{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T06:11:23Z","timestamp":1778220683297,"version":"3.51.4"},"posted":{"date-parts":[[2026,4,22]]},"group-title":"Immunology","reference-count":163,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T00:00:00Z","timestamp":1776816000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,4,24]]},"abstract":"<jats:title>Summary<\/jats:title>\n                <jats:p>\n                  Respiratory viral infections in early childhood are major drivers of acute morbidity and long-term airway disease, yet how distinct viruses remodel the pediatric nasal mucosa at cellular resolution remains unresolved. Here, we generated a single-cell RNA sequencing atlas of 335,174 nasal epithelial and immune cells from 132 children under five years of age with SARS-CoV-2, rhinovirus, or respiratory syncytial virus (RSV) infection, alongside uninfected controls. Mapping viral transcripts to individual cells revealed virus-specific infected epithelial states: an NF-kB-responsive ciliated subset in SARS-CoV-2 and a previously undescribed\n                  <jats:italic>KRT17+<\/jats:italic>\n                  squamous-like subset in RSV. We delineated divergent mucosal response programs, including a robust interferon (IFN) response in SARS-CoV-2, an IL-13-responsive secretory program in rhinovirus, and heightened inflammatory and cytotoxic immune activation in RSV. In RSV, specific immune subsets and elevated IFN-response signatures were associated with disease severity, whereas rhinovirus-induced wheeze was marked by expansion of a\n                  <jats:italic>CST1<\/jats:italic>\n                  + goblet cell subset. Integration of asthma genome-wide association data with our atlas revealed a\n                  <jats:italic>KRT13+<\/jats:italic>\n                  hillock-like squamous epithelial subset enriched for expression of childhood-onset asthma risk loci. Finally, we demonstrate that this resource enables high-resolution annotation of independent pediatric cohorts in Kolkata, India and rural Bangladesh. Together, this atlas establishes a comprehensive view of antiviral immunity in the pediatric nasal mucosa and defines virus-specific mucosal immune programs relevant to disease severity and asthma risk in early life.\n                <\/jats:p>","DOI":"10.64898\/2026.04.20.719671","type":"posted-content","created":{"date-parts":[[2026,4,23]],"date-time":"2026-04-23T04:10:18Z","timestamp":1776917418000},"source":"Crossref","is-referenced-by-count":0,"title":["Unique nasal cell states induced by common pediatric respiratory viruses"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6292-1006","authenticated-orcid":false,"given":"Jaclyn M. L.","family":"Walsh","sequence":"first","affiliation":[{"name":"Division of Gastroenterology, Hepatology, and Nutrition, Boston Children\u2019s Hospital, Boston, MA, USA;"},{"name":"Department of Immunology, Harvard Medical School, Boston, MA, USA;"},{"name":"Program in Immunology, Harvard Medical School, Boston, MA, USA;"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4985-8505","authenticated-orcid":false,"given":"Lillian J.","family":"Juttukonda","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology, Hepatology, and Nutrition, Boston Children\u2019s Hospital, Boston, MA, USA;"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA;"},{"name":"Division of Newborn Medicine, Boston Medical Center, Boston, MA, USA;"},{"name":"Department of Pediatrics, Chobanian and Avedisian School of Medicine, Boston University, Boston, MA, USA;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4357-2343","authenticated-orcid":false,"given":"Ying","family":"Tang","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology, Hepatology, and Nutrition, Boston Children\u2019s Hospital, Boston, MA, USA;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ankita","family":"Chatterjee","sequence":"additional","affiliation":[{"name":"John.C. Martin Center for Liver Research & Innovations, Kolkata, India;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marc","family":"Elosua-Bayes","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology, Hepatology, and Nutrition, Boston Children\u2019s Hospital, Boston, MA, USA;"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA;"},{"name":"Cell Discovery Network, Boston Children\u2019s Hospital, Boston, MA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Erica","family":"Langan","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology, Hepatology, and Nutrition, Boston Children\u2019s Hospital, Boston, MA, USA;"},{"name":"Program in Immunology, Harvard Medical School, Boston, MA, USA;"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA;"},{"name":"Harvard-MIT MD\/PhD Program, Boston, MA, USA;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amanda","family":"Frischmann","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology, Hepatology, and Nutrition, Boston Children\u2019s Hospital, Boston, MA, USA;"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Faith","family":"Taliaferro","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology, Hepatology, and Nutrition, Boston Children\u2019s Hospital, Boston, MA, USA;"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA;"},{"name":"Department of Pediatrics, Massachusetts General Hospital, Boston, MA, USA;"},{"name":"Harvard Medical School, Boston, MA, USA;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hannah R.","family":"Matthews","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology, Hepatology, and Nutrition, Boston Children\u2019s Hospital, Boston, MA, USA;"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA;"},{"name":"Department of Immunology and Infectious Diseases, Harvard T.H. 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Chan School of Public Health, Boston, MA, USA;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kyle","family":"Kimler","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology, Hepatology, and Nutrition, Boston Children\u2019s Hospital, Boston, MA, USA;"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA;"},{"name":"Cell Discovery Network, Boston Children\u2019s Hospital, Boston, MA, USA"},{"name":"Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA;"},{"name":"Institute of Medical Engineering & Science, MIT, Cambridge, MA, USA;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chris M.","family":"Lent","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology, Hepatology, and Nutrition, Boston Children\u2019s Hospital, Boston, MA, USA;"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Deb 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