Age-related pharyngeal microbiome and host transcriptomic signatures underlying fever responses in RSV bronchiolitis

Ying Li; Jingyuan Zhang; Haizhou Liu; Muhammad Noman; Muhammad Arif Rizwan; Ismaila Damilare Isiaka; Hebin Chen; Wenqing Li; Nan Zhao; Yan Li; Yamin Sun; Xiaoxia Lu; Di Liu; Yi Yan

doi:10.1016/j.virs.2026.05.002

June 2026

Citation: Ying Li, Jingyuan Zhang, Haizhou Liu, Muhammad Noman, Muhammad Arif Rizwan, Ismaila Damilare Isiaka, Hebin Chen, Wenqing Li, Nan Zhao, Yan Li, Yamin Sun, Xiaoxia Lu, Di Liu, Yi Yan. Age-related pharyngeal microbiome and host transcriptomic signatures underlying fever responses in RSV bronchiolitis .VIROLOGICA SINICA, 2026, 41(3) : 574-585. http://dx.doi.org/10.1016/j.virs.2026.05.002

Age-related pharyngeal microbiome and host transcriptomic signatures underlying fever responses in RSV bronchiolitis

Ying Li ^a,b,c,d ,
Jingyuan Zhang ^c,d ,
Haizhou Liu ^a ,
Muhammad Noman ^a,b ,
Muhammad Arif Rizwan ^a,b ,
Ismaila Damilare Isiaka ^a,b ,
Hebin Chen ^c,d ,
Wenqing Li ^c,d ,
Nan Zhao ^c,d ,
Yan Li ^c,d,e ,
Yamin Sun ^f ,
Xiaoxia Lu ^{c,d
,,} ,
Di Liu ^{a,b
,,} ,
Yi Yan ^{c,d
,,}

a. State Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;
b. University of Chinese Academy of Sciences, Beijing 101409, China;
c. Department of Respiratory Medicine, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China;
d. Pediatric Respiratory Disease Laboratory, Institute of Maternal and Child Health, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China;
e. Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China;
f. National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 101409, China

Corresponding author: Xiaoxia Lu, lusi74@163.com
Di Liu, liud@wh.iov.cn
Yi Yan, yanyi_1996@163.com
Received Date: 07 January 2026
Accepted Date: 12 May 2026
Available online: 14 May 2026

Abstract

Respiratory syncytial virus (RSV) bronchiolitis is the leading cause of hospitalization in infancy and exhibits pronounced age-dependent clinical heterogeneity. Fever becomes increasingly prevalent with age, yet whether febrile representation reflects a uniform inflammatory and immune phenotype across infancy remains unclear. In this prospective cohort of infants hospitalized with RSV bronchiolitis, we performed an integrated analysis of clinical features, pharyngeal microbiome composition, host transcriptomic profiles, and host-microbe interaction networks, with particular attention to age-related variation in fever-associated patterns. Clinically, fever prevalence exhibited a strong age-dependent increase across infancy. Correspondingly, canonical correspondence analysis identified age and fever as dominant gradients related to variation in both pharyngeal microbiome composition and host gene expression. Although no significant age-dependent correlations were observed at the global microbial and host transcriptomic levels in the fever-age interaction model, distinct patterns of microbial and host responses related to fever were observed across different age groups. Specifically, ranked gene set enrichment analysis indicated that febrile infants in early infancy showed relative attenuation of host defense-related programs, whereas older infants showed stronger enrichment of antiviral and inflammatory effector pathways, with more selective regulatory and signaling-associated patterns in late infancy. Integrated host-microbe network analysis further delineated a coherent developmental trajectory of fever-associated interaction architectures, evolving from densely interconnected regulatory networks in early infancy to modular, selectively coupled, host-centered configurations with advancing age. Together, febrile responses in RSV bronchiolitis should not be interpreted as a uniform biological phenotype across infancy and support age-aware interpretation of fever in pediatric RSV infection.
- Respiratory syncytial virus (RSV)
- , Bronchiolitis
- , Age-dependent
- , Fever
- , Host response
- , Airway microbiome

References
1. Blomqvist, A., Engblom, D., 2018. Neural Mechanisms of Inflammation-Induced Fever. Neuroscientist 24, 381-399.
2. Brand, H.K., Ahout, I.M., de Ridder, D., van Diepen, A., Li, Y., Zaalberg, M., Andeweg, A., Roeleveld, N., de Groot, R., Warris, A., Hermans, P.W., Ferwerda, G., Staal, F.J., 2015. Olfactomedin 4 Serves as a Marker for Disease Severity in Pediatric Respiratory Syncytial Virus (RSV) Infection. PLoS One 10, e0131927.
3. Chen, S., Zhou, Y., Chen, Y., Gu, J., 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884-i890.
4. Colosia, A., Costello, J., McQuarrie, K., Kato, K., Bertzos, K., 2023. Systematic literature review of the signs and symptoms of respiratory syncytial virus. Influenza Other Respir Viruses 17, e13100.
5. de Steenhuijsen Piters, W.A., Heinonen, S., Hasrat, R., Bunsow, E., Smith, B., Suarez-Arrabal, M.C., Chaussabel, D., Cohen, D.M., Sanders, E.A., Ramilo, O., Bogaert, D., Mejias, A., 2016. Nasopharyngeal Microbiota, Host Transcriptome, and Disease Severity in Children with Respiratory Syncytial Virus Infection. Am J Respir Crit Care Med 194, 1104-1115.
6. Do, L.A.H., Pellet, J., van Doorn, H.R., Tran, A.T., Nguyen, B.H., Tran, T.T.L., Tran, Q.H., Vo, Q.B., Tran Dac, N.A., Trinh, H.N., Nguyen, T.T.H., Le Binh, B.T., Nguyen, H.M.K., Nguyen, M.T., Thai, Q.T., Vo, T.V., Ngo, N.Q.M., Dang, T.K.H., Cao, N.H., Tran, T.V., Ho, L.V., De Meulder, B., Auffray, C., Hofstra, J.J., Farrar, J., Bryant, J.E., de Jong, M., Hibberd, M.L., 2017. Host Transcription Profile in Nasal Epithelium and Whole Blood of Hospitalized Children Under 2 Years of Age With Respiratory Syncytial Virus Infection. J Infect Dis 217, 134-146.
7. Dobin, A., Davis, C.A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., Gingeras, T.R., 2013. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15-21.
8. Feng, Q., Feng, Z., Yang, B., Han, S., Wen, S., Lu, G., Jin, R., Xu, B., Zhang, H., Xu, L., Xie, Z., 2023. Metatranscriptome Reveals Specific Immune and Microbial Signatures of Respiratory Syncytial Virus Infection in Children. Microbiol Spectr 11, e0410722.
9. Feng, Z., Xie, Z., Xu, L., 2025. Current antiviral therapies and promising drug candidates against respiratory syncytial virus infection. Virol Sin 40, 147-156.
10. Fujiogi, M., Raita, Y., Perez-Losada, M., Freishtat, R.J., Celedon, J.C., Mansbach, J.M., Piedra, P.A., Zhu, Z., Camargo, C.A., Jr., Hasegawa, K., 2022. Integrated relationship of nasopharyngeal airway host response and microbiome associates with bronchiolitis severity. Nat Commun 13, 4970.
11. Hall, C.B., Weinberg, G.A., Iwane, M.K., Blumkin, A.K., Edwards, K.M., Staat, M.A., Auinger, P., Griffin, M.R., Poehling, K.A., Erdman, D., Grijalva, C.G., Zhu, Y., Szilagyi, P., 2009. The burden of respiratory syncytial virus infection in young children. N Engl J Med 360, 588-598.
12. Hartmann, K., Liese, J.G., Kemmling, D., Prifert, C., Weissbrich, B., Thilakarathne, P., Diels, J., Weber, K., Streng, A., 2022. Clinical Burden of Respiratory Syncytial Virus in Hospitalized Children Aged </=5 Years (INSPIRE Study). J Infect Dis 226, 386-395.
13. Hasegawa, K., Mansbach, J.M., Ajami, N.J., Espinola, J.A., Henke, D.M., Petrosino, J.F., Piedra, P.A., Shaw, C.A., Sullivan, A.F., Camargo, C.A., Jr., the, M.-I., 2016. Association of nasopharyngeal microbiota profiles with bronchiolitis severity in infants hospitalised for bronchiolitis. Eur Respir J 48, 1329-1339.
14. Hu, M., Bogoyevitch, M.A., Jans, D.A., 2020. Impact of Respiratory Syncytial Virus Infection on Host Functions: Implications for Antiviral Strategies. Physiol Rev 100, 1527-1594.
15. Kawakami, C., Sato, A., Sumita, H., Isozaki, A., Shimizu, H., Kanetaka, T., Maehara, K., Ao, K., Nariai, A., Takeshita, F., Kizu, R., Mori, M., 2018. Fever Responses Are Enhanced with Advancing Age during Respiratory Syncytial Virus Infection among Children under 24 Months Old. Tohoku J Exp Med 245, 217-222.
16. Kollmann, T.R., Levy, O., Montgomery, R.R., Goriely, S., 2012. Innate immune function by Toll-like receptors: distinct responses in newborns and the elderly. Immunity 37, 771-783.
17. Kristensen, M., de Steenhuijsen Piters, W.A.A., Wildenbeest, J., van Houten, M.A., Zuurbier, R.P., Hasrat, R., Arp, K., Chu, M., Billard, M., Heikkinen, T., Cunningham, S., Snape, M., Drysdale, S.B., Thwaites, R.S., Martinon-Torres, F., Pollard, A.J., Openshaw, P.J.M., Aerssen, J., Binkowska, J., Bont, L., Bogaert, D., investigators, R.E.S.v.C.i.E., 2024. The respiratory microbiome is linked to the severity of RSV infections and the persistence of symptoms in children. Cell Rep Med 5, 101836.
18. Langmead, B., Salzberg, S.L., 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357-359.
19. Li, Y., Wang, X., Blau, D.M., Caballero, M.T., Feikin, D.R., Gill, C.J., Madhi, S.A., Omer, S.B., Simoes, E.A.F., Campbell, H., Pariente, A.B., Bardach, D., Bassat, Q., Casalegno, J.-S., Chakhunashvili, G., Crawford, N., Danilenko, D., Do, L.A.H., Echavarria, M., Gentile, A., Gordon, A., Heikkinen, T., Huang, Q.S., Jullien, S., Krishnan, A., Lopez, E.L., Markic, J., Mira-Iglesias, A., Moore, H.C., Moyes, J., Mwananyanda, L., Nokes, D.J., Noordeen, F., Obodai, E., Palani, N., Romero, C., Salimi, V., Satav, A., Seo, E., Shchomak, Z., Singleton, R., Stolyarov, K., Stoszek, S.K., von Gottberg, A., Wurzel, D., Yoshida, L.-M., Yung, C.F., Zar, H.J., Abram, M., Aerssens, J., Alafaci, A., Balmaseda, A., Bandeira, T., Barr, I., Batinovic, E., Beutels, P., Bhiman, J., Blyth, C.C., Bont, L., Bressler, S.S., Cohen, C., Cohen, R., Costa, A.-M., Crow, R., Daley, A., Dang, D.-A., Demont, C., Desnoyers, C., Diez-Domingo, J., Divarathna, M., du Plessis, M., Edgoose, M., Ferolla, F.M., Fischer, T.K., Gebremedhin, A., Giaquinto, C., Gillet, Y., Hernandez, R., Horvat, C., Javouhey, E., Karseladze, I., Kubale, J., Kumar, R., Lina, B., Lucion, F., MacGinty, R., Martinon-Torres, F., McMinn, A., Meijer, A., Milic, P., Morel, A., Mulholland, K., Mungun, T., Murunga, N., Newbern, C., Nicol, M.P., Odoom, J.K., Openshaw, P., Ploin, D., Polack, F.P., Pollard, A.J., Prasad, N., Puig-Barbera, J., Reiche, J., Reyes, N., Rizkalla, B., Satao, S., Shi, T., Sistla, S., Snape, M., Song, Y., Soto, G., Tavakoli, F., Toizumi, M., Tsedenbal, N., van den Berge, M., Vernhes, C., von Mollendorf, C., Walaza, S., Walker, G., Nair, H., 2022. Global, regional, and national disease burden estimates of acute lower respiratory infections due to respiratory syncytial virus in children younger than 5 years in 2019: a systematic analysis. The Lancet 399, 2047-2064.
20. Liao, Y., Smyth, G.K., Shi, W., 2014. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923-930.
21. Love, M.I., Huber, W., Anders, S., 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15, 550.
22. Lu, B., Yan, Y., Dong, L., Han, L., Liu, Y., Yu, J., Chen, J., Yi, D., Zhang, M., Deng, X., Wang, C., Wang, R., Wang, D., Wei, H., Liu, D., Yi, C., 2021. Integrated characterization of SARS-CoV-2 genome, microbiome, antibiotic resistance and host response from single throat swabs. Cell Discov 7, 19.
23. Lu, J., Breitwieser, F.P., Thielen, P., Salzberg, S.L., 2017. Bracken: estimating species abundance in metagenomics data. PeerJ Comput Sci 3.
24. Mariani, T.J., Qiu, X., Chu, C., Wang, L., Thakar, J., Holden-Wiltse, J., Corbett, A., Topham, D.J., Falsey, A.R., Caserta, M.T., Walsh, E.E., 2017. Association of Dynamic Changes in the CD4 T-Cell Transcriptome With Disease Severity During Primary Respiratory Syncytial Virus Infection in Young Infants. J Infect Dis 216, 1027-1037.
25. Marsh, R.L., Kaestli, M., Chang, A.B., Binks, M.J., Pope, C.E., Hoffman, L.R., Smith-Vaughan, H.C., 2016. The microbiota in bronchoalveolar lavage from young children with chronic lung disease includes taxa present in both the oropharynx and nasopharynx. Microbiome 4, 37.
26. Mazur, N.I., Martinon-Torres, F., Baraldi, E., Fauroux, B., Greenough, A., Heikkinen, T., Manzoni, P., Mejias, A., Nair, H., Papadopoulos, N.G., Polack, F.P., Ramilo, O., Sharland, M., Stein, R., Madhi, S.A., Bont, L., Respiratory Syncytial Virus, N., 2015. Lower respiratory tract infection caused by respiratory syncytial virus: current management and new therapeutics. Lancet Respir Med 3, 888-900.
27. Mejias, A., Dimo, B., Suarez, N.M., Garcia, C., Suarez-Arrabal, M.C., Jartti, T., Blankenship, D., Jordan-Villegas, A., Ardura, M.I., Xu, Z., Banchereau, J., Chaussabel, D., Ramilo, O., 2013. Whole blood gene expression profiles to assess pathogenesis and disease severity in infants with respiratory syncytial virus infection. PLoS Med 10, e1001549.
28. Mejias, A., Ramilo, O., 2020. Respiratory syncytial virus treatment and the respiratory microbiome. Lancet Respir Med 8, 941-943.
29. Muller, W.J., Madhi, S.A., Seoane Nunez, B., Baca Cots, M., Bosheva, M., Dagan, R., Hammitt, L.L., Llapur, C.J., Novoa, J.M., Saez Llorens, X., Grenham, A., Kelly, E.J., Mankad, V.S., Shroff, M., Takas, T., Leach, A., Villafana, T., Group, M.S., 2023. Nirsevimab for Prevention of RSV in Term and Late-Preterm Infants. N Engl J Med 388, 1533-1534.
30. Poole, A., Urbanek, C., Eng, C., Schageman, J., Jacobson, S., O'Connor, B.P., Galanter, J.M., Gignoux, C.R., Roth, L.A., Kumar, R., Lutz, S., Liu, A.H., Fingerlin, T.E., Setterquist, R.A., Burchard, E.G., Rodriguez-Santana, J., Seibold, M.A., 2014. Dissecting childhood asthma with nasal transcriptomics distinguishes subphenotypes of disease. J Allergy Clin Immunol 133, 670-678 e612.
31. Ralston, S.L., Lieberthal, A.S., Meissner, H.C., 2015. Ralston SL, Lieberthal AS, Meissner HC, et al. Clinical Practice Guideline: The Diagnosis, Management, and Prevention of Bronchiolitis. Pediatrics. 2014;134(5):e1474-e1502. Pediatrics 136, 782.
32. Rohart, F., Gautier, B., Singh, A., Le Cao, K.A., 2017. mixOmics: An R package for 'omics feature selection and multiple data integration. PLoS Comput Biol 13, e1005752.
33. Rosas-Salazar, C., Chirkova, T., Gebretsadik, T., Chappell, J.D., Peebles, R.S., Jr., Dupont, W.D., Jadhao, S.J., Gergen, P.J., Anderson, L.J., Hartert, T.V., 2023. Respiratory syncytial virus infection during infancy and asthma during childhood in the USA (INSPIRE): a population-based, prospective birth cohort study. Lancet 401, 1669-1680.
34. Schroeder, A.R., Mansbach, J.M., Stevenson, M., Macias, C.G., Fisher, E.S., Barcega, B., Sullivan, A.F., Espinola, J.A., Piedra, P.A., Camargo, C.A., Jr., 2013. Apnea in children hospitalized with bronchiolitis. Pediatrics 132, e1194-1201.
35. Wei, P., Zhang, L., Hu, Q., Zhu, A., Zhuang, Z., Zhang, Z., Zhang, S., Chen, J., Xiong, X., Qu, B., Zhang, Y., Chen, L., Xu, Z., Chen, Z., Zhong, Q., Xing, X., Li, X., Gao, J., He, Y., Xie, G., Shang, J., Guo, X., Jiang, J., Shi, Y., Zhao, J., Wang, Y., Zhao, J., Jin, Y., 2026. Integrated multiplex PCR and metatranscriptomics reveal upper-lower airway microbial landscapes in pediatric respiratory infections. Virol Sin 41, 58-69.
36. Wood, D.E., Lu, J., Langmead, B., 2019. Improved metagenomic analysis with Kraken 2. Genome Biol 20, 257.
37. Wu, T., Hu, E., Xu, S., Chen, M., Guo, P., Dai, Z., Feng, T., Zhou, L., Tang, W., Zhan, L., Fu, X., Liu, S., Bo, X., Yu, G., 2021. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. Innovation (Camb) 2, 100141.
38. Yu, D., Zhang, C., Qi, Y., Liu, Z., Yang, D., Zhao, N., Ke, Z., Lu, X., Li, Y., 2025. RSV Vaccines: Targeting Prefusion F and G Proteins from Structural Design to Clinical Application. Vaccines (Basel) 13.
39. Zhao, S., Shang, Y., Yin, Y., Zou, Y., Xu, Y., Zhong, L., Zhang, H., Zhang, H., Zhao, D., Shen, T., Huang, D., Chen, Q., Yang, Q., Yang, Y., Dong, X., Li, L., Chen, Z., Liu, E., Deng, L., Jiang, W., Cheng, H., Nong, G., Wang, X., Chen, Y., Ding, R., Zhou, W., Zheng, Y., Shen, Z., Lu, X., Hao, C., Zhu, X., Jia, T., Wu, Y., Zou, G., Rito, K., Wu, J.Z., Liu, H., Ni, X., Group, A.S., 2024. Ziresovir in Hospitalized Infants with Respiratory Syncytial Virus Infection. N Engl J Med 391, 1096-1107.
40. Zivanovic, N., Oner, D., Abraham, Y., McGinley, J., Drysdale, S.B., Wildenbeest, J.G., Crabbe, M., Vanhoof, G., Thys, K., Thwaites, R.S., Robinson, H., Bont, L., Openshaw, P.J.M., Martinon-Torres, F., Investigators, R., Pollard, A.J., Aerssens, J., 2023. Single-cell immune profiling reveals markers of emergency myelopoiesis that distinguish severe from mild respiratory syncytial virus disease in infants. Clin Transl Med 13, e1507.
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Age-related pharyngeal microbiome and host transcriptomic signatures underlying fever responses in RSV bronchiolitis

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Age-related pharyngeal microbiome and host transcriptomic signatures underlying fever responses in RSV bronchiolitis

Corresponding author: Xiaoxia Lu, lusi74@163.com

Corresponding author: Di Liu, liud@wh.iov.cn

Corresponding author: Yi Yan, yanyi_1996@163.com

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