Single-cell profiling of Ebola virus disease In Vivo reveals viral and host dynamics

Abstract

Ebola virus (EBOV) causes epidemics with high mortality yet remains understudied due to the challenge of experimentation in high-containment and outbreak settings. Here, we used single-cell transcriptomics and CyTOF-based single-cell protein quantification to characterize peripheral immune cells during EBOV infection in rhesus monkeys. We obtained 100,000 transcriptomes and 15,000,000 protein profiles, finding that immature, proliferative monocyte-lineage cells with reduced antigen-presentation capacity replace conventional monocyte subsets, while lymphocytes upregulate apoptosis genes and decline in abundance. By quantifying intracellular viral RNA, we identify molecular determinants of tropism among circulating immune cells and examine temporal dynamics in viral and host gene expression. Within infected cells, EBOV downregulates STAT1 mRNA and interferon signaling, and it upregulates putative pro-viral genes (e.g., DYNLL1 and HSPA5), nominating pathways the virus manipulates for its replication. This study sheds light on EBOV tropism, replication dynamics, and elicited immune response and provides a framework for characterizing host-virus interactions under maximum containment.

We thank E. Normandin, K. Siddle, S. Reilly, S. Weingarten-Gabbay, C. Myhrvold, K. DeRuff, M. Rudy, N. Barkas, M. Babadi, C. Edwards, M. Reyes, N. Hacohen, A. Regev, and E. Hodis for helpful comments on this work. We thank S. Wolock for useful feedback and for providing scripts and processed data for investigating the human bone marrow samples. We thank D. Schwarz and New England Biolabs for generously providing SauCas9 and technical advice. We thank A. Matthews and M. Kemball for help in project management and administration. We thank S. Knemeyer and SciStories for illustrations. This work is supported by the US Food and Drug Administration (FDA) contracts HHSF223201810172C and HHSF223201610018C , National Institute of Allergy and Infectious Diseases (NIAID) U19AI110818 , and HHMI . This work was partially supported by NIAID Interagency agreement NOR15003-001-0000 . The nonhuman primate work completed at the NIAID Integrated Research Facility was supported in part by the NIAID Division of Intramural Research and NIAID Division of Clinical Research and was performed under Battelle Memorial Institute Contract (No. HHSN272200700016I ), and manuscript drafting was performed under Laulima Government Solutions, LLC . Contract (No. HHSN272201800013C ). J.L. performed this work as an employee of Battelle. J.R.K., B.D.-K., R.A., and R.S.B. are current employees of Laulima Government Solutions. D.K. was supported by award number T32GM007753 from the National Institute of General Medical Sciences (NIGMS). A.E.L. was supported by the National Science Foundation (NSF) under Grant No. DGE 1144152 . M.M. was a Gilead Fellow of the Life Sciences Research Foundation . K.G.B was supported by a K01 ( NIH-TW010853 ) and an ASTMH Shope fellowship . A.K.S. was supported by the Searle Scholars Program , the Beckman Young Investigator Program , a Sloan Fellowship in Chemistry , NIH 5U24AI118672 , and the Bill and Melinda Gates Foundation . The CyTOF facility at the trans-NIH Center for Human Immunology is supported by funding from the Intramural Research Program of the NIH . The authors are solely responsible for the content of this paper, which does not necessarily represent the official views of the US Department of Health and Human Services (HHS), the NIH, the NIGMS, the FDA, or the institutions and companies affiliated with the authors.

Peer Reviewed

"Article signat per 27autors/es: Dylan Kotliar, Aaron E Lin, James Logue, Travis K Hughes, Nadine M Khoury, Siddharth S Raju, Marc H Wadsworth, Han Chen, Jonathan R Kurtz, Bonnie Dighero-Kemp, Zach B Bjornson, Nilanjan Mukherjee, Brian A Sellers, Nancy Tran, Matthew R Bauer, Gordon C Adams, Ricky Adams, John L Rinn, Marta Melé, Stephen F Schaffner, Garry P Nolan, Kayla G Barnes, Lisa E Hensley, David R McIlwain, Alex K Shalek, Pardis C Sabeti, Richard S Bennett "

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