Description
The dynamics of the COVID-19 pandemic have exhibited different patterns over the course of the first two years. In Germany, early outbreaks that facilitated onward spread in the country were followed by seasonal waves of infection, caused by environmental and behavioural changes. After the introduction of different SARS-CoV-2 variants of concern (VOC), these temporal infection profiles were extended by variant replacement patterns with successive waves caused by Alpha, Delta and Omicron. To track the evolution of SARS-CoV-2 and thus the emergence of new variants, systematic viral genome sequencing was implemented nationally. However, these genomes also hold valuable information on the transmission history of the virus. To extract this information in a phylodynamic birth-death-sampling framework, we use publicly available sequence data and quantify the transmission dynamics of SARS-CoV-2 in Germany during these different time periods. Starting in early 2020, we date the most recent common ancestor of one of the earliest outbreaks in the country, revealing traces of an initial superspreading event quantified through a change in the inferred reproductive number. Continuing in 2021, we infer a longer temporal profile of the reproductive number of SARS-CoV-2 in parts of Bavaria. This highlights the local impact of interventions and seasons on the reproductive number. From SARS-CoV-2 genomes sampled in Berlin in December 2021 we finally estimate the relative increase in the transmission rate of the Omicron compared to the Delta variant in the area, evincing a lower Omicron transmission advantage than in the global context. Taken together, these results provide further insights into and quantifications of the transmission as well as evolutionary dynamics of SARS-CoV-2 over the course of the pandemic in Germany, relying only on genomic sequences and their sampling dates as data source.
