Advancing Precision Vaccinology by Molecular and Genomic Surveillance of Severe Acute Respiratory Syndrome Coronavirus 2 in Germany, 2021

作者：Djin Ye Oh, Martin Hölzer, Sofia Paraskevopoulou, Maria Trofimova, Felix Hartkopf, Matthias Budt, Marianne Wedde, Hugues Richard, Berit Haldemann, Teresa Domaszewska, Janine Reiche, Kathrin Keeren, Aleksandar Radonić, Julia Patricia Ramos Calderón, Maureen Rebecca Smith, Annika Brinkmann, Kathrin Trappe, Oliver Drechsel, Kathleen Klaper, Sascha Hein, Eberhard Hildt, Walter Haas, Sébastien Calvignac‐Spencer, Torsten Semmler, Ralf Dürrwald, Andrea Thürmer, Christian Drosten, Stephan Fuchs, Stefan Kröger, Max von Kleist, Thorsten Wolff, Barbara Biere, Konrad A. Bode, Victor M. Corman, Michael Erren, Patrick Finzer, Roger Grosser, Manuel Haffner, Beate Hermann, Christina Kiel, Andi Krumbholz, Kristian Meinck, Andreas Nitsche, Markus Petzold, Thomas Schwanz, Florian Szabados, Friedemann Tewald, Carsten Tiemann · 发表于：Clinical Infectious Diseases · 年份：2022 · DOI：10.1093/cid/ciac399 · 被引用次数：27 · 研究领域：SARS-CoV-2 and COVID-19 Research、vaccines and immunoinformatics approaches、Immune responses and vaccinations

BACKGROUND: Comprehensive pathogen genomic surveillance represents a powerful tool to complement and advance precision vaccinology. The emergence of the Alpha variant in December 2020 and the resulting efforts to track the spread of this and other severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern led to an expansion of genomic sequencing activities in Germany. METHODS: At Robert Koch Institute (RKI), the German National Institute of Public Health, we established the Integrated Molecular Surveillance for SARS-CoV-2 (IMS-SC2) network to perform SARS-CoV-2 genomic surveillance at the national scale, SARS-CoV-2-positive samples from laboratories distributed across Germany regularly undergo whole-genome sequencing at RKI. RESULTS: We report analyses of 3623 SARS-CoV-2 genomes collected between December 2020 and December 2021, of which 3282 were randomly sampled. All variants of concern were identified in the sequenced sample set, at ratios equivalent to those in the 100-fold larger German GISAID sequence dataset from the same time period. Phylogenetic analysis confirmed variant assignments. Multiple mutations of concern emerged during the observation period. To model vaccine effectiveness in vitro, we employed authentic-virus neutralization assays, confirming that both the Beta and Zeta variants are capable of immune evasion. The IMS-SC2 sequence dataset facilitated an estimate of the SARS-CoV-2 incidence based on genetic evolution rates. Together wi...