Genetic diversity of astroviruses detected in wild aquatic birds in Hong Kong.

Wild waterfowl serve as a reservoir of some astroviruses. Fecal samples from wild waterfowl collected at Hong Kong's Marshes were tested using pan-astrovirus reverse transcription-PCR. Positive samples underwent subsequent host identification using DNA barcoding. Based on deduced partial sequences, noteworthy samples from three astrovirus groups (mammalian, avian and unclassified astroviruses) were further analyzed by next-generation sequencing. One sample of Avastrovirus 4 clade, MP22-196, had a nearly complete genome identified. The results of ORF2 phylogenetic analysis and genetic distance analysis indicate that Avastrovirus 4 is classified as a distinct subclade within Avastrovirus. MP22-196 has typical astrovirus genome characteristics. The unique characteristics and potential differences of this genome, compared to other avian astrovirus sequences, involve the identification of a modified sgRNA sequence situated near the ORF2 start codon, which precedes the ORF1b stop codon. Additionally, the 3' UTR of MP22-196 is shorter than other avian astroviruses. This study expands our understanding of the Avastrovirus 4 clade.

Managing temperature in open quantum systems strongly coupled with structured environments.

In non-perturbative non-Markovian open quantum systems, reaching either low temperatures with the hierarchical equations of motion (HEOM) or high temperatures with the Thermalized Time Evolving Density Operator with Orthogonal Polynomials Algorithm (T-TEDOPA) formalism in Hilbert space remains challenging. We compare different ways of modeling the environment. Sampling the Fourier transform of the bath correlation function, also called temperature dependent spectral density, proves to be very effective. T-TEDOPA [Tamascelli et al., Phys. Rev. Lett. 123, 090402 (2019)] uses a linear chain of oscillators with positive and negative frequencies, while HEOM is based on the complex poles of an optimized rational decomposition of the temperature dependent spectral density [Xu et al., Phys. Rev. Lett. 129, 230601 (2022)]. Resorting to the poles of the temperature independent spectral density and of the Bose function separately is an alternative when the problem due to the huge number of Bose poles at low temperatures is circumvented. Two examples illustrate the effectiveness of the HEOM and T-TEDOPA approaches: a benchmark pure dephasing case and a two-bath model simulating the dynamics of excited electronic states coupled through a conical intersection. We show the efficiency of T-TEDOPA to simulate dynamics at a finite temperature by using either continuous spectral densities or only all the intramolecular oscillators of a linear vibronic model calibrated from ab initio data of a phenylene ethynylene dimer.

Environmentally Driven Symmetry Breaking Quenches Dual Fluorescence in Proflavine.

Nonadiabatic couplings between several electronic excited states are ubiquitous in many organic chromophores and can significantly influence optical properties. A recent experimental study demonstrated that the proflavine molecule exhibits surprising dual fluorescence in the gas phase, which is suppressed in polar solvent environments. Here, we uncover the origin of this phenomenon by parametrizing a linear-vibronic coupling Hamiltonian from spectral densities of system-bath coupling constructed along molecular dynamics trajectories, fully accounting for interactions with the condensed-phase environment. The finite-temperature absorption, steady-state emission, and time-resolved emission spectra are then computed using powerful, numerically exact tensor network approaches. We find that the dual fluorescence in vacuum is driven by a single well-defined coupling mode but is quenched in solution due to dynamic solvent-driven symmetry breaking that mixes the two low-lying electronic states. We expect the computational framework developed here to be widely applicable to the study of non-Condon effects in complex condensed-phase environments.

Stability of SARS-CoV-2 on Commercial Aircraft Interior Surfaces with Implications for Effective Control Measures.

BACKGROUND: The COVID-19 pandemic from 2019 to 2022 devastated many aspects of life and the economy, with the commercial aviation industry being no exception. One of the major concerns during the pandemic was the degree to which the internal aircraft environment contributed to virus transmission between humans and, in particular, the stability of SARS-CoV-2 on contact surfaces in the aircraft cabin interior. METHOD: In this study, the stability of various major strains of SARS-CoV-2 on interior aircraft surfaces was evaluated using the TCID50 assessment. RESULTS: In contrast to terrestrial materials, SARS-CoV-2 was naturally less stable on common contact points in the aircraft interior, and, over a 4 h time period, there was a 90% reduction in culturable virus. Antiviral and surface coatings were extremely effective at mitigating the persistence of the virus on surfaces; however, their benefit was diminished by regular cleaning and were ineffective after 56 days of regular use and cleaning. Finally, successive strains of SARS-CoV-2 have not evolved to be more resilient to survival on aircraft surfaces. CONCLUSIONS: We conclude that the mitigation strategies for SARS-CoV-2 on interior aircraft surfaces are more than sufficient, and epidemiological evidence over the past three years has not found that surface spread is a major route of transmission.

Effect of Surface Porosity on SARS-CoV-2 Fomite Infectivity.

Previous reports indicated the low stability of severe actute respiratory syndrome coronovirus 2 (SARS-CoV-2) on various porous surfaces, but the role of porosity was unclear because there was no direct comparison between porous and nonporous solids of the same chemistry. Through comparing pairs of solids with very similar chemistry, we find that porosity is important: porous glass has a much lower infectivity than nonporous glass. However, porosity is not sufficient to lower infectivity; permeability, which is the ability of a liquid to move through a material, is the important parameter. We show this by comparing a pair of porous CuO coatings where the pores are accessible in one case and inaccessible in the other case. When the pores are inaccessible, the infectivity remains similar to that for nonporous solids. Thus, for both glass and CuO, it is the access to porosity that decreases the infectivity of extracted liquid droplets. Having established the importance of permeability, there is the open question of the mechanism of changing the infectivity of SARS-CoV-2. Several hypotheses are possible, such as increasing the difficulty of extracting the virus from the solid, changing the drying time, increasing the surface area of active ingredient, etc. Reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) measurements show that less viral DNA is extracted from a permeable surface, suggesting that the virus becomes trapped in the pores. Finally, we consider the effect of drying. We show that permeability and the water contact angle on the solid have effects on the drying time of a contaminated droplet, which may in turn affect infectivity.

Evaluation of RT-qPCR Primer-Probe Sets to Inform Public Health Interventions Based on COVID-19 Sewage Tests.

Sewage surveillance is increasingly employed as a supplementary tool for COVID-19 control. Experiences learnt from large-scale trials could guide better interpretation of the sewage data for public health interventions. Here, we compared the performance of seven commonly used primer-probe sets in RT-qPCR and evaluated the usefulness in the sewage surveillance program in Hong Kong. All selected primer-probe sets reliably detected SARS-CoV-2 in pure water at 7 copies per µL. Sewage matrix did not influence RT-qPCR determination of SARS-CoV-2 concentrated from a small-volume sewage (30 mL) but introduced inhibitory impacts on a large-volume sewage (920 mL) with a ΔCt of 0.2-10.8. Diagnostic performance evaluation in finding COVID-19 cases showed that N1 was the best single primer-probe set, while the ORF1ab set is not recommended. Sewage surveillance using the N1 set for over 3200 samples effectively caught the outbreak trend and, importantly, had a 56% sensitivity and a 96% specificity in uncovering the signal sources from new cases and/or convalescent patients in the community. Our study paves the way for selecting detection primer-probe sets in wider applications in responding to the COVID-19 pandemic.

Comparison of virus concentration methods and RNA extraction methods for SARS-CoV-2 wastewater surveillance.

Wastewater surveillance is a promising tool for population-level monitoring of the spread of infectious diseases, such as the coronavirus disease 2019 (COVID-19). Different from clinical specimens, viruses in community-scale wastewater samples need to be concentrated before detection because viral RNA is highly diluted. The present study evaluated eleven different virus concentration methods for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater. First, eight concentration methods of different principles were compared using spiked wastewater at a starting volume of 30 mL. Ultracentrifugation was the most effective method with a viral recovery efficiency of 25 ± 6%. The second-best option, AlCl3 precipitation method, yielded a lower recovery efficiency, only approximately half that of the ultracentrifugation method. Second, the potential of increasing method sensitivity was explored using three concentration methods starting with a larger volume of 1000 mL. Although ultracentrifugation using a large volume outperformed the other two large-volume methods, it only yielded a comparable method sensitivity as the ultracentrifugation using a small volume (30 mL). Thus, ultracentrifugation using less volume of wastewater is more preferable considering the sample processing throughput. Third, a comparison of two viral RNA extraction methods showed that the lysis-buffer-based extraction method resulted in higher viral recovery efficiencies, with cycle threshold (Ct) values 0.9-4.2 lower than those obtained for the acid-guanidinium-phenol-based method using spiked samples. These results were further confirmed by using positive wastewater samples concentrated by ultracentrifugation and extracted separately by the two viral RNA extraction methods. In summary, concentration using ultracentrifugation followed by the lysis buffer-based extraction method enables sensitive and robust detection of SARS-CoV-2 for wastewater surveillance.

Transparent Anti-SARS-CoV-2 and Antibacterial Silver Oxide Coatings.

Transparent antimicrobial coatings can maintain the aesthetic appeal of surfaces and the functionality of a touch-screen while adding the benefit of reducing disease transmission. We fabricated an antimicrobial coating of silver oxide particles in a silicate matrix on glass. The matrix was grown by a modified Stöber sol-gel process with vapor-phase water and ammonia. A coating on glass with 2.4 mg of Ag2O per mm2 caused a reduction of 99.3% of SARS-CoV-2 and >99.5% of Pseudomonas aeruginosa, Staphylococcus aureus, and methicillin-resistant Staphylococcus aureus compared to the uncoated glass after 1 h. We envisage that screen protectors with transparent antimicrobial coatings will find particular application to communal touch-screens, such as in supermarkets and other check-out or check-in facilities where a number of individuals utilize the same touch-screen in a short interval.

A human pluripotent stem cell-based model of SARS-CoV-2 infection reveals an ACE2-independent inflammatory activation of vascular endothelial cells through TLR4.

To date, the direct causative mechanism of SARS-CoV-2-induced endotheliitis remains unclear. Here, we report that human ECs barely express surface ACE2, and ECs express less intracellular ACE2 than non-ECs of the lungs. We ectopically expressed ACE2 in hESC-ECs to model SARS-CoV-2 infection. ACE2-deficient ECs are resistant to the infection but are more activated than ACE2-expressing ones. The virus directly induces endothelial activation by increasing monocyte adhesion, NO production, and enhanced phosphorylation of p38 mitogen-associated protein kinase (MAPK), NF-κB, and eNOS in ACE2-expressing and -deficient ECs. ACE2-deficient ECs respond to SARS-CoV-2 through TLR4 as treatment with its antagonist inhibits p38 MAPK/NF-κB/ interleukin-1ß (IL-1ß) activation after viral exposure. Genome-wide, single-cell RNA-seq analyses further confirm activation of the TLR4/MAPK14/RELA/IL-1ß axis in circulating ECs of mild and severe COVID-19 patients. Circulating ECs could serve as biomarkers for indicating patients with endotheliitis. Together, our findings support a direct role for SARS-CoV-2 in mediating endothelial inflammation in an ACE2-dependent or -independent manner.

Microcavity-like exciton-polaritons can be the primary photoexcitation in bare organic semiconductors.

Strong-coupling between excitons and confined photonic modes can lead to the formation of new quasi-particles termed exciton-polaritons which can display a range of interesting properties such as super-fluidity, ultrafast transport and Bose-Einstein condensation. Strong-coupling typically occurs when an excitonic material is confided in a dielectric or plasmonic microcavity. Here, we show polaritons can form at room temperature in a range of chemically diverse, organic semiconductor thin films, despite the absence of an external cavity. We find evidence of strong light-matter coupling via angle-dependent peak splittings in the reflectivity spectra of the materials and emission from collective polariton states. We additionally show exciton-polaritons are the primary photoexcitation in these organic materials by directly imaging their ultrafast (5 × 106 m s-1), ultralong (~270 nm) transport. These results open-up new fundamental physics and could enable a new generation of organic optoelectronic and light harvesting devices based on cavity-free exciton-polaritons.

Transparent and Sprayable Surface Coatings that Kill Drug-Resistant Bacteria Within Minutes and Inactivate SARS-CoV-2 Virus.

Antimicrobial coatings are one method to reduce the spread of microbial diseases. Transparent coatings preserve the visual properties of surfaces and are strictly necessary for applications such as antimicrobial cell phone screens. This work describes transparent coatings that inactivate microbes within minutes. The coatings are based on a polydopamine (PDA) adhesive, which has the useful property that the monomer can be sprayed, and then the monomer polymerizes in a conformal film at room temperature. Two coatings are described (1) a coating where PDA is deposited first and then a thin layer of copper is grown on the PDA by electroless deposition (PDA/Cu) and (2) a coating where a suspension of Cu2O particles in a PDA solution is deposited in a single step (PDA/Cu2O). In the second coating, PDA menisci bind Cu2O particles to the solid surface. Both coatings are transparent and are highly efficient in inactivating microbes. PDA/Cu kills >99.99% of Pseudomonas aeruginosa and 99.18% of methicillin-resistant Staphylococcus aureus (MRSA) in only 10 min and inactivates 99.98% of SARS-CoV-2 virus in 1 h. PDA/Cu2O kills 99.94% of P. aeruginosa and 96.82% of MRSA within 10 min and inactivates 99.88% of SARS-CoV-2 in 1 h.

SARS-CoV-2 virus transfers to skin through contact with contaminated solids.

Transfer of SARS-CoV-2 from solids to fingers is one step in infection via contaminated solids, and the possibility of infection from this route has driven calls for increased frequency of handwashing during the COVID-19 pandemic. To analyze this route of infection, we measured the percentage of SARS-CoV-2 that was transferred from a solid to an artificial finger. A droplet of SARS-CoV-2 suspension (1 µL) was placed on a solid, and then artificial skin was briefly pressed against the solid with a light force (3 N). Transfer from a variety of solids was detected, and transfer from the non-porous solids, glass, stainless steel, and Teflon, was substantial when the droplet was still wet. The viral titer for the finger was 13-16% or 0.8-0.9 log less than for the input droplet. Transfer still occurred after the droplet evaporated, but was smaller, 3-9%. We found a lower level of transfer from porous solids but did not find a significant effect of solid wettability for non-porous solids.

Reduction of Infectivity of SARS-CoV-2 by Zinc Oxide Coatings.

We developed antimicrobial coatings from ZnO particles that reduce the infectivity of SARS-CoV-2 suspensions by >99.9% in 1 h. The advantage of a coating is that it can be applied to a variety of objects, e.g., hand rails and door knobs, to hinder the spread of disease. Two porous coatings were prepared: one from submicrometer zinc oxide particles bound with silica menisci and the other from zinc oxide tetrapods bound with polyurethane. Experiments on glass coatings show that infectivity depends on porosity for hydrophilic materials, wherein aqueous droplets are imbibed into the pores.

Influence of non-adiabatic effects on linear absorption spectra in the condensed phase: Methylene blue.

Modeling linear absorption spectra of solvated chromophores is highly challenging as contributions are present both from coupling of the electronic states to nuclear vibrations and from solute-solvent interactions. In systems where excited states intersect in the Condon region, significant non-adiabatic contributions to absorption line shapes can also be observed. Here, we introduce a robust approach to model linear absorption spectra accounting for both environmental and non-adiabatic effects from first principles. This model parameterizes a linear vibronic coupling (LVC) Hamiltonian directly from energy gap fluctuations calculated along molecular dynamics (MD) trajectories of the chromophore in solution, accounting for both anharmonicity in the potential and direct solute-solvent interactions. The resulting system dynamics described by the LVC Hamiltonian are solved exactly using the thermalized time-evolving density operator with orthogonal polynomials algorithm (T-TEDOPA). The approach is applied to the linear absorption spectrum of methylene blue in water. We show that the strong shoulder in the experimental spectrum is caused by vibrationally driven population transfer between the bright S1 and the dark S2 states. The treatment of the solvent environment is one of many factors that strongly influence the population transfer and line shape; accurate modeling can only be achieved through the use of explicit quantum mechanical solvation. The efficiency of T-TEDOPA, combined with LVC Hamiltonian parameterizations from MD, leads to an attractive method for describing a large variety of systems in complex environments from first principles.

Exciton Diffusion in Highly-Ordered One Dimensional Conjugated Polymers: Effects of Back-Bone Torsion, Electronic Symmetry, Phonons and Annihilation.

Many optoelectronic devices based on organic materials require rapid and long-range singlet exciton transport. Key factors controlling exciton transport include material structure, exciton-phonon coupling and electronic state symmetry. Here, we employ femtosecond transient absorption microscopy to study the influence of these parameters on exciton transport in one-dimensional conjugated polymers. We find that excitons with 21Ag- symmetry and a planar backbone exhibit a significantly higher diffusion coefficient (34 ± 10 cm2 s-1) compared to excitons with 11Bu+ symmetry (7 ± 6 cm2 s-1) with a twisted backbone. We also find that exciton transport in the 21Ag- state occurs without exciton-exciton annihilation. Both 21Ag- and 11Bu+ states are found to exhibit subdiffusive behavior. Ab initio GW-BSE calculations reveal that this is due to the comparable strengths of the exciton-phonon interaction and exciton coupling. Our results demonstrate the link between electronic state symmetry, backbone torsion and phonons in exciton transport in π-conjugated polymers.

Cupric Oxide Coating That Rapidly Reduces Infection by SARS-CoV-2 via Solids.

The ongoing COVID-19 pandemic has created a need for coatings that reduce infection from SARS-CoV-2 via surfaces. Such a coating could be used on common touch surfaces (e.g., door handles and railings) to reduce both disease transmission and fear of touching objects. Herein, we describe the design, fabrication, and testing of a cupric oxide anti-SARS-CoV-2 coating. Rapid loss of infectivity is an important design criterion, so a porous hydrophilic coating was created to allow rapid infiltration of aqueous solutions into the coating where diffusion distances to the cupric oxide surface are short and the surface area is large. The coating was deposited onto glass from a dispersion of cuprous oxide in ethanol and then thermally treated at 700 °C for 2 h to produce a CuO coating that is ≈30 µm thick. The heat treatment oxidized the cuprous oxide to cupric oxide and sintered the particles into a robust film. The SARS-CoV-2 infectivity from the CuO film was reduced by 99.8% in 30 min and 99.9% in 1 h compared to that from glass. The coating remained hydrophilic for at least 5 months, and there was no significant change in the cross-hatch test of robustness after exposure to 70% ethanol or 3 wt % bleach.

Matrix Product State Simulations of Non-Equilibrium Steady States and Transient Heat Flows in the Two-Bath Spin-Boson Model at Finite Temperatures.

Simulating the non-perturbative and non-Markovian dynamics of open quantum systems is a very challenging many body problem, due to the need to evolve both the system and its environments on an equal footing. Tensor network and matrix product states (MPS) have emerged as powerful tools for open system models, but the numerical resources required to treat finite-temperature environments grow extremely rapidly and limit their applications. In this study we use time-dependent variational evolution of MPS to explore the striking theory of Tamascelli et al. (Phys. Rev. Lett. 2019, 123, 090402.) that shows how finite-temperature open dynamics can be obtained from zero temperature, i.e., pure wave function, simulations. Using this approach, we produce a benchmark dataset for the dynamics of the Ohmic spin-boson model across a wide range of coupling strengths and temperatures, and also present a detailed analysis of the numerical costs of simulating non-equilibrium steady states, such as those emerging from the non-perturbative coupling of a qubit to baths at different temperatures. Despite ever-growing resource requirements, we find that converged non-perturbative results can be obtained, and we discuss a number of recent ideas and numerical techniques that should allow wide application of MPS to complex open quantum systems.

Désinfection à la chaleur humide des respirateurs N95, inactivation du SRAS-CoV-2 et effets sur les propriétés des respirateurs.

CONTEXTE: La demande sans précédent de respirateurs N95 durant la pandémie de maladie à coronavirus 2019 (COVID-19) a entraîné une pénurie mondiale. Nous avons validé un protocole de décontamination rapide et économique répondant aux normes réglementaires afin de permettre la réutilisation sûre de ce type de masque. MÉTHODES: Nous avons contaminé 4 modèles courants de respirateurs N95 avec le coronavirus du syndrome respiratoire aigu sévère 2 (SRAS-CoV-2) et avons évalué l'inactivation virale après une désinfection de 60 minutes à 70 °C et à une humidité relative de 0 %. De même, nous avons étudié l'efficacité de la désinfection thermique, à une humidité relative allant de 0 % à 70 %, de masques contaminés à Escherichia coli. Enfin, nous avons examiné des masques soumis à de multiples cycles de désinfection thermique: nous avons évalué leur intégrité structurelle à l'aide d'un microscope à balayage, et leurs propriétés protectrices au moyen des normes du National Institute for Occupational Safety and Health des États-Unis relatives à la filtration particulaire, à la résistance respiratoire et à l'ajustement. RÉSULTATS: Une seule désinfection thermique a suffi pour que le SRAS-CoV-2 ne soit plus décelable sur les masques étudiés. En ce qui concerne les masques contaminés à E. coli, une culture de 24 heures a révélé que la bactérie n'était pratiquement plus décelable sur les masques désinfectés à 70 °C et à une humidité relative de 50 %, contrairement aux masques non désinfectés (densité optique à une longueur d'onde de 600 nm : 0,02 ± 0,02 contre 2,77 ± 0,09; p < 0,001), mais qu'elle persistait sur les masques traités à une humidité relative moindre. Les masques ayant subi 10 cycles de désinfection avaient toujours des fibres de diamètre semblable à celui des fibres des masques non traités, et ils répondaient encore aux normes d'ajustement, de filtration et de résistance respiratoire. INTERPRÉTATION: La désinfection thermique a réussi à décontaminer les respirateurs N95 sans compromettre leur intégrité structurelle ni modifier leurs propriétés. Elle pourrait se faire dans les hôpitaux et les établissements de soins de longue durée avec de l'équipement facilement accessible, ce qui réduirait la pénurie de N95.

Static Disorder in Excitation Energies of the Fenna-Matthews-Olson Protein: Structure-Based Theory Meets Experiment.

Inhomogeneous broadening of optical lines of the Fenna-Matthews-Olson (FMO) light-harvesting protein is investigated by combining a Monte Carlo sampling of low-energy conformational substates of the protein with a quantum chemical/electrostatic calculation of local transition energies (site energies) of the pigments. The good agreement between the optical spectra calculated for the inhomogeneous ensemble and the experimental data demonstrates that electrostatics is the dominant contributor to static disorder in site energies. Rotamers of polar amino acid side chains are found to cause bimodal distribution functions of site energy shifts, which can be probed by hole burning and single-molecule spectroscopy. When summing over the large number of contributions, the resulting distribution functions of the site energies become Gaussians, and the correlations in site energy fluctuations at different sites practically average to zero. These results demonstrate that static disorder in the FMO protein is in the realm of the central limit theorem of statistics.

First principles modeling of exciton-polaritons in polydiacetylene chains.

Exciton-polaritons in organic materials are hybrid states that result from the strong interaction of photons and the bound excitons that these materials host. Organic polaritons hold great interest for optoelectronic applications; however, progress toward this end has been impeded by the lack of a first principles approach that quantifies light-matter interactions in these systems, which would allow the formulation of molecular design rules. Here, we present a theoretical framework that combines first principles calculations for excitons with classical electrodynamics in order to quantify light-matter interactions. We exemplify our approach by studying variants of the conjugated polymer polydiacetylene, and we show that a large polymer conjugation length is critical toward strong exciton-photon coupling, hence underlying the importance of pure structures without static disorder. By comparing to our experimental reflectivity measurements, we show that the coupling of excitons to vibrations, manifested by phonon side bands in the absorption, has a strong impact on the magnitude of light-matter coupling over a range of frequencies. Our approach opens the way toward a deeper understanding of polaritons in organic materials, and we highlight that a quantitatively accurate calculation of the exciton-photon interaction would require accounting for all sources of disorder self-consistently.