications for communicating changes in genome packaging to the overall stability of the virus particle. Amide hydrogen/deuterium exchange mass spectrometry (HDXMS) of whole viruses is a powerful probe for uncovering virus allostery. Here we critically discuss advancements in understanding virus dynamics by HDXMS with single particle cryo-EM and computational approaches., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Facing the escalating threat of viruses worldwide, the development of efficient sensor elements for rapid virus detection has never been more critical. Traditional point-of-care (POC) sensors struggle due to their reliance on fragile biological receptors and limited adaptability to viral strains. In this study, we introduce a nanosensor design for receptor-free virus recognitions using near-infrared (NIR) fluorescent single-walled carbon nanotubes (SWCNTs) functionalized with a poly(ethylene glycol) (PEG)-phospholipid (PEG-lipid) array. Three-dimensional (3D) corona interfaces of the nanosensor array enable selective and sensitive detection of diverse viruses, including Ebola, Lassa, H3N2, H1N1, Middle East respiratory syndrome (MERS), severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1), and SARS-CoV-2, even without any biological receptors. The PEG-lipid components, designed considering chain length, fatty acid saturation, molecular weight, and end-group moieties, allow for precise quantification of viral recognition abilities. High-throughput automated screening of the array demonstrates how the physicochemical properties of the PEG-lipid/SWCNT 3D corona interfaces correlate with viral detection efficiency. Utilizing molecular dynamics and AutoDock simulations, we investigated the impact of PEG-lipid components on 3D corona interface formation, such as surface coverage and hydrodynamic radius and specific molecular interactions based on chemical potentials. Our findings not only enhance detection specificity across various antigens but also accelerate the development of sensor materials for promptly identifying and responding to emerging antigen threats.

ViralZone (http://viralzone.expasy.org) is a knowledge repository for viruses that links biological knowledge and databases. It contains data on virion structure, genome, proteome, replication cycle and host-virus interactions. The new update provides better access to the data through contextual popups and higher resolution images in Scalable Vector Graphics (SVG) format. These images are designed to be dynamic and interactive with human viruses to give users better access to the data. In addition, a new coronavirus-specific resource provides regularly updated data on variants and molecular biology of SARS-CoV-2. Other virus-specific resources have been added to the database, particularly for HIV, herpesviruses and poxviruses., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Living viruses characterized by distinctive biological functions including specific targeting, gene invasion, immune modulation, and so forth have been receiving intensive attention from researchers worldwide owing to their promising potential for producing numerous theranostic modalities against diverse pathological conditions. Nevertheless, concerns during applications, such as rapid immune clearance, altering immune activation modes, insufficient gene transduction efficiency, and so forth, highlight the crucial issues of excessive therapeutic doses and the associated biosafety risks. To address these concerns, synthetic nanomaterials featuring unique physical/chemical properties are frequently exploited as efficient drug delivery vehicles or treatments in biomedical domains. By constant endeavor, researchers nowadays can create adaptable living virus-based nanohybrids (LVN) that not only overcome the limitations of virotherapy, but also combine the benefits of natural substances and nanotechnology to produce novel and promising therapeutic and diagnostic agents. In this review, we discuss the fundamental physiochemical properties of the viruses, and briefly outline the basic construction methodologies of LVN. We then emphasize their distinct diagnostic and therapeutic performances for various diseases. Furthermore, we survey the foreseeable challenges and future perspectives in this interdisciplinary area to offer insights. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Therapeutic Approaches and Drug Discovery > Emerging Technologies., (© 2023 Wiley Periodicals LLC.)

Around 30% of the scientific papers published on imprinted polymers describe the recognition of proteins, nucleic acids, viruses, and cells. The straightforward synthesis from only one up to six functional monomers and the simple integration into a sensor are significant advantages as compared with enzymes or antibodies. Furthermore, they can be synthesized against toxic substances and structures of low immunogenicity and allow multi-analyte measurements via multi-template synthesis. The affinity is sufficiently high for protein biomarkers, DNA, viruses, and cells. However, the cross-reactivity of highly abundant proteins is still a challenge., (© 2023. The Author(s), under exclusive license to Springer Nature Switzerland AG.)

The removal of viruses by filtration is a critical unit operation to ensure the overall safety of monoclonal antibody (mAb) products. Many mAbs show very low filtrate flux during virus removal filtration, although there are still significant uncertainties regarding both the mechanisms and antibody properties that determine the filtration behavior. Experiments were performed with three highly purified mAbs through three different commercial virus filters (Viresolve Pro, Viresolve NFP, and Pegasus SV4) with different pore structures and chemistries. The flux decline observed during mAb filtration was largely reversible, even under conditions where the filtrate flux with the mAb was more than 100-fold smaller than the corresponding buffer flux. The extent of flux decline was highly correlated with the hydrodynamic diameter of the mAb as determined by dynamic light scattering (DLS). The mAb with the lowest filtrate flux for all three membranes showed the largest attractive intermolecular interactions and the greatest hydrophobicity, with the latter determined by binding to a butyl resin in an analytical hydrophobic interaction chromatography (HIC) column. These results strongly suggest that the flux behavior is dominated by reversible self-association of the mAbs, providing important insights into the design of more effective virus filtration processes and in the early identification of problematic mAbs/solution conditions., (© 2023 The Authors. Biotechnology Journal published by Wiley-VCH GmbH.)

Before the resolution revolution, cryoelectron microscopy (cryo-EM) single-particle analysis (SPA) already achieved resolutions beyond 4 Å for certain icosahedral viruses, enabling ab initio atomic model building of these viruses. As the only samples that achieved such high resolution at that time, cryo-EM method development was closely intertwined with the improvement of reconstructions of symmetrical viruses. Viral morphology exhibits significant diversity, ranging from small to large, uniform to non-uniform, and from containing single symmetry to multiple symmetries. Furthermore, viruses undergo conformational changes during their life cycle. Several methods, such as asymmetric reconstruction, Ewald sphere correction, cryoelectron tomography (cryo-ET), and sub-tomogram averaging (STA), have been developed and applied to determine virus structures in vivo and in vitro. This review outlines current advanced cryo-EM methods for high-resolution structure determination of viruses and summarizes accomplishments obtained with these approaches. Moreover, persisting challenges in comprehending virus structures are discussed and we propose potential solutions., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023. Published by Elsevier Ltd.)

Advancements in the field of cryo-electron microscopy (cryo-EM) have greatly contributed to our current understanding of virus structures and life cycles. In this review, we discuss the application of single particle cryo-electron microscopy (EM) for the structure elucidation of small enveloped icosahedral viruses, namely, alpha- and flaviviruses. We focus on technical advances in cryo-EM data collection, image processing, three-dimensional reconstruction, and refinement strategies for obtaining high-resolution structures of these viruses. Each of these developments enabled new insights into the alpha- and flavivirus architecture, leading to a better understanding of their biology, pathogenesis, immune response, immunogen design, and therapeutic development., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Recently, Maassen et al. measured an appreciable pH difference between the bulk solution and the solution in the lumen of virus-like particles, self-assembled in an aqueous buffer solution containing the coat proteins of a simple plant virus and polyanions (Maassen, S. J.; et al. Small 2018 , 14 , 1802081). They attribute this to the Donnan effect, caused by an imbalance between the number of negative charges on the encapsulated polyelectrolyte molecules and the number of positive charges on the RNA binding domains of the coat proteins that make up the virus shell or capsid. By applying Poisson-Boltzmann theory, we confirm this conclusion and show that simple Donnan theory is accurate even for the smallest of viruses and virus-like particles. This, in part, is due to the additional screening caused by the presence of a large number of immobile charges in the cavity of the shell. The presence of a net charge on the outer surface of the capsid we find in practice to not have a large effect on the pH shift. Hence, Donnan theory can indeed be applied to connect the local pH and the amount of encapsulated material. The large shifts up to a full pH unit that we predict must have consequences for applications of virus capsids as nanocontainers in bionanotechnology and artificial cell organelles.

While the application of cryogenic electron microscopy (cryo-EM) to helical polymers in biology has a long history, due to the huge number of helical macromolecular assemblies in viruses, bacteria, archaea, and eukaryotes, the use of cryo-EM to study synthetic soft matter noncovalent polymers has been much more limited. This has mainly been due to the lack of familiarity with cryo-EM in the materials science and chemistry communities, in contrast to the fact that cryo-EM was developed as a biological technique. Nevertheless, the relatively few structures of self-assembled peptide nanotubes and ribbons solved at near-atomic resolution by cryo-EM have demonstrated that cryo-EM should be the method of choice for a structural analysis of synthetic helical filaments. In addition, cryo-EM has also demonstrated that the self-assembly of soft matter polymers has enormous potential for polymorphism, something that may be obscured by techniques such as scattering and spectroscopy. These cryo-EM structures have revealed how far we currently are from being able to predict the structure of these polymers due to their chaotic self-assembly behavior.

It is difficult to overestimate the urgency of the problem of well-timed diagnosis of viral infections. According to the WHO, dozens of outbreaks of viral diseases are recorded annually, both in developing and developed countries. Moreover, the seasonal flu virus alone is capable of infecting up to 20% of the population, even in European countries with a high level of medicine. And the annual number of deaths due to viral infections, according to official statistics, exceeds 600 thousand people around the world. That's why the provision of a reliable and fairly rapid diagnosis of viruses, along with subsequent therapy, makes a significant contribution to reducing the incidence of mortality. Despite the fact that PCR-based methods currently remain the most common method for identifying viruses in clinical practice, as recent experience shows, in addition to the already known disadvantages, in the event of large outbreaks, such test systems may simply not be in the required amount. In this regard, it is necessary to supplement and improve the existing tools for identification and research of clinically significant viruses. The MALDI-TOF mass spectrometry method combines a degree of accuracy and versatility, sufficient both for the identification of clinical strains isolated from patients, and for the study of the phenotypic properties of viruses in research laboratories and centers. This article presents and summarizes the main data on the existing or potential application of the method of time-of-flight mass spectrometry with matrix-associated laser desorption / ionization for the identification or study of viruses., Competing Interests: The authors declare no conflict of interest.

Liquid-electron microscopy (EM), the room temperature correlate to cryo-EM, is an exciting new technique delivering real-time data of dynamic reactions in solution. Here, we explain how liquid-EM gained popularity in recent years by examining key experiments conducted on viral assemblies and host-pathogen interactions. We describe developing workflows for specimen preparation, data collection, and computing processes that led to the first high-resolution virus structures in a liquid environment. Equally important, we review why liquid-electron tomography may become the next big thing in biomedical research due to its ability to monitor live viruses entering cells within seconds. Taken together, we pose the idea that liquid-EM can serve as a dynamic complement to current cryo-EM methods, inspiring the "real-time revolution" in nanoscale imaging., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Gastroenteritis, as one of the main worldwide health challenges, especially in children, leads to 3-6 million deaths annually and causes nearly 20% of the total deaths of children aged ˂5 years, of which ~1.5 million gastroenteritis deaths occur in developing nations. Viruses are the main causative agent (~70%) of gastroenteritis episodes and their specific and early diagnosis via laboratory assays is very helpful for having successful antiviral therapy and reduction in infection burden. Regarding this importance, the present literature is the first review of updated improvements in the employing of different types of biosensors such as electrochemical, optical, and piezoelectric for sensitive, simple, cheap, rapid, and specific diagnosis of human gastroenteritis viruses. The Introduction section is a general discussion about the importance of viral gastroenteritis, types of viruses that cause gastroenteritis, and reasons for the combination of conventional diagnostic tests with biosensors for fast detection of viruses associated with gastroenteritis. Following the current laboratory detection tests for human gastroenteritis viruses and their limitations (with subsections: Electron Microscope (EM), Cell Culture, Immunoassay, and Molecular Techniques), structural features and significant aspects of various biosensing methods are discussed in the Biosensor section. In the next sections, basic information on viruses causing gastroenteritis and recent developments for fabrication and testing of different biosensors for each virus detection are covered, and the prospect of future developments in designing different biosensing platforms for gastroenteritis virus detection is discussed in the Conclusion and Future Directions section as well.

Asymmetric structural elements are typically not readily visualized in icosahedral viruses that have other obvious symmetrical features and most asymmetry has gone unresolved for decades. Asymmetric features may be incorporated during assembly or maturation or develop during key steps in the infectious cycle of the virus. However, resolving asymmetric features requires abandoning capsid-wide symmetry averaging and relying on special applications during single-particle cryogenic electron microscopy (cryo-EM) analysis. Thanks to the advances in the cryo-EM field, we are learning more about asymmetry of viruses. Here we summarize some of what is currently known about asymmetric structural features using as examples members of the Togaviridae, Flaviviridae, Herpesviridae, Parvoviridae, and Papillomaviridae., (Copyright © 2022 Elsevier B.V. All rights reserved.)

As epitomised by the COVID-19 pandemic, diseases caused by viruses are one of the greatest health and economic burdens to human society. Viruses are 'nanostructures', and their small size (typically less than 200 nm in diameter) can make it challenging to obtain images of their morphology and structure. Recent advances in fluorescence microscopy have given rise to super-resolution techniques, which have enabled the structure of viruses to be visualised directly at a resolution in the order of 20 nm. This mini-review discusses how recent state-of-the-art super-resolution imaging technologies are providing new nanoscale insights into virus structure., (Copyright © 2022 The Author. Published by Elsevier B.V. All rights reserved.)

An efficient chromatography-based virus purification method has been developed and validated for the non-pathogenic infectious virus PRD1. Compared to the conventional method that consists of relatively time-consuming and labour-intensive precipitation and density gradient ultracentrifugation steps, the method developed here is performed in a single flow using tandem-coupled anion exchange and size exclusion chromatography (AIEX-SEC) columns. This inline approach helps to minimize the loss of virus in the process and streamlines time consumption, since no physical transfer of the sample is required between purification steps. In the development process, sample feed composition, dynamic binding capacity and elution conditions for the AIEX resin as well as different exclusion limits for SEC resins were optimized to achieve maximal yield of pure infectious viruses. Utilizing this new approach, a high-quality virus sample was produced from a lysate feed in 320 min with a total yield of 13 mg purified particles per litre of cell lysate, constituting a 3.5-fold yield increase as compared to the conventional method, without compromising the high specific infectivity of the product (6 × 10 12 to 7 × 10 12 pfu/mg of protein). The yield of infectious viruses of the lysate feed was 54%. The easy scalability of chromatography-based methods provide a direct route to industrial usage without any significant changes needed to be made to the purification regime. This is especially interesting as the method has high potential to be used for purification of various viruses and nanoparticles, including adenovirus., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)

Virus removal filtration is a critical step in the manufacture of monoclonal antibody products, providing a robust size-based removal of both enveloped and non-enveloped viruses. Many monoclonal antibodies show very large reductions in filtrate flux during virus filtration, with the mechanisms governing this behavior and its dependence on the properties of the virus filter and antibody remaining largely unknown. Experiments were performed using the highly asymmetric Viresolve® Pro and the relatively homogeneous Pegasus™ SV4 virus filters using a highly purified monoclonal antibody. The filtrate flux for a 4 g/L antibody solution through the Viresolve® Pro decreased by about 10-fold when the filter was oriented with the skin side down but by more than 1000-fold when the asymmetric filter orientation was reversed and used with the skin side up. The very large flux decline observed with the skin side up could be eliminated by placing a large pore size prefilter directly on top of the virus filter; this improvement in filtrate flux was not seen when the prefilter was used inline or as a batch prefiltration step. The increase in flux due to the prefilter was not related to the removal of large protein aggregates or to an alteration in the extent of concentration polarization. Instead, the prefilter appears to transiently disrupt reversible associations of the antibodies caused by strong intermolecular attractions. These results provide important insights into the role of membrane morphology and antibody properties on the filtrate flux during virus filtration., (© 2022 American Institute of Chemical Engineers.)

Tilapia Lake Virus Disease (TiLVD) is caused by Tilapia Lake Virus (TiLV), and it has a cumulative mortality rate of up to 90% in Nile tilapia (Oreochromis niloticus). TiLV is a negative enveloped single-stranded RNA virus with 10 genomic segments. Segment 5 (S5) and segment 6 (S6) were predicted to include a signaling peptide, suggesting that the encoded proteins of these two segments may exist as part of the virus envelope. Based on bioinformatic predictions, the S5 and S6 proteins in this study were produced, including S5 27-343 , S5 27-172 , S5 196-272 , S6 30-317 , S6 30-190 , and S6 200-317. All proteins were tested for their expression in Escherichia coli. Only S5 196-272 and S6 200-317 were expressed as soluble and insoluble proteins, respectively. The soluble protein was purified using affinity chromatography, whereas the insoluble protein was solubilized using 6 M urea lysis buffer before purification. Both proteins were further purified using gel filtration chromatography, and the results showed a symmetric peak of both proteins suggested a high degree of uniformity in the conformation of these proteins. Antigenicity results indicated that these proteins were recognized by serum from TiLV-infected fish. The immunization tests revealed that serum antibodies levels in Nile tilapia produced by S5 196-272 and S6 200-317 were significantly increased (p-value < 0.05) at 7 days post-immunization (dpi) compared to antibody levels on Day 0 (D0). All the results combined suggested a potential vaccine candidate of S5 and S6 for TiLV protection in Nile tilapia., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Quantitative physicochemical perspective on life processes has been a great asset, in bioengineering and biotechnology. The quantitative physicochemical approach can be applied to practically all organisms, including viruses, if their chemical composition and thermodynamic properties are known. In this paper, a new method is suggested for determining elemental composition of viruses, based on atom counting. The atom counting method requires knowledge of genetic sequence, protein sequences and protein copy numbers. An algorithm was suggested for a program that finds elemental composition of various viruses (DNA or RNA, enveloped or non-enveloped). Except for the nucleic acid, capsid proteins, lipid bilayer and carbohydrates, this method includes membrane proteins, as well as spike proteins. The atom counting method has been compared with the existing molecular composition and geometric methods on 5 viruses of different morphology, as well as experimentally determined composition of the poliovirus. The atom counting method was found to be more accurate in most cases. The three methods were found to be complementary, since they require different kind of input information. Moreover, since the 3 methods rest on different assumptions, results of one model can be compared to those of the other two., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Viruses are macromolecular machineries that hijack cellular metabolism for replication. Enveloped viruses comprise a large variety of RNA and DNA viruses, many of which are notorious human or animal pathogens. Despite their importance, the presence of lipid bilayers in their assembly has made most enveloped viruses too pleomorphic to be reconstructed as a whole by traditional structural biology methods. Furthermore, structural biology of the viral lifecycle was hindered by the sample thickness. Here, I review the recent advances in the applications of cryo-electron tomography (cryo-ET) on enveloped viral structures and intracellular viral activities., Competing Interests: Declaration of interests No interests to declare., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Liquid-liquid phase separation (LLPS) is critical for assembling membraneless organelles (MLOs) such as nucleoli, P-bodies, and stress granules, which are involved in various physiological processes and pathological conditions. While the critical role of RNA in the formation and the maintenance of MLOs is increasingly appreciated, there is still a lack of specific resources for LLPS-related RNAs. Here, we presented RPS (http://rps.renlab.org), a comprehensive database of LLPS-related RNAs in 20 distinct biomolecular condensates from eukaryotes and viruses. Currently, RPS contains 21,613 LLPS-related RNAs with three different evidence types, including 'Reviewed', 'High-throughput' and 'Predicted'. RPS provides extensive annotations of LLPS-associated RNA properties, including sequence features, RNA structures, RNA-protein/RNA-RNA interactions, and RNA modifications. Moreover, RPS also provides comprehensive disease annotations to help users to explore the relationship between LLPS and disease. The user-friendly web interface of RPS allows users to access the data efficiently. In summary, we believe that RPS will serve as a valuable platform to study the role of RNA in LLPS and further improve our understanding of the biological functions of LLPS., (© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Despite filamentous viruses represent an important portion of the universe of viruses, their 3D structures available are quite limited, particularly if compared to the large number of structures of icosahedral viruses present in the Protein Data Bank. As a matter of fact, flexible filamentous viruses cannot be grown as single crystals and past structural studies have mostly been limited to X-ray fiber diffraction or to the determination of the structure of isolated viral proteins. Only very recently, several structures of filamentous viruses have become available, owing to the recent development of cryo-electron microscopy. This technique has given a strong impulse to the field and has allowed the building of reliable molecular models of entire viruses, in some cases at a nearly atomic resolution level. In this paper we briefly describe the architecture of filamentous viruses that infect bacteria, archaea, plants and humans. It is easy to foresee that more new structures of filamentous viruses will become available soon and they will allow a better understanding of the rules underlying the structural organization of these organisms so relevant for the life on our planet., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Trapping by active sites on surfaces plays important roles in various chemical and biological processes, including catalysis, enzymatic reactions, and viral entry into host cells. However, the mechanisms of these processes remain not well understood, mostly because the existing theoretical descriptions are not fully accounting for the role of the surfaces. Here, we present a theoretical investigation on the dynamics of surface-assisted trapping by specific active sites. In our model, a diffusing particle can occasionally reversibly bind to the surface and diffuse on it before reaching the final target site. An approximate theoretical framework is developed, and its predictions are tested by Brownian dynamics computer simulations. It is found that the surface diffusion can be crucial in mediating trapping by active sites. Our theoretical predictions work reasonably well as long as the area of the active site is much smaller than the overall surface area. Potential applications of our approach are discussed.

Viruses are obligate parasites that depend on a host cell for replication and survival. Consequently, to fully understand the viral processes involved in infection and replication, it is fundamental to study them in the cellular context. Often, viral infections induce significant changes in the subcellular organization of the host cell due to the formation of viral factories, alteration of cell cytoskeleton and/or budding of newly formed particles. Accurate 3D mapping of organelle reorganization in infected cells can thus provide valuable information for both basic virus research and antiviral drug development. Among the available techniques for 3D cell imaging, cryo-soft X-ray tomography stands out for its large depth of view (allowing for 10 µm thick biological samples to be imaged without further thinning), its resolution (about 50 nm for tomographies, sufficient to detect viral particles), the minimal requirements for sample manipulation (can be used on frozen, unfixed and unstained whole cells) and the potential to be combined with other techniques (i.e., correlative fluorescence microscopy). In this review we describe the fundamentals of cryo-soft X-ray tomography, its sample requirements, its advantages and its limitations. To highlight the potential of this technique, examples of virus research performed at BL09-MISTRAL beamline in ALBA synchrotron are also presented.

The viral protein containers that encapsulate a virus' genetic material are repurposed as virus-like particles in a host of nanotechnology applications, including cargo delivery, storage, catalysis, and vaccination. These viral architectures have evolved to sit on the knife's edge between stability, to provide adequate protection for their genetic cargoes, and instability, to enable their efficient and timely release in the host cell environment upon environmental cues. By introducing a percolation theory for viral capsids, we demonstrate that the geometric characteristics of a viral capsid in terms of its subunit layout and intersubunit interaction network are key for its disassembly behavior. A comparative analysis of all alternative homogeneously tiled capsid structures of the same stoichiometry identifies evolutionary drivers favoring specific viral geometries in nature and offers a guide for virus-like particle design in nanotechnology.

The rapid growth in the global human population has increased the prevalence of emerging infectious diseases, which poses a major risk to public health. In search of effective clinical solutions, the acquisition of knowledge and understanding of biomolecular processes associated with viral pathogens represents a prerequisite. In this context, biophysical engineering approaches are particularly promising since they can resolve biomolecular interactions systematically by circumventing the complexities associated with experiments involving natural biological systems. The engineering approaches encompass the design and construction of biomimetic platforms that simulate the physiological system. This approach enables us to characterize, measure, and quantitatively analyze biomolecular interactions.In this Account, we summarize biophysical measurements that our group has successfully adopted to develop broad-spectrum antiviral drugs based on the lipid envelope antiviral disruption (LEAD) strategy, targeting the structural integrity of the outer viral membrane to abrogate viral infectivity. We particularly focus on the engineering aspects related to the design and construction of the tethered lipid vesicle platform, which closely mimics the viral membrane. We first outline the development of the LEAD agents screening platform that integrates soft matter design components with biomaterials and surface functionalization strategies to facilitate parallel measurements tracking peptide-induced destabilization of nanoscale, virus-mimicking vesicles with tunable size and composition. Then, we describe how this platform can be effectively employed to gain insights into the membrane curvature dependency of certain peptides. The fundamental knowledge acquired through this systematic process is crucial in the identification and subsequent development of antiviral drug candidates. In particular, we highlight the development of curvature-sensitive α-helical (AH) peptides as a broad-spectrum antiviral agent that has been demonstrated as an effective therapeutic treatment against multiple enveloped viruses. Also, we introduce a tethered cluster of vesicles to mimic clusters of enveloped viruses, exhibiting higher infectivity levels in the biological system. Then, we discuss key considerations, including experimental artifacts, namely dye leakage and imaging-related photobleaching, and corresponding corrective measures to improve the accuracy of quantitative interpretation. With the ongoing development and application of the tethered lipid vesicle platform, there is a compelling opportunity to explore fundamental biointerfacial science and develop a new class of broad-spectrum antiviral agents to prepare for the future membrane-enveloped viral pandemics.

It is intriguing to think that over millions of years, groups of nucleic acids got the chance to hold together with groups of proteins to build up what today is called a virus. Their only goal is to guarantee a successful replication inside a host. If their genome information is preserved, the task is accomplished. Viruses have evolved to infect organisms and propagate with high degree of adaptation, as it is the case of the SARS-CoV-2, agent of the 2020 world pandemic. The technological progress observed in the field of structural biology, especially in cryo-EM, has offered scientists the possibility of a better understanding of virus origins, behavior, and structural organization. In this minireview we summarize few perspectives about the origins and organization of viruses and the advances of cryo-EM to aid structural virologists to sample the virosphere., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Recent research has highlighted the immense potential of the quantum dot (QD)-based single-virus tracking (SVT) technique in virology. In these experiments, the infection behaviors of single viruses or viral components, labeled with QDs, could be tracked on time scales of milliseconds to hours in host cells. The trajectories of individual viruses are reconstructed with nanometer accuracy, and the underlying dynamic information on virus infection can be extracted to uncover the infection mechanisms of viruses. Therefore, QD-based single-virus tracking (QSVT) is an exquisitely selective and powerful approach to investigating how viruses are internalized in host cells dynamically to release their genome for viral replication and assembly that ensure the completion of viral life cycles.QDs are better candidates than organic dyes and fluorescent proteins for virus labeling and subsequent SVT due to the following considerations: (i) the high brightness of QDs makes it possible to label a virus with sufficient brightness using very few QDs or even just one QD; (ii) the extraordinary photostability of QDs allows one to track the infection process long term and quantify low probability events; (iii) the color-tunable emission property of QDs ensures multicolor labeling of various components of a virus simultaneously; and (iv) the abundant surface ligands of QDs facilitate the conjugation of a virus with a variety of labeling strategies. Therefore, the photoproperties of QDs make it possible to perform multicolor long-term SVT experiments quantitatively. Nowadays, the QD-based SVT (QSVT) technique has made prodigious achievements in unraveling the entry, trafficking, and uncoating mechanisms of viruses. This fascinating technique can provide spatiotemporal dynamic information on the viral journey in unprecedented detail and has revolutionized our understanding of virus infection.In this Account, we first introduce the advantages and the limitations of conventional SVT in virological research and the unique features of QDs as labels in the SVT field. We subsequently focus on the principles and related methods of QSVT and the current state of QD chemistry and QD-based virus labeling that resolves many issues associated with the tracking of individual viruses in live cells. Then we emphasize some new findings by this technique in the study of infection mechanisms. Finally, we will provide our insights into future challenges on this topic. With this Account, we hope to further stimulate the development of QSVT with a combined effort from different disciplines and, more importantly, to accelerate the applications of QSVT in virological research.

The emergence of novel viral infections of zoonotic origin and mutations of existing human pathogenic viruses represent a serious concern for public health. It warrants the establishment of better interventions and protective therapies to combat the virus and prevent its spread. Surface glycoproteins catalyzing the fusion of viral particles and host cells have proven to be an excellent target for antivirals as well as vaccines. This review focuses on recent advances for computational structure-based design of antivirals and vaccines targeting viral fusion machinery to control seasonal and emerging respiratory viruses.

Host plasma membrane protein SERINC5 is incorporated into budding retrovirus particles where it blocks subsequent entry into susceptible target cells. Three structurally unrelated proteins encoded by diverse retroviruses, human immunodeficiency virus type 1 (HIV-1) Nef, equine infectious anemia virus (EIAV) S2, and ecotropic murine leukemia virus (MLV) GlycoGag, disrupt SERINC5 antiviral activity by redirecting SERINC5 from the site of virion assembly on the plasma membrane to an internal RAB7+ endosomal compartment. Pseudotyping retroviruses with particular glycoproteins, e.g., vesicular stomatitis virus glycoprotein (VSV G), renders the infectivity of particles resistant to inhibition by virion-associated SERINC5. To better understand viral determinants for SERINC5-sensitivity, the effect of SERINC5 was assessed using HIV-1, MLV, and Mason-Pfizer monkey virus (M-PMV) virion cores, pseudotyped with glycoproteins from Arenavirus, Coronavirus, Filovirus, Rhabdovirus, Paramyxovirus, and Orthomyxovirus genera. SERINC5 restricted virions pseudotyped with glycoproteins from several retroviruses, an orthomyxovirus, a rhabdovirus, a paramyxovirus, and an arenavirus. Infectivity of particles pseudotyped with HIV-1, amphotropic-MLV (A-MLV), or influenza A virus (IAV) glycoproteins, was decreased by SERINC5, whether the core was provided by HIV-1, MLV, or M-PMV. In contrast, particles pseudotyped with glycoproteins from M-PMV, parainfluenza virus 5 (PIV5), or rabies virus (RABV) were sensitive to SERINC5, but only with particular retroviral cores. Resistance to SERINC5 did not correlate with reduced SERINC5 incorporation into particles, route of viral entry, or absolute infectivity of the pseudotyped virions. These findings indicate that some non-retroviruses may be sensitive to SERINC5 and that, in addition to the viral glycoprotein, the retroviral core influences sensitivity to SERINC5.

Nanotechnology is the science of nano-sized particles/structures (~100 nm) having a high surface-to-volume ratio that can modulate the physical, chemical and biological properties of the chemical compositions. In last few decades, nanoscience has attracted the attention of the scientific community worldwide due to its potential uses in the pharmacy, medical diagnostics and disease treatment, energy, electronics, agriculture, chemical and space industries. The properties of nanoparticles (NPs) are size and shape dependent. These characteristic features of nanoparticles can be explored for various other applications such as computer transistors, chemical sensors, electrometers, memory schemes, reusable catalysts, biosensing, antimicrobial activity, nanocomposites, medical imaging, tumor detection and drug delivery. Therefore, synthesizing nanoparticles of desired size, structure, monodispersity and morphology is crucial for the aforementioned applications. Recent advancements in nanotechnology aim at the synthesis of nanoparticles/materials using reliable, innoxious and novel ecofriendly techniques. In contrast to the traditional methods, the biosynthesis of nanoparticles of a desired nature and structure using the microbial machinery is not only quicker and safer but more environmentally friendly. Various microbes, including bacteria, actinobacteria, fungi, yeast, microalgae and viruses, have recently been explored for the synthesis of metal, metal oxide and other important NPs through intracellular and extracellular processes. Some bacteria and microalgae possess specific potential to fabricate distinctive nanomaterials such as exopolysaccharides, nanocellulose, nanoplates and nanowires. Moreover, their ability to synthesize nanoparticles can be enhanced using genetic engineering approaches. Thus, the use of microorganisms for synthesis of nanoparticles is unique and has a promising future. The present review provides explicit information on different strategies for the synthesis of nanoparticles using microbial cells; their applications in bioremediation, agriculture, medicine and diagnostics; and their future prospects.

Aptamers are short single-stranded DNA or RNA oligonucleotides selected by the technique of systematic evolution of ligands by exponential enrichment (SELEX). Aptamers have been demonstrated to bind various targets from small-molecule to cells or even tissues in the way of antibodies. Thus, they are called chemical antibodies. We summarize and evaluate recent developments in aptamer-based sensors (for short aptasensors) for virus detection in this review. These aptasensors are mainly classified into optical and electronic aptasensors based on the type of transducer. Nowadays, the smartphone has become the most widely used mobile device with billions of users worldwide. Considering the ongoing COVID-19 outbreak, smartphone-based aptasensors for a portable and point-of-care test (POCT) of COVID-19 detection will be of great importance in the future., (© 2021 Wiley-VCH GmbH.)

The development of organic nanoparticles that fluoresce in the near-infrared, especially in the second near-infrared (NIR-II) window, improves in vivo fluorescence imaging due to deeper penetration and higher spatiotemporal resolution. We report two kinds of NIR-II fluorescent molecules with twisted intramolecular charge-transfer (TICT) and aggregation-induced emission (AIE) characteristics. The virus-like particles (VLPs) of simian virus 40 (SV40) were used as templates to encapsulate the molecules in a well-defined structure (referred to as CH1-SV40 and CH2-SV40). The CH1-SV40 dots exhibited a highly uniform size of 21.5 nm, strong fluorescence, high photostability, and good biocompatibility in vitro and in vivo. Their fluorescence spectrum exhibited a peak at 955 nm, with a tail extending to 1200 nm. Moreover, the CH1-SV40 dots, with a quantum yield of 13.03%, enabled blood vessel imaging and image-guided surgery with a high signal-to-background ratio. Overall, the hybrid nanoparticles represent a new kind of NIR-II AIE nanoprobes for biomedical imaging.

JSPR is a single particle cryo-EM image processing and 3D reconstruction software developed in the Jiang laboratory at Purdue University. It began as a few refinement scripts for symmetric and asymmetric reconstructions of icosahedral viruses, but has grown into a comprehensive suite of tools for building ab initio reconstructions, high resolution refinements of viruses, protein complexes of arbitrary symmetries including helical tubes/filaments, and image file handling utilities. In this review, we will present examples achieved using JSPR and demonstrate recently implemented features of JSPR such as multi-aberration "alignments" and automatic optimization of masking for the assessment of map resolution using "true" FSC., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Nonlinear electrokinetics (EK), specifically electrophoresis of the second kind, dielectrophoresis (DEP) and electrorotation (EROT), have gained significant interest recently for their flexibility and labeless discriminant manner of operation. The current applications of these technologies are a clear advancement from what they were when first discovered, but also still show strong signs of future growth. The present review article presents a discussion of the current uses of microscale nonlinear EK technologies as analytical, sensing, and purification tools for microorganisms. The discussion is focused on some of the latest discoveries with various nonlinear EK microfluidic techniques, such as DEP particle trapping and EROT for particle assessments, for the analysis of microorganisms ranging from viruses to parasites. Along the way, special focus was given to key research articles from within the past two years to provide the most up-to-date knowledge on the current state-of-the-art within the field of microscale EK, and from there, an outlook on where the future of the field is headed is also included., (© 2020 Wiley-VCH GmbH.)

Photodynamic therapy (PDT) is a promising therapy due to its efficiency and accuracy. The photosensitizer is delivered to the target lesion and locally activated. Viral nanoparticles (VNPs) have been explored as delivery vehicles for PDT in recent years because of their favorable properties, including simple manufacture and good safety profile. They have great potential as drug delivery carriers in medicine. Here, we review the development of PDT photosensitizers and discuss applications of VNP-mediated photodynamic therapies and the performance of VNPs in the treatment of tumor cells and antimicrobial therapy. Furthermore, future perspectives are discussed for further developing novel viral nanocarriers or improving existing viral vectors.

Viruses deploy genetically encoded strategies to coopt host machinery and support viral replicative cycles. Here, we use protein structure similarity to scan for molecular mimicry, manifested by structural similarity between viral and endogenous host proteins, across thousands of cataloged viruses and hosts spanning broad ecological niches and taxonomic range, including bacteria, plants and fungi, invertebrates, and vertebrates. This survey identified over 6,000,000 instances of structural mimicry; more than 70% of viral mimics cannot be discerned through protein sequence alone. We demonstrate that the manner and degree to which viruses exploit molecular mimicry varies by genome size and nucleic acid type and identify 158 human proteins that are mimicked by coronaviruses, providing clues about cellular processes driving pathogenesis. Our observations point to molecular mimicry as a pervasive strategy employed by viruses and indicate that the protein structure space used by a given virus is dictated by the host proteome. A record of this paper's transparent peer review process is included in the Supplemental Information., Competing Interests: Declaration of Interests The authors declare no competing interests., (Copyright © 2020 Elsevier Inc. All rights reserved.)

We investigate aspects of topology in protein folding. For this we numerically simulate the temperature driven folding and unfolding of the slipknotted archaeal virus protein AFV3-109. Due to knottiness the (un)folding is a topological process, it engages the entire backbone in a collective fashion. Accordingly we introduce a topological approach to model the process. Our simulations reveal that the (un)folding of AFV3-109 slipknot proceeds through a folding intermediate that has the topology of a trefoil knot. We observe that the final slipknot causes a slight swelling of the folded AFV3-109 structure. We disclose the relative stability of the strands and helices during both the folding and unfolding processes. We confirm results from previous studies that pointed out that it can be very demanding to simulate the formation of knotty self-entanglement, and we explain how the problems are circumvented: The slipknotted AFV3-109 protein is a very slow folder with a topologically demanding pathway, which needs to be properly accounted for in a simulation description. When we either increase the relative stiffness of bending, or when we decrease the speed of ambient cooling, the rate of slipknot formation rapidly increases., Competing Interests: The authors have declared that no competing interests exist.

VIrus Particle ExploreR data base (VIPERdb) (http://viperdb.scripps.edu) is a curated repository of virus capsid structures and a database of structure-derived data along with various virus specific information. VIPERdb has been continuously improved for over 20 years and contains a number of virus structure analysis tools. The release of VIPERdb v3.0 contains new structure-based data analytics tools like Multiple Structure-based and Sequence Alignment (MSSA) to identify hot-spot residues within a selected group of structures and an anomaly detection application to analyze and curate the structure-derived data within individual virus families. At the time of this writing, there are 931 virus structures from 62 different virus families in the database. Significantly, the new release also contains a standalone database called 'Virus World database' (VWdb) that comprises all the characterized viruses (∼181 000) known to date, gathered from ICTVdb and NCBI, and their capsid protein sequences, organized according to their virus taxonomy with links to known structures in VIPERdb and PDB. Moreover, the new release of VIPERdb includes a service-oriented data engine to handle all the data access requests and provides an interface for futuristic data analytics using machine leaning applications., (© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)