High burden of viruses and bacterial pathobionts drives heightened nasal innate immunity in children with and without SARS-CoV-2

Recent work indicates that heightened nasal innate immunity in children may impact SARS-CoV-2 pathogenesis. Here, we identified drivers of nasal innate immune activation in children using cytokine profiling and multiplex pathogen detection in 291 pediatric nasopharyngeal samples from the 2022 Omicron surge. Nasal viruses and bacterial pathobionts were highly prevalent, especially in younger children (81% of symptomatic and 37% asymptomatic children overall; 91% and 62% in subjects <5 yrs). For SARS-CoV-2, viral load was highest in young children, and viral load in single infections or combined viral loads in coinfections best predicted nasal CXCL10, a biomarker of the mucosal interferon response. Bacterial pathobionts correlated with high nasal IL-1β and TNF, but not CXCL10, and viral-bacterial coinfections showed a combined immunophenotype. These findings reveal virus and bacteria as drivers of heightened nasal innate immunity in children and suggest that frequent host-pathogen interactions shape responses to respiratory viruses in this age group. ### Competing Interest Statement Dr. Foxman is an inventor on a pending patent application WO2019/217296 A1 and provisional patent application No 63/293386. Dr. Foxman and Dr. Landry are inventors on pending patent application WO2018/071498 Al. Dr. Schulz is a consultant for Hugo Health, consultant for Detect Inc, a point-of-care diagnostics company; co-founder of Refacto Health, and has received funds from Merck, Regeneron, the Shenzen Center for Health Information, and the Beijing National Center for Cardiac Diseases. The other authors declare no competing interests. ### Funding Statement This study was funded by the National Institutes of Health (T32AI055403 received by TAW), Fast Grants for COVID-19 research from the Mercatus Center (George Mason University, Fairfax, VA, USA; received by EFF), the Rita Allen Foundation (received by EFF) and the Gruber Foundation (received by TAW). ### 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: In this study, we collected a total of 306 residual nasopharyngeal swab samples from patients presenting to the pediatric emergency department between January 11-23, 2022 and were screened for SARS-CoV-2. 15 samples were excluded from further analysis due to low Ct for the internal control (albumin, Ct>33), leaving 291 samples for analysis. The study protocol was reviewed and ethical approval was given by the Yale Human Investigations Committee, the institutional review board at the Yale School of Medicine, (protocol #2000027656) and the study was determined to not require specific patient consent. 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 All data produced in the present work are contained in the manuscript. Extended data analyses, original code for mediation analysis and data visualizations, and extended demographics data will be deposited in Mendeley Data at the DOI 10.17632/g8ckr9zxbx.1 and will be available at the time of peer-reviewed publication.