{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,6,8]],"date-time":"2026-06-08T07:42:55Z","timestamp":1780904575056,"version":"3.54.1"},"posted":{"date-parts":[[2026,2,5]]},"group-title":"Microbiology","reference-count":101,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T00:00:00Z","timestamp":1770249600000},"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":[[2026,2,5]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>\n                  Respiratory syncytial virus (RSV) is a major cause of morbidity and mortality in infants globally. Specific nasal bacterial genera are differentially associated with RSV severity in infants:\n                  <jats:italic>Haemophilus<\/jats:italic>\n                  and\n                  <jats:italic>Streptococcus<\/jats:italic>\n                  with more severe disease and\n                  <jats:italic>Dolosigranulum<\/jats:italic>\n                  with healthy controls or milder outcomes. We hypothesized these differential bacterial effects begin at the epithelial level. Therefore, we established human nasal epithelial organoids differentiated at air-liquid interface (HNO-ALI) as a model system to assess effects of individual nasal microbionts on the epithelial response to subsequent RSV infection and of RSV on those microbionts. Infant-derived HNO-ALI were monocolonized with either\n                  <jats:italic>Streptococcus pneumoniae,<\/jats:italic>\n                  nontypeable\n                  <jats:italic>Haemophilus influenzae,<\/jats:italic>\n                  or\n                  <jats:italic>Dolosigranulum pigrum<\/jats:italic>\n                  one day before viral infection. RSV reduced colonizing\n                  <jats:italic>S. pneumoniae<\/jats:italic>\n                  and\n                  <jats:italic>D. pigrum<\/jats:italic>\n                  levels without affecting\n                  <jats:italic>H. influenzae. S. pneumoniae<\/jats:italic>\n                  precolonization uniquely reduced RSV levels during infection.\n                  <jats:italic>S. pneumoniae<\/jats:italic>\n                  precolonization also modulated the epithelial transcriptional response to RSV infection more so than\n                  <jats:italic>H. influenzae<\/jats:italic>\n                  or\n                  <jats:italic>D. pigrum<\/jats:italic>\n                  , with a pronounced effect on genes involved in immune response, cell cycle, stress, and growth signaling. Gene set enrichment analysis showed\n                  <jats:italic>S. pneumoniae<\/jats:italic>\n                  precolonization blunted RSV-induced increase in inflammatory and immune responses, consistent with\n                  <jats:italic>S. pneumoniae<\/jats:italic>\n                  also modulating RSV-induced cytokine production. Furthermore,\n                  <jats:italic>S. pneumoniae<\/jats:italic>\n                  precolonization blocked RSV-mediated dysregulation of cell-cycle genes, consistent with preventing arrest. Bacterial rescue of cell-cycle progression is a potential mechanism for reduced infectious virion production, since cell-cycle arrest enhances RSV replication. HNO-ALI facilitated elucidation of bacterial-viral-epithelial interplay at a frequent site of viral infection, directly linking nasal bacterial colonization to RSV infection dynamics.\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>IMPORTANCE<\/jats:title>\n                  <jats:p>\n                    Most RSV-related hospitalizations occur in healthy young children, yet predictors of RSV severity in this population are limited. The nasal passages are a major microbiota site exposed to frequent respiratory viral infections. Specific nasal bacterial genera\/species correlate with RSV clinical outcomes; however, the biological basis of these associations is poorly defined. Here, we established human nasal epithelial organoids differentiated at air-liquid interface (HNO-ALI) as a tractable experimental system for defining the interplay between bacteria, virus, and epithelial cells in the human nasal passages, enabling mechanistic insight into how the nasal microbiota contribute to RSV disease severity. Using this approach, we found that precolonization with each of the common nasal bacteria\n                    <jats:italic>S. pneumoniae<\/jats:italic>\n                    ,\n                    <jats:italic>H. influenzae<\/jats:italic>\n                    , or\n                    <jats:italic>D. pigrum<\/jats:italic>\n                    differentially affected the nasal epithelial response to RSV infection. This work highlights that the nasal epithelium actively integrates microbial and viral signals and that variation in bacterial colonization can shape viral infection trajectories.\n                  <\/jats:p>\n                <\/jats:sec>","DOI":"10.64898\/2026.02.05.703985","type":"posted-content","created":{"date-parts":[[2026,2,6]],"date-time":"2026-02-06T04:10:17Z","timestamp":1770351017000},"source":"Crossref","is-referenced-by-count":1,"title":["<i>Streptococcus pneumoniae<\/i>\n                  colonization modulates human nasal epithelial responses to respiratory syncytial virus infection"],"prefix":"10.64898","author":[{"given":"Leah A.","family":"Kafer","sequence":"first","affiliation":[{"name":"Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isabel F.","family":"Escapa","sequence":"additional","affiliation":[{"name":"Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea I.","family":"Boyd","sequence":"additional","affiliation":[{"name":"Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alejandra Rivera","family":"Tostado","sequence":"additional","affiliation":[{"name":"Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amal","family":"Kambal","sequence":"additional","affiliation":[{"name":"Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah E.","family":"Blutt","sequence":"additional","affiliation":[{"name":"Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vasanthi","family":"Avadhanula","sequence":"additional","affiliation":[{"name":"Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0100-2919","authenticated-orcid":false,"given":"Pedro A.","family":"Piedra","sequence":"additional","affiliation":[{"name":"Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA"},{"name":"Division of Infectious Diseases, Texas Children\u2019s Hospital and Department of Pediatrics Baylor College of Medicine, Houston, Texas, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1542-1679","authenticated-orcid":false,"given":"Katherine P.","family":"Lemon","sequence":"additional","affiliation":[{"name":"Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA"},{"name":"Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA"},{"name":"Division of Infectious Diseases, Texas Children\u2019s Hospital and Department of Pediatrics Baylor College of Medicine, Houston, Texas, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026021008111213000_2026.02.05.703985v1.1","first-page":"e36342","article-title":"Respiratory Syncytial Virus: A Comprehensive Review of Transmission, Pathophysiology, and Manifestation","volume":"15","year":"2023","journal-title":"Cureus"},{"key":"2026021008111213000_2026.02.05.703985v1.2","doi-asserted-by":"publisher","DOI":"10.1016\/s0140-6736(22)00478-0"},{"key":"2026021008111213000_2026.02.05.703985v1.3","doi-asserted-by":"publisher","DOI":"10.1586\/eri.11.92"},{"key":"2026021008111213000_2026.02.05.703985v1.4","doi-asserted-by":"crossref","first-page":"101447","DOI":"10.1016\/j.lanepe.2025.101447","article-title":"Risk factors for severe outcomes of respiratory syncytial virus infection in children: a nationwide cohort study in Sweden","volume":"58","year":"2025","journal-title":"Lancet Reg Health Eur"},{"key":"2026021008111213000_2026.02.05.703985v1.5","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(24)00138-7"},{"key":"2026021008111213000_2026.02.05.703985v1.6","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa0804877"},{"key":"2026021008111213000_2026.02.05.703985v1.7","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2015.03.008"},{"key":"2026021008111213000_2026.02.05.703985v1.8","doi-asserted-by":"publisher","DOI":"10.1183\/13993003.00152-2016"},{"key":"2026021008111213000_2026.02.05.703985v1.9","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.201602-0220OC"},{"key":"2026021008111213000_2026.02.05.703985v1.10","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-017-0395-y"},{"key":"2026021008111213000_2026.02.05.703985v1.11","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-50217-w"},{"key":"2026021008111213000_2026.02.05.703985v1.12","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1093\/infdis\/jiaa576","article-title":"Airway Gene Expression Correlates of Respiratory Syncytial Virus Disease Severity and Microbiome Composition in Infants","volume":"223","year":"2021","journal-title":"J Infect Dis"},{"key":"2026021008111213000_2026.02.05.703985v1.13","doi-asserted-by":"crossref","unstructured":"Alba C , Aparicio M , Gonz\u00e1lez-Mart\u00ednez F , Gonz\u00e1lez-S\u00e1nchez IM , P\u00e9rez-Moreno J , Castillo DTB , Rodr\u00edguez MJ , Rodr\u00edguez-Fern\u00e1ndez R , Fern\u00e1ndez L . 2021. Nasal and Fecal Microbiota and Immunoprofiling of Infants With and Without RSV Bronchiolitis. Frontiers in Microbiology 12.","DOI":"10.3389\/fmicb.2021.667832"},{"key":"2026021008111213000_2026.02.05.703985v1.14","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiaa577"},{"key":"2026021008111213000_2026.02.05.703985v1.15","doi-asserted-by":"crossref","unstructured":"Fujiogi M , Raita Y , P\u00e9rez-Losada M , Freishtat JR , Celed\u00f3n CJ , Mansbach MJ , Piedra AP , Zhu Z , Camargo AC , Hasegawa K . 2022. Integrated relationship of nasopharyngeal airway host response and microbiome associates with bronchiolitis severity. Nature Communications 13.","DOI":"10.1038\/s41467-022-32323-y"},{"key":"2026021008111213000_2026.02.05.703985v1.16","doi-asserted-by":"crossref","first-page":"101836","DOI":"10.1016\/j.xcrm.2024.101836","article-title":"The respiratory microbiome is linked to the severity of RSV infections and the persistence of symptoms in children","volume":"5","author":"investigators RESvCiE","year":"2024","journal-title":"Cell Rep Med"},{"key":"2026021008111213000_2026.02.05.703985v1.17","doi-asserted-by":"crossref","first-page":"1141","DOI":"10.1111\/pai.13524","article-title":"Respiratory syncytial virus and airway microbiota \u2013 A complex interplay and its reflection on morbidity","volume":"32","year":"2021","journal-title":"Pediatr Allergy Immunol"},{"key":"2026021008111213000_2026.02.05.703985v1.18","doi-asserted-by":"crossref","unstructured":"Caserta MT , Mariani TJ , Walsh EE , Gill SR , Gill AL , Corbett A , Harrington D , Chu C , Qiu X . 2026. Nasal Biomarkers of Acute Illness Severity and Predictors of Recurrent Wheeze in Respiratory Syncytial Virus (RSV) Infected Infants. The Journal of Infectious Diseases.","DOI":"10.1093\/infdis\/jiag049"},{"key":"2026021008111213000_2026.02.05.703985v1.19","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2017.10.023"},{"key":"2026021008111213000_2026.02.05.703985v1.20","doi-asserted-by":"publisher","DOI":"10.1080\/14787210.2019.1621168"},{"key":"2026021008111213000_2026.02.05.703985v1.21","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2020.07.004"},{"key":"2026021008111213000_2026.02.05.703985v1.22","doi-asserted-by":"publisher","DOI":"10.1111\/resp.13179"},{"key":"2026021008111213000_2026.02.05.703985v1.23","doi-asserted-by":"crossref","first-page":"912","DOI":"10.1093\/infdis\/jiab481","article-title":"Nasopharyngeal Codetection of Haemophilus influenzae and Streptococcus pneumoniae Shapes Respiratory Syncytial Virus Disease Outcomes in Children","volume":"225","year":"2022","journal-title":"J Infect Dis"},{"key":"2026021008111213000_2026.02.05.703985v1.24","doi-asserted-by":"crossref","unstructured":"Lin G-L , Drysdale BS , Snape DM , O\u2019Connor D , Brown A , Macintyre-Cockett G , Mellado-Gomez E , Cesare DM , Ansari AM , Bonsall D , Bray EJ , Jolley AK , Bowden R , Aerssens J , Bont L , Openshaw MJP , Martinon-Torres F , Nair H , Golubchik T , Pollard JA . 2024. Targeted metagenomics reveals association between severity and pathogen co-detection in infants with respiratory syncytial virus. Nature Communications 15.","DOI":"10.1038\/s41467-024-46648-3"},{"key":"2026021008111213000_2026.02.05.703985v1.25","doi-asserted-by":"crossref","first-page":"727","DOI":"10.3390\/microorganisms8050727","article-title":"The Ability of Respiratory Commensal Bacteria to Beneficially Modulate the Lung Innate Immune Response Is a Strain Dependent Characteristic","volume":"8","year":"2020","journal-title":"Microorganisms"},{"key":"2026021008111213000_2026.02.05.703985v1.26","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0127098"},{"key":"2026021008111213000_2026.02.05.703985v1.27","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.00873"},{"key":"2026021008111213000_2026.02.05.703985v1.28","doi-asserted-by":"publisher","DOI":"10.1128\/msphere.00984-21"},{"key":"2026021008111213000_2026.02.05.703985v1.29","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-3687-8_9"},{"key":"2026021008111213000_2026.02.05.703985v1.30","doi-asserted-by":"crossref","unstructured":"Rijsbergen CL , Dijk VALL , Engel MFM , Vries DDR , Swart DLR . 2021. In Vitro Modelling of Respiratory Virus Infections in Human Airway Epithelial Cells \u2013 A Systematic Review. Frontiers in Immunology 12.","DOI":"10.3389\/fimmu.2021.683002"},{"key":"2026021008111213000_2026.02.05.703985v1.31","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.201304-0750OC"},{"key":"2026021008111213000_2026.02.05.703985v1.32","doi-asserted-by":"crossref","first-page":"3062","DOI":"10.1111\/all.16196","article-title":"Network analysis reveals age\u2013 and virus-specific circuits in nasal epithelial cells of extremely premature infants","volume":"79","year":"2024","journal-title":"Allergy"},{"key":"2026021008111213000_2026.02.05.703985v1.33","doi-asserted-by":"crossref","first-page":"366","DOI":"10.7774\/cevr.2025.14.e30","article-title":"Cytokine responses to respiratory syncytial virus infection in well-differentiated infant nasal epithelial cell cultures","volume":"14","year":"2025","journal-title":"Clin Exp Vaccine Res"},{"key":"2026021008111213000_2026.02.05.703985v1.34","doi-asserted-by":"publisher","DOI":"10.1096\/fj.14-254359"},{"key":"2026021008111213000_2026.02.05.703985v1.35","doi-asserted-by":"publisher","DOI":"10.1186\/s12931-016-0382-z"},{"key":"2026021008111213000_2026.02.05.703985v1.36","doi-asserted-by":"crossref","unstructured":"Sachs N , Papaspyropoulos A , Zomer-van Ommen DD , Heo I , Bottinger L , Klay D , Weeber F , Huelsz-Prince G , Iakobachvili N , Amatngalim GD , de Ligt J , van Hoeck A , Proost N , Viveen MC , Lyubimova A , Teeven L , Derakhshan S , Korving J , Begthel H , Dekkers JF , Kumawat K , Ramos E , van Oosterhout MF , Offerhaus GJ , Wiener DJ , Olimpio EP , Dijkstra KK , Smit EF , van der Linden M , Jaksani S , van de Ven M , Jonkers J , Rios AC , Voest EE , van Moorsel CH , van der Ent CK , Cuppen E , van Oudenaarden A , Coenjaerts FE , Meyaard L , Bont LJ , Peters PJ , Tans SJ , van Zon JS , Boj SF , Vries RG , Beekman JM , Clevers H . 2019. Long-term expanding human airway organoids for disease modeling. EMBO J 38.","DOI":"10.15252\/embj.2018100300"},{"key":"2026021008111213000_2026.02.05.703985v1.37","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.03511-21"},{"key":"2026021008111213000_2026.02.05.703985v1.38","doi-asserted-by":"publisher","DOI":"10.1016\/j.jinf.2024.106305"},{"key":"2026021008111213000_2026.02.05.703985v1.39","doi-asserted-by":"crossref","first-page":"e0049325","DOI":"10.1128\/msphere.00493-25","article-title":"Nasal microbionts differentially colonize and elicit cytokines in human nasal epithelial organoids","volume":"10","year":"2025","journal-title":"mSphere"},{"key":"2026021008111213000_2026.02.05.703985v1.40","doi-asserted-by":"crossref","first-page":"106617","DOI":"10.1016\/j.jinf.2025.106617","article-title":"Single cell sequencing analysis of respiratory syncytial virus-infected pediatric and adult human nose organoids reveals age differences, proliferative diversity and identifies novel cellular tropism","volume":"91","year":"2025","journal-title":"J Infect"},{"key":"2026021008111213000_2026.02.05.703985v1.41","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0038052"},{"key":"2026021008111213000_2026.02.05.703985v1.42","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00806-09"},{"key":"2026021008111213000_2026.02.05.703985v1.43","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1110203109"},{"key":"2026021008111213000_2026.02.05.703985v1.44","doi-asserted-by":"publisher","DOI":"10.1097\/00005537-200004000-00021"},{"key":"2026021008111213000_2026.02.05.703985v1.45","doi-asserted-by":"crossref","unstructured":"Marks LR , Reddinger RM , Hakansson AP . 2012. High levels of genetic recombination during nasopharyngeal carriage and biofilm formation in Streptococcus pneumoniae. mBio 3.","DOI":"10.1128\/mBio.00200-12"},{"key":"2026021008111213000_2026.02.05.703985v1.46","doi-asserted-by":"crossref","unstructured":"Basset A , Herd M , Daly R , Dove SL , Malley R . 2017. The Pneumococcal Type 1 Pilus Genes Are Thermoregulated and Are Repressed by a Member of the Snf2 Protein Family. J Bacteriol 199.","DOI":"10.1128\/JB.00078-17"},{"key":"2026021008111213000_2026.02.05.703985v1.47","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00400-21"},{"key":"2026021008111213000_2026.02.05.703985v1.48","doi-asserted-by":"publisher","DOI":"10.1128\/JB.01022-15"},{"key":"2026021008111213000_2026.02.05.703985v1.49","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.76.11.5654-5666.2002"},{"key":"2026021008111213000_2026.02.05.703985v1.50","doi-asserted-by":"publisher","DOI":"10.1002\/ppul.24715"},{"key":"2026021008111213000_2026.02.05.703985v1.51","doi-asserted-by":"publisher","DOI":"10.1097\/01.MLG.0000159527.76949.93"},{"key":"2026021008111213000_2026.02.05.703985v1.52","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0102368"},{"key":"2026021008111213000_2026.02.05.703985v1.53","doi-asserted-by":"publisher","DOI":"10.1016\/j.jaci.2017.07.018"},{"key":"2026021008111213000_2026.02.05.703985v1.54","doi-asserted-by":"publisher","DOI":"10.1136\/thorax-2023-220230"},{"key":"2026021008111213000_2026.02.05.703985v1.55","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiac404"},{"key":"2026021008111213000_2026.02.05.703985v1.56","doi-asserted-by":"publisher","DOI":"10.1042\/bj2650621"},{"key":"2026021008111213000_2026.02.05.703985v1.57","doi-asserted-by":"publisher","DOI":"10.1038\/nrd.2018.45"},{"key":"2026021008111213000_2026.02.05.703985v1.58","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1016\/S2213-2600(21)00103-X","article-title":"Interleukin-6: obstacles to targeting a complex cytokine in critical illness","volume":"9","year":"2021","journal-title":"Lancet Respir Med"},{"key":"2026021008111213000_2026.02.05.703985v1.59","doi-asserted-by":"publisher","DOI":"10.1097\/INF.0b013e3182a14407"},{"key":"2026021008111213000_2026.02.05.703985v1.60","doi-asserted-by":"publisher","DOI":"10.1097\/MD.0000000000001512"},{"key":"2026021008111213000_2026.02.05.703985v1.61","doi-asserted-by":"publisher","DOI":"10.1016\/j.cytogfr.2011.06.001"},{"key":"2026021008111213000_2026.02.05.703985v1.62","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiw191"},{"key":"2026021008111213000_2026.02.05.703985v1.63","doi-asserted-by":"publisher","DOI":"10.1038\/ni.3503"},{"key":"2026021008111213000_2026.02.05.703985v1.64","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.272.9.5846"},{"key":"2026021008111213000_2026.02.05.703985v1.65","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2006.01.005"},{"key":"2026021008111213000_2026.02.05.703985v1.66","doi-asserted-by":"publisher","DOI":"10.1016\/j.smim.2021.101516"},{"key":"2026021008111213000_2026.02.05.703985v1.67","doi-asserted-by":"publisher","DOI":"10.1016\/j.cytogfr.2014.07.016"},{"key":"2026021008111213000_2026.02.05.703985v1.68","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0172953"},{"key":"2026021008111213000_2026.02.05.703985v1.69","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.05164-11"},{"key":"2026021008111213000_2026.02.05.703985v1.70","doi-asserted-by":"crossref","first-page":"22972","DOI":"10.1038\/srep22972","article-title":"Pneumococcal Pneumolysin Induces DNA Damage and Cell Cycle Arrest","volume":"6","year":"2016","journal-title":"Sci Rep"},{"key":"2026021008111213000_2026.02.05.703985v1.71","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.201407-1240OC"},{"key":"2026021008111213000_2026.02.05.703985v1.72","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.201703-0554OC"},{"key":"2026021008111213000_2026.02.05.703985v1.73","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciaf184"},{"key":"2026021008111213000_2026.02.05.703985v1.74","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1016\/S2213-2600(24)00148-6","article-title":"Interactions between respiratory syncytial virus and Streptococcus pneumoniae in the pathogenesis of childhood respiratory infections: a systematic review","volume":"12","year":"2024","journal-title":"Lancet Respir Med"},{"key":"2026021008111213000_2026.02.05.703985v1.75","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2010834117"},{"key":"2026021008111213000_2026.02.05.703985v1.76","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiu473"},{"key":"2026021008111213000_2026.02.05.703985v1.77","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00425-21"},{"key":"2026021008111213000_2026.02.05.703985v1.78","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.69.8.4870-4873.2001"},{"key":"2026021008111213000_2026.02.05.703985v1.79","doi-asserted-by":"crossref","first-page":"e0187721","DOI":"10.1128\/aac.01877-21","article-title":"A Humanized Monoclonal Antibody Potentiates Killing of Diverse Biofilm-Forming Respiratory Tract Pathogens by Antibiotics","volume":"66","year":"2022","journal-title":"Antimicrob Agents Chemother"},{"key":"2026021008111213000_2026.02.05.703985v1.80","doi-asserted-by":"publisher","DOI":"10.1177\/2211068214561025"},{"key":"2026021008111213000_2026.02.05.703985v1.81","doi-asserted-by":"crossref","first-page":"1649","DOI":"10.1128\/jcm.34.7.1649-1653.1996","article-title":"Rapid diagnosis of respiratory syncytial virus infections in immunocompromised adults","volume":"34","year":"1996","journal-title":"J Clin Microbiol"},{"key":"2026021008111213000_2026.02.05.703985v1.82","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts635"},{"key":"2026021008111213000_2026.02.05.703985v1.83","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-12-323"},{"key":"2026021008111213000_2026.02.05.703985v1.84","doi-asserted-by":"crossref","unstructured":"Danecek P , Bonfield JK , Liddle J , Marshall J , Ohan V , Pollard MO , Whitwham A , Keane T , McCarthy SA , Davies RM , Li H . 2021. Twelve years of SAMtools and BCFtools. Gigascience 10.","DOI":"10.1093\/gigascience\/giab008"},{"key":"2026021008111213000_2026.02.05.703985v1.85","doi-asserted-by":"crossref","first-page":"1521","DOI":"10.12688\/f1000research.7563.1","article-title":"Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences","volume":"4","year":"2015","journal-title":"F1000Res"},{"key":"2026021008111213000_2026.02.05.703985v1.86","first-page":"8","article-title":". vegan: Community Ecology Package","volume":"2","year":"2025","journal-title":"vR package version"},{"key":"2026021008111213000_2026.02.05.703985v1.87","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0550-8"},{"key":"2026021008111213000_2026.02.05.703985v1.88","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2010-11-10-r106"},{"key":"2026021008111213000_2026.02.05.703985v1.89","doi-asserted-by":"publisher","DOI":"10.1093\/biostatistics\/kxw041"},{"key":"2026021008111213000_2026.02.05.703985v1.90","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0506580102"},{"key":"2026021008111213000_2026.02.05.703985v1.91","doi-asserted-by":"publisher","DOI":"10.1101\/060012"},{"key":"2026021008111213000_2026.02.05.703985v1.92","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.cels.2015.12.004","article-title":"The Molecular Signatures Database (MSigDB) hallmark gene set collection","volume":"1","year":"2015","journal-title":"Cell Syst"},{"key":"2026021008111213000_2026.02.05.703985v1.93","unstructured":"Dolgalev I. 2025. msigdbr: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format, vR package version 25.1.1. https:\/\/igordot.github.io\/msigdbr\/."},{"key":"2026021008111213000_2026.02.05.703985v1.94","doi-asserted-by":"publisher","DOI":"10.2307\/2346101"},{"key":"2026021008111213000_2026.02.05.703985v1.95","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005752"},{"key":"2026021008111213000_2026.02.05.703985v1.96","unstructured":"Team RC . 2025. R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, https:\/\/www.r-project.org\/."},{"key":"2026021008111213000_2026.02.05.703985v1.97","unstructured":"team P. 2025. R Studio: Integrated Development Environment for R, Posit Software, PBC, Boston, MA. http:\/\/www.posit.co\/."},{"key":"2026021008111213000_2026.02.05.703985v1.98","doi-asserted-by":"crossref","first-page":"1686","DOI":"10.21105\/joss.01686","article-title":"Welcome to the Tidyverse","volume":"4","year":"2019","journal-title":"Journal of Open Source Software"},{"key":"2026021008111213000_2026.02.05.703985v1.99","first-page":"1","article-title":"Fitting Linear Mixed-Effects Models Using lme4","volume":"67","year":"2015","journal-title":"Journal of Statistical Software"},{"key":"2026021008111213000_2026.02.05.703985v1.100","doi-asserted-by":"crossref","unstructured":"Kuznetsova A , Brockhoff BP , Christensen BHR . 2017. lmerTest Package: Tests in Linear Mixed Effects Models. Journal of Statistical Software 82.","DOI":"10.18637\/jss.v082.i13"},{"key":"2026021008111213000_2026.02.05.703985v1.101","unstructured":"Lenth RV . 2024. emmeans: Estimated Marginal Means, aka Least-Squares Means, https:\/\/rvlenth.github.io\/emmeans\/."}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.02.05.703985","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,10]],"date-time":"2026-02-10T16:11:24Z","timestamp":1770739884000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.02.05.703985"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2,5]]},"references-count":101,"URL":"https:\/\/doi.org\/10.64898\/2026.02.05.703985","relation":{},"subject":[],"published":{"date-parts":[[2026,2,5]]},"subtype":"preprint"}}