The COVID-19 pandemic, caused by SARS coronavirus 2 (SARS-CoV-2), has resulted in excess morbidity and mortality as well as economic decline. To characterise the systemic host immune response to SARS-CoV-2, we performed single-cell RNA-sequencing coupled with analysis of cell surface proteins and T and B lymphocyte antigen receptor repertoires, providing molecular profiling of over 800,000 peripheral blood mononuclear cells from a cohort of 130 patients with COVID-19. Our cohort, from three UK centres, spans the spectrum of clinical presentations and disease severities ranging from asymptomatic to critical.
For more information, please read our manuscript published in Nature Medicine:
Emily Stephenson, Gary Reynolds, Rachel A Botting, Fernando J Calero-Nieto, Michael Morgan, Zewen Kelvin Tuong, Karsten Bach, Waradon Sungnak, Kaylee B Worlock, Masahiro Yoshida, Natsuhiko Kumasaka, Katarzyna Kania, Justin Engelbert, Bayanne Olabi, Jarmila Stremenova Spegarova, Nicola K Wilson, Nicole Mende, Laura Jardine, Louis CS Gardner, Issac Goh, Dave Horsfall, Jim McGrath, Simone Webb, Michael W Mather, Rik GH Lindeboom, Emma Dann, Ni Huang, Krzysztof Polanski, Elena Prigmore, Florian Gothe, Jonathan Scott, Rebecca P Payne, Kenneth F Baker, Aidan T Hanrath, Ina CD Schim van der Loeff, Andrew S Barr, Amada Sanchez-Gonzalez, Laura Bergamaschi, Federica Mescia, Josephine L Barnes, Eliz Kilich, Angus de Wilton, Anita Saigal, Aarash Saleh, Sam M Janes, Claire M Smith, Nusayhah Gopee, Caroline Wilson, Paul Coupland, Jonathan M Coxhead, Vladimir Y Kiselev, Stijn van Dongen, Jaume Bacardit, Hamish W King, Anthony J Rostron, A John Simpson, Sophie Hambleton, Elisa Laurenti, Paul A Lyons, Kerstin B Meyer, Marko Z Nikolic, Christopher JA Duncan, Ken Smith, Sarah A Teichmann, Menna R Clatworthy, John C Marioni, Berthold Gottgens, Muzlifah Haniffa. Single-cell multi-omics analysis of the immune response in COVID-19. Nature Medicine 2021.04.20; doi: https://dx.doi.org/10.1038/s41591-021-01329-2
Original preprint:
Emily Stephenson, Gary Reynolds, Rachel A Botting, Fernando J Calero-Nieto, Michael Morgan, Zewen Kelvin Tuong, Karsten Bach, Waradon Sungnak, Kaylee B Worlock, Masahiro Yoshida, Natsuhiko Kumasaka, Katarzyna Kania, Justin Engelbert, Bayanne Olabi, Jarmila Stremenova Spegarova, Nicola K Wilson, Nicole Mende, Laura Jardine, Louis CS Gardner, Issac Goh, Dave Horsfall, Jim McGrath, Simone Webb, Michael W Mather, Rik GH Lindeboom, Emma Dann, Ni Huang, Krzysztof Polanski, Elena Prigmore, Florian Gothe, Jonathan Scott, Rebecca P Payne, Kenneth F Baker, Aidan T Hanrath, Ina CD Schim van der Loeff, Andrew S Barr, Amada Sanchez-Gonzalez, Laura Bergamaschi, Federica Mescia, Josephine L Barnes, Eliz Kilich, Angus de Wilton, Anita Saigal, Aarash Saleh, Sam M Janes, Claire M Smith, Nusayhah Gopee, Caroline Wilson, Paul Coupland, Jonathan M Coxhead, Vladimir Y Kiselev, Stijn van Dongen, Jaume Bacardit, Hamish W King, Anthony J Rostron, A John Simpson, Sophie Hambleton, Elisa Laurenti, Paul A Lyons, Kerstin B Meyer, Marko Z Nikolic, Christopher JA Duncan, Ken Smith, Sarah A Teichmann, Menna R Clatworthy, John C Marioni, Berthold Gottgens, Muzlifah Haniffa. The cellular immune response to COVID-19 deciphered by single cell multi-omics across three UK centres. medRxiv 2021.01.13.21249725; doi: https://doi.org/10.1101/2021.01.13.21249725
Explore the full COVID-19 cell atlas here.
Data is available under COVID-19 PBMC Ncl-Cambridge-UCL. Interactive view available here.
BCR AIRR files are available here.
Please email the corresponding authors in the main manuscript for other requests (https://www.nature.com/articles/s41591-021-01329-2).
For specific queries related to this repository, please contact one of the following:
https://github.com/MikeDMorgan
