COVID-19 outbreak and genomic investigation in an inpatient behavioral health unit

Background

Inpatient behavioral health units (BHUs) had unique challenges in implementing interventions to mitigate coronavirus disease 2019 (COVID-19) transmission, in part due to socialization in BHU settings. The objective of this study was to identify the transmission routes and the efficacy of the mitigation strategies employed during a COVID-19 outbreak in an inpatient BHU during the Omicron surge from December 2021 to January 2022.

Methods

An outbreak investigation was performed after identifying 2 COVID-19-positive BHU inpatients on December 16 and 20, 2021. Mitigation measures involved weekly point prevalence testing for all inpatients, healthcare workers (HCWs), and staff, followed by infection prevention mitigation measures and molecular surveillance. Whole-genome sequencing on a subset of COVID-19-positive individuals was performed to identify the outbreak source. Finally, an outbreak control sustainability plan was formulated for future BHU outbreak resurgences.

Results

We identified 35 HCWs and 8 inpatients who tested positive in the BHU between December 16, 2021, and January 17, 2022. We generated severe acute respiratory coronavirus virus 2 (SARS-CoV-2) genomes from 15 HCWs and all inpatients. Phylogenetic analyses revealed 3 distinct but genetically related clusters: (1) an HCW and inpatient outbreak likely initiated by staff, (2) an HCW and inpatient outbreak likely initiated by an inpatient visitor, and (3) an HCW-only cluster initiated by staff.

Conclusions

Distinct transmission clusters are consistent with multiple, independent SARS-CoV-2 introductions with further inpatient transmission occurring in communal settings. The implemented outbreak control plan comprised of enhanced personal protective equipment requirements, limited socialization, and molecular surveillance likely minimized disruptions to patient care as a model for future pandemics.

Time domain DNP at 1.2 T

We present the results of an experimental pulsed DNP study at 1.2 T (33.5 GHz/51 MHz electron and 1H Larmor frequencies, respectively). The results include a comparison of constant-amplitude NOVEL (CA-NOVEL), ramped-amplitude NOVEL (RA-NOVEL) and the frequency-swept integrated solid effect (FS-ISE) experiments all of which were performed at the NOVEL matching condition, ω1S=ω0I, where ω1S is the electron Rabi frequency andω0I the proton Larmor frequency. To the best of our knowledge, this is the first pulsed DNP study carried out at field higher than X-band (0.35 T) using the NOVEL condition. A combination of high microwave power (∼150 W) and a microwave cavity with a high Q (∼500) allowed us to satisfy the NOVEL matching condition. We also observed stretched solid effect (S2E) contributions in the Zeeman field profiles when chirped pulses are applied. Furthermore, the high quality factor of the cavity limits the concentration of the radical to ∼5 mM and generates a hysteresis in the FS-ISE experiments. Nevertheless, we observe very high DNP enhancements that are comparable to the results at X-band. These promising outcomes suggest the importance of further studies at even higher fields that delineate the instrumentation and methods required for time domain DNP.

Environmental and Personal Protective Equipment Contamination during Simulated Healthcare Activities

Providing care to patients with an infectious disease can result in the exposure of healthcare workers (HCWs) to pathogen-containing bodily fluids. We performed a series of experiments to characterize the magnitude of environmental contamination—in air, on surfaces and on participants—associated with seven common healthcare activities. The seven activities studied were bathing, central venous access, intravenous access, intubation, physical examination, suctioning and vital signs assessment. HCWs with experience in one or more activities were recruited to participate and performed one to two activities in the laboratory using task trainers that contained or were contaminated with fluorescein-containing simulated bodily fluid. Fluorescein was quantitatively measured in the air and on seven environmental surfaces. Fluorescein was quantitatively and qualitatively measured on the personal protective equipment (PPE) worn by participants. A total of 39 participants performed 74 experiments, involving 10–12 experimental trials for each healthcare activity. Healthcare activities resulted in diverse patterns and levels of contamination in the environment and on PPE that are consistent with the nature of the activity. Glove and gown contamination were ubiquitous, affirming the value of wearing these pieces of PPE to protect HCW’s clothing and skin. Though intubation and suctioning are considered aerosol-generating procedures, fluorescein was detected less frequently in air and at lower levels on face shields and facemasks than other activities, which suggests that the definition of aerosol-generating procedure may need to be revised. Face shields may protect the face and facemask from splashes and sprays of bodily fluids and should be used for more healthcare activities.

Ramped-amplitude NOVEL

We present a pulsed dynamic nuclear polarization (DNP) study using a ramped-amplitude nuclear orientation via electron spin locking (RA-NOVEL) sequence that utilizes a fast arbitrary waveform generator (AWG) to modulate the microwave pulses together with samples doped with narrow-line radicals such as 1,3-bisdiphenylene-2-phenylallyl (BDPA), sulfonated-BDPA (SA-BDPA), and trityl-OX063. Similar to ramped-amplitude cross polarization in solid-state nuclear magnetic resonance, RA-NOVEL improves the DNP efficiency by a factor of up to 1.6 compared to constant-amplitude NOVEL (CA-NOVEL) but requires a longer mixing time. For example, at τ_mix = 8 μs, the DNP efficiency reaches a plateau at a ramp amplitude of ∼20 MHz for both SA-BDPA and trityl-OX063, regardless of the ramp profile (linear vs. tangent). At shorter mixing times (τ_mix = 0.8 μs), we found that the tangent ramp is superior to its linear counterpart and in both cases there exists an optimum ramp size and therefore ramp rate. Our results suggest that RA-NOVEL should be used instead of CA-NOVEL as long as the electronic spin lattice relaxation T_1e is sufficiently long and/or the duty cycle of the microwave amplifier is not exceeded. To the best of our knowledge, this is the first example of a time domain DNP experiment that utilizes modulated microwave pulses. Our results also suggest that a precise modulation of the microwave pulses can play an important role in optimizing the efficiency of pulsed DNP experiments and an AWG is an elegant instrumental solution for this purpose.

Anisotropic 2H NMR spin-lattice relaxation in L alpha-phase cerebroside bilayers

A series of 2H NMR inversion recovery experiments in the L alpha phase of the cerebroside N-palmitoylgalactosylsphingosine (NPGS) have been performed. In these liquid crystalline lipid bilayers we have observed substantial anisotropy in the spin-lattice relaxation of the CD2 groups in the acyl chains. The form and magnitude of the anisotropy varies with position in the chain, being positive in the upper region, decreasing to zero at the 4-position, and reversing sign at the lower chain positions. It is also shown that addition of cholesterol to the bilayer results in profound changes in the anisotropy. These observations are accounted for by a simple motional model of discrete hops among nine sites, which result from the coupling of two modes of motion--long-axis rotational diffusion and gauche-trans isomerization. This model is employed in quantitative simulations of the spectral line shapes and permits determination of site populations and motional rates. These results, plus preliminary results in sphingomyelin and lecithin bilayers, illustrate the utility of T1 anisotropy measurements as a probe of dynamics in L alpha-phase bilayers.