Single-cell multi-omics analysis of the immune response in COVID-19.
Stephenson E., Reynolds G., Botting RA., Calero-Nieto FJ., Morgan MD., Tuong ZK., Bach K., Sungnak W., Worlock KB., Yoshida M., Kumasaka N., Kania K., Engelbert J., Olabi B., Spegarova JS., Wilson NK., Mende N., Jardine L., Gardner LCS., Goh I., Horsfall D., McGrath J., Webb S., Mather MW., Lindeboom RGH., Dann E., Huang N., Polanski K., Prigmore E., Gothe F., Scott J., Payne RP., Baker KF., Hanrath AT., Schim van der Loeff ICD., Barr AS., Sanchez-Gonzalez A., Bergamaschi L., Mescia F., Barnes JL., Kilich E., de Wilton A., Saigal A., Saleh A., Janes SM., Smith CM., Gopee N., Wilson C., Coupland P., Coxhead JM., Kiselev VY., van Dongen S., Bacardit J., King HW., Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID-19 BioResource Collaboration None., Rostron AJ., Simpson AJ., Hambleton S., Laurenti E., Lyons PA., Meyer KB., Nikolić MZ., Duncan CJA., Smith KGC., Teichmann SA., Clatworthy MR., Marioni JC., Göttgens B., Haniffa M.
Analysis of human blood immune cells provides insights into the coordinated response to viral infections such as severe acute respiratory syndrome coronavirus 2, which causes coronavirus disease 2019 (COVID-19). We performed single-cell transcriptome, surface proteome and T and B lymphocyte antigen receptor analyses of over 780,000 peripheral blood mononuclear cells from a cross-sectional cohort of 130 patients with varying severities of COVID-19. We identified expansion of nonclassical monocytes expressing complement transcripts (CD16+C1QA/B/C+) that sequester platelets and were predicted to replenish the alveolar macrophage pool in COVID-19. Early, uncommitted CD34+ hematopoietic stem/progenitor cells were primed toward megakaryopoiesis, accompanied by expanded megakaryocyte-committed progenitors and increased platelet activation. Clonally expanded CD8+ T cells and an increased ratio of CD8+ effector T cells to effector memory T cells characterized severe disease, while circulating follicular helper T cells accompanied mild disease. We observed a relative loss of IgA2 in symptomatic disease despite an overall expansion of plasmablasts and plasma cells. Our study highlights the coordinated immune response that contributes to COVID-19 pathogenesis and reveals discrete cellular components that can be targeted for therapy.