Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak.

An outbreak of over 1,000 COVID-19 cases in Provincetown, Massachusetts (MA), in July 2021-the first large outbreak mostly in vaccinated individuals in the US-prompted a comprehensive public health response, motivating changes to national masking recommendations and raising questions about infection and transmission among vaccinated individuals. To address these questions, we combined viral genomic and epidemiological data from 467 individuals, including 40% of outbreak-associated cases. The Delta variant accounted for 99% of cases in this dataset; it was introduced from at least 40 sources, but 83% of cases derived from a single source, likely through transmission across multiple settings over a short time rather than a single event. Genomic and epidemiological data supported multiple transmissions of Delta from and between fully vaccinated individuals. However, despite its magnitude, the outbreak had limited onward impact in MA and the US overall, likely due to high vaccination rates and a robust public health response.

Adaptive periodicity in the infectivity of malaria gametocytes to mosquitoes.

Daily rhythms in behaviour, physiology and molecular processes are expected to enable organisms to appropriately schedule activities according to consequences of the daily rotation of the Earth. For parasites, this includes capitalizing on periodicity in transmission opportunities and for hosts/vectors, this may select for rhythms in immune defence. We examine rhythms in the density and infectivity of transmission forms (gametocytes) of rodent malaria parasites in the host's blood, parasite development inside mosquito vectors and potential for onwards transmission. Furthermore, we simultaneously test whether mosquitoes exhibit rhythms in susceptibility. We reveal that at night, gametocytes are twice as infective, despite being less numerous in the blood. Enhanced infectiousness at night interacts with mosquito rhythms to increase sporozoite burdens fourfold when mosquitoes feed during their rest phase. Thus, changes in mosquito biting time (owing to bed nets) may render gametocytes less infective, but this is compensated for by the greater mosquito susceptibility.

Two-dimensional photonic crystal chemical and biomolecular sensors.

We review recent progress in the development of two-dimensional (2-D) photonic crystal (PC) materials for chemical and biological sensing applications. Self-assembly methods were developed in our laboratory to fabricate 2-D particle array monolayers on mercury and water surfaces. These hexagonal arrays strongly forward Bragg diffract light to report on their array spacings. By embedding these 2-D arrays onto responsive hydrogel surfaces, 2-D PC sensing materials can be fabricated. The 2-D PC sensors utilize responsive polymer hydrogels that are chemically functionalized to show volume phase transitions in selective response to particular chemical species. Novel hydrogels were also developed in our laboratory by cross-linking proteins while preserving their native structures to maintain their selective binding affinities. The volume phase transitions swell or shrink the hydrogels, which alter their 2-D array spacings, and shift their diffraction wavelengths. These shifts can be visually detected or spectrally measured. These 2-D PC sensing materials have been used for the detection of many analytes, such as pH, surfactants, metal ions, proteins, anionic drugs, and ammonia. We are exploring the use of organogels that use low vapor pressure ionic liquids as their mobile phases for sensing atmospheric analytes.

Removable interpenetrating network enables highly-responsive 2-D photonic crystal hydrogel sensors.

Responsive hydrogels functionalized with molecular recognition agents can undergo large volume changes upon interactions with specific chemical species. These responsive hydrogels can function as chemical sensing materials if the hydrogel volumes are monitored by using devices such as photonic crystals (PhC). An important criterion of merit is the responsiveness of these sensing hydrogels. Generally, hydrogel responsiveness is inversely proportional to the hydrogel crosslink density because the elastic constants scale with the crosslink density. The responsivities of these hydrogel sensors dramatically increase as their hydrogel crosslinker concentrations decrease. Unfortunately, the resulting highly responsive hydrogels become fragile at low crosslink densities, and are hard to fabricate and utilize. To temporarily increase the mechanical strengths of these highly responsive hydrogels we developed a method to incorporate a removable reinforcing interpenetrating hydrogel network. We demonstrate the utility of this approach by incorporating an interpenetrating PVA hydrogel within a weak, low crosslinked pH sensitive hydrogel through a freeze-thaw process. These interpenetrating PVA hydrogels are indefinitely stable at room temperature, but easily dissolved on transient heating to 70 °C. The pH sensing hydrogel response is unaffected by this incorporation and subsequent dissolution of the interpenetrating PVA hydrogel. These sacrificial hydrogels enable the fabrication and utilization of highly responsive hydrogel sensing materials.

Responsive ionic liquid-polymer 2D photonic crystal gas sensors.

We developed novel air-stable 2D polymerized photonic crystal (2DPC) sensing materials for visual detection of gas phase analytes such as water and ammonia by utilizing a new ionic liquid, ethylguanidine perchlorate (EGP) as the mobile phase. Because of the negligible ionic liquid vapor pressure these 2DPC sensors are indefinitely air stable and, therefore, can be used to sense atmospheric analytes. 2D arrays of ~640 nm polystyrene nanospheres were attached to the surface of crosslinked poly(hydroxyethyl methacrylate) (pHEMA)-based polymer networks dispersed in EGP. The wavelength of the bright 2D photonic crystal diffraction depends sensitively on the 2D array particle spacing. The volume phase transition response of the EGP-pHEMA system to water vapor or gaseous ammonia changes the 2DPC particle spacing, enabling the visual determination of the analyte concentration. Water absorbed by EGP increases the Flory-Huggins interaction parameter, which shrinks the polymer network and causes a blue shift in the diffracted light. Ammonia absorbed by the EGP deprotonates the pHEMA-co-acrylic acid carboxyl groups, swelling the polymer which red shifts the diffracted light.

Evidence of transmission from fully vaccinated individuals in a large outbreak of the SARS-CoV-2 Delta variant in Provincetown, Massachusetts.

Multiple summer events, including large indoor gatherings, in Provincetown, Massachusetts (MA), in July 2021 contributed to an outbreak of over one thousand COVID-19 cases among residents and visitors. Most cases were fully vaccinated, many of whom were also symptomatic, prompting a comprehensive public health response, motivating changes to national masking recommendations, and raising questions about infection and transmission among vaccinated individuals. To characterize the outbreak and the viral population underlying it, we combined genomic and epidemiological data from 467 individuals, including 40% of known outbreak-associated cases. The Delta variant accounted for 99% of sequenced outbreak-associated cases. Phylogenetic analysis suggests over 40 sources of Delta in the dataset, with one responsible for a single cluster containing 83% of outbreak-associated genomes. This cluster was likely not the result of extensive spread at a single site, but rather transmission from a common source across multiple settings over a short time. Genomic and epidemiological data combined provide strong support for 25 transmission events from, including many between, fully vaccinated individuals; genomic data alone provides evidence for an additional 64. Together, genomic epidemiology provides a high-resolution picture of the Provincetown outbreak, revealing multiple cases of transmission of Delta from fully vaccinated individuals. However, despite its magnitude, the outbreak was restricted in its onward impact in MA and the US, likely due to high vaccination rates and a robust public health response.

A Conserved TCRß Signature Dominates a Highly Polyclonal T-Cell Expansion During the Acute Phase of a Murine Malaria Infection.

CD4+ αß T-cells are key mediators of the immune response to a first Plasmodium infection, undergoing extensive activation and splenic expansion during the acute phase of an infection. However, the clonality and clonal composition of this expansion has not previously been described. Using a comparative infection model, we sequenced the splenic CD4+ T-cell receptor repertoires generated over the time-course of a Plasmodium chabaudi infection. We show through repeat replicate experiments, single-cell RNA-seq, and analyses of independent RNA-seq data, that following a first infection - within a highly polyclonal expansion - T-effector repertoires are consistently dominated by TRBV3 gene usage. Clustering by sequence similarity, we find the same dominant clonal signature is expanded across replicates in the acute phase of an infection, revealing a conserved pathogen-specific T-cell response that is consistently a hallmark of a first infection, but not expanded upon re-challenge. Determining the host or parasite factors driving this conserved response may uncover novel immune targets for malaria therapeutic purposes.

Stimuli-Responsive Pure Protein Organogel Sensors and Biocatalytic Materials.

Utilizing protein chemistry in organic solvents has important biotechnology applications. Typically, organic solvents negatively impact protein structure and function. Immobilizing proteins via cross-links to a support matrix or to other proteins is a common strategy to preserve the native protein function. Recently, we developed methods to fabricate macroscopic responsive pure protein hydrogels by lightly cross-linking the proteins with glutaraldehyde for chemical sensing and enzymatic catalysis applications. The water in the resulting protein hydrogel can be exchanged for organic solvents. The resulting organogel contains pure organic solvents as their mobile phases. The organogel proteins retain much of their native protein function, i.e., protein-ligand binding and enzymatic activity. A stepwise ethylene glycol (EG) solvent exchange was performed to transform these hydrogels into organogels with a very low vapor pressure mobile phase. These responsive organogels are not limited by solvent/mobile phase evaporation. The solvent exchange to pure EG is accompanied by a volume phase transition (VPT) that decreases the organogel volume compared to that of the hydrogel. Our organogel sensor systems utilize shifts in the particle spacing of an attached two-dimensional photonic crystal (2DPC) to report on the volume changes induced by protein-ligand binding. Our 2DPC bovine serum albumin (BSA) organogels exhibit VPT that swell the organogels in response to the BSA binding of charged ligands like ibuprofen and fatty acids. To our knowledge, this is the first report of a pure protein organogel VPT induced by protein-ligand binding. Catalytic protein organogels were also fabricated that utilize the enzyme organophosphorus hydrolase (OPH) to hydrolyze toxic organophosphate (OP) nerve agents. Our OPH organogels retain significant enzymatic activity. The OPH organogel rate of OP hydrolysis is ∼160 times higher than that of un-cross-linked OPH monomers in a 1:1 ethylene glycol/water mixture.