Integrated Genomic and Virological SARS-CoV-2 Surveillance in Germany 2022/23: Monitoring Viral Evolution and Epidemiological Characteristics

Integrated Genomic and Virological SARS-CoV-2 Surveillance in Germany 2022/23: Monitoring Viral Evolution and Epidemiological Characteristics | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Integrated Genomic and Virological SARS-CoV-2 Surveillance in Germany 2022/23: Monitoring Viral Evolution and Epidemiological Characteristics Thorsten Wolff, Christin Mache, Romy Kerber, Jessica Schulze, and 16 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6708651/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted You are reading this latest preprint version Abstract The continued emergence of new SARS-CoV-2 variants with increased transmissibility and immunoevasive properties highlights the necessity to complement genomic pathogen surveillance with epidemiological data and laboratory-based evaluation of virus variants. Throughout this study, we analyzed over 4,500 SARS-CoV-2 genomes gathered from a nationwide laboratory network from December 1st, 2021, to April 30th, 2023. Lineage assignments revealed ongoing dynamic viral evolution in this advanced phase of the COVID-19 pandemic with subsequent replacements of dominant variants from Delta to Omicron lineages BA.1, BA.2, BA.5.1, and BQ.1, to XBB recombinants. Case-based data analysis showed a higher incidence of BA.2 infections in children compared to other lineages within the same age groups. Furthermore, a multivariable logistic regression model identified male sex and increasing age as significant predictors of hospitalization. Evaluation of representative virus isolates in primary cell cultures suggested an ongoing adaptation to the upper human respiratory tract for Omicron BA.2, BQ.1.1, XBB.1.5, and XBB.1.9.2, as well as increased propagation of XBB.1.9.2 in an alveolar infection model. Collectively, this study underscores the public health importance of implementing strategies to assess the risk of emerging SARS-CoV-2 lineages and demonstrates ongoing intrinsic adaptation of SARS-CoV-2 variants to all compartments of the human respiratory tract. Biological sciences/Microbiology/Virology/SARS-CoV-2 Health sciences/Diseases/Infectious diseases/Viral infection SARS-CoV-2 COVID-19 genomic surveillance virus evolution epidemiology viral infection pandemic response Full Text Additional Declarations There is NO Competing Interest. Supplementary Files MacheXKerberetalsupplementarydata.pdf Supplementary Information Cite Share Download PDF Status: Under Review Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-6708651","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":461056376,"identity":"4c601b11-5d50-43a2-bf2e-da8b33a5eb04","order_by":0,"name":"Thorsten 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