Project description:During the COVID-19 pandemic, US populations have experienced elevated rates of financial and psychological distress that could lead to increases in suicide rates. Rapid ongoing mental health monitoring is critical for early intervention, especially in regions most affected by the pandemic, yet traditional surveillance data are available only after long lags. Novel information on real-time population isolation and concerns stemming from the pandemic's social and economic impacts, via cellular mobility tracking and online search data, are potentially important interim surveillance resources. Using these measures, we employed transfer function model time-series analyses to estimate associations between daily mobility indicators (proportion of cellular devices completely at home and time spent at home) and Google Health Trends search volumes for terms pertaining to economic stress, mental health, and suicide during 2020 and 2021 both nationally and in New York City. During the first pandemic wave in early-spring 2020, over 50% of devices remained completely at home and searches for economic stressors exceeded 60,000 per 10 million. We found large concurrent associations across analyses between declining mobility and increasing searches for economic stressor terms (national proportion of devices at home: cross-correlation coefficient (CC) = 0.6 (p-value <0.001)). Nationally, we also found strong associations between declining mobility and increasing mental health and suicide-related searches (time at home: mood/anxiety CC = 0.53 (<0.001), social stressor CC = 0.51 (<0.001), suicide seeking CC = 0.37 (0.006)). Our findings suggest that pandemic-related isolation coincided with acute economic distress and may be a risk factor for poor mental health and suicidal behavior. These emergent relationships warrant ongoing attention and causal assessment given the potential for long-term psychological impact and suicide death. As US populations continue to face stress, Google search data can be used to identify possible warning signs from real-time changes in distributions of population thought patterns.
Project description:BackgroundGovernments around the world have implemented non-pharmaceutical interventions to limit the transmission of COVID-19. While lockdowns and physical distancing have proven effective for reducing COVID-19 transmission, there is still limited understanding of how NPI measures are reflected in indicators of human mobility. Further, there is a lack of understanding about how findings from high-income settings correspond to low and middle-income contexts.MethodsIn this study, we assess the relationship between indicators of human mobility, NPIs, and estimates of R t , a real-time measure of the intensity of COVID-19 transmission. We construct a multilevel generalised linear mixed model, combining local disease surveillance data from subnational districts of Ghana with the timing of NPIs and indicators of human mobility from Google and Vodafone Ghana.FindingsWe observe a relationship between reductions in human mobility and decreases in R t during the early stages of the COVID-19 epidemic in Ghana. We find that the strength of this relationship varies through time, decreasing after the most stringent period of interventions in the early epidemic.InterpretationOur findings demonstrate how the association of NPI and mobility indicators with COVID-19 transmission may vary through time. Further, we demonstrate the utility of combining local disease surveillance data with large scale human mobility data to augment existing surveillance capacity and monitor the impact of NPI policies.
Project description:Human mobility has become a major variable of interest during the COVID-19 pandemic and central to policy decisions all around the world. To measure individual mobility, research relies on a variety of indicators that commonly stem from two main data sources: survey self-reports and behavioral mobility data from mobile phones. However, little is known about how mobility from survey self-reports relates to popular mobility estimates using data from the Global System for Mobile Communications (GSM) and the Global Positioning System (GPS). Spanning March 2020 until April 2021, this study compares self-reported mobility from a panel survey in Austria to aggregated mobility estimates utilizing (1) GSM data and (2) Google's GPS-based Community Mobility Reports. Our analyses show that correlations in mobility changes over time are high, both in general and when comparing subgroups by age, gender, and mobility category. However, while these trends are similar, the size of relative mobility changes over time differs substantially between different mobility estimates. Overall, while our findings suggest that these mobility estimates manage to capture similar latent variables, especially when focusing on changes in mobility over time, researchers should be aware of the specific form of mobility different data sources capture.
Project description:Following a pandemic disease outbreak, people travel to areas with low infection risk, but at the same time the epidemiological situation worsens as mobility flows to those areas increase. These feedback effects from epidemiological conditions to inflows and from inflows to subsequent infections are underexplored to date. This study investigates the two-way relationship between mobility flows and COVID-19 cases in a context of unrestricted mobility without COVID-19 vaccines. To this end, we merge data on COVID-19 cases in Spain during the summer of 2020 at the province level with mobility records based on mobile position tracking. Using a control function approach, we find that a 1% increase in arrivals translates into a 3.5% increase in cases in the following week and 5.6% ten days later. A simulation exercise shows the cases would have dropped by around 64% if the Second State of Alarm had been implemented earlier.
Project description:ImportanceIt is unknown how well cell phone location data portray social distancing strategies or if they are associated with the incidence of coronavirus disease 2019 (COVID-19) cases in a particular geographical area.ObjectiveTo determine if cell phone location data are associated with the rate of change in new COVID-19 cases by county across the US.Design, setting, and participantsThis cohort study incorporated publicly available county-level daily COVID-19 case data from January 22, 2020, to May 11, 2020, and county-level daily cell phone location data made publicly available by Google. It examined the daily cases of COVID-19 per capita and daily estimates of cell phone activity compared with the baseline (where baseline was defined as the median value for that day of the week from a 5-week period between January 3 and February 6, 2020). All days and counties with available data after the initiation of stay-at-home orders for each state were included.ExposuresThe primary exposure was cell phone activity compared with baseline for each day and each county in different categories of place.Main outcomes and measuresThe primary outcome was the percentage change in COVID-19 cases 5 days from the exposure date.ResultsBetween 949 and 2740 US counties and between 22 124 and 83 745 daily observations were studied depending on the availability of cell phone data for that county and day. Marked changes in cell phone activity occurred around the time stay-at-home orders were issued by various states. Counties with higher per-capita cases (per 100 000 population) showed greater reductions in cell phone activity at the workplace (β, -0.002; 95% CI, -0.003 to -0.001; P < 0.001), areas classified as retail (β, -0.008; 95% CI, -0.011 to -0.005; P < 0.001) and grocery stores (β, -0.006; 95% CI, -0.007 to -0.004; P < 0.001), and transit stations (β, -0.003, 95% CI, -0.005 to -0.002; P < 0.001), and greater increase in activity at the place of residence (β, 0.002; 95% CI, 0.001-0.002; P < 0.001). Adjusting for county-level and state-level characteristics, counties with the greatest decline in workplace activity, transit stations, and retail activity and the greatest increases in time spent at residential places had lower percentage growth in cases at 5, 10, and 15 days. For example, counties in the lowest quartile of retail activity had a 45.5% lower growth in cases at 15 days compared with the highest quartile (SD, 37.4%-53.5%; P < .001).Conclusions and relevanceOur findings support the hypothesis that greater reductions in cell phone activity in the workplace and retail locations, and greater increases in activity at the residence, are associated with lesser growth in COVID-19 cases. These data provide support for the value of monitoring cell phone location data to anticipate future trends of the pandemic.
Project description:One of the main problems in controlling COVID-19 epidemic spread is the delay in confirming cases. Having information on changes in the epidemic evolution or outbreaks rise before laboratory-confirmation is crucial in decision making for Public Health policies. We present an algorithm to estimate on-stream the number of COVID-19 cases using the data from telephone calls to a COVID-line. By modelling the calls as background (proportional to population) plus signal (proportional to infected), we fit the calls in Province of Buenos Aires (Argentina) with coefficient of determination R 2 > 0.85. This result allows us to estimate the number of cases given the number of calls from a specific district, days before the laboratory results are available. We validate the algorithm with real data. We show how to use the algorithm to track on-stream the epidemic, and present the Early Outbreak Alarm to detect outbreaks in advance of laboratory results. One key point in the developed algorithm is a detailed track of the uncertainties in the estimations, since the alarm uses the significance of the observables as a main indicator to detect an anomaly. We present the details of the explicit example in Villa Azul (Quilmes) where this tool resulted crucial to control an outbreak on time. The presented tools have been designed in urgency with the available data at the time of the development, and therefore have their limitations which we describe and discuss. We consider possible improvements on the tools, many of which are currently under development.
Project description:BackgroundThe COVID-19 pandemic exacerbated existing racial/ethnic health disparities in the United States. Monitoring nationwide Twitter conversations about COVID-19 and race/ethnicity could shed light on the impact of the pandemic on racial/ethnic minorities and help address health disparities.ObjectiveThis paper aims to examine the association between COVID-19 tweet volume and COVID-19 cases and deaths, stratified by race/ethnicity, in the early onset of the pandemic.MethodsThis cross-sectional study used geotagged COVID-19 tweets from within the United States posted in April 2020 on Twitter to examine the association between tweet volume, COVID-19 surveillance data (total cases and deaths in April), and population size. The studied time frame was limited to April 2020 because April was the earliest month when COVID-19 surveillance data on racial/ethnic groups were collected. Racially/ethnically stratified tweets were extracted using racial/ethnic group-related keywords (Asian, Black, Latino, and White) from COVID-19 tweets. Racially/ethnically stratified tweets, COVID-19 cases, and COVID-19 deaths were mapped to reveal their spatial distribution patterns. An ordinary least squares (OLS) regression model was applied to each stratified dataset.ResultsThe racially/ethnically stratified tweet volume was associated with surveillance data. Specifically, an increase of 1 Asian tweet was correlated with 288 Asian cases (P<.001) and 93.4 Asian deaths (P<.001); an increase of 1 Black tweet was linked to 47.6 Black deaths (P<.001); an increase of 1 Latino tweet was linked to 719 Latino deaths (P<.001); and an increase of 1 White tweet was linked to 60.2 White deaths (P<.001).ConclusionsUsing racially/ethnically stratified Twitter data as a surveillance indicator could inform epidemiologic trends to help estimate future surges of COVID-19 cases and potential future outbreaks of a pandemic among racial/ethnic groups.
Project description:Here, we describe Antigen-TCR Pairing and Multiomic Analysis of T-cells (APMAT), which is an integrated experimental-computational framework designed for the high-throughput capture and analysis of antigen specific CD8 T cells, with paired antigen, TCR sequence, and transcriptome information from the same single cells, from many patient samples in parallel.
Project description:BackgroundAdverse mental health consequences of COVID-19, including anxiety and depression, have been widely predicted but not yet accurately measured. There are a range of physical health risk factors for COVID-19, but it is not known if there are also psychiatric risk factors. In this electronic health record network cohort study using data from 69 million individuals, 62 354 of whom had a diagnosis of COVID-19, we assessed whether a diagnosis of COVID-19 (compared with other health events) was associated with increased rates of subsequent psychiatric diagnoses, and whether patients with a history of psychiatric illness are at a higher risk of being diagnosed with COVID-19.MethodsWe used the TriNetX Analytics Network, a global federated network that captures anonymised data from electronic health records in 54 health-care organisations in the USA, totalling 69·8 million patients. TriNetX included 62 354 patients diagnosed with COVID-19 between Jan 20, and Aug 1, 2020. We created cohorts of patients who had been diagnosed with COVID-19 or a range of other health events. We used propensity score matching to control for confounding by risk factors for COVID-19 and for severity of illness. We measured the incidence of and hazard ratios (HRs) for psychiatric disorders, dementia, and insomnia, during the first 14 to 90 days after a diagnosis of COVID-19.FindingsIn patients with no previous psychiatric history, a diagnosis of COVID-19 was associated with increased incidence of a first psychiatric diagnosis in the following 14 to 90 days compared with six other health events (HR 2·1, 95% CI 1·8-2·5 vs influenza; 1·7, 1·5-1·9 vs other respiratory tract infections; 1·6, 1·4-1·9 vs skin infection; 1·6, 1·3-1·9 vs cholelithiasis; 2·2, 1·9-2·6 vs urolithiasis, and 2·1, 1·9-2·5 vs fracture of a large bone; all p<0·0001). The HR was greatest for anxiety disorders, insomnia, and dementia. We observed similar findings, although with smaller HRs, when relapses and new diagnoses were measured. The incidence of any psychiatric diagnosis in the 14 to 90 days after COVID-19 diagnosis was 18·1% (95% CI 17·6-18·6), including 5·8% (5·2-6·4) that were a first diagnosis. The incidence of a first diagnosis of dementia in the 14 to 90 days after COVID-19 diagnosis was 1·6% (95% CI 1·2-2·1) in people older than 65 years. A psychiatric diagnosis in the previous year was associated with a higher incidence of COVID-19 diagnosis (relative risk 1·65, 95% CI 1·59-1·71; p<0·0001). This risk was independent of known physical health risk factors for COVID-19, but we cannot exclude possible residual confounding by socioeconomic factors.InterpretationSurvivors of COVID-19 appear to be at increased risk of psychiatric sequelae, and a psychiatric diagnosis might be an independent risk factor for COVID-19. Although preliminary, our findings have implications for clinical services, and prospective cohort studies are warranted.FundingNational Institute for Health Research.
Project description:IntroductionThe response to the COVID-19 pandemic became increasingly politicized in the U.S., and the political affiliation of state leaders may contribute to policies affecting the spread of the disease. This study examines the differences in COVID-19 infection, death, and testing by governor party affiliation across the 50 U.S. states and the District of Columbia.MethodsA longitudinal analysis was conducted in December 2020 examining COVID-19 incidence, death, testing, and test positivity rates from March 15, 2020 through December 15, 2020. A Bayesian negative binomial model was fit to estimate the daily risk ratios and posterior intervals comparing rates by gubernatorial party affiliation. The analyses adjusted for state population density, rurality, Census region, age, race, ethnicity, poverty, number of physicians, obesity, cardiovascular disease, asthma, smoking, and presidential voting in 2020.ResultsFrom March 2020 to early June 2020, Republican-led states had lower COVID-19 incidence rates than Democratic-led states. On June 3, 2020, the association reversed, and Republican-led states had a higher incidence (risk ratio=1.10, 95% posterior interval=1.01, 1.18). This trend persisted through early December 2020. For death rates, Republican-led states had lower rates early in the pandemic but higher rates from July 4, 2020 (risk ratio=1.18, 95% posterior interval=1.02, 1.31) through mid-December 2020. Republican-led states had higher test positivity rates starting on May 30, 2020 (risk ratio=1.70, 95% posterior interval=1.66, 1.73) and lower testing rates by September 30, 2020 (risk ratio=0.95, 95% posterior interval=0.90, 0.98).ConclusionsGubernatorial party affiliation may drive policy decisions that impact COVID-19 infections and deaths across the U.S. Future policy decisions should be guided by public health considerations rather than by political ideology.