Identification of SARS-CoV-2 variants in indoor dust.

Environmental surveillance of pathogens underlying infectious disease is critical to ensure public health. Recent efforts to track SARS-CoV-2 have utilized wastewater sampling to infer community trends in viral abundance and variant composition. Indoor dust has also been used for building-level inferences, though to date no sequencing data providing variant-scale resolution have been reported from dust samples, and strategies to monitor circulating variants in dust are needed to help inform public health decisions. In this study, we demonstrate that SARS-CoV-2 lineages can be detected and sequenced from indoor bulk dust samples. We collected 93 vacuum bags from April 2021 to March 2022 from buildings on The Ohio State University's (OSU) Columbus campus, and the dust was used to develop and apply an amplicon-based whole-genome sequencing protocol to identify the variants present and estimate their relative abundances. Three variants of concern were detected in the dust: Alpha, Delta, and Omicron. Alpha was found in our earliest sample in April 2021 with an estimated frequency of 100%. Delta was the primary variant present from October of 2021 to January 2022, with an average estimated frequency of 91% (±1.3%). Omicron became the primary variant in January 2022 and was the dominant strain in circulation through March with an estimated frequency of 87% (±3.2%). The detection of these variants on OSU's campus correlates with the circulation of these variants in the surrounding population (Delta p<0.0001 and Omicron p = 0.02). Overall, these results support the hypothesis that dust can be used to track COVID-19 variants in buildings.

Soft X-ray Absorption Spectroscopy of Liquids and Solutions.

X-ray absorption spectroscopy (XAS) is an electronic absorption technique for which the initial state is a deeply buried core level. The photon energies corresponding to such transitions are governed primarily by the binding energies of the initial state. Because the binding energies of core electrons vary significantly among atomic species, this makes XAS an element-selective spectroscopy. Proper interpretation of XA spectra can provide detailed information on the local chemical and geometric environment of the target atom. The introduction of liquid microjet and flow cell technologies into XAS experiments has enabled the general study of liquid samples. Liquids studied to date include water, alcohols, and solutions with relevance to biology and energy technology. This Review summarizes the experimental techniques employed in XAS studies of liquid samples and computational methods used for interpretation of the resulting spectra and summarizes salient experiments and results obtained in the XAS investigations of liquids.

Communication: Hydrogen bonding interactions in water-alcohol mixtures from X-ray absorption spectroscopy.

While methanol and ethanol are macroscopically miscible with water, their mixtures exhibit negative excess entropies of mixing. Despite considerable effort in both experiment and theory, there remains significant disagreement regarding the origin of this effect. Different models for the liquid mixture structure have been proposed to address this behavior, including the enhancement of the water hydrogen bonding network around the alcohol hydrophobic groups and microscopic immiscibility or clustering. We have investigated mixtures of methanol, ethanol, and isopropanol with water by liquid microjet X-ray absorption spectroscopy on the oxygen K-edge, an atom-specific probe providing details of both inter- and intra-molecular structure. The measured spectra evidence a significant enhancement of hydrogen bonding originating from the methanol and ethanol hydroxyl groups upon the addition of water. These additional hydrogen bonding interactions would strengthen the liquid-liquid interactions, resulting in additional ordering in the liquid structures and leading to a reduction in entropy and a negative enthalpy of mixing, consistent with existing thermodynamic data. In contrast, the spectra of the isopropanol-water mixtures exhibit an increase in the number of broken alcohol hydrogen bonds for mixtures containing up to 0.5 water mole fraction, an observation consistent with existing enthalpy of mixing data, suggesting that the measured negative excess entropy is a result of clustering or micro-immiscibility.

Properties of aqueous nitrate and nitrite from x-ray absorption spectroscopy.

Nitrate and nitrite ions are of considerable interest, both for their widespread use in commercial and research contexts and because of their central role in the global nitrogen cycle. The chemistry of atmospheric aerosols, wherein nitrate is abundant, has been found to depend on the interfacial behavior of ionic species. The interfacial behavior of ions is determined largely by their hydration properties; consequently, the study of the hydration and interfacial behavior of nitrate and nitrite comprises a significant field of study. In this work, we describe the study of aqueous solutions of sodium nitrate and nitrite via X-ray absorption spectroscopy (XAS), interpreted in light of first-principles density functional theory electronic structure calculations. Experimental and calculated spectra of the nitrogen K-edge XA spectra of bulk solutions exhibit a large 3.7 eV shift between the XA spectra of nitrate and nitrite resulting from greater stabilization of the nitrogen 1s energy level in nitrate. A similar shift is not observed in the oxygen K-edge XA spectra of NO3 (-) and NO2 (-). The hydration properties of nitrate and nitrite are found to be similar, with both anions exhibiting a similar propensity towards ion pairing.

X-Ray absorption spectroscopy of LiBF4 in propylene carbonate: a model lithium ion battery electrolyte.

Since their introduction into the commercial marketplace in 1991, lithium ion batteries have become increasingly ubiquitous in portable technology. Nevertheless, improvements to existing battery technology are necessary to expand their utility for larger-scale applications, such as electric vehicles. Advances may be realized from improvements to the liquid electrolyte; however, current understanding of the liquid structure and properties remains incomplete. X-ray absorption spectroscopy of solutions of LiBF4 in propylene carbonate (PC), interpreted using first-principles electronic structure calculations within the eXcited electron and Core Hole (XCH) approximation, yields new insight into the solvation structure of the Li(+) ion in this model electrolyte. By generating linear combinations of the computed spectra of Li(+)-associating and free PC molecules and comparing to the experimental spectrum, we find a Li(+)-solvent interaction number of 4.5. This result suggests that computational models of lithium ion battery electrolytes should move beyond tetrahedral coordination structures.

Electrokinetic detection for X-ray spectra of weakly interacting liquids: n-decane and n-nonane.

The introduction of liquid microjets into soft X-ray absorption spectroscopy enabled the windowless study of liquids by this powerful atom-selective high vacuum methodology. However, weakly interacting liquids produce large vapor backgrounds that strongly perturb the liquid signal. Consequently, solvents (e.g., hydrocarbons, ethers, ketones, etc.) and solutions of central importance in chemistry and biology have been inaccessible by this technology. Here we describe a new detection method, upstream detection, which greatly reduces the vapor phase contribution to the X-ray absorption signal while retaining important advantages of liquid microjet sample introduction (e.g., minimal radiation damage). The effectiveness of the upstream detection method is demonstrated in this first study of room temperature liquid hydrocarbons: n-nonane and n-decane. Good agreement with first principles' calculations indicates that the eXcited electron and Core Hole theory adequately describes the subtle interactions in these liquids that perturb the electronic structure of the unoccupied states probed in core-level experiments.

Cation-cation contact pairing in water: guanidinium.

The formation of like-charge guanidinium-guanidinium contact ion pairs in water is evidenced and characterized by X-ray absorption spectroscopy and first-principles spectral simulations based on molecular dynamics sampling. Observed concentration-induced nitrogen K-edge resonance shifts result from π* state mixing and the release of water molecules from each first solvation sphere as two solvated guanidinium ions associate into a stacked pair configuration. Possible biological implications of this counterintuitive cation-cation pairing are discussed.