The MS2 Coat Protein Shell is Likely Assembled Under Tension: A Novel Role for the MS2 Bacteriophage A Protein as Revealed by Small-angle Neutron Scattering

Small concentrations, big results: μM addition of photoactive iron oxides with PMS, PDS, or H2O2, leads to enhanced removal of viruses at near-neutral pH

The photo-Fenton process is effective for pathogen removal, and its low-cost versions can be applied in resource-poor contexts. Herein, a photo-Fenton-like system was proposed using low concentrations of iron oxides (hematite and magnetite) and persulfates (peroxymonosulfate - PMS, and peroxydisulfate - PDS), which exhibited excellent inactivation performance towards MS2 bacteriophages. In the presence of bacteria, MS2 inactivation was inhibited in H2O2 and PDS systems but promoted in PMS-involved systems. The inactivation efficacy of all the proposed systems for mixed bacteria and viruses was greater than that of the sole bacteria, showing potential practical applications. The inactivation performance of humic acid-incorporated iron oxides mediating photo-Fenton-like processes was also studied; except for the PMS-involved system, the inactivation efficacy of the H2O2- and PDS-involved systems was inhibited, but the PDS-involved system was still acceptable (< 2 h). Reactive species exploration experiments indicated that ·OH was the main radical in the H2O2 and PDS systems, whereas 1O2 played a key role in the PMS-involved system. In summary, hematite- and magnetite-mediated persulfate-assisted photo-Fenton-like systems at low concentrations can be used as alternatives to the photo-Fenton process for virus inactivation in sunny areas, providing more possibilities for point-of-use drinking water treatment in developing countries.

The presence of RNA cargo is suspected to modify the surface hydrophobicity of the MS2 phage

The surface hydrophobicity of native or engineered non-enveloped viruses and virus-like particles (VLPs) is a key parameter regulating their fate in living and artificial aqueous systems. Its modulation is mainly depending on the structure and environment of particles. Nevertheless, unexplained variations have been reported between structurally similar viruses and with pH. This indicates that some modulating factors of their hydrophobicity remain to be identified. Herein we investigate the potential involvement of RNA cargo in the MS2 phage used as non-enveloped RNA virus model, by examining the SDS-induced electrophoretic mobility shift (SEMS) determined for native MS2 virions and corresponding RNA-free VLPs at various pH. Interestingly, the SEMS of VLPs was larger and more variable from pH 5 to 9 compared to native virions. These observations are discussed in term of RNA-dependent changes in surface hydrophobicity, suggesting that RNA cargo may be a major modulator/regulator of this viral parameter.

Virus Removal and Inactivation Mechanisms during Iron Electrocoagulation: Capsid and Genome Damages and Electro-Fenton Reactions

Virus destabilization and inactivation are critical considerations in providing safe drinking water. We demonstrate that iron electrocoagulation simultaneously removed (via sweep flocculation) and inactivated a non-enveloped virus surrogate (MS2 bacteriophage) under slightly acidic conditions, resulting in highly effective virus control (e.g., 5-logs at 20 mg Fe/L and pH 6.4 in 30 min). Electrocoagulation simultaneously generated H₂O₂ and Fe(II) that can potentially trigger electro-Fenton reactions to produce reactive oxygen species such as ^•OH and high valent oxoiron(IV) that are capable of inactivating viruses. To date, viral attenuation during water treatment has been largely probed by evaluating infective virions (as plaque forming units) or genomic damage (via the quantitative polymerase chain reaction). In addition to these existing means of assessing virus attenuation, a novel technique of correlating transmission electron micrographs of electrocoagulated MS2 with their computationally altered three-dimensional electron density maps was developed to provide direct visual evidence of capsid morphological damages during electrocoagulation. The majority of coliphages lost at least 10-60% of the capsid protein missing a minimum of one of the 5-fold and two of 3- and 2-fold regions upon electrocoagulation, revealing substantial localized capsid deformation. Attenuated total reflectance-Fourier transform infrared spectroscopy revealed potential oxidation of viral coat proteins and modification of their secondary structures that were attributed to reactive oxygen species. Iron electrocoagulation simultaneously disinfects and coagulates non-enveloped viruses (unlike conventional coagulation), adding to the robustness of multiple barriers necessary for public health protection and appears to be a promising technology for small-scale distributed water treatment.

Cupric ion in combination with hydrogen peroxide and hydroxylamine applied to inactivation of different microorganisms

The microbial inactivation by cupric ion (Cu(II)) in combination with hydrogen peroxide (H₂O₂) and hydroxylamine (HA) was investigated for twelve different microorganisms (five Gram-negative bacteria, three Gram-positive bacteria, and four bacteriophages). The inactivation efficacy, protein oxidation, and RNA (or DNA) damage were monitored during and after treatment by Cu(II), Cu(II)/HA, Cu(II)/H₂O₂ and Cu(II)/HA/H₂O₂. The rate of microbial inactivation by the (combined) microbicides generally increased in the order of Cu(II) < Cu(II)/H₂O₂ < Cu(II)/HA < Cu(II)/HA/H₂O₂; Cu(II)/HA/H₂O₂ resulted in 0.18-0.31, 0.10-0.18, and 0.55-3.83 log inactivation/min for Gram-negative bacteria, Gram-positive bacteria, and bacteriophages, respectively. The degrees of protein oxidation and RNA (or DNA) damage increased in the order of Cu(II) < Cu(II)/HA < Cu(II)/H₂O₂ < Cu(II)/HA/H₂O₂. In particular, Cu(II)/HA/H₂O₂ led to exceptionally fast inactivation of the viruses. Gram-positive bacteria tended to show higher resistance to microbicides than other microbial species. The microbicidal effects of the combined microbicides on the target microorganisms were explained by the roles of Cu(I) and Cu(III) generated by the redox reactions of Cu(II) with H₂O₂, HA, and oxygen. Major findings of this study indicate that Cu(II)-based combined microbicides are promising disinfectants for different waters contaminated by pathogenic microorganisms.

Visualizing a viral genome with contrast variation small angle X-ray scattering

Despite the threat to human health posed by some single-stranded RNA viruses, little is understood about their assembly. The goal of this work is to introduce a new tool for watching an RNA genome direct its own packaging and encapsidation by proteins. Contrast variation small-angle X-ray scattering (CV-SAXS) is a powerful tool with the potential to monitor the changing structure of a viral RNA through this assembly process. The proteins, though present, do not contribute to the measured signal. As a first step in assessing the feasibility of viral genome studies, the structure of encapsidated MS2 RNA was exclusively detected with CV-SAXS and compared with a structure derived from asymmetric cryo-EM reconstructions. Additional comparisons with free RNA highlight the significant structural rearrangements induced by capsid proteins and invite the application of time-resolved CV-SAXS to reveal interactions that result in efficient viral assembly.

Revealing Sources of Variation for Reproducible Imaging of Protein Assemblies by Electron Microscopy

Electron microscopy plays an important role in the analysis of functional nano-to-microstructures. Substrates and staining procedures present common sources of variation for the analysis. However, systematic investigations on the impact of these sources on data interpretation are lacking. Here we pinpoint key determinants associated with reproducibility issues in the imaging of archetypal protein assemblies, protein shells, and filaments. The effect of staining on the morphological characteristics of the assemblies was assessed to reveal differential features for anisotropic (filaments) and isotropic (shells) forms. Commercial substrates and coatings under the same staining conditions gave comparable results for the same model assembly, while highlighting intrinsic sample variations including the density and heterogenous distribution of assemblies on the substrate surface. With no aberrant or disrupted structures observed, and putative artefacts limited to substrate-associated markings, the study emphasizes that reproducible imaging must correlate with an optimal combination of substrate stability, stain homogeneity, accelerating voltage, and magnification.

Progress in the study of virus detection methods: The possibility of alternative methods to validate virus inactivation

Virus inactivation validation studies have been widely applied in the risk assessment of biogenic material-based medical products, such as biological products, animal tissue-derived biomaterials, and allogeneic biomaterials, to decrease the risk of virus transmission. Traditional virus detection methods in an inactivation validation study utilize cell culture as a tool to quantify the infectious virus by observing cytopathic effects (CPEs) after virus inactivation. However, this is susceptible to subjective factors because CPEs must be observed by experts under a microscope during virus titration. In addition, this method is costly and time- and labor-consuming. Molecular biological technologies such as quantitative polymerase chain reaction (qPCR) have been widely used for virus detection but cannot distinguish infectious and noninfectious viruses. Therefore, qPCR cannot be directly applied to virus inactivation validation studies. In this paper, methods to detect viruses and progress in the challenge of differentiating infectious and noninfectious viruses with the combination of pretreatment and qPCR techniques such as the integrated cell culture-qPCR (ICC-qPCR) method are reviewed. In addition, the advantages and disadvantages of each new method, as well as its prospect in virus inactivation validation studies, are discussed.

Conceptual model and experimental framework to determine the contributions of direct and indirect photoreactions to the solar disinfection of MS2, phiX174, and adenovirus

Sunlight inactivates waterborne viruses via direct (absorption of sunlight by the virus) and indirect processes (adsorption of sunlight by external chromophores, which subsequently generate reactive species). While the mechanisms underlying these processes are understood, their relative importance remains unclear. This study establishes an experimental framework to determine the kinetic parameters associated with a virus' susceptibility to solar disinfection and proposes a model to estimate disinfection rates and to apportion the contributions of different inactivation processes. Quantum yields of direct inactivation were determined for three viruses (MS2, phiX174, and adenovirus), and second-order rate constants associated with indirect inactivation by four reactive species ((1)O2, OH(•), CO3(•-), and triplet states) were established. PhiX174 exhibited the greatest quantum yield (1.4 × 10(-2)), indicating that it is more susceptible to direct inactivation than MS2 (2.9 × 10(-3)) or adenovirus (2.5 × 10(-4)). Second-order rate constants ranged from 1.7 × 10(7) to 7.0 × 10(9) M(-1) s(-1) and followed the sequence MS2 > adenovirus > phiX174. A predictive model based on these parameters accurately estimated solar disinfection of MS2 and phiX174 in a natural water sample and approximated that of adenovirus within a factor of 6. Inactivation mostly occurred by direct processes, though indirect inactivation by (1)O2 also contributed to the disinfection of MS2 and adenovirus.

Mechanisms of MS2 bacteriophage removal by fouled ultrafiltration membrane subjected to different cleaning methods

An ultrafiltration unit with a polyvinylidene fluoride (PVDF) membrane of 40 nm nominal pore size was used to study bacteriophage MS2 removal under different membrane conditions: pristine membrane, membrane fouled by soluble microbial product (SMP) extracted from membrane bioreactor (MBR) feedwater, backwashed membrane, and chemically cleaned membrane. The order of MS2 removal by these membranes was as follows: fouled membrane > backwashed membrane > chemically cleaned membrane ≈ pristine membrane. A linear correlation between membrane relative permeability and MS2 removal was found. Mass balance analysis showed a high percentage of MS2 in the concentrate for the fouled membrane as compared with the pristine membrane. Quartz crystal microbalance (QCM) results showed faster kinetics of MS2 adhesion to the pristine membrane than to the SMP-fouled membrane. In agreement with QCM results, an attractive force between MS2 and the pristine membrane was detected using an atomic force microscope (AFM), whereas a repulsive force was detected for the interaction between MS2 and the fouled membrane. The presence of SMP on the membrane surface led to higher rejection of MS2 due to both pore blocking and repulsion between MS2 and the SMP layer. Chemical cleaning removed most of the SMP foulant and as a result led to a lower MS2 removal.

Mechanical and assembly units of viral capsids identified via quasi-rigid domain decomposition

Key steps in a viral life-cycle, such as self-assembly of a protective protein container or in some cases also subsequent maturation events, are governed by the interplay of physico-chemical mechanisms involving various spatial and temporal scales. These salient aspects of a viral life cycle are hence well described and rationalised from a mesoscopic perspective. Accordingly, various experimental and computational efforts have been directed towards identifying the fundamental building blocks that are instrumental for the mechanical response, or constitute the assembly units, of a few specific viral shells. Motivated by these earlier studies we introduce and apply a general and efficient computational scheme for identifying the stable domains of a given viral capsid. The method is based on elastic network models and quasi-rigid domain decomposition. It is first applied to a heterogeneous set of well-characterized viruses (CCMV, MS2, STNV, STMV) for which the known mechanical or assembly domains are correctly identified. The validated method is next applied to other viral particles such as L-A, Pariacoto and polyoma viruses, whose fundamental functional domains are still unknown or debated and for which we formulate verifiable predictions. The numerical code implementing the domain decomposition strategy is made freely available.

The genetic material of viruses is packaged inside capsids constituted from a few tens to thousands of proteins. The latter can organize in multimers that serve as fundamental blocks for the viral shell assembly or that control the capsid conformational transitions and response to mechanical stress. In this work, we introduce and apply a computational scheme that identifies the fundamental protein blocks from the structural fluctuations of the capsids in thermal equilibrium. These can be derived from phenomenological elastic network models with minimal computational expenditure. Accordingly, the basic functional protein units of a capsid can be obtained from the sole input of the capsid crystal structure. The method is applied to a heterogeneous set of viruses of various size and geometries. These include well-characterised instances for validation purposes, as well as debated ones for which predictions are formulated.

Impact of the virus purification protocol on aggregation and electrokinetics of MS2 phages and corresponding virus-like particles

Previous experimental and theoretical studies have established that electrokinetic and aggregation properties of soft MS2 phages are not only governed by the physico-chemical features of their proteinaceous outer surface but are also significantly impacted by those of their inner RNA component (Dika et al. Appl. Environ. Microbiol., 2011, 14, 4939-4948). These conclusions contradict the recent findings of Nguyen et al. (Soft Matter, 2011, 7, 10449-10456) who reported identical electrokinetic and aggregation characteristics for MS2 and corresponding virus like particles (VLPs) that lack the internal RNA component. We demonstrate here that this contradiction originates from the different purification methods adopted prior to measurements. More generally, we show that stability and electrohydrodynamics of viruses differ according to purification by (i) dialysis, (ii) isopycnic centrifugation in the cesium chloride gradient, and (iii) precipitation using polyethylene glycol (PEG). Methods (i) and (iii) lead to aggregation of MS2 phages at pH ≤ 4 and pH ≤ 6 in 1-100 mM NaNO3 solutions, respectively, while under such conditions aggregation is not observed for MS2 and VLP suspensions prepared according to (ii). In addition, VLPs prepared following methods (i) and (iii) aggregate only at the isoelectric point (pH ~ 3-4) in 1 mM NaNO3 solution. Electrophoretic mobility data of stable MS2 and VLP particles were further examined using a recent formalism for electrokinetics of soft multilayered colloids. The analysis qualitatively shows how the purification protocol may affect either the outer particle surface properties and/or the inner particle content. Finally, the non-DLVO aggregation behavior of MS2 and VLPs purified via the above protocols is discussed in terms of the possible change in corresponding interparticular interactions.

Virus inactivation mechanisms: impact of disinfectants on virus function and structural integrity

Oxidative processes are often harnessed as tools for pathogen disinfection. Although the pathways responsible for bacterial inactivation with various biocides are fairly well understood, virus inactivation mechanisms are often contradictory or equivocal. In this study, we provide a quantitative analysis of the total damage incurred by a model virus (bacteriophage MS2) upon inactivation induced by five common virucidal agents (heat, UV, hypochlorous acid, singlet oxygen, and chlorine dioxide). Each treatment targets one or more virus functions to achieve inactivation: UV, singlet oxygen, and hypochlorous acid treatments generally render the genome nonreplicable, whereas chlorine dioxide and heat inhibit host-cell recognition/binding. Using a combination of quantitative analytical tools, we identified unique patterns of molecular level modifications in the virus proteins or genome that lead to the inhibition of these functions and eventually inactivation. UV and chlorine treatments, for example, cause site-specific capsid protein backbone cleavage that inhibits viral genome injection into the host cell. Combined, these results will aid in developing better methods for combating waterborne and foodborne viral pathogens and further our understanding of the adaptive changes viruses undergo in response to natural and anthropogenic stressors.

Inactivation of aerosolized Bacillus atrophaeus (BG) endospores and MS2 viruses by combustion of reactive materials

Accidental release of biological agents from a bioweapon facility may contaminate large areas, possibly causing disastrous environmental consequences. To address this issue, novel halogen-containing reactive materials are being designed with the added capability to inactivate viable airborne microorganisms. This study determined the efficiency of combustion products of such materials to inactivate aerosolized bacteria and viruses. Spores of Bacillus atrophaeus and MS2 viruses dispersed in dry air were exposed for subsecond time intervals to hydrocarbon flames seeded with different reactive powders so that bioaerosol particles interacted with the combustion products in a controlled high-temperature environment. The experiments were designed to quantify differences in the biocidal effects of different reactive material powders including Al and Mg, a B•Ti nanocomposite, an 8Al•MoO(3) nanothermite, and a novel Al•I(2) nanocomposite. Compared to pure hydrocarbon flame, powder-seeded flame (with no iodine) produced about an order of magnitude greater inactivation of bacterial spores. The iodine-containing material increased the spore inactivation by additional 2 orders of magnitude. The aerosolized MS2 viruses (generally not as stress-resistant as spores) were fully inactivated when exposed to combustion of either the iodinated or noniodinated powders. Overall, the study suggests a great biocidal potential of combustion products generated by novel iodine-containing nanocomposite materials.

Bacteriophage inactivation by UV-A illuminated fullerenes: role of nanoparticle-virus association and biological targets

Inactivation rates of the MS2 bacteriophage and (1)O(2) generation rates by four different photosensitized aqueous fullerene suspensions were in the same order: aqu-nC(60) < C(60)(OH)(6) ≈ C(60)(OH)(24) < C(60)(NH(2))(6). Alterations to capsid protein secondary structures and protein oxidation were inferred by detecting changes in infrared vibrational frequencies and carbonyl groups respectively. MS2 inactivation appears to be the result of loss of capsid structural integrity (localized deformation) and the reduced ability to eject genomic RNA into its bacterial host. Evidence is also presented for possible capsid rupture in MS2 exposed to UV-A illuminated C(60)(NH(2))(6) through TEM imagery and detection of RNA infrared fingerprints in ATR-FTIR spectra. Fullerene-virus mixtures were also directly visualized in the aqueous phase using a novel enhanced darkfield transmission optical microscope fitted with a hyperspectral imaging (HSI) spectrometer. Perturbations in intermolecular extended chains, HSI, and electrostatic interactions suggest that inactivation is a function of the relative proximity between nanoparticles and viruses and (1)O(2) generation rate. MS2 log survival ratios were linearly related to CT (product of (1)O(2) concentration C and exposure time T) demonstrating the applicability of classical Chick-Watson kinetics for all fullerenes employed in this study. Results suggest that antiviral properties of fullerenes can be increased by adjusting the type of surface functionalization and extent of cage derivatization thereby increasing the (1)O(2) generation rate and facilitating closer association with biological targets.

Antiviral properties of polymeric aziridine- and biguanide-modified core-shell magnetic nanoparticles

Polycationic superparamagnetic nanoparticles (∼150-250 nm) were evaluated as virucidal agents. The particles possess a core-shell structure, with cores consisting of magnetite clusters and shells of functional silica covalently bound to poly(hexamethylene biguanide) (PHMBG), polyethyleneimine (PEI), or PEI terminated with aziridine moieties. Aziridine was conjugated to the PEI shell through cationic ring-opening polymerization. The nanometric core-shell particles functionalized with biguanide or aziridine moieties are able to bind and inactivate bacteriophage MS2, herpes simplex virus HSV-1, nonenveloped infectious pancreatic necrosis virus (IPNV), and enveloped viral hemorrhagic septicaemia virus (VHSV). The virus-particle complexes can be efficiently removed from the aqueous milieu by simple magnetocollection.

Energies and pressures in viruses: contribution of nonspecific electrostatic interactions

We summarize some aspects of electrostatic interactions in the context of viruses. A simplified but, within well defined limitations, reliable approach is used to derive expressions for electrostatic energies and the corresponding osmotic pressures in single-stranded RNA viruses and double-stranded DNA bacteriophages. The two types of viruses differ crucially in the spatial distribution of their genome charge which leads to essential differences in their free energies, depending on the capsid size and total charge in a quite different fashion. Differences in the free energies are trailed by the corresponding characteristics and variations in the osmotic pressure between the inside of the virus and the external bathing solution.

Impact of internal RNA on aggregation and electrokinetics of viruses: comparison between MS2 phage and corresponding virus-like particles

We compare for the first time the electrokinetic and aggregation properties of MS2 phage (pH 2.5 to 7, 1 to 100 mM NaNO(3) electrolyte concentration) with those of the corresponding virus-like particles (VLPs), which lack entirely the inner viral RNA component. In line with our previous work (J. Langlet, F. Gaboriaud, C. Gantzer, and J. F. L. Duval, Biophys. J. 94:3293-3312, 2008), it is found that modifying the content of RNA within the virus leads to very distinct electrohydrodynamic and aggregation profiles for MS2 and MS2 VLPs. Under the given pH and concentration conditions, MS2 VLPs exhibit electrophoretic mobility larger in magnitude than that of MS2, and both have similar isoelectric point (IEP) values (∼4). The electrokinetic results reflect a greater permeability of MS2 VLPs to electroosmotic flow, developed within/around these soft particles during their migration under the action of the applied electrical field. Results also support the presence of some remaining negatively charged component within the VLPs. In addition, MS2 phage systematically forms aggregates at pH values below the IEP, regardless of the magnitude of the solution ionic strength, whereas MS2 VLPs aggregate under the strict condition where the pH is relatively equal to the IEP at sufficiently low salt concentrations (<10 mM). It is argued that the stability of VLPs against aggregation and the differences between electrokinetics of MS2 and corresponding VLPs conform to recently developed formalisms for the stability and electrohydrodynamics of soft multilayered particles. The differences between the surface properties of these two kinds of particles reported here suggest that VLPs may not be appropriate for predicting the behavior of pathogenic viruses in aqueous media.

Quantitative characterization of virus-like particles by asymmetrical flow field flow fractionation, electrospray differential mobility analysis, and transmission electron microscopy

Here we characterize virus-like particles (VLPs) by three very distinct, orthogonal, and quantitative techniques: electrospray differential mobility analysis (ES-DMA), asymmetric flow field-flow fractionation with multi-angle light scattering detection (AFFFF-MALS) and transmission electron microscopy (TEM). VLPs are biomolecular particles assembled from viral proteins with applications ranging from synthetic vaccines to vectors for delivery of gene and drug therapies. VLPs may have polydispersed, multimodal size distributions, where the size distribution can be altered by subtle changes in the production process. These three techniques detect subtle size differences in VLPs derived from the non-enveloped murine polyomavirus (MPV) following: (i) functionalization of the surface of VLPs with an influenza viral peptide fragment; (ii) packaging of foreign protein internally within the VLPs; and (iii) packaging of genomic DNA internally within the VLPs. These results demonstrate that ES-DMA and AFFFF-MALS are able to quantitatively determine VLP size distributions with greater rapidity and statistical significance than TEM, providing useful technologies for product development and process analytics.

The three-dimensional structure of genomic RNA in bacteriophage MS2: implications for assembly

Using cryo-electron microscopy, single particle image processing and three-dimensional reconstruction with icosahedral averaging, we have determined the three-dimensional solution structure of bacteriophage MS2 capsids reassembled from recombinant protein in the presence of short oligonucleotides. We have also significantly extended the resolution of the previously reported structure of the wild-type MS2 virion. The structures of recombinant MS2 capsids reveal clear density for bound RNA beneath the coat protein binding sites on the inner surface of the T=3 MS2 capsid, and show that a short extension of the minimal assembly initiation sequence that promotes an increase in the efficiency of assembly, interacts with the protein capsid forming a network of bound RNA. The structure of the wild-type MS2 virion at approximately 9 A resolution reveals icosahedrally ordered density encompassing approximately 90% of the single-stranded RNA genome. The genome in the wild-type virion is arranged as two concentric shells of density, connected along the 5-fold symmetry axes of the particle. This novel RNA fold provides new constraints for models of viral assembly.