Virological characteristics of the SARS-CoV-2 Omicron BA.2 spike.

Soon after the emergence and global spread of the SARS-CoV-2 Omicron lineage BA.1, another Omicron lineage, BA.2, began outcompeting BA.1. The results of statistical analysis showed that the effective reproduction number of BA.2 is 1.4-fold higher than that of BA.1. Neutralization experiments revealed that immunity induced by COVID vaccines widely administered to human populations is not effective against BA.2, similar to BA.1, and that the antigenicity of BA.2 is notably different from that of BA.1. Cell culture experiments showed that the BA.2 spike confers higher replication efficacy in human nasal epithelial cells and is more efficient in mediating syncytia formation than the BA.1 spike. Furthermore, infection experiments using hamsters indicated that the BA.2 spike-bearing virus is more pathogenic than the BA.1 spike-bearing virus. Altogether, the results of our multiscale investigations suggest that the risk of BA.2 to global health is potentially higher than that of BA.1.

Virological characteristics of the SARS-CoV-2 Omicron BA.2 subvariants, including BA.4 and BA.5.

After the global spread of the SARS-CoV-2 Omicron BA.2, some BA.2 subvariants, including BA.2.9.1, BA.2.11, BA.2.12.1, BA.4, and BA.5, emerged in multiple countries. Our statistical analysis showed that the effective reproduction numbers of these BA.2 subvariants are greater than that of the original BA.2. Neutralization experiments revealed that the immunity induced by BA.1/2 infections is less effective against BA.4/5. Cell culture experiments showed that BA.2.12.1 and BA.4/5 replicate more efficiently in human alveolar epithelial cells than BA.2, and particularly, BA.4/5 is more fusogenic than BA.2. We further provided the structure of the BA.4/5 spike receptor-binding domain that binds to human ACE2 and considered how the substitutions in the BA.4/5 spike play roles in ACE2 binding and immune evasion. Moreover, experiments using hamsters suggested that BA.4/5 is more pathogenic than BA.2. Our multiscale investigations suggest that the risk of BA.2 subvariants, particularly BA.4/5, to global health is greater than that of original BA.2.

Attenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variant.

The emergence of the Omicron variant of SARS-CoV-2 is an urgent global health concern1. In this study, our statistical modelling suggests that Omicron has spread more rapidly than the Delta variant in several countries including South Africa. Cell culture experiments showed Omicron to be less fusogenic than Delta and than an ancestral strain of SARS-CoV-2. Although the spike (S) protein of Delta is efficiently cleaved into two subunits, which facilitates cell-cell fusion2,3, the Omicron S protein was less efficiently cleaved compared to the S proteins of Delta and ancestral SARS-CoV-2. Furthermore, in a hamster model, Omicron showed decreased lung infectivity and was less pathogenic compared to Delta and ancestral SARS-CoV-2. Our multiscale investigations reveal the virological characteristics of Omicron, including rapid growth in the human population, lower fusogenicity and attenuated pathogenicity.

Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation.

During the current coronavirus disease 2019 (COVID-19) pandemic, a variety of mutations have accumulated in the viral genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and, at the time of writing, four variants of concern are considered to be potentially hazardous to human society1. The recently emerged B.1.617.2/Delta variant of concern is closely associated with the COVID-19 surge that occurred in India in the spring of 2021 (ref. 2). However, the virological properties of B.1.617.2/Delta remain unclear. Here we show that the B.1.617.2/Delta variant is highly fusogenic and notably more pathogenic than prototypic SARS-CoV-2 in infected hamsters. The P681R mutation in the spike protein, which is highly conserved in this lineage, facilitates cleavage of the spike protein and enhances viral fusogenicity. Moreover, we demonstrate that the P681R-bearing virus exhibits higher pathogenicity compared with its parental virus. Our data suggest that the P681R mutation is a hallmark of the virological phenotype of the B.1.617.2/Delta variant and is associated with enhanced pathogenicity.

Increased flexibility of the SARS-CoV-2 RNA-binding site causes resistance to remdesivir.

Mutations continue to accumulate within the SARS-CoV-2 genome, and the ongoing epidemic has shown no signs of ending. It is critical to predict problematic mutations that may arise in clinical environments and assess their properties in advance to quickly implement countermeasures against future variant infections. In this study, we identified mutations resistant to remdesivir, which is widely administered to SARS-CoV-2-infected patients, and discuss the cause of resistance. First, we simultaneously constructed eight recombinant viruses carrying the mutations detected in in vitro serial passages of SARS-CoV-2 in the presence of remdesivir. We confirmed that all the mutant viruses didn't gain the virus production efficiency without remdesivir treatment. Time course analyses of cellular virus infections showed significantly higher infectious titers and infection rates in mutant viruses than wild type virus under treatment with remdesivir. Next, we developed a mathematical model in consideration of the changing dynamic of cells infected with mutant viruses with distinct propagation properties and defined that mutations detected in in vitro passages canceled the antiviral activities of remdesivir without raising virus production capacity. Finally, molecular dynamics simulations of the NSP12 protein of SARS-CoV-2 revealed that the molecular vibration around the RNA-binding site was increased by the introduction of mutations on NSP12. Taken together, we identified multiple mutations that affected the flexibility of the RNA binding site and decreased the antiviral activity of remdesivir. Our new insights will contribute to developing further antiviral measures against SARS-CoV-2 infection.

Multiple mutations of SARS-CoV-2 Omicron BA.2 variant orchestrate its virological characteristics.

IMPORTANCE: Most studies investigating the characteristics of emerging SARS-CoV-2 variants have been focusing on mutations in the spike proteins that affect viral infectivity, fusogenicity, and pathogenicity. However, few studies have addressed how naturally occurring mutations in the non-spike regions of the SARS-CoV-2 genome impact virological properties. In this study, we proved that multiple SARS-CoV-2 Omicron BA.2 mutations, one in the spike protein and another downstream of the spike gene, orchestrally characterize this variant, shedding light on the importance of Omicron BA.2 mutations out of the spike protein.

Ruthenium and palladium bimetallic nanoparticles achieving functional parity with a rhodium cocatalyst for TiO2-photocatalyzed ring hydrogenation of benzoic acid.

Our previous study showed that a rhodium (Rh) cocatalyst is indispensable for ring hydrogenation of benzoic acid over a titanium(IV) oxide (TiO2) photocatalyst. In this study, we explored ring hydrogenation under an Rh-free condition by using two kinds of cocatalyst that were inactive for this reaction when used solely. Cyclohexanecarboxylic acid as the ring hydrogenation product was successfully obtained when ruthenium (Ru) and palladium (Pd) were simultaneously loaded on TiO2, indicating that this bimetallic system can be used in place of an Rh cocatalyst in ring hydrogenation. The state and distribution of Ru and Pd in particles loaded on TiO2 were investigated by transmission electron microscopy, X-ray photon spectroscopy, and X-ray absorption near edge structure analysis. The functions of Ru and Pd as cocatalysts are discussed on the basis of results of characterization and activity tests. The effects of different contents of Ru and Pd in Ru-Pd/TiO2 prepared by a two-step photodeposition method on catalytic activity and the features of the reaction system were investigated in detail.

High-Entropy Intermetallics Serve Ultrastable Single-Atom Pt for Propane Dehydrogenation.

Propane dehydrogenation has been a promising propylene production process that can compensate for the increasing global demand for propylene. However, Pt-based catalysts with high stability at ≥600 °C have barely been reported because the catalysts typically result in short catalyst life owing to side reactions and coke formation. Herein, we report a new class of heterogeneous catalysts using high-entropy intermetallics (HEIs). Pt-Pt ensembles, which cause side reactions, are entirely diluted by the component inert metals in PtGe-type HEIs. The resultant HEI (PtCoCu) (GeGaSn)/Ca-SiO2 exhibited an outstandingly high catalytic stability, even at 600 °C (kd-1 = τ = 4146 h = 173 d), and almost no deactivation of the catalyst was observed for 2 months for the first time. Detailed experimental studies and theoretical calculations demonstrated that the combination of the site-isolation and entropy effects upon multi-metallization of PtGe drastically enhanced the desorption of propylene and the thermal stability, eventually suppressing the side reactions even at high reaction temperatures.

Genetic characteristics of archival noroviruses detected from the 1970s to the 1990s.

The genetic characterization of archival specimens is important for evaluating the evolutionary processes of noroviruses. Complete viral genome sequences, GVIII.1[GII.P28] and GIX.1[GII.P15], were determined from two archival specimens collected in Tokyo, Japan, in 1986 and 1995. In addition, complete VP1 and partial RdRp sequences of four samples collected between 1975 and 1983 were determined. Two viruses were classified as GI.5[P5] and GI.9[P9]; however, the viruses from the other two samples could not be assigned to any known genotypes using norovirus typing tools and phylogenetic analysis, suggesting that they might be untypable genotypes. Further evolutionary analysis of these viruses is warranted.

Local Structure and L1- and L3-Edge X-ray Absorption Near Edge Structures of Middle Lanthanoid Elements (Eu, Gd, Tb, and Dy) in Their Complex Oxides.

Relationship between the local structures of middle lanthanoid elements (Ln; Eu, Gd, Tb, and Dy) in their complex oxides and the characteristic features of the L1-edge and L3-edge X-ray absorption near edge structure (XANES) was investigated. There was a significant correlation between the pre-edge peak areas of the Ln L1-edge or the full widths at half maximum of the white line of the Ln L3-edge XANES spectra and the abstract physical indexes defined by bond angles formed by the middle Ln elements and the two adjacent oxygen atoms, which act as indicators of local configurational disorder of the target element. Theoretical simulation based on multiple scattering theory revealed that the pre-edge peak in the Ln L1-edge XANES spectra originates due to the p-d hybridization that occurs above the Fermi energy. This systematic survey demonstrated a universal method to estimate the local structure of the middle Ln elements by means of XANES spectroscopy.

Catalytic amino acid production from biomass-derived intermediates.

Amino acids are the building blocks for protein biosynthesis and find use in myriad industrial applications including in food for humans, in animal feed, and as precursors for bio-based plastics, among others. However, the development of efficient chemical methods to convert abundant and renewable feedstocks into amino acids has been largely unsuccessful to date. To that end, here we report a heterogeneous catalyst that directly transforms lignocellulosic biomass-derived α-hydroxyl acids into α-amino acids, including alanine, leucine, valine, aspartic acid, and phenylalanine in high yields. The reaction follows a dehydrogenation-reductive amination pathway, with dehydrogenation as the rate-determining step. Ruthenium nanoparticles supported on carbon nanotubes (Ru/CNT) exhibit exceptional efficiency compared with catalysts based on other metals, due to the unique, reversible enhancement effect of NH3 on Ru in dehydrogenation. Based on the catalytic system, a two-step chemical process was designed to convert glucose into alanine in 43% yield, comparable with the well-established microbial cultivation process, and therefore, the present strategy enables a route for the production of amino acids from renewable feedstocks. Moreover, a conceptual process design employing membrane distillation to facilitate product purification is proposed and validated. Overall, this study offers a rapid and potentially more efficient chemical method to produce amino acids from woody biomass components.

Design, Identification, and Evolution of a Surface Ruthenium(II/III) Single Site for CO Activation.

RuII compounds are widely used in catalysis, photocatalysis, and medical applications. They are usually obtained in a reductive environment as molecular O2 can oxidize RuII to RuIII and RuIV . Here we report the design, identification and evolution of an air-stable surface [bipy-RuII (CO)2 Cl2 ] site that is covalently mounted onto a polyphenylene framework. Such a RuII site was obtained by reduction of [bipy-RuIII Cl4 ]- with simultaneous ligand exchange from Cl- to CO. This structural evolution was witnessed by a combination of in situ X-ray and infrared spectroscopy studies. The [bipy-RuII (CO)2 Cl2 ] site enables oxidation of CO with a turnover frequency of 0.73×10-2  s-1 at 462 K, while the RuIII site is completely inert. This work contributes to the study of structure-activity relationship by demonstrating a practical control over both geometric and electronic structures of single-site catalysts at molecular level.

The Electrophilicity of Surface Carbon Species in the Redox Reactions of CuO-CeO2 Catalysts.

Electronic metal-support interactions (EMSI) describe the electron flow between metal sites and a metal oxide support. It is generally used to follow the mechanism of redox reactions. In this study of CuO-CeO2 redox, an additional flow of electrons from metallic Cu to surface carbon species is observed via a combination of operando X-ray absorption spectroscopy, synchrotron X-ray powder diffraction, near ambient pressure near edge X-ray absorption fine structure spectroscopy, and diffuse reflectance infrared Fourier transform spectroscopy. An electronic metal-support-carbon interaction (EMSCI) is proposed to explain the reaction pathway of CO oxidation. The EMSCI provides a complete picture of the mass and electron flow, which will help predict and improve the catalytic performance in the selective activation of CO2 , carbonate, or carbonyl species in C1 chemistry.

Low-temperature NO oxidation using lattice oxygen in Fe-site substituted SrFeO3-δ.

Improvement of the low-temperature activity for NO oxidation catalysts is a crucial issue to improve the NOx storage performance in automotive catalysts. We have recently reported that the lattice oxygen species in SrFeO3-δ (SFO) are reactive in the oxidation of NO to NO2 at low temperatures. The oxidation of NO using lattice oxygen species is a powerful means to oxidize NO in such kinetically restricted temperature regions. This paper shows that Fe-site substitution of SFO with Mn or Co improves the properties of lattice oxygen such as the temperature and amount of oxygen release/storage, resulting in the enhancement of the activity for NO oxidation in a low-temperature range. In particular, NO oxidation on SrFe0.8Mn0.2O3-δ is found to proceed even at extremely low temperatures <423 K. From oxygen release/storage profiles obtained by temperature-programmed reactions, Co doping into SFO increases the amount of released oxygen owing to the reducibility of the Co species and promotes the phase transformation to the brownmillerite phase. On the other hand, Mn doping does not increase the oxygen release amount and suppresses the phase transformation. However, it significantly decreases the oxygen migration barrier of SFO. Substitution with Mn renders the structure of SFO more robust and maintains the perovskite structure after the release of oxygen. Thus, the oxygen release properties are strongly dependent on the crystal structure change before and after oxygen release from the perovskite structure, which has a significant effect on NO oxidation and the NOx storage performance.

Catalytic Production of Alanine from Waste Glycerol.

Chemical synthesis of amino acids directly from biomass feedstock is rare. Reported here is a one-step protocol to convert crude glycerol, from the biodiesel industry, into 43 % alanine over a Ru1 Ni7 /MgO catalyst. The multifunctional catalytic system promotes glycerol conversion into lactic acid, and then into alanine. X-ray absorption spectroscopy and scanning transmission electron microscopy revealed the existence of bimetallic RuNi species, whereas density-functional theory calculations suggested Ni-doped Ru substantially decreased the Ea of C-H bond dissociation of lactate alkoxide to form pyruvate, which is the rate-determining step. The catalytic route established in this work creates new opportunities for glycerol utilization and enriches the substrate scope of renewable feedstock to access value-added amino acids.

Zeolite-Encaged Pd-Mn Nanocatalysts for CO2 Hydrogenation and Formic Acid Dehydrogenation.

A CO2 -mediated hydrogen storage energy cycle is a promising way to implement a hydrogen economy, but the exploration of efficient catalysts to achieve this process remains challenging. Herein, sub-nanometer Pd-Mn clusters were encaged within silicalite-1 (S-1) zeolites by a ligand-protected method under direct hydrothermal conditions. The obtained zeolite-encaged metallic nanocatalysts exhibited extraordinary catalytic activity and durability in both CO2 hydrogenation into formate and formic acid (FA) dehydrogenation back to CO2 and hydrogen. Thanks to the formation of ultrasmall metal clusters and the synergic effect of bimetallic components, the PdMn0.6 @S-1 catalyst afforded a formate generation rate of 2151 molformate molPd -1 h-1 at 353 K, and an initial turnover frequency of 6860 mol H 2 molPd -1 h-1 for CO-free FA decomposition at 333 K without any additive. Both values represent the top levels among state-of-the-art heterogeneous catalysts under similar conditions. This work demonstrates that zeolite-encaged metallic catalysts hold great promise to realize CO2 -mediated hydrogen energy cycles in the future that feature fast charge and release kinetics.

Atomically Dispersed Pt1-Polyoxometalate Catalysts: How Does Metal-Support Interaction Affect Stability and Hydrogenation Activity?

Unlike nanostructured metal catalysts, supported single-atom catalysts (SACs) contain only atomically dispersed metal atoms, hinting at much more pronounced metal-support effects. Herein, we take a series of polyoxometalate-supported Pt catalysts as examples to quantitatively investigate the stability of Pt atoms on oxide supports and how the Pt-support interaction influences the catalytic performance. For this entire series, we show that the Pt atoms prefer to stay at a 4-fold hollow site of one polyoxometalate molecule and that the least adsorption energy to obtain sintering-resistant Pt SACs is 5.50 eV, which exactly matches the cohesive energy of bulk Pt metal. Further, we compared their catalytic performance in several hydrogenation reactions and simulated the reaction pathways of propene hydrogenation by density functional theory (DFT) calculations. Both experimental and theoretical approaches suggest that despite the Pt1-support interactions being different, the reaction pathways of various Pt1-polyoxometalate catalysts are very similar and their effective reaction barriers are close to each other and as low as 24 kJ/mol, indicating the possibility of obtaining SACs with improved stability without compromising activity. DFT calculations show that all reaction elementary steps take place only on the Pt atom without involving neighboring O atoms and that hydrogenation proceeds from the molecularly adsorbed H2 species. Pt SACs give a weaker H2 adsorption energy than Pt clusters or surfaces, resulting in small adsorption equilibrium constants and small apparent activation barriers, which agree between experiment and theory.

Local Structure Study of Lanthanide Elements by X-Ray Absorption Near Edge Structure Spectroscopy.

This paper describes a systematic study of the spectra and local structures of lanthanide (Ln) L-edge XANES. We found that Ln L1 and L3 -edge XANES spectra exhibit characteristic features correlated to their local symmetry through experimental and theoretical simulations. We also propose a simple local structure index criterion for a combination of XANES study and theoretical simulation. Possible solutions of intrinsic problems such as low resolution of characteristic features in the Ln L-edge XANES and site distributions are also discussed.

Self-regeneration of a Ni-Cu alloy catalyst during a three-way catalytic reaction.

Ni-Cu alloy supported on γ-Al2O3 catalysts prepared by high-temperature hydrogen reduction exhibit high catalytic activity and durability for a three-way catalytic reaction under both oxidative and reductive conditions because of their self-regenerating feature. DFT calculations showed that Ni-oxide was reduced to Ni metal by CO in the presence of Cu metal because of the Ni-Cu alloy effect but was not in the absence of Cu metal.

Dynamic Behavior of Rh Species in Rh/Al2O3 Model Catalyst during Three-Way Catalytic Reaction: An Operando X-ray Absorption Spectroscopy Study.

The dynamic behavior of Rh species in 1 wt% Rh/Al2O3 catalyst during the three-way catalytic reaction was examined using a micro gas chromatograph, a NOx meter, a quadrupole mass spectrometer, and time-resolved quick X-ray absorption spectroscopy (XAS) measurements at a public beamline for XAS, BL01B1 at SPring-8, operando. The combined data suggest different surface rearrangement behavior, random reduction processes, and autocatalytic oxidation processes of Rh species when the gas is switched from a reductive to an oxidative atmosphere and vice versa. This study demonstrates an implementation of a powerful operando XAS system for heterogeneous catalytic reactions and its importance for understanding the dynamic behavior of active metal species of catalysts.