The dataset includes 864 genomic sequences obtained from COVID-19 patients aged 18 years old and above within the NYU Langone Health system between March 12 and May 10, 2020. Patients reflected the health system's catchment area (i.e., the greater New York City metropolitan area). rRNA-depleted total RNA was sequenced, underwent quality control, and analyzed to produce phylogenetic trees. Further...

To construct a fixed time-scaled phylogenetic tree, the investigators combined 828 viral genome sequences obtained from COVID-19 patients at NYU Langone Health between March and May 2020 with 1,899 background sequences that were contributed to the Nextstrain repository. A total of 2,727 SARS-CoV-2 genomic sequences are available in the dataset. The supporting R code included with the dataset will produce...

A Delta-Omicron recombinant of the SARS-CoV-2 virus was sequenced and isolated from an immunosuppressed and unvaccinated male kidney transplant patient who received Sotrovimab for treatment of COVID-19. Further clinical details and medical history of the patient are described in the associated publication. Sotrovimab is a therapeutic monoclonal antibody (mAb) used to treat infections by the BA.1 Omicron...

This dataset contains a list of accession numbers of SARS-CoV-2 genomes obtained from 76 patients at NYU Langone Health who were fully vaccinated with the BNT162b2 (Pfizer/BioNTech), mRNA-1273 (Moderna), or JNJ-78436735 (Janssen) COVID-19 mRNA vaccines but had breakthrough infections between February 1 and April 30, 2021. 37 were male and 39 were female; the median age of patients was 48 years. There...

Investigators obtained high quality SARS-CoV-2 sequences from 132 vaccinated and 283 unvaccinated individuals who were seen at NYU Langone Health facilities between May 1, 2021 and August 3, 2021. Fully vaccinated individuals received either two doses of the BNT162b2 (Pfizer/BioNTech) or mRNA-1273 (Moderna) vaccines, or a single-dose of the COVID-19 Janssen vaccine. Breakthrough infections were defined...

Data was abstracted from NYU Langone Health electronic health records, the Perlmutter Cancer Center Data Hub, and the NYU Langone Health SARS-CoV-2 Data Mart for all patients treated for breast cancer at Perlmutter Cancer Center either through telemedicine or in-person between February 1, 2020 and May 1, 2020 to determine the incidence of SARS-CoV-2 infection associated with treatment with cytotoxic...

To study and compare longitudinal immune responses to two-dose BNT162b2 mRNA vaccinations, investigators recruited 15 adults with a history of laboratory-confirmed COVID-19 and 21 adults who did not have COVID-19. Participants' ages ranged from 21 to 65 years old. Peripheral immune responses were assessed via blood samples drawn before and after each vaccine dose. A total of five samples were collected...

This is a retrospective cohort study of COVID-19 hospitalized patients with different degrees of severity. They performed this study to analyze the generation of autoimmune antibodies to common antigens. This study included 115 hospitalized patients with SARS-CoV-2 infection and 42 uninfected controls. Sample collection was performed as part of routine clinical care for COVID-19 patients at the time...

This study examined autoimmune antibodies to annexin A2, which is a phospholipid-binding protein expressed in the lung and other organs, in COVID-19 patients. Annexin A2 is critical for fibrinolysis, lung elasticity, cell membrane repair, and integrity of the pulmonary vasculature. Therefore, antagonism of annexin A2 may explain many of the clinical features of severe COVID-19 cases. This study analyzed...

Exosomes mediate intercellular communication by transporting substrates with a variety of functions related to tissue homeostasis and disease. Recently, a subset of exosomes was labeled as defensosomes that are assembled during bacterial infection. Defensosomes mediate host defense by binding and inhibiting pore-forming toxins secreted by bacterial pathogens through incorporating protein receptors...