Human SARS-CoV-2 challenge resolves local and systemic response dynamics

The COVID-19 pandemic is an ongoing global health threat, yet our understanding of the cellular disease dynamics remains limited. In our unique COVID-19 human challenge study we used single cell genomics of nasopharyngeal swabs and blood to temporally resolve abortive, transient and sustained infections in 16 seronegative individuals challenged with preAlpha-SARS-CoV-2. Our analyses revealed rapid changes in cell type proportions and dozens of highly dynamic cellular response states in epithelial and immune cells associated with specific timepoints or infection status. We observed that the interferon response in blood precedes the nasopharynx, and that nasopharyngeal immune infiltration occurred early in transient but later in sustained infection, and thus correlated with preventing sustained infection. Ciliated cells showed an acute response phase, upregulated MHC class II while infected, and were most permissive for viral replication, whilst nasal T cells and macrophages were infected non-productively. We resolve 54 T cell states, including acutely activated T cells that clonally expanded while carrying convergent SARS-CoV-2 motifs. Our novel computational pipeline (Cell2TCR) identifies activated antigen-responding clonotype groups and motifs in any dataset. Together, we show that our detailed time series data (covid19cellatlas.org) can serve as a 'Rosetta stone' for the epithelial and immune cell responses, and reveals early dynamic responses associated with protection from infection. ### Competing Interest Statement R.G.H.L., L.M.D. and S.A.T. are inventors on a filed patent that is related to the detection and application of activated T cells. In the past three years, S.A.T. has received remuneration for Scientific Advisory Board Membership from Sanofi, GlaxoSmithKline, Foresite Labs and Qiagen. S.A.T. is a co-founder and holds equity in Transition Bio. P.M. is a Medical Research Council (MRC)-GlaxoSmithKline EMINENT clinical training fellow with project funding unrelated to the topic of this Comment and receives co-funding from the National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre. P.M. reports consultancy fees from SOBI, AbbVie, UCB, Lilly, Boehringer Ingelheim, and EUSA Pharma all unrelated to this submission. A.M., A.C., M.K., M.M. and A.B. are full time employees at hVIVO Services Ltd. ### Clinical Trial NCT04865237 ### Funding Statement This research was funded in whole, or in part, by the Wellcome Trust Grant 206194, 220540/Z/20/A and 211276/Z/18/Z, and by Action Medical Research (GN2911, to M.Z.N. and K.B.M.). M.Z.N. acknowledges funding from a MRC Clinician Scientist Fellowship (MR/W00111X/1). M.Z.N. and J.L.B. acknowledge funding from the Rutherford Fund Fellowship allocated by the MRC UK Regenerative Medicine Platform 2 (MR/5005579/1). M.Y. was funded by The Jikei University School of Medicine and Action Medical Research (GN2911). K.B.W. acknowledges funding from University College London, Birkbeck MRC Doctoral Training Programme. L.M.D is supported by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 955321. M.N. acknowledges funding from the Wellcome Trust (207511/Z/17/Z) and by NIHR Biomedical Research Funding to UCL and UCLH. R.H. is a NIHR Senior Investigator. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The UK Health Research Authority - Ad Hoc Specialist Ethics Committee gave ethical approval for this work (reference: 20/UK/2001 and 20/UK/0002). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes The data presented in this study can be explored and analyzed interactively through our COVID-19 Cell Atlas web portal (https://covid19cellatlas.org), currently accessible via early-access at http://covid19-challenge-study.cellgeni.sanger.ac.uk/ . The cell by feature count matrices are also available to download at the web portal. The cell state annotation models are available in the CellTypist model repository (https://www.celltypist.org/models). A reference for our MT-GPR model to infer time since viral exposure on PBMC data is available at our GitHub repository (https://github.com/Teichlab/COVID-19\_Challenge\_Study). The raw sequencing data will be made available via the European Genome-Phenome Archive, which will be made available under managed data access. Cell2TCR is available at our GitHub repository (https://github.com/Teichlab/Cell2TCR). Code that was used for data analysis is available at our GitHub repository (https://github.com/Teichlab/COVID-19\_Challenge\_Study).