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Background <p>The continued emergence of SARS-CoV-2 variants with increased transmissibility and immunoevasive properties highlights the necessity to complement genomic surveillance with epidemiological data and laboratory-based assessment of viral phenotypes. Effective surveillance tools must be scalable, cost-efficient, and able to detect and characterize emerging variants in timely manner.</p> Methods <p>We utilized the Integrated Molecular Surveillance for SARS-CoV-2 (IMSSC2) network to conduct nationwide integrated SARS-CoV-2 genomic surveillance in Germany. SARS-CoV-2-positive samples from diagnostic laboratories were routinely subjected to whole genome sequencing. Epidemiological data from COVID-19 cases infected with BA.1, BA.2, BA.5.1, BQ.1.1, XBB.1.5, XBB.1.9.1, and XBB.1.9.2, notified between 1 December 2021 and 30 April 2023, were analyzed. Complementary, representative virus isolates were examined for immunoevasive properties and replication in human respiratory infection models.</p> Results <p>Lineage assignments of 4595 SARS-CoV-2 genomes indicate ongoing viral evolution with successive replacement of dominant variants from Delta to Omicron lineages BA.1, BA.2, BA.5.1, BQ.1, and XBB recombinants. Age-stratified epidemiological analyses show higher proportions of BA.1 and BA.2 infections in children. Multivariable logistic regression identifies male sex and increasing age as significant predictors of hospitalization. Phenotypic characterization suggests ongoing adaptation of Omicron variants BA.2, BQ.1.1, XBB.1.5, and XBB.1.9.2 to the upper human respiratory tract and enhanced propagation of XBB.1.9.2 in an alveolar infection model.</p> Conclusion <p>Integrated genomic, epidemiological and virological approaches enable early assessment of emerging SARS-CoV-2 lineages and demonstrate ongoing adaptation across the human respiratory tract. Our findings show that geographically representative, scalable surveillance provides robust insights into viral evolution, supporting sustainable surveillance beyond the acute pandemic phase.</p>

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Monitoring viral evolution and epidemiological characteristics of SARS-CoV-2 during 2022–2023 using Integrated Genomic Surveillance

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年5月26日

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  • Christin Mache,
  • Romy Kerber,
  • Jessica Schulze,
  • Marie Lataretu,
  • Susan Abunijela,
  • Yusra Seyam,
  • Sofia Paraskevopoulou,
  • Djin-Ye Oh,
  • Maximilian Arlt,
  • Aleksandar Radonić,
  • Somayyeh Sedaghatjoo,
  • Matthias Budt,
  • Ann-Sophie Lehfeld,
  • Felix Hartkopf,
  • Ralf Dürrwald,
  • Torsten Semmler,
  • Walter Haas,
  • Stephan Fuchs,
  • Stefan Kröger,
  • Thorsten Wolff,
  • Gerald von Hermanni,
  • Felix Stelter,
  • Laura Gropp,
  • Bernhard Miller,
  • Patrick Chhatwal,
  • Christina Kiel,
  • Abdullah Al Mamun,
  • Konrad A. Bode,
  • Veronika Balau,
  • Anja Kruggel,
  • Roger Grosser,
  • Aida Bajraktarevic,
  • Ralf Ignatius,
  • Juliane Flindt,
  • Ingo Neumann,
  • Manuel Haffner,
  • Jana Löbner,
  • Karsten Mydlak,
  • Andi Krumbholz,
  • Thomas Lorentz,
  • Semir Doric,
  • Thomas Müller,
  • Denise Buhlmann,
  • Beate Hermann,
  • Claudia Gerlich,
  • Andreas Gerritzen,
  • Carsten Tiemann,
  • Udo Geipel,
  • Bettina Georg,
  • Meike Voss,
  • Sandra Dehn,
  • Friedemann Tewald,
  • Patrick Finzer,
  • Lea Klar,
  • Florian Szabados,
  • Michael Erren,
  • Jerzy Roch Nofer,
  • Alexa Laubner,
  • Markus Petzold,
  • Annika Brinkmann,
  • Andreas Nitsche,
  • Christin Mache,
  • Jessica Schulze

摘要

Background

The continued emergence of SARS-CoV-2 variants with increased transmissibility and immunoevasive properties highlights the necessity to complement genomic surveillance with epidemiological data and laboratory-based assessment of viral phenotypes. Effective surveillance tools must be scalable, cost-efficient, and able to detect and characterize emerging variants in timely manner.

Methods

We utilized the Integrated Molecular Surveillance for SARS-CoV-2 (IMSSC2) network to conduct nationwide integrated SARS-CoV-2 genomic surveillance in Germany. SARS-CoV-2-positive samples from diagnostic laboratories were routinely subjected to whole genome sequencing. Epidemiological data from COVID-19 cases infected with BA.1, BA.2, BA.5.1, BQ.1.1, XBB.1.5, XBB.1.9.1, and XBB.1.9.2, notified between 1 December 2021 and 30 April 2023, were analyzed. Complementary, representative virus isolates were examined for immunoevasive properties and replication in human respiratory infection models.

Results

Lineage assignments of 4595 SARS-CoV-2 genomes indicate ongoing viral evolution with successive replacement of dominant variants from Delta to Omicron lineages BA.1, BA.2, BA.5.1, BQ.1, and XBB recombinants. Age-stratified epidemiological analyses show higher proportions of BA.1 and BA.2 infections in children. Multivariable logistic regression identifies male sex and increasing age as significant predictors of hospitalization. Phenotypic characterization suggests ongoing adaptation of Omicron variants BA.2, BQ.1.1, XBB.1.5, and XBB.1.9.2 to the upper human respiratory tract and enhanced propagation of XBB.1.9.2 in an alveolar infection model.

Conclusion

Integrated genomic, epidemiological and virological approaches enable early assessment of emerging SARS-CoV-2 lineages and demonstrate ongoing adaptation across the human respiratory tract. Our findings show that geographically representative, scalable surveillance provides robust insights into viral evolution, supporting sustainable surveillance beyond the acute pandemic phase.