Longitudinal home self-collection of capillary blood using homeRNA correlates interferon and innate viral defense pathways with SARS-CoV-2 viral clearance

Blood transcriptional profiling is a powerful tool to evaluate immune responses to infection; however, blood collection via traditional phlebotomy remains a barrier to precise characterization of the immune response in dynamic infections (e.g., respiratory viruses). Here we present an at-home self-collection methodology, home RNA, to study the host transcriptional response during acute SARS-CoV-2 infections. This method uniquely enables high frequency measurement of the host immune kinetics in non-hospitalized adults during the acute and most dynamic stage of their infection. COVID-19+ and healthy participants self-collected blood every other day for two weeks with daily nasal swabs and symptom surveys to track viral load kinetics and symptom burden, respectively. While healthy uninfected participants showed remarkably stable immune kinetics with no significant dynamic genes, COVID-19+ participants, on the contrary, depicted a robust response with over 418 dynamic genes associated with interferon and innate viral defense pathways. When stratified by vaccination status, we detected distinct response signatures between unvaccinated and breakthrough (vaccinated) infection subgroups; unvaccinated individuals portrayed a response repertoire characterized by higher innate antiviral responses, interferon signaling, and cytotoxic lymphocyte responses while breakthrough infections portrayed lower levels of interferon signaling and enhanced early cell-mediated response. Leveraging cross-platform longitudinal sampling (nasal swabs and blood), we observed that IFI27 , a key viral response gene, tracked closely with SARS-CoV-2 viral clearance in individual participants. Taken together, these results demonstrate that at-home sampling can capture key host antiviral responses and facilitate frequent longitudinal sampling to detect transient host immune kinetics during dynamic immune states. One Sentence Summary Self-blood collection using home RNA captures temporal dynamics in host transcriptional immune response during acute SARS-CoV-2 infection. ### Competing Interest Statement AW reports receiving clinical trial support to their institution from Pfizer, Ansun Biopharma, Allovir, and GlaxoSmithKline/Vir; receiving personal fees from Kyorin Pharmaceuticals; and receiving grants from Amazon and VB Tech outside the submitted work. MB reports clinical research support from Ansun Biopharma, Amazon, GSK, Vir Biotechnology, Gilead Sciences, Regeneron, Ridgeback, and Merck and personal fees from Allovir, Kyorin Pharmaceuticals and Merck, outside the submitted work. ABT has ownership in Stacks to the Future, LLC, but the work in this manuscript is unrelated. FYL, AJH, and ABT have filed a patent through the University of Washington technology transfer office on the homeRNA technology: A. Theberge, E. Berthier, A. Haack, D. Kennedy, F. Lim. Fluid transfer system for applications including stabilizing biological fluids. US Patent Application 17/361,322 (Publication Number: US20210402406A1). Filed 06/29/2021 (Priority Date: 06/30/2020) ### Funding Statement The study was funded by National Institutes of Health grants R01AI153087 (AW) and R35GM128648 (ABT, for in-lab developments of homeRNA), Fred Hutchinson Cancer Center COVID-19 Pilot grant (AW), and a Packard Research Fellowship from the David and Lucile Packard Foundation (ABT). ### 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: IRB of Fred Hutchinson Cancer Center gave ethical approval for this work. 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 and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data are available in the main text or the supplementary materials. Gene expression data available upon request. All statistical analyses were conducted using R. Packages used to perform analyses are specified in the statistical section. Scripts developed to perform analyses are available upon request.