SARS-CoV-2 human challenge reveals single-gene blood transcriptional biomarkers that discriminate early and late phases of acute respiratory viral infections.

Evaluation of host-response blood transcriptional signatures of viral infection have so far failed to test whether these biomarkers reflect different biological processes that may be leveraged for distinct translational applications. We addressed this question in the SARS-CoV-2 human challenge model. We found differential time profiles for interferon (IFN) stimulated blood transcriptional responses represented by measurement of single genes. MX1 transcripts correlated with a rapid and transient wave of type 1 IFN stimulated genes (ISG) across all cell types, which may precede PCR detection of replicative infection. Another ISG, IFI27, showed a delayed but sustained response restricted to myeloid peripheral blood mononuclear cells, attributable to gene and cell-specific epigenetic regulation. These findings were reproducible in diverse respiratory virus challenges, and in natural infection with SARS-CoV-2 or unselected respiratory viruses. The MX1 response achieved superior diagnostic accuracy in early infection, correlation with viral load and identification of virus culture positivity, with potential to stratify patients for time sensitive antiviral treatment. IFI27 achieved superior diagnostic accuracy across the time course of symptomatic infection. Compared to blood, measurement of these responses in nasal mucosal samples was less sensitive and did not discriminate between early and late phases of infection. ### Competing Interest Statement SAT. has received remuneration for Scientific Advisory Board Membership from Sanofi, GlaxoSmithKline, Foresite Labs and Qiagen. SAT is a co-founder and holds equity in Transition Bio. AM, AC, MK, MM and AB are full time employees at hVIVO Services Ltd. ### Funding Statement This research was supported by the Wellcome Trust (224530/Z/21/Z). AL acknowledges funding by the NIHR Health Protection Research Units (HPRU) in Respiratory Infections (NIHR200927). BMC acknowledges funding by the Rosetrees Foundation. CMB, MK and ML acknowledge funding by NIHR Biomedical Research to Imperial College London. CMW acknowledges funding from the Medical Research Council (MR/T016329/1). CT acknowledges funding from the Wellcome Trust (102186/B/13/Z). LCKB acknowledges funding from the NIHR (Academic Clinical Fellowship Programme). LMD acknowledges funding from the European Union Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 955321. M.Z.N. acknowledges funding from a MRC Clinician Scientist Fellowship (MR/W00111X/1), Action Medical Research (GN2911) and funding from the Rutherford Fund Fellowship allocated by the MRC UK Regenerative Medicine Platform 2 (MR/5005579/1). MN 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. RKG acknowledges funding from the National Institute for Health Research (NIHR302829). ### 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: Regulatory approvals for the human studies presented herein were provided by the UK Health Research Authority under the following reference numbers: 20/UK/2001 and 20/UK/0002 for the SARS-CoV-2 challenge study; 20/NW/0231 for the INSTINCT study; 19/LO/1441 for the H3N2 influenza challenge study. 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 Processed RNAseq data will be made available after peer reviewed publication at ArrayExpress for the SARS-CoV-2 challenge study (accession number: E-MTAB-12993), H3N2 influenza challenge study (accession numbers: E-MTAB-13038 and E-MTAB-13041). Raw sequencing data from these studies and the INSTINCT SARS-CoV-2 household contact study will be made available via the European Genome-Phenome Archive under managed data access.