The impact of the first three months of the COVID-19 pandemic on the Australian trans community.

Background: Trans and gender diverse individuals (people who identify with a gender different to what was presumed for them at birth) are one of the most medically and socially marginalized groups in our community. The COVID-19 pandemic may compound preexisting depression and thoughts of self-harm or suicide. Aim: We aimed to explore the impact of the COVID-19 pandemic on the Australian trans community. Methods: An online cross-sectional survey was conducted between 1st May 2020 and 30th June 2020, amidst strict Australia-wide social restrictions. Australian trans people aged ≥16 years were eligible to participate. Survey questions explored the impact of the COVID-19 pandemic on living situation, employment, financial situation, and healthcare. Logistic regression to assess negative impacts due to COVID-19 on depression and thoughts of self-harm or suicide (measured by Patient Health Questionnaire-9 (PHQ-9) are presented as odds ratios (95% confidence interval)). Results: Of 1019 participants, 49.6% reported experiencing financial strain, 22% had reduced working hours, and 22.4% were unemployed (three times the national rate). Concerningly, 61.1% experienced clinically significant symptoms of depression (Patient Health Questionnaire-9 score ≥10), considerably higher than pre-COVID rates for the trans community and over twice the national rate. Moreover, 49% reported thoughts of self-harm or suicide (over three times the national rate) which was more likely if a person experienced cancelation or postponement of gender-affirming surgery (OR 1.56 (1.04, 2.35)), financial strain (OR 1.80 (1.36, 2.38)), or felt unsafe or afraid in their household (OR 1.96 (1.23, 3.08)). Discussion: Given rates of clinically significant depression and thoughts of self-harm or suicide are far higher in trans people than the general population, specific strategies to improve mental health in the trans community during the COVID-19 pandemic must be made a priority for policymakers, researchers, and health service providers to prevent suicide.Supplemental data for this article is available online at https://doi.org/10.1080/26895269.2021.1890659.

The spatial and temporal distribution of SARS-CoV-2 from the built environment of COVID-19 patient rooms: A multicentre prospective study.

BackgroundSARS-CoV-2 can be detected from the built environment (e.g., floors), but it is unknown how the viral burden changes over space and time surrounding an infected patient. Characterising these data can help advance our understanding and interpretation of surface swabs from the built environment. MethodsWe conducted a prospective study at two hospitals in Ontario, Canada between January 19, 2022 and February 11, 2022. We performed serial floor sampling for SARS-CoV-2 in rooms of patients newly hospitalized with COVID-19 in the past 48 hours. We sampled the floor twice daily until the occupant moved to another room, was discharged, or 96 hours had elapsed. Floor sampling locations included: 1m from the hospital bed, 2m from the hospital bed, and at the rooms threshold to the hallway (typically 3 - 5m from the hospital bed). The samples were analyzed for the presence of SARS-CoV-2 using qPCR. We calculated the sensitivity of detecting SARS-CoV-2 in a patient with COVID-19, and we evaluated how the percentage of positive swabs and the cycle threshold of the swabs changed over time. We also compared the cycle threshold between the two hospitals. ResultsOver the 6-week study period we collected 164 floor swabs from the rooms of 13 patients. The overall percentage of swabs positive for SARS-CoV-2 was 93% and the median cycle threshold (for positive swabs) was 33.7 (IQR: 30.9, 37.5). On day 0 of swabbing the percentage of swabs positive for SARS-CoV-2 was 81.1% and the median cycle threshold was 33.7 (IQR: 32.1, 38.3) compared to swabs performed on day 2 or later where the percentage of swabs positive for SARS-CoV-2 was 98.1% and the cycle threshold was 33.4 (IQR: 30.7, 35.7). We found that viral detection did not change with increasing time (since the first sample collection) over the sampling period, OR 1.65 per day (95% CI 0.68, 4.02; p = 0.27). Similarly, viral detection did not change with increasing distance from the patients bed (1m, 2m, or 3m), OR 0.85 per metre (95% CI 0.38, 1.88; p = 0.69). The cycle threshold was lower (e.g. more virus) in The Ottawa Hospital (median Cq 30.8) where the floors are cleaned once daily rather than the Toronto hospital (median Cq 37.3) where floors were cleaned twice daily. ConclusionsWe were able to detect SARS-CoV-2 on the floors of rooms of patients with COVID-19 and the viral burden did not vary over time or by distance from the bed. These results suggest floor swabbing for the detection of SARS-CoV-2 in a built environment such as a hospital room is both accurate and robust to variation in sampling location and duration of occupancy.

Detection of COVID-19 Outbreaks in Long-Term Care Homes Using Built Environment Testing for SARS-CoV-2: A Multicentre Prospective Study

BackgroundEnvironmental surveillance of SARS-CoV-2 via wastewater has become an invaluable tool for population-level surveillance of COVID-19. Built environment sampling may provide a more spatially refined approach for surveillance of COVID-19 in congregate living settings and other high risk settings (e.g., schools, daycares). MethodsWe conducted a prospective study in 10 long-term care homes (LTCHs) across three cities in Ontario, Canada between September 2021 and May 2022. Floor surfaces were sampled weekly at multiple locations (range 10 to 24 swabs per building) within each building and analyzed for the presence of SARS-CoV-2 using RT-qPCR. The exposure variable was detection of SARS-CoV-2 on floors. The primary outcome was the presence of a COVID-19 outbreak in the week that floor sampling was performed. ResultsOver the 9-month study period, we collected 3848 swabs at 10 long-term care homes. During the study period, 19 COVID-19 outbreaks occurred with 103 cumulative weeks under outbreak. During outbreak periods, the proportion of floor swabs positive for SARS-CoV-2 was 50% (95% CI: 47-53) with a median quantification cycle of 37.3 (IQR 35.2-38.7). During non-outbreak periods the proportion of floor swabs positive was 18% (95% CI:17-20) with a median quantification cycle of 38.0 (IQR 36.4-39.1). Using the proportion of positive floor swabs for SARS-CoV-2 to predict COVID-19 outbreak status in a given week, the area under the receiver operating curve (AUROC) was 0.85 (95% CI: 0.78-0.92). Using thresholds of [≥]10%, [≥]30%, and [≥]50% of floor swabs positive for SARS-CoV-2 yielded positive predictive values for outbreak of 0.57 (0.49-0.66), 0.73 (0.63-0.81), and 0.73 (0.6-0.83) respectively and negative predictive values of 0.94 (0.87-0.97), 0.85 (0.78-0.9), and 0.75 (0.68-0.81) respectively. Among 8 LTCHs with an outbreak and swabs performed in the antecedent week, 5 had positive floor swabs exceeding 10% at least five days prior to outbreak identification. For 3 of these 5 LTCHs, positivity of floor swabs exceeded 10% more than 10 days before the outbreak being identified. ConclusionsDetection of SARS-CoV-2 on floors is strongly associated with COVID-19 outbreaks in LTCHs. These data suggest a potential role for floor sampling in improving early outbreak identification.

A Titratable Cell Lysis-on-Demand System for Droplet-Compartmentalized Ultrahigh-Throughput Screening in Functional Metagenomics and Directed Evolution.

Water-in-oil emulsion droplets are an attractive format for ultrahigh-throughput screening in functional metagenomics and directed evolution applications that allow libraries with more than 107 members to be characterized in a day. Single library members are compartmentalized in droplets that are generated in microfluidic devices and tested for the presence of target biocatalysts. The target proteins can be produced intracellularly, for example, in bacterial hosts in-droplet cell lysis is therefore necessary to allow the enzymes to encounter the substrate to initiate an activity assay. Here, we present a titratable lysis-on-demand (LoD) system enabling the control of the cell lysis rate in Escherichia coli. We demonstrate that the rate of cell lysis can be controlled by adjusting the externally added inducer concentration. This LoD system is evaluated both at the population level (by optical density measurements) and at the single-cell level (on single-cell arrays and in alginate microbeads). Additionally, we validate the LoD system by droplet screening of a phosphotriesterase expressed from E. coli, with cell lysis triggered by inducer concentrations in the µM range. The LoD system yields sufficient release of the intracellularly produced enzymes to bring about a detectable quantity of product (measured by fluorescence in flow cytometry of double emulsions), while leaving viable cells for the downstream recovery of the genetic material.

SARS-CoV-2 Detection from the Built Environment and Wastewater and Its Use for Hospital Surveillance

BackgroundSARS-CoV-2 causes significant morbidity and mortality in health care settings. Our understanding of the distribution of this virus in the built healthcare environment and wastewater, and relationship to disease burden, is limited. MethodsWe performed a prospective multi-center study of environmental sampling of SARS-CoV-2 from hospital surfaces and wastewater and evaluated their relationships with regional and hospital COVID-19 burden. We developed and validated a qPCR-based approach to surface sampling, and swab samples were collected weekly from different locations and surfaces across two tertiary care hospital campuses for a 10-week period during the pandemic, along with wastewater samples. ResultsOver a 10-week period, 963 swab samples were collected and analyzed. We found 61 (6%) swabs positive for SARS-CoV-2, with the majority of these (n=51) originating from floor samples. Wards that actively managed patients with COVID-19 had the highest frequency of positive samples (p<0.01). Detection frequency in built environment swabs was significantly associated with active cases in the hospital throughout the study (p<0.025). Wastewater viral signal changes appeared to predate change in case burden. ConclusionsEnvironment sampling for SARS-CoV-2, in particular from floors, may offer a unique and resolved approach to surveillance of COVID-19.