Acknowledgements
This work was funded by European Union DG Research through projects Prepare (GA602525), Compare (GA643476), and EVAg (GA653316); by European Union DG SANCO through EVD-LabNet, as well as by the German Ministry of Research through projects RAPID (01KI1723A) and DZIF (301-4-7-01.703).
We gratefully acknowledge the authors, the originating and submitting laboratories for their sequence and metadata shared through GISAID, on which this research is based. All authors of data may be contacted directly via www.gisaid.org: National Institute for Viral Disease Control and Prevention, China CDC (Wenjie Tan, Xiang Zhao, Wenling Wang, Xuejun Ma, Yongzhong Jiang, Roujian Lu, Ji Wang, Weimin Zhou, Peihua Niu, Peipei Liu,Faxian Zhan, Weifeng Shi, Baoying Huang, Jun Liu, Li Zhao, Yao Meng, Xiaozhou He, Fei Ye, Na Zhu, Yang Li, Jing Chen, Wenbo Xu, George F. Gao, Guizhen Wu); Wuhan Institute of Virology, Chinese Academy of Sciences (Peng Zhou, Xing-Lou Yang, Ding-Yu Zhang, Lei Zhang, Yan Zhu, Hao-Rui Si, Zhengli Shi); Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (Lili Ren, Jianwei Wang, Qi Jin, Zichun Xiang, Yongjun Li, Zhiqiang Wu, Chao Wu, Yiwei Liu); and National Institute for Communicable Disease Control and Prevention (ICDC), China CDC (Zhang Y-Z, Wu, F, Chen Y-M, Pei Y-Y, Xu L, Wang W, Zhao S, Yu B, Hu Y, Tao Z-W, Song Z-G, Tian J-H, Zhang Y-L, Liu Y, Zheng J-J, Dai F-H, Wang Q-M, She J-L and Zhu T-Y)
We thank Marta Zuchowski, Sigrid Kersten, and Joerg Hofmann for help with sample logistics. In vitro-transcribed control RNA for the E gene assay can be acquired from author C. D. through the European Virus Archive platform (www.european-virus-archive.com),

Conflict of interest: None declared.
Authors’ contributions: VMC: Planned and conducted experiments, conceptualised the laboratory work
OL: Planned and conducted experiments, conceptualised the laboratory work
MK: Planned and conducted experiments
RM: Planned and conducted experiments, conceptualised the laboratory work
AM: Planned and conducted experiments, conceptualised the laboratory work
DKWC: Planned and conducted experiments
TB: Planned and conducted experiments
SB: Planned and conducted experiments
JS: Planned and conducted experiments
MLS: Planned and conducted experiments
DGJCM: Planned and conducted experiments
BLH: Planned and conducted experiments
BvdV: Planned and conducted experiments
SvdB: Planned and conducted experiments
LW: Planned and conducted experiments
GG: Planned and conducted experiments
JLR: Contributed to overall study conceptualization
JE: Planned and conducted experiments, conceptualised the laboratory work
MZ: Planned laboratory work, contributed to overall study conceptualization
MP: Planned laboratory work, contributed to overall study conceptualization
HG: Contributed to overall study conceptualization
CR: Planned experiments, conceptualised the laboratory work
MPGK: Planned experiments, conceptualised the laboratory work
CD: Planned experiments, conceptualised the laboratory work, conceptualised the overall study, wrote the manuscript draft.

Supplementary Data
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