[Abstract]
In late 2019 and through 2020, the COVID-19 pandemic swept the world, presenting both scientific and medical challenges associated with understanding and treating a previously unknown disease. To help address the need for great understanding of COVID-19, the scientific community mobilized and banded together rapidly to characterize SARS-CoV-2 infection, pathogenesis and its distinct disease trajectories. The urgency of COVID-19 provided a pressing use-case for leveraging relatively new tools, technologies, and nascent collaborative networks. Single-cell biology is one such example that has emerged over the last decade as a powerful approach that provides unprecedented resolution to the cellular and molecular underpinnings of biological processes. Early foundational work within the single-cell community, including the Human Cell Atlas, utilized published and unpublished data to characterize the putative target cells of SARS-CoV-2 sampled from diverse organs based on expression of the viral receptor ACE2 and associated entry factors TMPRSS2 and CTSL (Muus et al., 2020; Sungnak et al., 2020; Ziegler et al., 2020). This initial characterization of reference data provided an important foundation for framing infection and pathology in the airway as well as other organs. However, initial community analysis was limited to samples derived from uninfected donors and other previously-sampled disease indications. This report provides an overview of a single-cell data resource derived from samples from COVID-19 patients along with initial observations and guidance on data reuse and exploration.
Competing Interest Statement
A.K.S. reports compensation for consulting and/or SAB membership from Honeycomb Biotechnologies, Cellarity, Repertoire Immune Medicines, Ochre Bio, and Dahlia Biosciences.
Funding Statement
Funding for this project and those involved in it came from the Chan Zuckerberg Initiative, Wellcome Trust, Wellcome Sanger Core funds, a Rutherford Fund Fellowship, the MRC and the UK Regenerative Medicine Platform (MR/5005579/1 to MZN). Rosetrees Trust (MZN & KBMM, Executive Committee on Research at MGH (M.B.G & A-C.V.), a grant from the National Institute of Health, and the American Lung Association COVID-19 Action Initiative grant, and an anonymous gift through the Broad Institute to support the COVID-19 single-cell genomics work. Please see the Acknowledgement section for a list of all funds and grant numbers.
Author Declarations
I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.
Yes
The details of the IRB/oversight body that provided approval or exemption for the research described are given below:
Please see details of the individual studies and cohorts detailed in the manuscript under the "Ethics Declarations" section.
All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.
Yes
I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).
Yes
I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.
Yes
Data Availability
Processed data is openly and freely available to explore via the covid19cellatlas.org website. The underlying processed data is also openly and freely available for download and reuse with requested attention to the community standards that the authors outline. Data will be updated and shared going forward to encourage prepublication reuse.
