# COVIDPBMC

### Multi-omics profiling of peripheral immune system response to SARS-CoV-2 infection.

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***](https://www.nature.com/articles/s41591-021-01329-2):

*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*

## Web portal

<a href="https://www.sanger.ac.uk/" rel="Wellcome Trust Sanger Institute"><img src="https://www.covid19cellatlas.org/logos/sanger.png" height="100"></a>

<a href="https://data.humancellatlas.org/" rel="Human cell atlas"><img src="https://www.covid19cellatlas.org/logos/human-cell-atlas.png" height="100"></a>

<a href="https://chanzuckerberg.com/" rel="Chan-Zuckerberg Initiative"><img src="https://www.covid19cellatlas.org/logos/chan-zuckerberg-initiative.png" height="100"></a>

Explore the full COVID-19 cell atlas [here](https://www.covid19cellatlas.org/).

Data is available under `COVID-19 PBMC Ncl-Cambridge-UCL`. Interactive view available [here](https://covid19cellatlas.org/haniffa21).

## Research Groups

<a href="https://haniffalab.com" rel="Haniffa Lab"><img src="https://avatars0.githubusercontent.com/u/44367631?s=200&v=4" height="100"></a>

[Haniffa Lab github](https://github.com/haniffalab) [![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/haniffalab.svg?style=social&label=Follow%20%40haniffalab)](https://twitter.com/haniffalab)

<a href="https://www.teichlab.org" rel="Teichmann Lab"><img src="http://static1.squarespace.com/static/56d85b53c6fc08fe12541664/t/580e213129687fbc612f9a5c/1610115725446/?format=1500w" height="100"></a>

[Teichmann Lab github](https://github.com/Teichlab) [![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/teichlab.svg?style=social&label=Follow%20%40teichlab)](https://twitter.com/teichlab)

<a href="https://github.com/MarioniLab" rel="Marioni Lab"><img src="https://avatars3.githubusercontent.com/u/16623186?s=200&v=4" height="100"></a>

[Marioni Lab github](https://github.com/MarioniLab) [![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/marionilab.svg?style=social&label=Follow%20%40marionilab)](https://twitter.com/marionilab)

[Göttgens Lab](http://www.haem.cam.ac.uk/staff/senior-staff/professor-bertie-gottgens/)

<a href="https://clatworthylab.github.io/" rel="Clatworthy Lab"><img src="https://clatworthylab.github.io/assets/img/clatworthylab_bold.svg" height="100"></a> [![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/clatworthylab.svg?style=social&label=Follow%20%40clatworthylab)](https://twitter.com/clatworthylab)

[Clatworthy Lab](https://www.med.cam.ac.uk/clatworthy/)

## BCR analysis package

<a href="https://sc-dandelion.readthedocs.io/" rel="dandelion"><img src="https://github.com/zktuong/dandelion/blob/master/docs/notebooks/img/dandelion_logo.png" height="100"></a>

[dandelion github](https://github.com/zktuong/dandelion)

BCR AIRR files are available [here](https://github.com/clatworthylab/COVID_analysis).

## Contacts

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 [![Twitter URL](http://i.imgur.com/wWzX9uB.png)](https://twitter.com/MDMorgan_cam)

https://github.com/greynolds81 [![Twitter URL](http://i.imgur.com/wWzX9uB.png)](https://twitter.com/gary_d_reynolds)

https://github.com/zktuong [![Twitter URL](http://i.imgur.com/wWzX9uB.png)](https://twitter.com/KelvinTuong)