Standardization and Comparison of Emergency Use Authorized COVID-19 Assays and Testing Laboratories (preprint)

SARS-CoV-2, the causal agent of the global COVID-19 pandemic, made its appearance at the end of 2019 and is still circulating in the population. The pandemic led to an urgent need for fast, reliable, and widely available testing. After December 2020, the emergence of new variants of SARS-CoV-2 led to additional challenges since new and existing tests had to detect variants to the same extent as the original Wuhan strain. When an antigen-based test is submitted to the Food and Drug Administration (FDA) for Emergency Use Authorization (EUA) consideration it is benchmarked against PCR comparator assays, which yield cycle threshold (CT) data as an indirect indicator of viral load - the lower the CT, the higher the viral load of the sample and the higher the CT, the lower the viral load. The FDA mandates that 10-20% of clinical samples used to evaluate the antigen test have to be low positive. Low positive, as defined by the FDA, are clinical samples in which the CT of the SARS-CoV-2 target gene is within 3 CT of the mean CT value of the approved comparator tests Limit of Detection (LOD). While all comparator tests are PCR-based, the results from different PCR assays used are not uniform. Results vary depending on assay platform, target gene, LOD and laboratory methodology. The emergence and dominance of the Omicron variant further challenged this approach as the fraction of low positive clinical samples dramatically increased as compared to earlier SARS-CoV-2 variants. This led to 20-40% of clinical samples having high CT values and therefore assays vying for an EUA were failing to achieve the 80% Percent Positive Agreement (PPA) threshold required. Here we describe the methods and statistical analyses used to establish a predefined cutoff, based on genome copies per ml (GE/ml) to classify samples as low positive (less than the cutoff GE/ml) or high positive (greater than the cutoff GE/mL). CT 30 for the E gene target using Cobas(R) SARS-CoV-2-FluA/B platform performed at TriCore Reference Laboratories, and this low positive cutoff value was used for two EUA authorizations. Using droplet digital PCR and methods described here, a value 49,447.72 was determined as the GE/ml equivalent for the low positive cutoff. The CT cutoff corresponding to 49447.72 GE/ml was determined across other platforms and laboratories. The methodology and statistical analysis described here can now be used for standardization of all comparators used for FDA submissions with a goal towards establishing uniform criteria for EUA authorization. MotivationThe motivation for this work was the need to establish a predefined cutoff based on genome copies per ml (GE/ml) rather than Ct, which can vary depending on the laboratory and assay used. A GE/ml-based threshold was necessary to define what constituted low positives" for samples that were included in data sets submitted to the FDA for emergency use approval for SARS-CoV-2 antigen tests.

Environmental reservoirs of the drug-resistant pathogenic yeast Candida auris.

Candia auris is an emerging human pathogenic yeast; yet, despite phenotypic attributes and genomic evidence suggesting that it probably emerged from a natural reservoir, we know nothing about the environmental phase of its life cycle and the transmission pathways associated with it. The thermotolerant characteristics of C. auris have been hypothesised to be an environmental adaptation to increasing temperatures due to global warming (which may have facilitated its ability to tolerate the mammalian thermal barrier that is considered a protective strategy for humans against colonisation by environmental fungi with pathogenic potential). Thus, C. auris may be the first human pathogenic fungus to have emerged as a result of climate change. In addition, the release of antifungal chemicals, such as azoles, into the environment (from both pharmaceutical and agricultural sources) is likely to be responsible for the environmental enrichment of resistant strains of C. auris; however, the survival and dissemination of C. auris in the natural environment is poorly understood. In this paper, we critically review the possible pathways through which C. auris can be introduced into the environment and evaluate the environmental characteristics that can influence its persistence and transmission in natural environments. Identifying potential environmental niches and reservoirs of C. auris and understanding its emergence against a backdrop of climate change and environmental pollution will be crucial for the development of effective epidemiological and environmental management responses.

Yardstick for managing cough, part 2: In children.

Nationwide statistics in the United States and Australia reveal that cough of undifferentiated duration is the most common complaint for which patients of all ages seek medical care in the ambulatory setting. Management of chronic cough is one of the most common reasons for new patient visits to respiratory specialists. Because symptomatic cough is such a common problem and so much has been learned about how to diagnose and treat cough of all durations but especially chronic cough, this 2-part yardstick has been written to review in a practical way the evidence-based guidelines most of which have been developed from high-quality systematic reviews on how best to manage cough of all durations in adults, adolescents, and children. Chronic cough in children is often benign and self-limiting. Using established and validated protocols and specific pointers (clues in history, findings on examination) can aid the clinician in identifying causes when present and improve outcomes. In this manuscript, part 2 of the 2-part series, we provide evidence-based, expert opinion recommendations on the management of chronic cough in the pediatric patient (<14 years of age).

Evaluation of Measurement Properties and Differential Item Functioning in the English and French Versions of the University of California, Los Angeles, Loneliness Scale-6: A Scleroderma Patient-Centered Intervention Network (SPIN) Study.

OBJECTIVE: Loneliness has been associated with poorer health-related quality of life but has not been studied in patients with systemic sclerosis (SSc). The current study was undertaken to examine and compare the psychometric properties of the English and French versions of the University of California, Los Angeles, Loneliness Scale-6 (ULS-6) in patients with SSc during the COVID-19 pandemic. METHODS: This study used baseline cross-sectional data from 775 adults enrolled in the Scleroderma Patient-Centered Intervention Network (SPIN) COVID-19 Cohort. Reliability and validity of ULS-6 scores overall and between languages were evaluated using confirmatory factor analysis (CFA), differential item functioning (DIF) through the multiple-indicator multiple-cause (MIMIC) model, omega/alpha calculation, and correlations of hypothesized convergent relationships. RESULTS: CFA for the total sample supported the single-factor structure (comparative fit index [CFI] 0.96, standardized root mean residual [SRMR] 0.03), and all standardized factor loadings for items were large (0.60-0.86). The overall MIMIC model with language as a covariate fit well (CFI 0.94, SRMR 0.04, root mean square error of approximation 0.11). Statistically significant DIF was found for 3 items across language (ßitem2  = 0.14, P < 0.001; ßitem4  = -0.07, P = 0.01; ßitem6  = 0.13, P < 0.001), but these small differences were without practical measurement implications. Analyses demonstrated high internal consistency with no language-based convergent validity differences. CONCLUSION: Analyses demonstrated evidence of acceptable reliability and validity of ULS-6 scores in English- and French-speaking adults with SSc. DIF analysis supported use of the ULS-6 to examine comparative experiences of loneliness without adjusting for language.

Heterogenous Treatment Effects Following Inspiratory Muscle Training during Recovery from Post-Acute COVID-19 Syndrome.

PURPOSE: To investigate whether heterogeneous treatment effects occur for changes in inspiratory muscle strength, perceived dyspnoea, and health-related quality of life (QoL), following eight-weeks unsupervised home-based inspiratory muscle training (IMT) in adults with post-acute COVID-19 syndrome. METHODS: In total, 147 adults with self-reported prior COVID-19 either completed an eight-week home-based IMT intervention (n = 111; 92 females; 48 ± 11 years; 9.3 ± 3.6 months post-acute COVID-19 infection) or acted as "usual care" wait list controls (n = 36; 34 females; 49 ± 12 years; 9.4 ± 3.2 months post-acute COVID-19 infection). RESULTS: Applying a Bayesian framework, we found clear evidence of heterogeneity of treatment response for inspiratory muscle strength: the estimated difference between standard deviations (SDs) of the IMT and control groups was 22.8 cmH2O (75% Credible Interval (CrI): 4.7-37.7) for changes in maximal inspiratory pressure (MIP), and 86.8 pressure time-units (PTUs; 75% CrI: 55.7-116.7) for sustained MIP (SMIP). Conversely, there were minimal differences in the SDs between the IMT and the control group for changes in perceived dyspnoea and health-related QoL, providing no evidence of heterogeneous treatment effects. Higher cumulative power during the IMT intervention was related to changes in MIP (ß = 10.9 [95% CrI: 5.3-16.8] cmH2O per 1SD) and SMIP (ß = 63.7 [32.2-95.3] PTUs per 1SD), clearly indicating an IMT dose response for changes in inspiratory muscle strength. Older age (>50 years), a longer time post-acute COVID-19 (>3 months), and greater severity of dyspnoea at baseline were also associated with smaller improvements in inspiratory muscle strength. CONCLUSIONS: Heterogenous individual responses occurred following an eight-week home-based IMT programme in people with post-acute COVID-19 syndrome. Consistent with standard exercise theory, larger improvements in inspiratory muscle strength are strongly related to a greater cumulative dose of IMT.

A Comparison of Pediatric Mental Health Diagnoses and Selective Serotonin Reuptake Inhibitor Prescribing Before and During the COVID-19 Pandemic.

PURPOSE: To assess the rate of mental health diagnoses and selective serotonin reuptake inhibitor (SSRI) prescribing before and during the Coronavirus Disease 2019 pandemic. METHODS: We conducted a cross-sectional study at an ambulatory pediatric clinic. A prepandemic (June 2018 to June 2019) and intrapandemic (June 2020 to June 2021) cohort were reviewed. The rate of mental health visits and new SSRI prescriptions were compared. Chi-squared analyses demonstrated a variance of statistical significance. RESULTS: From 15,414 encounters (9,791 prepandemic and 5,623 intrapandemic), 397 mental health encounters were identified. 231 (4.1%) encounters occurred during the pandemic (vs. 1.7% prepandemic) and 63 (27.3%) SSRIs were prescribed (vs. 5.4% prepandemic). Mental health encounters (prevalence ratio 2.42, 95% confidence interval, 1.99-2.95, p < .001) and SSRI prescriptions (prevalence ratio 5.03, 95% confidence interval, 2.58-9.82, p < .001) were higher during the pandemic. DISCUSSION: Our findings demonstrate increased rates of SSRI prescribing and mental health diagnoses during the Coronavirus Disease 2019 pandemic, suggesting an increased incidence of these conditions. Clinicians should be prepared to manage and screen for mental health conditions.

SARS-CoV-2 antibody responses associate with sex, age and disease severity in previously uninfected people admitted to hospital with COVID-19: An ISARIC4C prospective study.

The SARS-CoV-2 pandemic enables the analysis of immune responses induced against a novel coronavirus infecting immunologically naïve individuals. This provides an opportunity for analysis of immune responses and associations with age, sex and disease severity. Here we measured an array of solid-phase binding antibody and viral neutralising Ab (nAb) responses in participants (n=337) of the ISARIC4C cohort and characterised their correlation with peak disease severity during acute infection and early convalescence. Overall, the responses in a Double Antigen Binding Assay (DABA) for antibody to the receptor binding domain (anti-RBD) correlated well with IgM as well as IgG responses against viral spike, S1 and nucleocapsid protein (NP) antigens. DABA reactivity also correlated with nAb. As we and others reported previously, there is greater risk of severe disease and death in older men, whilst the sex ratio was found to be equal within each severity grouping in younger people. In older males with severe disease (mean age 68 years), peak antibody levels were found to be delayed by one to two weeks compared with women, and nAb responses were delayed further. Additionally, we demonstrated that solid-phase binding antibody responses reached higher levels in males as measured via DABA and IgM binding against Spike, NP and S1 antigens. In contrast, this was not observed for nAb responses. When measuring SARS-CoV-2 RNA transcripts (as a surrogate for viral shedding) in nasal swabs at recruitment, we saw no significant differences by sex or disease severity status. However, we have shown higher antibody levels associated with low nasal viral RNA indicating a role of antibody responses in controlling viral replication and shedding in the upper airway. In this study, we have shown discernible differences in the humoral immune responses between males and females and these differences associate with age as well as with resultant disease severity.

Mental health symptoms in scleroderma during COVID-19: a Scleroderma Patient-centred Intervention Network (SPIN) cohort longitudinal study.

OBJECTIVES: People with systemic sclerosis (SSc) are vulnerable in COVID-19 and face challenges related to shifting COVID-19 risk and protective restrictions. We evaluated mental health symptom trajectories in people with SSc through March 2022. METHODS: The longitudinal Scleroderma Patient-centred Intervention Network (SPIN) COVID-19 cohort was launched in April 2020 and included participants from the ongoing SPIN Cohort and external enrolees. Analyses included estimated means with 95% CIs for anxiety and depression symptoms pre-COVID-19 for ongoing SPIN Cohort participants and anxiety, depression, loneliness, and fear of COVID-19 for all participants across 28 COVID-19 assessments up to March 2022. We conducted sensitivity analyse including estimating trajectories using only responses from participants who completed >90% of items for ≥21 of 28 possible assessments ("completers") and stratified analyses for all outcomes by sex, age, country, and SSc subtype. RESULTS: Anxiety symptoms increased in early 2020 but returned to pre-COVID-19 levels by mid-2020 and remained stable through March 2022. Depression symptoms did not initially change but were slightly lower by mid-2020 compared to pre-COVID-19 and were stable through March 2022. COVID-19 fear started high and decreased. Loneliness did not change across the pandemic. Results were similar for completers and for all subgroups. CONCLUSIONS: People with SSc continue to face COVID-19 challenges related to ongoing risk, the opening of societies, and removal of protective restrictions. People with SSc, in aggregate, appear to be weathering the pandemic well, but health care providers should be mindful that some individuals may benefit from mental health support.

Yardstick for managing cough, part 1: In adults and adolescent patients older than 14 years of age.

Nationwide statistics in the United States and Australia reveal that cough of undifferentiated duration is the most common complaint for which patients of all ages seek medical care in the ambulatory setting. Management of chronic cough is one of the most common reasons for new patient visits to pulmonologists. Because symptomatic cough is such a common problem and so much has been learned about how to diagnose and treat cough of all durations but especially chronic cough, this 2-part yardstick has been written to review in a practical way the latest evidence-based guidelines most of which have been developed from recent high quality systematic reviews on how best to manage cough of all durations in adults, adolescents, and children. In this manuscript, part 1 of the 2-part series, we provide evidence-based, and expert opinion recommendations on the management of chronic cough in adult and adolescent patients (>14 years of age).

Prevalence of SARS-CoV-2 infection in Baja California, Mexico: Findings from a community-based survey in February 2021 in the Mexico-United States border

Between March 2020 and February 2021, the state of Baja California, Mexico, which borders the United States, registered 46,118 confirmed cases of COVID-19 with a mortality rate of 238.2 deaths per 100,000 residents. Given limited access to testing, the population prevalence of SARS-CoV-2 infection is unknown. The objective of this study is to estimate the seroprevalence and real time polymerase chain reaction (RT-PCR) prevalence of SARS-CoV-2 infection in the three most populous cities of Baja California prior to scale-up of a national COVID-19 vaccination campaign. Probabilistic three-stage clustered sampling was used to conduct a population-based household survey of residents five years and older in the three cities. RT-PCR testing was performed on nasopharyngeal swabs and SARS-CoV-2 seropositivity was determined by IgG antibody testing using fingerstick blood samples. An interviewer-administered questionnaire assessed participants' knowledge, attitudes, and preventive practices regarding COVID-19. In total, 1,126 individuals (unweighted sample) were surveyed across the three cities. Overall prevalence of SARS-CoV-2 infection by RT-PCR was 7.8% (95% CI 5.5–11.0) and IgG seroprevalence was 21.1% (95% CI 17.4–25.2). There was no association between border crossing in the past 6 months and SARS-CoV-2 prevalence (unadjusted OR 0.40, 95%CI 0.12–1.30). While face mask use and frequent hand washing were common among participants, quarantine or social isolation at home to prevent infection was not. Regarding vaccination willingness, 30.4% (95% CI 24.4–3 7.1) of participants said they were very unlikely to get vaccinated. Given the high prevalence of active SARS-CoV-2 infection in Baja California at the end of the first year of the pandemic, combined with its low seroprevalence and the considerable proportion of vaccine hesitancy, this important area along the Mexico-United States border faces major challenges in terms of health literacy and vaccine uptake, which need to be further explored, along with its implications for border restrictions in future epidemics.

Exploring research team members' and trial participants' perceptions of acceptability and implementation within one videoconference-based supportive care program for individuals affected by systemic sclerosis during COVID-19: a qualitative interview study.

The SPIN-CHAT Program was designed to support mental health among individuals with systemic sclerosis (SSc; commonly known as scleroderma) and at least mild anxiety symptoms at the onset of COVID-19. The program was formally evaluated in the SPIN-CHAT Trial. Little is known about program and trial acceptability, and factors impacting implementation from the perspectives of research team members and trial participants. Thus, the propose of this follow-up study was to explore research team members' and trial participants' experiences with the program and trial to identify factors impacting acceptability and successful implementation. Data were collected cross-sectionally through one-on-one, videoconference-based, semi-structured interviews with 22 research team members and 30 purposefully recruited trial participants (Mage = 54.9, SD = 13.0 years). A social constructivist paradigm was adopted, and data were analyzed thematically. Data were organized into seven themes: (i) getting started: the importance of prolonged engagement and exceeding expectations; (ii) designing the program and trial: including multiple features; (iii) training: research team members are critical to positive program and trial experiences; (iv) offering the program and trial: it needs to be flexible and patient-oriented; (v) maximizing engagement: navigating and managing group dynamics; (vi) delivering a videoconference-based supportive care intervention: necessary, appreciated, and associated with some barriers; and (vii) refining the program and trial: considering modification when offered beyond the period of COVID-19 restrictions. Trial participants were satisfied with and found the SPIN-CHAT Program and Trial to be acceptable. Results offer implementation data that can guide the design, development, and refinement of other supportive care programs seeking to promote psychological health during and beyond COVID-19.

The Scleroderma Patient-centered Intervention Network COVID-19 Home-isolation Activities Together (SPIN-CHAT) Program, a videoconference-based supportive care program, was designed to protect and enhance mental health in individuals affected by systemic sclerosis (commonly known as scleroderma) with at least mild anxiety symptoms during the COVID-19 pandemic. A trial was conducted to evaluate the SPIN-CHAT Program, and results were generally positive. However, important gaps in knowledge remained. Specifically, research team members' and participants' perceptions of SPIN-CHAT Trial acceptability (including satisfaction) and factors impacting implementation of the SPIN-CHAT Program had not yet been explored. To fill this gap, we conducted one-on-one, videoconference-based, semi-structured interviewed with 22 research team members and 30 purposefully recruited trial participants. Interviews sought to gain insights into research team members' and trial participants' experiences within the SPIN-CHAT Program, delivery preferences, and aspects that were/were not beneficial. Findings suggest research team members and participants valued the SPIN-CHAT Program and found the trial to be acceptable. Results also highlight important factors to consider when designing, developing, and/or refining videoconference-based supportive care programs.

COVID-19 disease and immune dysregulation.

The SARS-CoV-2 virus has complex and divergent immune alterations in differing hosts and over disease evolution. Much of the nuanced COVID-19 disease immune dysregulation was originally dominated by innate cytokine changes, which has since been replaced with a more complex picture of innate and adaptive changes characterized by simultaneous hyperinflammatory and immunosuppressive phenomena in effector cells. These intricacies are summarized in this review as well as potential relevance from acute infection to a multisystem inflammatory syndrome commonly seen in children. Additional consideration is made for the influence of variant to variant host cellular changes and the impact of potential vaccination upon these phenotypes. Finally, therapeutic benefit for immune alterations are discussed.

Critical care pharmacy workforce: a 2020 re-evaluation of the UK deployment and characteristics.

INTRODUCTION: Critical care pharmacists improve the quality and efficiency of medication therapy whilst reducing treatment costs where they are available. UK critical care pharmacist deployment was described in 2015, highlighting a deficit in numbers, experience level, and critical care access to pharmacy services over the 7-day week. Since then, national workforce standards have been emphasised, quality indicators published, and service commissioning documents produced, reinforced by care quality assessments. Whether these initiatives have resulted in further development of the UK critical care pharmacy workforce is unknown. This evaluation provides a 2020 status update. METHODS: The 2015 electronic data entry tool was updated and circulated for completion by UK critical care pharmacists. The tool captured workforce data disposition as it was just prior to the COVID-19 pandemic, at critical care unit level. MAIN FINDINGS: Data were received for 334 critical care units from 203 organisations (96% of UK critical care units). Overall, 98.2% of UK critical care units had specific clinical pharmacist time dedicated to the unit. The median weekday pharmacist input to each level 3 equivalent bed was 0.066 (0.043-0.088) whole time equivalents, a significant increase from the median position in 2015 (+ 0.021, p < 0.0001). Despite this progress, pharmacist availability remains below national minimum standards (0.1/level 3 equivalent bed). Most units (71.9%) had access to prescribing pharmacists. Geographical variation in pharmacist staffing levels were evident, and weekend services remain extremely limited. CONCLUSIONS: Availability of clinical pharmacists in UK adult critical care units is improving. However, national standards are not routinely met despite widely publicised quality indicators, commissioning specifications, and assessments. Additional measures are needed to address persistent deficits and realise gains in organisational and patient-level outcomes. These measures must include promotion of cross-professional collaborative working, adjusted funding models, and a nationally recognised training pathway for critical care pharmacists.

Unexpected Moments in Telemedicine.

Who would have thought that a telehealth visit might sometimes be more intimate, more informative, more revelatory than an in-person one?Much has now been written about the utilization of telehealth/telemedicine during the coronavirus disease 2019 (COVID-19) pandemic.

"It's hard for everyone" systemic barriers to home confinement to prevent community spread of COVID-19.

Rapid identification and isolation/quarantine of COVID-19 cases or close contacts, respectively, is a vital tool to support safe, in-person learning. However, safe isolation or quarantine for a young child also necessitates home confinement for at least one adult caregiver, as well as rapid learning material development by the teacher to minimize learning loss. The purpose of this study is to better understand barriers and supports to student home confinement. We conducted a mixed-methods study using focus group discussions and a self-administered online survey with parents and staff members from 12 elementary schools and childcare sites across San Diego County serving low-income and socially vulnerable families. Focus group participants reported that mental distress and loneliness, learning loss, childcare, food, income loss, and overcrowded housing were major barriers related to home confinement. The experiences described by FGD participants were prevalent in a concurrent community survey: 25% of participants reported that isolation would be extremely difficult for a household member who tested positive or was exposed to COVID-19, and 20% were extremely concerned about learning loss while in isolation or quarantine. Our findings suggest that there are serious structural impediments to safely completing the entire recommended course of isolation or quarantine, and that the potential for isolation or quarantine may also lead to increased hesitancy to access diagnostic testing.

BACKGROUND: During the COVID-19 pandemic, home confinement (isolation and quarantine) are important public health tools to keep children learning in-person at schools. However, isolation or quarantine for young children also means that often their caregivers must also go into home confinement, as well as forcing teachers to adapt their lessons to online teaching. PURPOSE: The purpose of this study is to better understand what makes home confinement comfortable or difficult for students and their families. METHODS: We did focus group discussions and shared an online survey with parents and staff members from 12 elementary schools and childcare centers across San Diego County vulnerable families. RESULTS: Focus group participants said that mental distress and loneliness, learning loss, childcare, food, income loss, and overcrowded housing made home confinement hard to do. Also 25% of survey participants said that isolation would be difficult for a household member who tested positive or was exposed to COVID-19, and 20% were really concerned about their child's learning loss if the family had to isolate or do quarantine. CONCLUSIONS: Our study's results suggest that there are serious structural issues for school families to safely go into isolation or quarantine, and because of this may make families more hesitant to get tested for COVID-19.

Challenges of COVID-19 Case Investigation and Contact Tracing in School Settings: An Initial Investigation.

BACKGROUND: Case investigation and contact tracing (CI/CT) are important public health tools to interrupt COVID-19 transmission. Our study aims to understand how parents and school staff perceive COVID-19 CI/CT. METHODS: Using a mixed methods approach, we distributed a community survey and conducted 15 focus group discussions (FGDs) in English and Spanish between December 2020 and March 2021 with 20 parents and 22 staff from schools in San Diego County ZIP Codes with COVID-19 rates in the top quintile as of August 2020. RESULTS: One in 4 survey respondents reported that they would be reluctant to participate in CI/CT. FGDs revealed themes of mistrust in government authorities, overburdened institutions, unfamiliarity with CI/CT, and uncertainty about its reliability. School community members emphasized that parents trust schools to be involved in CI/CT efforts, but schools are overwhelmed with this added responsibility. CONCLUSIONS: Investing in schools as community hubs is necessary so they can become important partners in prevention and mitigation in public health.

Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics (preprint)

The maturation of genomic surveillance in the past decade has enabled tracking of the emergence and spread of epidemics at an unprecedented level. During the COVID-19 pandemic, for example, genomic data revealed that local epidemics varied considerably in the frequency of SARS-CoV-2 lineage importation and persistence, likely due to a combination of COVID-19 restrictions and changing connectivity. Here, we show that local COVID-19 epidemics are driven by regional transmission, including across international boundaries, but can become increasingly connected to distant locations following the relaxation of public health interventions. By integrating genomic, mobility, and epidemiological data, we find abundant transmission occurring between both adjacent and distant locations, supported by dynamic mobility patterns. We find that changing connectivity significantly influences local COVID-19 incidence. Our findings demonstrate a complex meaning of 'local' when investigating connected epidemics and emphasize the importance of collaborative interventions for pandemic prevention and mitigation.

Safer at school early alert: an observational study of wastewater and surface monitoring to detect COVID-19 in elementary schools.

Background: Schools are high-risk settings for SARS-CoV-2 transmission, but necessary for children's educational and social-emotional wellbeing. Previous research suggests that wastewater monitoring can detect SARS-CoV-2 infections in controlled residential settings with high levels of accuracy. However, its effective accuracy, cost, and feasibility in non-residential community settings is unknown. Methods: The objective of this study was to determine the effectiveness and accuracy of community-based passive wastewater and surface (environmental) surveillance to detect SARS-CoV-2 infection in neighborhood schools compared to weekly diagnostic (PCR) testing. We implemented an environmental surveillance system in nine elementary schools with 1700 regularly present staff and students in southern California. The system was validated from November 2020 to March 2021. Findings: In 447 data collection days across the nine sites 89 individuals tested positive for COVID-19, and SARS-CoV-2 was detected in 374 surface samples and 133 wastewater samples. Ninety-three percent of identified cases were associated with an environmental sample (95% CI: 88%-98%); 67% were associated with a positive wastewater sample (95% CI: 57%-77%), and 40% were associated with a positive surface sample (95% CI: 29%-52%). The techniques we utilized allowed for near-complete genomic sequencing of wastewater and surface samples. Interpretation: Passive environmental surveillance can detect the presence of COVID-19 cases in non-residential community school settings with a high degree of accuracy. Funding: County of San Diego, Health and Human Services Agency, National Institutes of Health, National Science Foundation, Centers for Disease Control.