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

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.