Purpose Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide causing a global health emergency. Pa-COVID-19 aims to provide comprehensive data on clinical course, pathophysiology, immunology and outcome of COVID-19, to identify prognostic biomarkers, clinical scores, and therapeutic targets for improved clinical management and preventive interventions. Methods Pa-COVID-19 is a prospective observational cohort study of patients with confirmed SARS-CoV-2 infection treated at Charité -Universitätsmedizin Berlin. We collect data on epidemiology, demography, medical history, symptoms, clinical course, and pathogen testing and treatment. Systematic, serial blood sampling will allow deep molecular and immunological phenotyping, transcriptomic profiling, and comprehensive biobanking. Longitudinal data and sample collection during hospitalization will be supplemented by long-term follow-up. Results Outcome measures include the WHO clinical ordinal scale on day 15 and clinical, functional, and health-related quality-of-life assessments at discharge and during follow-up. We developed a scalable dataset to (i) suit national standards of care, (ii) facilitate comprehensive data collection in medical care facilities with varying resources, and (iii) allow for rapid implementation of interventional trials based on the standardized study design and data collection. We propose this scalable protocol as blueprint for harmonized data collection and deep phenotyping in COVID-19 in Germany. Conclusion We established a basic platform for harmonized, scalable data collection, pathophysiological analysis, and deep phenotyping of COVID-19, which enables rapid generation of evidence for improved medical care and identification of candidate therapeutic and preventive strategies. The electronic database accredited for interventional trials allows fast trial implementation for candidate therapeutic agents. Trial registration Registered at the German registry for clinical studies (DRKS00021688)

250; Text: 2404All rights reserved. No reuse allowed without permission.(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. infection with SARS-CoV-2, a newly-emerged zoonotic virus and poorly characterized human pathogen.Therefore, the sample size is not prospectively determined. Recruitment of participants will depend on the emergence and spread of the disease in Berlin, Germany and on the number of patients presenting at Charité -Universitätsmedizin Berlin. With the evolving outbreak, recruitment in other study centres will be considered in order to facilitate the establishment of a comprehensive clinical and molecular database. The study has no set end date. Inclusion criteriaProven infection with SARS-CoV-2 (positive pathogen testing). Willingness to participate in the study. Exclusion criteriaRefusal to participate by patient, parent or appropriate legal representative.Any conditions that prohibit supplemental blood-sampling. Data Collection Harmonized scalable dataset / electronic Case Report Form (eCRF)This protocol outlines the methodology of the Berlin prospective cohort for capturing data of COVID-19. The parameters were selected and adapted to local standards through a multidisciplinary expert review board consisting of clinical researchers at Charité,