HCA Research on COVID-19

The HCA community, in partnership with disease consortia, is committed to contributing our scientific expertise to combat the COVID-19 pandemic. We have acted quickly to analyze our existing data to glean insights into the biology of the disease, and to openly release these data and analyses as rapidly as possible. We will continue to apply our approaches to deepen scientific understanding of SARS-CoV-2 and COVID-19, with the goal of informing clinical care. Our work and resources to date are available below.

Recent Published Papers

  • Local and systemic responses to SARS-CoV-2 infection in children and adults.  Masahiro Yoshida, Kaylee B. Worlock, Ni Huang, Rik G. H. Lindeboom, Colin R. Butler, Natsuhiko Kumasaka, Cecilia Dominguez Conde, Lira Mamanova, Liam Bolt, Laura Richardson, Krzysztof Polanski, Elo Madissoon, Josephine L. Barnes, Jessica Allen-Hyttinen, Eliz Kilich, Brendan C. Jones, Angus de Wilton, Anna Wilbrey-Clark, Waradon Sungnak, J. Patrick Pett, Juliane Weller, Elena Prigmore, Henry Yung, Puja Mehta, Aarash Saleh, Anita Saigal, Vivian Chu, Jonathan M. Cohen, Clare Cane, Aikaterini Iordanidou, Soichi Shibuya, Ann-Kathrin Reuschl, Iván T. Herczeg, A. Christine Argento, Richard G. Wunderink, Sean B. Smith, Taylor A. Poor, Catherine A. Gao, Jane E. Dematte, NU SCRIPT Study Investigators, Gary Reynolds, Muzlifah Haniffa, Georgina S. Bowyer, Matthew Coates, Menna R. Clatworthy, Fernando J. Calero-Nieto, Berthold Göttgens, Christopher O’Callaghan, Neil J. Sebire, Clare Jolly, Paolo de Coppi, Claire M. Smith, Alexander V. Misharin, Sam M. Janes, Sarah A. Teichmann, Marko Z. Nikolić & Kerstin B. Meyer.
  • Implicating Gene and Cell Networks Responsible for Differential COVID-19 Host Responses via an Interactive Single Cell Web Portal. Kang Jin, Eric E. Bardes, Alexis Mitelpunkt, Jake Y. Wang, Surbhi Bhatnagar, Soma Sengupta, Daniel Pomeranz Krummel, Marc E. Rothenberg, Bruce J. Aronow.
  • Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity. Linh T. Bui, Nichelle I. Winters, Mei-I Chung, Chitra Joseph, Austin J. Gutierrez, Arun C. Habermann, Taylor S. Adams, Jonas C. Schupp, Sergio Poli, Lance M. Peter, Chase J. Taylor, Jessica B. Blackburn, Bradley W. Richmond, Andrew G. Nicholson, Doris Rassl, William A. Wallace, Ivan O. Rosas, R. Gisli Jenkins, Naftali Kaminski, Jonathan A. Kropski, Nicholas E. Banovich & Human Cell Atlas Lung Biological Network.
  • The network effect: studying COVID-19 pathology with the Human Cell Atlas.  Sarah Teichmann & Aviv Regev
  • SARS-CoV-2 receptor ACE2 and TMPRSS2 are predominantly expressed in a transient secretory cell type in subsegmental bronchial branches.  Soeren Lukassen, Robert Lorenz Chua, Timo Trefzer, Nicolas C. Kahn, Marc A. Schneider et al.
  • SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes.  Waradon Sungnak, Ni Huang, Christophe Bécavin, Marijn Berg, Rachel Queen, Monika Litvinukova, Carlos Talavera-López, Henrike Maatz, Daniel Reichart, Fotios Sampaziotis, Kaylee B. Worlock, Masahiro Yoshida, Josephine L. Barnes & HCA Lung Biological Network
  • COVID-19 severity correlates with airway epithelium–immune cell interactions identified by single-cell analysis.  Robert Lorenz Chua, Soeren Lukassen, et al 
  • SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is enriched in specific cell subsets across tissues.  Carly G.K. Ziegler, Samuel J. Allon, Sarah K. Nyquist et al
  • Co-expression of SARS-CoV-2 entry genes in the superficial adult human conjunctival, limbal and corneal epithelium suggests an additional route of entry via the ocular surface. Joseph Collin, Rachel Queen, Darin Zerti, Birthe Dorgau, Maria Georgiou, Ivo Djidrovski, Rafiqul Hussain, Jonathan M.Cox, Agatha Joseph, Paul Rooney, Steven Lisgo, Francisco Figueiredo, Lyle Armstrong, Majlinda Lako.
  • Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Christoph Muus, Malte D. Luecken, […]The Human Cell Atlas Lung Biological Network.
  • Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19.  Saskia Trump, Soeren Lukassen, […] Irina Lehmann.
  • SARS-CoV-2 infection of the oral cavity and saliva.   Ni Huang, Paola Pérez, […] Kevin M. Byrd 
  • COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets.  Toni M. Delorey, Carly G. K. Ziegler, […]Aviv Regev
  • Single-cell multi-omics analysis of the immune response in COVID-19.  Emily Stephenson, Gary Reynolds, […]Muzlifah Haniffa
  • A molecular single-cell lung atlas of lethal COVID-19.  Johannes C. Melms, Jana Biermann, Huachao Huang, Yiping Wang, Ajay Nair et al.
  • Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions.  Daniel Butler, Christopher Mozsary, Cem Meydan, Jonathan Foox, Joel Rosiene et al.
  • Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19.  Bernardes JP, Mishra N, Tran F, Bahmer T, Best L et al.
  • SARS-CoV-2 receptor networks in diabetic and COVID-19-associated kidney disease.  Menon R, Otto EA, Sealfon R, Nair V, Wong AK et al.
  • Myocyte-Specific Upregulation of ACE2 in Cardiovascular Disease.  Nicholas E. BanovichPascal BarbryKatharine E. BlackAlvis BrazmaJoseph Collin et al.
  • Pre-activated anti-viral innate immunity in the upper airways controls early SARS-CoV-2 infection in children

Posted Preprints

These preprints have not yet been peer-reviewed

Additional resources from HCA Members

Further Reading

Single-cell RNA-seq studies with COVID-19 infection:

The landscape of lung bronchoalveolar immune cells in COVID-19 revealed by single-cell RNA sequencing
Minfeng Liao, Yang Liu, Jin Yuan, Yanling Wen, Gang Xu, Juanjuan Zhao, Lin Chen, Jinxiu Li, Xin Wang, Fuxiang Wang, Lei Liu, Shuye Zhang, Zheng Zhang.

Immune Cell Profiling of COVID-19 Patients in the Recovery Stage by Single-Cell Sequencing
Wen Wen, Wenru Su, Hao Tang, Wenqing Le, Xiaopeng Zhang, Yingfeng Zheng, XiuXing Liu, Lihui Xie, Jianmin Li, Jinguo Ye, Xiuliang Cui, Yushan Miao, Depeng Wang, Jiantao Dong, Chuan-Le Xiao, Wei Chen, Hongyang Wang.

Blood single cell immune profiling reveals the interferon-MAPK pathway mediated adaptive immune response for COVID-19
Lulin Huang, Yi Shi, Bo Gong, Li Jiang, Xiaoqi Liu, Jialiang Yang, Juan Tang, Chunfang You, Qi Jiang, Bo Long, Tao Zeng, Mei Luo, Fanwei Zeng, Fanxin Zeng, Shuqiang Wang, Xingxiang Yang, Zhenglin Yang.

A single-cell atlas of the peripheral immune response to severe COVID-19
Aaron J Wilk, Arjun Rustagi, Nancy Q Zhao, Jonasel Roque, Giovanny J Martinez-Colon, Julia L McKechnie, Geoffrey T Ivison, Thanmayi Ranganath, Rosemary Vergara, Taylor Hollis, Laura J Simpson, Philip Grant, Aruna Subramanian, Angela J Rogers, Catherine A Blish.

Single-cell atlas of a non-human primate reveals new pathogenic mechanisms of COVID-19
Lei Han, Xiaoyu Wei, Chuanyu Liu, Giacomo Volpe, Zhifeng Wang, Taotao Pan, Yue Yuan, Ying Lei, Yiwei Lai, Carl Ward, Yeya Yu, Mingyue Wang, Quan Shi, Tao Wu, Liang Wu, Ya Liu, Chunqing Wang, Yuanhang Zhang, Haixi Sun, Hao Yu, Zhenkun Zhuang, Tingting Tang, Yunting Huang, Haorong Lu, Liqin Xu, Jiangshan Xu, Mengnan Cheng, Yang Liu, Chi Wai Wong, Tao Tan, Weizhi Ji, Patrick H. Maxwell, Huanming Yang, Jian Wang, Shida Zhu, Shiping Liu, Xun Xu, Yong Hou, Miguel A. Esteban, Longqi Liu, South China Greater Bay Area-Single Cell Consortium (SC-GBA-C).

Tocilizumab treatment in severe COVID-19 patients attenuates the inflammatory storm incited by monocyte centric immune interactions revealed by single-cell analysis
Chuang Guo, Bin Li, Huan Ma, Xiaofang Wang, Pengfei Cai, Qiaoni Yu, Lin Zhu, Liying Jin, Chen Jiang, Jingwen Fang, Qian Liu, Dandan Zong, Wen Zhang, Yichen Lu, Kun Li, Xuyuan Gao, Binqing Fu, Lianxin Liu, Xiaoling Ma, Jianping Weng, Haiming Wei, Tengchuan Jin, Jun Lin, Kun Qu.

General Enquiries

For further details, please contact: team@humancellatlas.org

Contacts for Journalists

For further details, please contact: press@humancellatlas.org