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• Rapid Acceleration of Diagnostics - Underserved Populations (RADx-UP): COVID-19 Testing and Prevention in Correctional Settings

  This study will work with diverse correctional facilities across MN, RI, WA, and FL to characterize the incidence of COVID-19 disease progression and related outcomes. The goal is to identify barriers and facilitators to develop strategies to improve testing in these under-served populations by: Increasing the reach, access, uptake, and impact of COVID-19 testing among incarcerated people and staff in prison and jails. Individuals in congregate settings have been disproportionately affected by COVID-19, with correctional settings accounting for 39 of the 50 largest cluster outbreaks in the country to date. Schema of Correctional Facilities: Correctional facilities are amplifiers of infectious diseases for structural reasons: 1) Dormitory-style living and overcrowded conditions make social distancing nearly impossible 2) They have a focus primarily on security not health 3) Their medical departments are under-resourced and often disconnected from local public health agencies. Correctional facilities must be the focus of urgent intervention to understand the incidence of COVID-19, how it spreads in correctional facilities, and durable long-term strategies to reduce transmission, including testing and vaccines. However, our work from the COVID Prison Project shows that correctional systems have implemented a range of testing strategies, without coordination, such that synthesizing the information on COVID-19 incidence, outcomes and optimal testing strategies (including repeat testing and contact tracing) has been challenging. Incarcerated people decline testing due to concerns about confidentiality, implications for release, and fear of placement in solitary confinement. Through interviews we will identify ethical concerns and potential solutions for COVID-19 testing and vaccine strategies in correctional facilities using a community-engaged strategy. The project's work from the COVID Prison Project shows that correctional systems have implemented a range of testing strategies, without coordination, such that synthesizing the information on COVID-19 incidence, outcomes and optimal testing strategies (including repeat testing and contact tracing) has been challenging. Incarcerated people decline testing due to concerns about confidentiality, implications for release, and fear of placement in solitary confinement. Through interviews we will Identify ethical concerns and potential solutions for COVID-19 testing and vaccine strategies in correctional facilities using a community-engaged strategy. Goals: 1. Identify ethical concerns and potential solutions for COVID-19 testing and vaccine strategies in correctional facilities using a community-engaged strategy. 2. Characterize incidence of COVID-19, disease progression, and related-outcomes and effectiveness of testing and contact tracing in correctional facilities. Participant Selection: a. Potential subjects must be currently incarcerated at key facilities in Washington, Rhode Island, Minnesota, and Florida. These facilities are Everglades Correctional Institution and Homestead Correctional Institution in Florida, Shakopee and Stillwater correctional facilities in Minnesota, the Rhode Island Department of Corrections, and Yakima County Jail in Washington. b. Participating correctional facilities in Florida, Minnesota, Rhode Island, and Washington will provide de-identified data on approximately 16,859 incarcerated adults and correctional staff. Data sources include deidentified data from medical records, administrative data, and policy documents pertaining to COVID-19. c. 3 series of focus groups (6, 12, 18 months) x 3 distinct groups (incarcerated people, medical providers, and correctional leaders) x 4 sites=36 total focus groups over the study period. d. Will utilize 74,812 COVID-19 tests to test and re-test a total of 16,859 incarcerated people and correctional staff for active infection over a six-month period in the FL, MN, and RI state prison systems and the Yakima County Jail in WA.

  Study phs003361

• Ex vivo RNA-seq in moderate COVID-19 monocytes

  This dataset was used to compare gene expression profiles of ex vivo isolated classical CD14+ monocytes from patients with moderate COVID-19 to those of healthy individuals. Blood samples were taken from patients with moderate COVID-19 admitted to hospitals in London (Hammersmith Hospital, Charing Cross Hospital, Saint Mary’s Hospital) 3-14 days after disease onset and 0-2 days after hospitalization and positive PCR, and before study treatment initiation. Moderate patients displayed mild or moderate COVID-19 pneumonia, defined as grade 3 or 4 WHO severity. Samples were collected from March 2020 to February 2021. Healthy donors were Imperial College staff with no prior diagnosis of or recent symptoms consistent with COVID-19, and where possible, were matched in age and sex distribution with COVID-19 patients. None of the participants of this study were COVID-19 vaccinated. Peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll Hypaque (GE Healthcare) gradient centrifugation <4 hours after blood collection. CD14+ monocytes were isolated using a positive selection magnetic sorting kit (StemCell Technologies, UK) from total PBMC and stimulated with vehicle, UV-inactivated SARS-CoV-2 (CoV-2). RNA was isolated using the RNeasy Micro Plus Kit (QIAGEN) following the manufacturer’s guidelines. RNA-sequencing was performed by the Oxford Genomics Centre. PolyA-enriched strand- specific libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kits (Illumina). All samples were pooled together and 150bp PE reads were sequenced on a Novaseq 6000 system.

  Dataset EGAD00001009800

• COVID-19 progression and convalescence in common variable immunodeficiency patients

  Longitudinal analysis of single-cell RNAseq datasets of PBMCs from COVID-19 CVID patients and controls.

  Dataset EGAD50000000543

• COVID-19 Postmortem Lung snRNA-seq

  A deeper understanding of the pathological mechanisms of SARS-CoV-2 infection is required to combat COVID-19. Through this dataset, we analyze postmortem lung cells from patients that are infected/uninfected with SARS-CoV-2 with snRNA-seq.

  Study EGAS00001004689

• Single-cell RNA-seq data of bronchoalveolar lavage (BAL) fluid in late severe COVID-19

  We performed single-cell RNA-sequencing of cells in the bronchoalveolar lavage (BAL) fluid of late severe COVID-19. This study provides detailed insights into the alveolar macrophage response to SARS-CoV-2 infection and reveals a profibrotic macrophage response in severe COVID-19 patients.

  Dataset EGAD00001008161

• Detecting PKD1 variants in Polycystic Kidney Disease patients by single-molecule long-read sequencing

  Cohort of 19 ADPKD patients characterized using long-read sequencing. The variant identification provided high sensitivity in identifying PKD1 pathogenic variants, with a diagnostic yield of 94.7%. This dataset includes all sequencing data (BAM files) of the 19 patients, in addition to their raw variants (unfiltered) obtained from the long-read sequencing as well as Sanger sequencing (VCF file).

  Dataset EGAD00001003103

• ScRNA-seq of PBMC and whole blood samples reveals a dysregulated myeloid cell compartment in severe COVID-19

  In a dual-center, two-cohort study, we performed single-cell RNA-sequencing of whole blood and peripheral blood mononuclear cells to determine changes in immune cell composition and activation in mild vs. severe COVID-19 over time. This study provides detailed insights into the systemic immune response to SARS-CoV-2 infection and reveals profound alterations in the myeloid cell compartment associated with severe COVID-19.

  Study EGAS00001004571

• WES dataset of a TIL-ACT metastatic melanoma cohort

  Whole-exome sequencing (WES) data from 13 patients with metastatic melanoma in a TIL-ACT cohort, generated to characterize tumor genomics and neoantigen landscapes relevant to adoptive T cell therapy.

  Dataset EGAD50000001731

• Rapid Acceleration of Diagnostics - Digital Health Technologies (RADx-DHT): NIH Digital Health Solutions for COVID-19: IBM Covid19 Contact Tracing and Data Exchange Tools

  The goal of this project is to develop both contact tracing and secure data exchange tools. The contact tracing solution securely combines data from a variety of sources (including manual self-report data and mobile device surveys) to enable tracing of contacts with individuals that have tested positive for COVID-19 or have been exposed to COVID-19. The data exchange solution is a secure mechanism that empowers users to control the data they share in the course of their return to work, including the ability to provide a verifiable health status claim. These tools are being used by an employer to evaluate the risk of allowing individuals to return to normal activities, and also the ability to trace user contact with individuals diagnosed with or suspected of having contracted COVID-19. DOI: https://rapids.ll.mit.edu/10.57895/h0an-m559

  Study phs002516

• Rapid Acceleration of Diagnostics - Digital Health Technologies (RADx-DHT): Covidseeker and COVID-19 Citizen Science: Leveraging Citizen Science and Real-Time Geospatial Temporal Mobile Data for Digital Contact Tracing and SARS-CoV-2 Hotspotting

  The Covidseeker and COVID-19 Citizen Science Study integrates a retrospectively-determined geolocation digital program into an established digital infrastructure housed within the NIH-funded Eureka platform to enroll SARS-CoV-2 positive and negative individuals. The solution also leverages the ongoing COVID-19 Citizen Science Study cohort both in-person and remotely to test and implement existing technology to enhance readily accessible contact tracing methods and identify “hot spots” of transmission of SARS-CoV-2. The tools are designed to alert users regarding overlap with SARS-CoV-2 infected individuals, identifying businesses that were visited by someone who later tested positive for COVID-19, and working with those businesses and public health departments on strategies to reduce the spread of the virus. DOI: https://rapids.ll.mit.edu/10.57895/me7r-vp06

  Study phs002519