Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

AbstractUnderstanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.</jats:p

Monitoring DNA Hybridization and Thermal Dissociation at the Silica/Water Interface Using Resonantly Enhanced Second Harmonic Generation Spectroscopy

The immobilization of oligonucleotide sequences onto glass supports is central to the field of biodiagnostics and molecular biology with the widespread use of DNA microarrays. However, the influence of confinement on the behavior of DNA immobilized on silica is not well understood owing to the difficulties associated with monitoring this buried interface. Second harmonic generation (SHG) is an inherently surface specific technique making it well suited to observe processes at insulator interfaces like silica. Using a universal 3-nitropyrolle nucleotide as an SHG-active label, we monitored the hybridization rate and thermal dissociation of a 15-mer of DNA immobilized at the silica/aqueous interface. The immobilized DNA exhibits hybridization rates on the minute time scale, which is much slower than hybridization kinetics in solution but on par with hybridization behavior observed at electrochemical interfaces. In contrast, the thermal dissociation temperature of the DNA immobilized on silica is on average 12 °C lower than the analogous duplex in solution, which is more significant than that observed on other surfaces like gold. We attribute the destabilizing affect of silica to its negatively charged surface at neutral pH that repels the hybridizing complementary DNA

Bimodal or Trimodal? The Influence of Starting pH on Site Identity and Distribution at the Low Salt Aqueous/Silica Interface

Second harmonic generation (SHG) is commonly employed to monitor processes at mineral oxide/liquid interfaces. Using SHG, we determine how the starting pH affects the acid–base chemistry of the silica/aqueous interface. We observe three different sites with p<i>K</i>_a values of approximately 3.8, 5.2, and ∼9 (p<i>K</i>_a-I, p<i>K</i>_a-II, p<i>K</i>_a-III, respectively), but the presence and relative abundance of these sites is very sensitive to the starting pH. For titrations initiated at pH 12, all three sites are observed, whereas only two sites are observed for titrations initiated at pH 2 or pH 7. Moreover, exposure to pH 2 facilitates the formation of p<i>K</i>_a-II and p<i>K</i>_a-III sites, while exposure to pH 7 results in p<i>K</i>_a-I and p<i>K</i>_a-III sites. Based on previous computational work, we assign these sites to three different hydrogen bonding environments at the interface including a hydrophobic site for the most acidic silanol corresponding to p<i>K</i>_a-I

The Influence of Gap Length on Cooperativity and Rate of Association in DNA-Modified Gold Nanoparticle Aggregates

Polyvalent gold nanoparticle–DNA conjugates hybridize with complementary linker DNA strands to form aggregates that exhibit sharp dissociation curves indicative of cooperative behavior. Introducing single-stranded gaps consisting of thymidines (T₁–T₂₀) into the linker strand resulted in a decrease in the number of duplexes that dissociate cooperatively. Upon adding one base insertion (T₁) the cooperative number drops from 6.3(2) to 2.8(2) duplexes. The cooperative number then increases slightly for the T₃ gap and thereafter decreases for T₈ and T₁₀, with a slight increase again for the T₂₀ gap. As the presence of a shared condensed cation cloud has been implicated in neighboring duplex cooperativity, we measured the salt-dependent behavior of T_<i>n</i> gap-linked unmodified duplexes and the number of ions released per duplex dissociation. Interestingly, the number of cations released for the duplexes with a longer gap sequence is significantly larger than the number released for a T₁ gap-linked duplex or a nicked duplex (T₀). Overall there is a correlation between the change in condensed cation density and the dissociation entropy for the unmodified T_<i>n</i> gap-linked duplexes, and the cooperative unit for the T_<i>n</i> gap-linked GNP–DNA aggregates. Using dynamic light scattering and changes in optical absorbance, we also found that aggregation of GNP–DNA is more rapid when hybridization occurs at a nicked versus gap site, which was previously observed but attributed to slower hybridization as a result of the longer linker strand. By comparing the aggregation rate of a prehybridized GNP–DNA:T₁₀-linker complex with a completely complementary GNP–DNA and a GNP–DNA that led to a T₁₀ gap, we were able to establish that the presence of the gap, not DNA length or accessibility, caused the decrease in aggregation rate. Our results support that flexibility in aggregates decreases the rate of aggregation as well as the extent of cooperativity, which has important implications in genomic DNA detection

Ketone Binding at Amino and Ureido Monolayer/Solvent Interfaces Studied by Nonlinear Optical Techniques

Understanding the influence of immobilization is key to advancing efforts in green chemistry based on supported catalyst materials. The binding of a model reactant 4-nitroacetophenone with amino and ureido organocatalytic monolayers has been investigated at the acetonitrile/solid interface using a combination of second harmonic generation (SHG) and sum frequency generation (SFG). By changing the ketone concentration in the bulk solvent, binding isotherms at each interface were determined from SHG measurements. Langmuir fitting of these isotherms yielded binding energies consistent with hydrogen bond formation. Surprisingly, the ketone had a lower binding affinity for ureido monolayers compared with its binding behavior at amino-modified surfaces despite the fact that urea can form two hydrogen bonds with carbonyl groups. This lower binding affinity was attributed to the presence of a hydrogen bond network within the ureido monolayer that must be disrupted to facilitate ketone binding. Vibrational SFG measurements of the urea groups in the N–H stretching region revealed two new peaks upon introduction of the ketone that were attributed to the ketone-bound urea. An observed phase change in these peaks supported that ketone binding not only disrupted the hydrogen-bonded network within the ureido monolayer but also led to significant reorientation of the ureido groups

Specific Cation Effects on the Bimodal Acid–Base Behavior of the Silica/Water Interface

Using nonresonant second harmonic generation spectroscopy, we have monitored the change in surface charge density of the silica/water interface over a broad pH range in the presence of different alkali chlorides. Planar silica is known to possess two types of surface sites with p<i>K</i>_a values of ∼4 and ∼9, which are attributed to different solvation environments of the silanols. We report that varying the alkali chloride electrolyte significantly changes the effective acid dissociation constant (p<i>K</i>_a^eff) for the less acidic silanol groups, with the silica/NaCl_aq and silica/CsCl_aq interfaces exhibiting the lowest and highest p<i>K</i>_a^eff values of 8.3(1) and 10.8(1), respectively. Additionally, the relative populations of the two silanol groups are also very sensitive to the electrolyte identity. The greatest percentage of acidic silanol groups was 60(2)% for the silica/LiCl_aq interface in contrast to the lowest value of 20(2)% for the silica/NaCl_aq interface. We attribute these changes in the bimodal behavior to the influence of alkali ions on the interfacial water structure and its corresponding effect on surface acidity

Halide-Induced Cooperative Acid–Base Behavior at a Negatively Charged Interface

Using second harmonic generation and sum frequency generation spectroscopy, we monitor the influence of sodium and potassium halides on acid–base processes at the negatively charged silica/aqueous electrolyte interface. We find that the two types of acidic silanols at the surface are very sensitive to the presence of halides in the aqueous phase. As the halide size increases, the pH at which half the more acidic sites are deprotonated (pH_0.5) shifts to lower pH. Conversely, the pH_0.5 of the less acidic sites shifts to higher pH with increasing halide size. We also observe titration curves of increasing sharpness as the halide size increases, indicative of positive cooperativity. Using a simple cooperative model, we find that the cooperative unit for the dissociation of more acidic surface sites is ∼1, 2, and 3 for the chloride, bromide, and iodide electrolytes, respectively, which reveals that the larger anions promote deprotonation among the more acidic silanol groups. We also find that the fraction of more acidic sites, proportional to the relative surface charge density at neutral pH, increases from 20% to 86% as the sodium halide is varied from chloride to iodide. As the percentage of more acidic sites and the surface charge at neutral pH increases, the effective acidity of the less acidic sites decreases, indicating that greater surface charge density renders the remaining silanol groups more difficult to deprotonate. As the relative amount of less acidic sites increases, their deprotonation events exhibit negative, rather than positive, cooperativity revealing charge repulsion between neighboring silanol groups

NEW MODEL SURFACES FOR MINERAL AEROSOLS: ANILINE-LINKED OLEFINS ON SILICA STUDIED WITH BROADBAND VIBRATIONAL SUM-FREQUENCY GENERATION

Author Institution: Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208Olefin-functionalized silica surfaces and their reactions apply to catalysis, materials science and atmospheric chemistry, however, their high vapor pressures make it difficult to study their heterogeneous reactions at room temperature. We use vibrational broadband sum frequency generation (SFG) to characterize glass surfaces functionalized with olefins, circumventing issues associated with the high vapor pressures of many olefins. Using various ester-, amide- and aniline-based linkers, a number of cyclic and acyclic olefins are chemically bound to borosilicate glass surfaces via siloxanes. These systems model the surfaces of atmospheric mineral-dust aerosols coated with biogenic unsaturated organic molecules that are often oxidized by tropospheric ozone. While aliphatic linkers contribute spectral peaks that overlap with the region of interest for studying olefin chemistry, spectra of aniline-based linkers show that their use minimizes linker-attributed spectral congestion in the aliphatic C-H spectral region. Studies of various aniline-linked olefins also elucidate the spectral features of cyclic olefins as compared to acyclic counterparts. These results demonstrate the effectiveness of using phenyl-linked olefins on silica for SFG studies of tailor-made organic surfaces designed to address complexity issues in catalysis, materials science and atmospheric chemistry