key: cord-1035356-o9o199o0 authors: Yi, Buqing; Poetsch, Anna R.; Stadtmüller, Marlena; Rost, Fabian; Winkler, Sylke; Dalpke, Alexander H. title: Phylogenetic analysis of SARS-CoV-2 lineage development across the first and second waves in Eastern Germany, 2020 date: 2021-05-14 journal: bioRxiv DOI: 10.1101/2021.04.29.441906 sha: 2add1e4847caff1097e6dc6b8b534353db79540c doc_id: 1035356 cord_uid: o9o199o0 SARS-CoV-2 lineages prevalent in the first and second waves in Eastern Germany were different, with many new variants including four predominant lineages in the second wave, having been introduced into Eastern Germany between August to October 2020, indicating the major cause of the second wave was the introduction of new variants. SARS-CoV-2 lineages prevalent in the first and second waves in Eastern Germany were different, with many new variants including four predominant lineages in the second wave, having been introduced into Eastern Germany between August to October 2020, indicating the major cause of the second wave was the introduction of new variants. In Germany, the first wave of the coronavirus disease (COVID-19) pandemic (March to May, 2020) showed visible regional differences: it was much milder in Eastern regions (Saxony, Saxony-Anhalt, Berlin, Brandenburg and Thuringia) compared to most other regions in Germany. However, the severity of the second wave (August to December, 2020) was similar in most regions in Germany. It is unclear how the second wave started in Eastern Germany where in June and July 2020 the number of COVID-19 cases was close to zero (Fig. 1A) . We therefore performed phylogenetic analysis of the predominant SARS-CoV-2 variants in the first and second waves in Eastern Germany. By dissecting the difference between the first wave and the second wave, we expect the information achieved through this study could provide insights into the cause of the second wave and can possibly help developing suitable strategies for preventing similar scenarios in future. For surveillance purpose, randomly selected SARS-CoV-2 positive samples from each state in Germany were sequenced by the Robert Koch Institute or by sequencing facilities of local universities. All sequences that passed stringent quality control were uploaded to GISAID (1). We used GISAID sequences from regions in Eastern Germany dating between March to December 2020 in this study (data collected on Feb. 28, 2021; Table S1 ). The number of genomes in each and time trees were constructed using the SARS-CoV-2-specific procedures taken from github.com/nextstrain/ncov (3, 4) . The first wave in Eastern Germany reached its peak in April 2020 (Fig. 1A) . Based on the frequency of detection in April (Fig. 1C&D) (Fig. 1C&D) . From August till October 2020 was the summer/autumn holiday season in Eastern Germany, and a lot of regional and international travelling took place during this period. Our analysis indicates that many new lineages were introduced into Eastern Germany from August to October 2020 (Fig. 1B&C ). For example, in August, 20 new lineages were first detected in Eastern Germany, such as (5), which means the chances of the introduction of these lineages were higher than other variants. In addition, travelling within Germany might also play a role here since no tests were required for regional travelers. In conclusion, the introduction of various SARS-CoV-2 lineages from August to October 2020 was the major driving force for the development of the second wave in Eastern Germany regions, instead of expansion of local circulating lineages from the first wave. Global initiative on sharing all influenza data -from vision to reality A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology TreeTime: Maximum-likelihood phylodynamic analysis Nextstrain: real-time tracking of pathogen evolution Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020 numbers in each month. C. Frequency of detection for each SARS-CoV-2 lineage in each month in Eastern Germany (range: 0 ~ 0.74, representing 0% ~ 74%; 0 is shown with deep blue, indicating no detection of the relevant variant in that month). Note: to achieve a better resolution, a few lineages that were detected only once across 2020 and with a frequency < 0.01 were omitted from the heatmap. D. Phylogenetic and time tree of SARS-CoV-2 genomes from Eastern Germany, March to December 2020. Each genome is denoted with Pangolin-lineage (PANGO Lineage). The names of lineages that were predominant in the first or second wave are colour labelled. The four lineages from the second wave B.1.177, B.1.258, B. 1.221 and B.1.160 had been circulating in multiple other European countries since June (5). We thank all researchers who are working around the clock to generate and share genome data on GISAID (http://www.gisaid.org) on which the analysis is based. We specifically thank colleagues at the Institute of Medical Microbiology and Virology, Technische Universität Dresden, for their work in performing SARS-CoV-2 sample testing and sequencing sample preparing, and we thank the Robert Koch Institute and Dresden Concept Genome Center for their sequencing efforts.