NOTE: This dataset is no longer being updated but is being kept for historical reference. For current data on respiratory illness visits and respiratory laboratory testing data please see Influenza, COVID-19, RSV, and Other Respiratory Virus Laboratory Surveillance and Inpatient, Emergency Department, and Outpatient Visits for Respiratory Illnesses. This is the place to look for important information about how to use this dataset, so please expand this box and read on! This is the source data for some of the metrics available at https://www.chicago.gov/city/en/sites/covid-19/home/reopening-chicago.html#reopeningmetrics. For all datasets related to COVID-19, see https://data.cityofchicago.org/browse?limitTo=datasets&sortBy=alpha&tags=covid-19. The National Syndromic Surveillance Program (NSSP), a collaboration among CDC, federal partners, local and state health departments, and academic and private sector partners, is used to capture information during an Emergency Department (ED) visit. ED data can include information that are collected before cases are diagnosed or laboratory results are confirmed, providing an early warning system for infections, like COVID-19. This dataset includes reports of COVID-19-Like illness (CLI) and COVID-19 diagnosed during an ED visit. CLI is defined as fever and cough or shortness of breath or difficulty breathing with or without the presence of a coronavirus diagnosis code. Visits meeting the CLI definition that also have mention of flu or influenza are excluded. This dataset also includes ED visits among persons who have been diagnosed or laboratory confirmed to have COVID-19. During the initial months of the COVID-19 pandemic COVID-19 diagnoses counts are artificially low, due to varying eligibility requirements and availability of testing. Over the course of the COVID-19 pandemic, public health best practices migrated from focusing on CLI to focusing on diagnosed cases. This dataset originally contained only CLI columns. In June 2021, the diagnosis columns were added, back filled to the start of the pandemic but with the caveat noted above. Roughly simultaneously, updating of the CLI columns was discontinued, although previously existing data were kept. Reflecting the new columns, the name of the dataset was changed from “COVID-Like Illness (CLI) Emergency Department Visits” to “COVID-Like Illness (CLI) and COVID-19 Diagnosis Emergency Department Visits” at the same time. Data Source: Illinois Hospital Emergency Departments reporting to CDPH through the National Syndromic Surveillance Project (NSSP)

Background: The current COVID-19 coronavirus pandemic is an emergency on a global scale, with huge swathes of the population required to remain indoors for prolonged periods to tackle the virus. In this new context, individuals' health-promoting routines are under greater strain, contributing to poorer mental and physical health. Additionally, individuals are required to keep up to date with latest health guidelines about the virus, which may be confusing in an age of social-media disinformation and shifting guidelines. To tackle these factors, we developed Elena+, a smartphone-based and conversational agent (CA) delivered pandemic lifestyle care intervention.Methods: Elena+ utilizes varied intervention components to deliver a psychoeducation-focused coaching program on the topics of: COVID-19 information, physical activity, mental health (anxiety, loneliness, mental resources), sleep and diet and nutrition. Over 43 subtopics, a CA guides individuals through content and tracks progress over time, such as changes in health outcome assessments per topic, alongside user-set behavioral intentions and user-reported actual behaviors. Ratings of the usage experience, social demographics and the user profile are also captured. Elena+ is available for public download on iOS and Android devices in English, European Spanish and Latin American Spanish with future languages and launch countries planned, and no limits on planned recruitment. Panel data methods will be used to track user progress over time in subsequent analyses. The Elena+ intervention is open-source under the Apache 2 license (MobileCoach software) and the Creative Commons 4.0 license CC BY-NC-SA (intervention logic and content), allowing future collaborations; such as cultural adaptions, integration of new sensor-related features or the development of new topics.Discussion: Digital health applications offer a low-cost and scalable route to meet challenges to public health. As Elena+ was developed by an international and interdisciplinary team in a short time frame to meet the COVID-19 pandemic, empirical data are required to discern how effective such solutions can be in meeting real world, emergent health crises. Additionally, clustering Elena+ users based on characteristics and usage behaviors could help public health practitioners understand how population-level digital health interventions can reach at-risk and sub-populations.

The C-19GA20 dataset was gathered online in April 2020 from school and university students between 14 to 24 years of age. It provides insightful information about the students’ mental health, social lives, attitude towards Covid-19, impact of the Covid-19 Pandemic on students’ education, and their experience with online learning. The data includes 5 major groups of variables: 1) Socio-demographic data - age group, gender, current place of stay, study level in their institution 2) 4 items for information regarding connectivity to the internet during the lockdown - device availability for exclusive use, internet bandwidth, top 5 online tools used most commonly, and screen time. 3) 9 items measured the impact of Covid-19 on the students’ social lives - their current situation of living, number of people around them where they live, their feelings towards meeting their friends, visiting their institution of study, events that would have been held offline. Students were asked about their top 5 past time activities during the lockdown and the amount of time they spend on social media online. 4) 6 items to gauge their experience with online learning during the lockdown - questions about feeling connected to their peers, maintaining discipline, structured learning, and the stress/burden felt by them due to online learning in the lockdown 5) 11 items to comprehensively gather information about the students’ mental health - how well have they adapted to stay-at-home instructions, their overall mood in the lockdown, feelings towards Covid 19, their prime concerns regarding their academic schedule, being updated and informed about Covid 19, the impact of social media on their beliefs. Finally, the students were asked to write about how they feel the pandemic has changed them as a person and affected their thinking process, and the students were asked to share a one-line message for the world during the lockdown.

Assembly statistics of SARS-CoV-2 genome across starting concentrations.

Assembly statistics for the SARS-CoV-2 genome generated from clinical samples.

This dataset is no longer being updated as of 5/11/2023. It is being retained on the Open Data Portal for its potential historical interest.

This table reports case classification and status data.

The "test mode" rows show confirmed and probable case counts for all Cambridge residents who have tested positive for COVID-19 or have been clinically diagnosed with the disease to date. The numbers represented in these rows reflect individual people (cases), not tests performed. If someone is clinically diagnosed and later gets an antibody test, for example, they will be removed from the “clinical diagnosis” category and added to the “antibody positive” category. Case classification is based on guidance from the Massachusetts Department of Public Health and is as follows:

Confirmed Case: A person with a positive viral (PCR) test for COVID-19. This test is also known as a molecular test.

Probable Case: A person with a positive antigen test. This test is also known as a rapid test.

A person who is a known contact of a confirmed case and has received a clinical diagnosis based on their symptoms. People in this category have not received a viral or antibody test. Whenever possible, lab results from a viral (PCR) test are used to confirm a clinical diagnosis, and if that is not feasible, antibody testing can be used.

Suspect Case: A person with a positive antibody test. This test is also known as a serology test.

The "case status" rows show current outcomes for all Cambridge residents who are classified as confirmed, probable, or suspect COVID-19 cases. Outcomes include:

Recovered Case: The Cambridge Public Health Department determines if a Cambridge COVID-19 case has recovered based on the Center for Disease Control and Prevention’s criteria for ending home isolation: https://www.cdc.gov/coronavirus/2019-ncov/hcp/disposition-in-home-patients.html. Staff from the Cambridge Public Health Department (CPHD) or the state’s Community Tracing Collaborative (CTC) follow up with all reported COVID-19 cases multiple times throughout their illness. It is through these conversations that CPHD or CTC staff determine when a Cambridge resident infected with COVID-19 has met the CDC criteria for ending isolation, which connotes recovery. While many people with mild COVID-19 illness will meet the CDC criteria for ending isolation (i.e., recovery) in under two weeks, people who survive severe illness might not meet the criteria for six weeks or more.

Active Case: This category reflects Cambridge COVID-19 cases who are currently infected. Note: There may be a delay in the time between a person being released from isolation (recovered) and when their recovery is reported.

Death: This category reflects total deaths among Cambridge COVID 19 cases.

Unknown Outcome: This category reflects Cambridge COVID-19 cases who public health staff have been unable to reach by phone or letter, or who have stopped responding to follow up from public health staff.

Splitgraph serves as an HTTP API that lets you run SQL queries directly on this data to power Web applications. For example:

See the Splitgraph documentation for more information.

Title: Improving efficiency of COVID-19 aggregate case and death surveillance data transmission for jurisdictions: current and future role of application programming interfaces (APIs) Authors: Diba Khan, Meeyoung Park, Samuel Lerma, Stephen Soroka, Denise Gaughan, Lyndsay Bottichio, Monika Bray, Mary Fukushima, Brooke Bregman, Caleb Wiedeman, William Duck, Deborah Dee, Adi Gundlapalli, and Amitabh B. Suthar CEDEP Program: EP Product type: publication Conference, meeting, or publication accepted to: Journal of the American Medical Informatics Association

Weekly updates have finished. The Retail Pharmacy Partnership dataset represents doses of vaccine allocated from the federal government directly to Pennsylvania’s retail pharmacy partners. The partners then determine which stores to send the allocated doses to, with the department’s input to ensure we are meeting the needs of all Pennsylvanians.
This dataset will be updated Wednesday’s at 12:00pm.

Per library breadth of coverage of SARS-CoV-2 genome across starting concentrations.

Early detection of SARS-CoV-2 infection is key to managing the current global pandemic, as evidence shows the virus is most contagious on or before symptom onset. Here, we introduce a low-cost, high-throughput method for diagnosing and studying SARS-CoV-2 infection. Dubbed Pathogen-Oriented Low-Cost Assembly & Re-Sequencing (POLAR), this method amplifies the entirety of the SARS-CoV-2 genome. This contrasts with typical RT-PCR-based diagnostic tests, which amplify only a few loci. To achieve this goal, we combine a SARS-CoV-2 enrichment method developed by the ARTIC Network (https://artic.network/) with short-read DNA sequencing and de novo genome assembly. Using this method, we can reliably (>95% accuracy) detect SARS-CoV-2 at a concentration of 84 genome equivalents per milliliter (GE/mL). The vast majority of diagnostic methods meeting our analytical criteria that are currently authorized for use by the United States Food and Drug Administration with the Coronavirus Disease 2019 (COVID-19) Emergency Use Authorization require higher concentrations of the virus to achieve this degree of sensitivity and specificity. In addition, we can reliably assemble the SARS-CoV-2 genome in the sample, often with no gaps and perfect accuracy given sufficient viral load. The genotypic data in these genome assemblies enable the more effective analysis of disease spread than is possible with an ordinary binary diagnostic. These data can also help identify vaccine and drug targets. Finally, we show that the diagnoses obtained using POLAR of positive and negative clinical nasal mid-turbinate swab samples 100% match those obtained in a clinical diagnostic lab using the Center for Disease Control’s 2019-Novel Coronavirus test. Using POLAR, a single person can manually process 192 samples over an 8-hour experiment at the cost of ~$36 per patient (as of December 7th, 2022), enabling a 24-hour turnaround with sequencing and data analysis time. We anticipate that further testing and refinement will allow greater sensitivity using this approach.

Per sample cost breakdown of reagents needed to perform the POLAR.

Early detection of SARS-CoV-2 infection is key to managing the current global pandemic, as evidence shows the virus is most contagious on or before symptom onset. Here, we introduce a low-cost, high-throughput method for diagnosing and studying SARS-CoV-2 infection. Dubbed Pathogen-Oriented Low-Cost Assembly & Re-Sequencing (POLAR), this method amplifies the entirety of the SARS-CoV-2 genome. This contrasts with typical RT-PCR-based diagnostic tests, which amplify only a few loci. To achieve this goal, we combine a SARS-CoV-2 enrichment method developed by the ARTIC Network (https://artic.network/) with short-read DNA sequencing and de novo genome assembly. Using this method, we can reliably (>95% accuracy) detect SARS-CoV-2 at a concentration of 84 genome equivalents per milliliter (GE/mL). The vast majority of diagnostic methods meeting our analytical criteria that are currently authorized for use by the United States Food and Drug Administration with the Coronavirus Disease 2019 (COVID-19) Emergency Use Authorization require higher concentrations of the virus to achieve this degree of sensitivity and specificity. In addition, we can reliably assemble the SARS-CoV-2 genome in the sample, often with no gaps and perfect accuracy given sufficient viral load. The genotypic data in these genome assemblies enable the more effective analysis of disease spread than is possible with an ordinary binary diagnostic. These data can also help identify vaccine and drug targets. Finally, we show that the diagnoses obtained using POLAR of positive and negative clinical nasal mid-turbinate swab samples 100% match those obtained in a clinical diagnostic lab using the Center for Disease Control’s 2019-Novel Coronavirus test. Using POLAR, a single person can manually process 192 samples over an 8-hour experiment at the cost of ~$36 per patient (as of December 7th, 2022), enabling a 24-hour turnaround with sequencing and data analysis time. We anticipate that further testing and refinement will allow greater sensitivity using this approach.