We gratefully acknowledge China National GeneBank at Shenzhen, China for the sequencing strategy and capacity support. We also gratefully acknowledge the laboratories that have contributed publicly available genomes via GISAID: The Public Health Agency of Sweden, Sweden; Public Health Ontario Laboratories, Canada; Pathogen Discovery, Respiratory Viruses Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, United States; Programme in Emerging Infectious Diseases, Duke-NUS Medical School, United State; Alaska State Virology Laboratory, United States; Respiratory Virus Unit, Microbiology Services Colindale, Public Health England, United Kingdom; Laboratory for Functional Genome Analysis, Dept. Genomics, Gene Center of the LMU Munich, Germany; Michigan Department of Health and Human Services, Bureau of Laboratories, United State; National Public Health Laboratory, National Centre for Infectious Diseases, Singapore; BGI-shenzhen & The First Affiliated Hospital of Guangzhou Medical University, China; NSW Health Pathology - Institute of Clinical Pathology and Medical Research; Westmead Hospital; University of Sydney, Australia; BCCDC Public Health Laboratory, Canada; COVID-19 Genomics UK (COG-UK) Consortium, United Kingdom; Guangdong Provincial Institution of Public Health, China; Department of Microbiology, Guangdong Provincial Center for Diseases Control and Prevention, China; Department of Health Technology and Informatics, Faculty of Health and Social Science, The Hong Kong Polytechnic University, Hong Kong; School of Public Health, The University of Hong Kong, Hong Kong; Pathogen Genomics Center, National Institute of Infectious Diseases, Japan; National Research Center for Translational Medicine (Shanghai), Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine & Shanghai Public Health Clinical Center, China; Seattle Flu Study, United States; UW Virology Lab, United States; National Institute for Viral Disease Control & Prevention, CCDC, China; Beijing Institute of Microbiology and Epidemiology, China; National Institute for Viral Disease Control and Prevention, China CDC, China; Inspection Center of Hangzhou Center for Disease Control and Prevention, China; Pathogen Genomics Lab King Abdullah University of Science and Technology (KAUST), Saudi Arabia; Chinese PLA Institute for Disease Control and Prevention, China; National Institute of Health. Department of medical Sciences, Ministry of Public Health, Thailand; Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Greece; Wellcome Sanger Institute for the COVID-19 Genomics UK Consortium, United Kingdom; State Key Laboratory of Biotherapy of Sichuan University, China; SeqCOVID-SPAIN consortium/IBV(CSIC), Spain; Oxford University Clinical Research Unit, Hanoi, Vietnam; Institute of Environmental Science and Research (ESR), New Zealand; Erasmus Medical Center, Netherlands.