Upper Respiratory Virome Signatures Reflect COVID-19 Severity and Post-Recovery Shifts

Upper Respiratory Virome Signatures Reflect COVID-19 Severity and Post-Recovery Shifts | Authorea try { document.documentElement.classList.add('js'); } catch (e) { } var _gaq = _gaq || []; _gaq.push(['_setAccount', 'G-8VDV14Y67G']); _gaq.push(['_trackPageview']); (function() { var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js'; var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); Skip to main content Preprints Collections Wiley Open Research IET Open Research Ecological Society of Japan All Collections About About Authorea FAQs Contact Us Quick Search anywhere Search for preprint articles, keywords, etc. Search Search ADVANCED SEARCH SCROLL This is a preprint and has not been peer reviewed. Data may be preliminary. 2 January 2026 V1 Latest version Share on Upper Respiratory Virome Signatures Reflect COVID-19 Severity and Post-Recovery Shifts Authors : Mudita Gosain 0000-0002-2660-7578 , Manjeet Kaur , Daizee Talukdar , Subhash Tanwar , Pradipta Jana , Sonali Porey Karmakar , Jyoti Verma , … Show All … , Susmita Bakshi , Kajal Kamboj , Priyanka Verma , Madhu Pareek , Sreevatsan Raghavan , Pallavi Kshetrapal 0000-0001-6219-5155 , Shinjini Bhatnagar , Jayanta Bhattacharya , Pramod Kumar Garg , Nitya Wadhwa , and Bhabatosh Das 0009-0001-5501-371X [email protected] Show Fewer Authors Info & Affiliations https://doi.org/10.22541/au.176734816.64501435/v1 170 views 95 downloads Contents Abstract Supplementary Material Information & Authors Metrics & Citations View Options References Figures Tables Media Share Abstract Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection profoundly impacts the upper respiratory tract, yet the dynamics of the resident virome across different stages of Coronavirus Disease 2019 (COVID-19) and recovery remain poorly understood. This study profiled virome and microbiome alterations in 143 SARS-CoV-2–positive adults, stratified by disease severity (Non-Severe, Severe, Critical), compared with 96 RT-PCR–negative controls. Nasal and oral swabs underwent targeted viral enrichment and next-generation sequencing, followed by virome profiling. The respiratory virome of SARS-CoV-2 positive individuals was dominated by SARS-CoV-2, with co-detected viruses such as Human Mastadenovirus C increasing with severity and persisting post-recovery. Alpha diversity was highest in Non-Severe cases and declined in Severe and Critical groups, indicating increasing virome disruption with disease severity. Beta diversity showed clear separation between controls and cases, and across severity levels. LEfSe identified distinct viral signatures differentiating infection status, and logistic regression of key viral taxa accurately classified Critical versus post-recovery samples (AUC = 0.91). Although the study focused on viruses, bacterial taxa including Rothia mucilaginosa and Haemophilus parahaemolyticus were also detected with severity-linked variation, highlighting viral–bacterial interactions. Longitudinal paired analysis revealed consistent post-recovery enrichment of Streptococcus-specific bacteriophages across all severity groups, suggesting restoration of Streptococcus-associated phage dynamics during convalescence. Overall, this study reveals SARS-CoV-2–associated alterations in the respiratory virome and microbiome and highlights specific microbial taxa with potential as biomarkers for disease severity and post-infection recovery. Supplementary Material File (2amsf.docx) Download 5.17 MB Information & Authors Information Version history V1 Version 1 02 January 2026 Copyright This work is licensed under a Non Exclusive No Reuse License. Keywords coronavirus pathogenesis respiratory tract sars coronavirus virus classification Authors Affiliations Mudita Gosain 0000-0002-2660-7578 Translational Health Science and Technology Institute View all articles by this author Manjeet Kaur Translational Health Science and Technology Institute View all articles by this author Daizee Talukdar Translational Health Science and Technology Institute View all articles by this author Subhash Tanwar Translational Health Science and Technology Institute View all articles by this author Pradipta Jana Translational Health Science and Technology Institute View all articles by this author Sonali Porey Karmakar Translational Health Science and Technology Institute View all articles by this author Jyoti Verma Translational Health Science and Technology Institute View all articles by this author Susmita Bakshi Translational Health Science and Technology Institute View all articles by this author Kajal Kamboj Translational Health Science and Technology Institute View all articles by this author Priyanka Verma Translational Health Science and Technology Institute View all articles by this author Madhu Pareek Translational Health Science and Technology Institute View all articles by this author Sreevatsan Raghavan Translational Health Science and Technology Institute View all articles by this author Pallavi Kshetrapal 0000-0001-6219-5155 Translational Health Science and Technology Institute View all articles by this author Shinjini Bhatnagar Translational Health Science and Technology Institute View all articles by this author Jayanta Bhattacharya Translational Health Science and Technology Institute View all articles by this author Pramod Kumar Garg All India Institute of Medical Sciences New Delhi View all articles by this author Nitya Wadhwa Translational Health Science and Technology Institute View all articles by this author Bhabatosh Das 0009-0001-5501-371X [email protected] Translational Health Science and Technology Institute View all articles by this author Metrics & Citations Metrics Article Usage 170 views 95 downloads .FvxKWukQNSOunydq8rnd { width: 100px; } Citations Download citation Mudita Gosain, Manjeet Kaur, Daizee Talukdar, et al. Upper Respiratory Virome Signatures Reflect COVID-19 Severity and Post-Recovery Shifts. Authorea . 02 January 2026. DOI: https://doi.org/10.22541/au.176734816.64501435/v1 If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download. For more information or tips please see 'Downloading to a citation manager' in the Help menu . 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