Table S1. an Excel File Containing Detailed Information About the Sequences of SARS Cov-2 Strains and Acknowledgement Used in This Study

Table S1. An excel file containing detailed information about the sequences of SARS CoV-2 strains and acknowledgement used in this study. We have used data till 2 May 2020. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GISAID's EpiFlu Database (www.gisaid.org) on which this research is based. The list is detailed in this Table S1. Ref. ID Accession ID Databases Location Virus name Collection date Originating Lab Submitting Lab Authors Division of Viral Diseases, Center for Division of Viral Diseases, Center for Jeong-Min Kim, Yoon-Seok Chung, Namjoo Laboratory Control of Infectious Laboratory Control of Infectious Lee, Mi-Seon Kim, Sang Hee Woo, Hye-Jun hCoV-19/South Diseases, Korea Centers for Diseases Diseases, Korea Centers for Diseases Jo, Sehee Park, Heui Man Kim, Myung Guk 1 EPI_ISL_412869 GISAID Asia / South Korea /Seoul Korea/KCDC05/2020 2020-01-30 Control and Prevention Control and Prevention Han Bin Fang, Xiang Li, Xiao Yu, Linlin Liu, Bo Yang, Faxian Zhan, Guojun Ye, Xixiang Huo, Junqiang Xu, Bo Yu, Kun Cai, Jing Li, hCoV-19/Tianmen/HBCDC- Tianmen Center for Disease Control and Hubei Provincial Center for Disease YiFa Zhu, Yangyang Tao,Xierong 2 EPI_ISL_412983 GISAID Asia / China / Hubei / Tianmen HB-07/2020 2020-02-08 Prevention Control and Prevention Li,Yongzhong Jiang.

Andrés E. Castillo, Bárbara Parra, Paz Tapia, Alejandra Acevedo, Jaime Lagos, Winston Andrade, Loredana Arata, Gabriel Leal, Gisselle Barra, Carolina Tambley, hCoV-19/Chile/Talca- Javier Tognarelli, Patricia Bustos, Soledad 3 EPI_ISL_414578 GISAID South America / Chile / Talca 2/2020 2020-03-04 Hospital de Talca, Chile Instituto de Salud Publica de Chile Ulloa, Rodrigo Fasce, Jorge Fernández. Oleg V. Pyankov, Sergey A. Bodnev, State Research Center of Virology and State Research Center of Virology and Tatyana V. Tregubchak, Alexander N. Europe / Russia / Republic of hCoV-19/Russia/Kabardino- Biotechnology VECTOR, Department of Biotechnology VECTOR, Department of Shvalov, Elena V. Gavrilova, Rinat A. 4 EPI_ISL_428893 GISAID Kabardino-Balkaria Balkaria-80501/2020 2020-03-23 Collection of Microorganisms Collection of Microorganisms Maksyutov hCoV- Chinese PLA Institute for Disease Chinese PLA Institute for Disease 5 EPI_ISL_430724 GISAID Asia / China / Beijing 19/Beijing/BJ752/2020 2020-02-08 Control and Prevention Control and Prevention Peng Li，Jinhui Li, Lizhong Li hCoV-19/Japan/UT- University of Wisconsin - Madison: University of Wisconsin Madison, AIDS Katarina Braun, Gage Moreno, Peter 6 EPI_ISL_418809 GISAID Asia / Japan / Tokyo NCGM02/2020 2020-02-01 Influenza Research Institute Vaccine Research Laboratories Halfmann, et al.

National Research Center for Translational Medicine (Shanghai), Shanghai Public Health Clinical Center, Ruijin Hospital affiliated to Shanghai Jiao Shengyue Wang, Xiaonan Zhang, Gang Lu, hCoV- Shanghai Medical College, Fudan Tong University School of Medicine & Yun Tan, Yun Ling, Hongzhou Lu, Saijuan 7 EPI_ISL_416333 GISAID Asia / China / Shanghai 19/Shanghai/SH0024/2020 2020-01-30 University Shanghai Public Health Clinical Center Chen Paola Resende, Fernando Motta, Luciana Appolinario, Sunando Roy, Aline Mattos, Instituto Oswaldo Cruz FIOCRUZ - Instituto Oswaldo Cruz FIOCRUZ - Milene Miranda, Cristiana Garcia, Braulia South America / Brazil / Rio de hCoV-19/Brazil/RJ- Laboratory of Respiratory Viruses and Laboratory of Respiratory Viruses and Caetano, Maria Ogrzewalska, Priscila Born, 8 EPI_ISL_427299 GISAID Janeiro / Niteroi 352/2020 2020-03-05 Measles (LVRS) Measles (LVRS) Jonathan Lopes, Marilda Siqueira Neris Garcia-Gonzalez, Inma Galán Vendrell, Sandra Carbo, Loreto Ferrús Abad, Paula Ruiz-Hueso, Mariana Reyes- Prieto, Vicente Soriano Chirona, Ivan Ansari, David Navarro, Maria Alma Bracho, Griselda De Marco, Beatriz Beamud, Lidia Servicio de Microbiología. Consorcio Sequencing and Bioinformatics Service Ruiz Roldan, Marta Pla Diaz, Llúcia Europe / Spain / Comunitat hCoV- Hospital General Universitario de and Molecular Epidemiology Research Martínez-Priego, Giuseppe D'Auria, 9 EPI_ISL_425219 GISAID Valenciana / Valencia 19/Spain/Valencia95/2020 2020-03-17 Valencia Group. FISABIO-Public Health Fernando Gonzalez-Candelas Ye Sheng, Tang Yun, Ling Hua,Yu Asia / China / Chongqinq / hCoV- Yongchuan District Center for Disease Chongqing Municipal Center for Disease zhen,Chen Shuang,Tan ZhangPing, Su 10 EPI_ISL_408478 GISAID Yongchuan 19/Chongqing/YC01/2020 2020-01-21 Control and Prevention Control and Prevention Kun, Li Qing, Tang Wenge, Rong Rong Fujian Center for Disease Control and Fujian Center for Disease Control and Chen Wei, Zhang Yanhua, He Wenxiang, 11 EPI_ISL_411060 GISAID Asia / China / Fujian hCoV-19/Fujian/8/2020 2020-01-21 Prevention Prevention Weng Yuwei Harrigan, Prystajecky, Krajden, Lee, hCoV- Kamelian, Lapointe, Choi, Hoang, Sekirov, North America / Canada / 19/Canada/BC_4799711/20 Levett, Tyson, Snutch, Loman, Quick, Li, 12 EPI_ISL_418830 GISAID British Columbia 20 2020-03-09 BCCDC Public Health Laboratory BCCDC Public Health Laboratory Gilmour hCoV-19/USA/UT- 13 EPI_ISL_417964 GISAID North America / USA / Utah 00014/2020 2020-03-13 Utah Public Health Laboratory Utah Public Health Laboratory Erin Young, Kelly Oakeson Anna Majer, Shari Tyson, Grace Seo, Kristyn Burak, Philip Mabon, Elsie Grudeski, Rhiannon Huzarewich, Russell Mandes, Jennifer Tanner, Natalie Knox, Morag Graham, Gary Van Domselaar, Robert Needle, Yang Yu, Adel Malek, Laura Gilbert, George Zahariadis, Nathalie hCoV- Bastien, Yan Li, Timothy Booth, Matthew 14 EPI_ISL_429815 GISAID North America / Canada / NL 19/Canada/NL_34/2020 2020-03-15 Public Health Laboratory National Microbiology Laboratory Gilmour Bixing Huang, Alyssa Pyke, Amanda De Jong, Andrew Van Den Hurk, Carmel Taylor, David Warrilow, Doris Genge, Elisabeth Gamez, Glen Hewitson, Ian Maxwell Mackay, Inga Sultana, Jamie McMahon, Jean Barcelon, Judy Northill, Mitchell Finger, Natalie Simpson, Neelima Nair, Peter Burtonclay, Peter Moore, Sarah hCoV- Wheatley, Sean Moody, Sonja Hall- Oceania / Australia / 19/Australia/QLDID931/202 Mendelin, Timothy Gardam, and Frederick 15 EPI_ISL_420879 GISAID Queensland / Brisbane 0 2020-03-25 Mater Pathology Public Health Virology Laboratory Moore

Guillermo M. Ruiz-Palacios, Pilar Ramos Cervantes, Violeta Ibarra Gonzalez, Fernando Ledesma Barrientos, Luis Alberto García Andrade, Alfredo Ponce de León Garduño, Irma López Martínez, Lucia Hernández Rivas, Gisela Barrera Badillo, Edgar Mendieta Condado, Fabiola Garcés Ayala, Adnan Araiza Rodríguez, José Ernesto Ramírez González, Celia Boukadida, Santiago Avila Ríos, Mario Mújica Sánchez, José Arturo Martínez Orozco, Eduardo Becerril Vargas, Joel Armando Vázquez Pérez, Victor Hugo Borja Aburto, Concepción Grajales Muñiz, Cesar Raúl González Bonilla, Carolina González Torres, Francisco Javier Gaytán Cervantes, José Esteban Muñoz Medina, Blanca Taboada, Alejandro Sánchez, Pavel Isa, North America / Mexico / hCoV-19/Mexico/CDMX- Instituto Nacional de Ciencias Medicas Instituto Nacional de Ciencias Medicas y Ricardo Grande, Gloria Vázquez, Francisco 16 EPI_ISL_426361 GISAID Mexico City INCMNSZ_01/2020 2020-03-12 y Nutricion Salvador Zubiran Nutricion Salvador Zubiran Pulido, Carlos F. Arias North America / USA / hCoV-19/USA/WA-UW- Pavitra Roychoudhury, Hong Xie, Keith 17 EPI_ISL_430918 GISAID Washington 5750/2020 2020-04-06 UW Virology Lab UW Virology Lab Jerome, Alexander Greninger Wenjie Tan，Xiaoqing Fu，Xiang Zhao，Wenling Wang， Peihua Niu，Roujian Lu,Yanhong Sun，Baoying hCoV-19/Yunnan/IVDC- National Institute for Viral Disease National Institute for Viral Disease Huang，Li Zhao，Fei Ye，Wenbo 18 EPI_ISL_408480 GISAID Asia / China / Yunnan / Kunming YN-003/2020 2020-01-17 Control and Prevention, China CDC Control & Prevention, CCDC Xu，George F. Gao，Guizhen Wu

Ying Tao, Krista Queen, Clinton R. Paden, Jing Zhang, Yan Li, Anna Uehara, Xiaoyan Pathogen Discovery, Respiratory Lu, Brian Lynch, Senthil Kumar K. Viruses Branch, Division of Viral Sakthivel, Brett L. Whitaker, Shifaq Kamili, North America / USA / Illinois / IL Department of Public Health Chicago Diseases, Centers for Dieases Control Lijuan Wang, Janna' R. Murray, Susan I. 19 EPI_ISL_404253 GISAID Chicago hCoV-19/USA/IL1/2020 2020-01-21 Laboratory and Prevention Gerber, Stephen Lindstrom, Suxiang Tong

Wenjie Tan, Jianan Xu, Wenling Wang, Peihua Niu, Roujian Lu, Huiping Yang, Asia / China / Sichuan / hCoV-19/Sichuan/IVDC- National Institute for Viral Disease National Institute for Viral Disease Xiang Zhao, Baoying Huang, Li Zhao, Fei 20 EPI_ISL_408484 GISAID Chengdu SC-001/2020 2020-01-15 Control and Prevention, China CDC Control & Prevention, CCDC Ye, Wenbo Xu, George F. Gao, Guizhen Wu Yan Li, Krista Queen, Clinton R. Paden, Pathogen Discovery, Respiratory Rachel Marine, Anna Uehara, Ying Tao, Viruses Branch, Division of Viral Jing Zhang, Haibin Wang, Mary S. Keckler, North America / USA / South hCoV- SC Dept of Health and Env. Control- Diseases, Centers for Disease Control Alison S. Laufer Halpin, Christopher A. 21 EPI_ISL_424842 GISAID Carolina 19/USA/SC_3575/2020 2020-03-07 Bureau of Laboratories and Prevention Elkins, Suxiang Tong Elbadry,M.A.; Subramaniam,K.; Lednicky Laboratory, Emerging Waltzek,T.B.; Gibson,J.C.; Pathogens Institute, University of Lednicky Laboratory, Emerging Stephenson,C.J.; Morris,J.G. Jr. and 22 EPI_ISL_434637 GISAID North America / USA / Florida hCoV-19/USA/UF-2/2020 2020-03-27 Florida. Pathogens Institute, University of Florida. Lednicky,J.A. Carlo M. Lapid, Francis A. Tablizo, Benedict A. Maralit, Jan Michael C. Yap, Raul V. Destura, Marissa M. Alejandria, El King D. Morado, Joshua Gregor A. Dizon, Jo- Hannah S. Llames, Shiela Mae M. Araiza, Kris P. Punayan, Kristianne Arielle D. Gabriel, Shebna Rose D. Fabilloren, Shana F. Genavia, Jarvin E. Nipales, Alessandra C. Sanchez, Haifa L.Gaza, Joy Ann Petronio-Santos, Julius Aaron Mejia, Maribell Dollete, Sonia Salamat, Christina hCoV- Tan, Bernard Demot, John Mark Velasco, 19/Philippines/PGC003/202 National Institutes of Health, University Eva Maria Cutiongco-de la Paz, and Cynthia 23 EPI_ISL_434555 GISAID Asia / Philippines / Manila 0 2020-03-26 of the Philippines Manila Philippine Genome Center P. Saloma

hCoV-19/Saudi Infectious Disease Research Majed Alghoribi, Sadeem Alhayli, Arabia/KAIMRC- Department, King Abdullah International Abdulrahman Alswaji, Liliane Okdah, 24 EPI_ISL_416432 GISAID Asia / Saudi Arabia / Riyadh Alghoribi/2020 2020-03-07 Clinical Microbiology Lab Medical Research Center (KAIMRC) Sameera Al Johani, Michel Doumith Paola Resende, Fernando Motta, Luciana Appolinario, Sunando Roy, Aline Mattos, Instituto Oswaldo Cruz FIOCRUZ - Milene Miranda, Cristiana Garcia, Braulia South America / Brazil / Santa hCoV-19/Brazil/SC- LACEN-SC - Laboratorio Central de Laboratory of Respiratory Viruses and Caetano, Maria Ogrzewalska, Priscila Born, 25 EPI_ISL_427305 GISAID Catarina / Joinville 766/2020 2020-03-10 Santa Catarina Measles (LVRS) Jonathan Lopes, Marilda Siqueira Inbar Cohen-Gihon, Ofir Israeli, Ohad Shifman, Dana Stein, Sharon Melamed, Nir Paran, Tomer Israely, Hagit Achdout, Yfat Yahalom Ronen, Hadas Tamir, Boaz Politi, Lilach Cherry, Einat Vitner, Orly Laskar, Shay Weiss, Michal Mandelboim, Oran Erster, Gili Regev-Yochay, Gadi Segal, hCoV- Shmuel Yitzhaki, Shmuel C. Shapira, Adi 26 EPI_ISL_419211 GISAID Asia / Israel / Ramat Gan 19/Israel/ISR_JP0320/2020 2020-02-23 Central Virology Laboratory Israel Institute for Biological Research Beth-Din, Anat Zvi Pathogen Discovery, Respiratory Anna Uehara, Ying Tao, Jing Zhang, Krista Viruses Branch, Division of Viral Queen, Clinton R. Paden, Yan Li, Haibin hCoV- Texas Department of State Health Diseases, Centers for Disease Control Wang, Jasmine Padilla, Justin Lee, Suxiang 27 EPI_ISL_419561 GISAID North America / USA / Texas 19/USA/TX_2020/2020 2020-02-29 Services Lab Services and Prevention Tong Microbiological Diagnostic Unit Public Health Laboratory and Victorian Infectious Diseases Reference hCoV- Victorian Infectious Diseases Reference Laboratory, The Peter Doherty Institute Caly L., Seemann T., Sait, M., Schultz M., 28 EPI_ISL_430689 GISAID Oceania / Australia / Victoria 19/Australia/VIC1315/2020 2020-04-11 Laboratory (VIDRL) for Infection and Immunity Druce J., Sherry, N. Fahd Al-Mulla, Sumi John, Rasheeba Iqbal, hCoV- Motasem Melhem, Ebaa AlOzairi, Sara Al- 29 EPI_ISL_416542 GISAID Asia / Kuwait / Dasman 19/Kuwait/KU17/2020 2020-03-02 Dasman Diabetes Institute Dasman Diabetes Institute Qabandi, Qais Al-Duwairi Shaikh Terkis Islam Pavel, Hazel Yetiskin, Gunsu Aydin, Can Holyavkin, Muhammet hCoV-19/Turkey/ERAGEM- Vaccine Research, Development and Ali Uygut, Zehra B Dursun, İlhami Celik, 30 EPI_ISL_424366 GISAID Europe / Turkey / Kayseri 001/2020 2020-03-17 Application Center, Erciyes University Gen Era Diagnostics Inc. Alper Iseri, Aykut Ozdarendeli

Chandima Jeewandara, Dinuka Ariyaratne, Laksiri Gomes, Deshni Jayathilaka, Ananda hCoV-19/Sri Wijewickrama, Eranga Narangoda, 31 EPI_ISL_428670 GISAID Asia / Sri Lanka Lanka/COV38/2020 2020-03-16 Centre for Dengue Research Centre for Dengue Research Damayanthi Idampitiya, Neelika Malaige Wenjie Tan, Zhaoguo Wang, Xiang Zhao, Wenling Wang, Peihua Niu, Roujian Lu, Ti Asia / China / Shandong / hCoV-19/Shandong/IVDC- National Institute for Viral Disease National Institute for Viral Disease Liu, Baoying Huang, Li Zhao, Fei Ye, 32 EPI_ISL_408482 GISAID Qingdao SD-001/2020 2020-01-19 Control and Prevention, China CDC Control & Prevention, CCDC Wenbo Xu, George F. Gao, Guizhen Wu

Kenneth Siu-Sing LEUNG, Timothy Ting- Leung NG, Alan Ka-Lun WU, Miranda Chong-Yee YAU, Hiu-Yin LAO, Ming-Pan CHOI, Kingsley King-Gee TAM, Lam- Kwong LEE, Barry Kin-Chung WONG, Alex Yat-Man HO, Kam-Tong Yip, Kwok-Cheung LUNG, Raymond Wai-To LIU, Eugene Yuk- Keung TSO, Wai-Shing LEUNG, Man-Chun CHAN, Yuk-Yung NG, Kit-Man SIN, Kitty Department of Health Technology and Sau-Chun FUNG, Sandy Ka-Yee CHAU, Department of Clinical Pathology, Informatics, Faculty of Health and Social Wing-Kin TO, Tak-Lun Que, David Ho- hCoV-19/Hong Pamela Youde Nethersole Eastern Science, The Hong Kong Polytechnic Keung SHUM, Shea Ping YIP, Wing 33 EPI_ISL_417193 GISAID Asia / Hong Kong Kong/HKPU32_0402/2020 2020-02-09 Hospital University Cheong YAM, Gilman Kit-Hang SIU JianXiong Li,Ying Xiong,Tian Gong,Yong Shi,Jun Zhou,Fang Xiao,ShiWen Jiangxi Province Center for Disease Jiangxi Province Center for Disease Liu,XiaoQing Liu,Gang Xu,DaJin Xiao,Xin 34 EPI_ISL_421256 GISAID Asia / China / Jiangxi / Jian hCoV-19/Jian/JX169/2020 2020-01-27 Control and Prevention Control and Prevention Ran,YanNi Zhang Guangdong Provincial Center for Bosheng Li, Haogao Gu, Lijun Liang, hCoV- Diseases Control and Zhencui Li, Hui-Ling Yen, Yao Hu, Yingchao Asia / China / Guangdong / 19/Guangdong/20SF753/20 Prevention;Guangdong Provincial School of Public Health, The University Song , Hanri Zeng, Tie Song, Jie Wu, Leo 35 EPI_ISL_428472 GISAID Zhuhai 20 2020-01-28 Institute of Public Health of Hong Kong L.M. Poon

Nato Kotaria, Marine Murtskhvaladze, Ann Machablishvili, Lela Sabadze, Mari Gavashelidze, Ana Papkiauri, Meri Pantsulaia, Gvantsa Brachveli, Tata Imnadze, Tamar Jashiashvili, Tea Tevdoradze, Ketevan Sidamonidze, Ekaterine Khmaladze, Ekaterine Zhghenti, Roena Sukhiashvili, Mariam Zakalashvili, Lela Urushadze, Magda Dgebuadze, Giorgi Tomashvili, Davit Tsaguria, Ekaterine Zangaladze, Nino Berishvili, Gvantsa R. G. Lugar Center for Public Health R. G. Lugar Center for Public Health Chanturia, Adam Kotorashvili, Maia Research, National Center for Disease Research, National Center for Disease Alkhazashvili, Irma Burjanadze, Anna hCoV-19/Georgia/Tb- Control and Public Health (NCDC) of Control and Public Health (NCDC) of Kasradze, Khatuna Zakhashvili, Paata 36 EPI_ISL_415643 GISAID Asia / Georgia / Tbilisi 468/2020 2020-03-10 Georgia. Georgia. Imnadze, Amiran Gamkrelidze. hCoV- 19/Portugal/IGC00009/202 Hospital Prof. Doutor Fernando João Costa, Cathy Paulino, Joao Sobral, 37 EPI_ISL_419386 GISAID Europe / Portugal / Lisbon 0 2020-03-18 Fonseca, EPE Instituto Gulbenkian de Ciência Susana Ladeiro, Ricardo Leite

Paola Resende, Allison Fabri, Joilson Xavier, Sunando Roy, Fernando Motta, Aline Mattos, Milene Miranda, Cristiana Instituto Oswaldo Cruz FIOCRUZ - Garcia, Braulia Caetano, Maria South America / Brazil / Espirito hCoV-19/Brazil/ES- LACEN/ES - Laboratório Central de Laboratory of Respiratory Viruses and Ogrzewalska, Jonathan Lopes, Luciana 38 EPI_ISL_415128 GISAID Santo / Vila Velha 225/2020 2020-02-29 Saúde Pública do Espírito Santo Measles (LVRS) Appolinario, Maria Nóbrega, Marilda Siqueira Yan Li, Krista Queen, Clinton R. Paden, Pathogen Discovery, Respiratory Rachel Marine, Anna Uehara, Ying Tao, Viruses Branch, Division of Viral Jing Zhang, Haibin Wang, Mary S. Keckler, hCoV- NV-Southern Nevada Public Health Diseases, Centers for Disease Control Alison S. Laufer Halpin, Christopher A. 39 EPI_ISL_424879 GISAID North America / USA / Nevada 19/USA/NV_0052/2020 2020-03-09 Laboratory and Prevention Elkins, Suxiang Tong Krista Queen, Yan Li, Ying Tao, Jing Zhang, Anne Uehara, Clinton R. Paden, Haibin Pathogen Discovery, Respiratory Wang, Rachel Marine, Mary S. Keckler, Viruses Branch, Division of Viral Alison S. Laufer Halpin, Jasmine Padilla, hCoV- Oregon State Public Health- Virology Diseases, Centers for Disease Control Justin Lee, Christopher A. Elkins, Suxiang 40 EPI_ISL_420794 GISAID North America / USA / Oregon 19/USA/OR_5430/2020 2020-03-01 section and Prevention Tong Institute of Microbiology and Institute of Microbiology and Tomaž Mark Zorec, Samo Zakotnik, Lucijan Immunology, Faculty of Medicine, Immunology, Faculty of Medicine, Skubic, Miša Korva, Tatjana Avšič - 41 EPI_ISL_420541 GISAID Europe / Slovenia hCoV-19/Slovenia/808/2020 2020-03-05 University of Ljubljana University of Ljubljana Županc, Mario Poljak

Jaqueline Goes de Jesus, Claudio Tavares Sacchi, Fabiana Cristina Pereira dos Santos, Ingra Morales Claro, Flávia Cristina da Silva Sales, Claudia Regina Gonçalves, Joshua Quick, Maria do Carmo Sampaio Tavares Timenetsky, Nicholas James South America / Brazil / Sao hCoV-19/Brazil/SPBR- Instituto Adolfo Lutz, Interdisciplinary Loman, Andrew Rambaut, Ester Cerdeira 42 EPI_ISL_413016 GISAID Paulo / Sao Paulo 02/2020 2020-02-28 Hospital Israelita Albert Einstein Procedures Center, Strategic Laboratory Sabino, Nuno Rodrigues Faria North America / USA / Alaska / hCoV-19/USA/AK- 43 EPI_ISL_431016 GISAID Ketchikan PHL016/2020 2020-03-18 Alaska State Virology Laboratory Alaska State Virology Laboratory Jack Chen, Ph.D. Ortwin Adams, Marcel Andree, Alexander Dilthey, Torsten Feldt, Sandra Hauka, Torsten Houwaart, Björn-Erik Jensen, Detlef Kindgen-Milles, Malte Kohns Europe / Germany / North Center of Medical Microbiology, Center of Medical Microbiology, Vasconcelos, Klaus Pfeffer, Tina Senff, Rhine Westphalia / Heinsberg hCoV-19/Germany/NRW- Virology, and Hospital Hygiene, Virology, and Hospital Hygiene, Daniel Strelow, Jörg Timm, Andreas 44 EPI_ISL_414499 GISAID District 04/2020 2020-02-26 University of Duesseldorf University of Duesseldorf Walker, Tobias Wienemann Aleksandra Milewska, Ewelina Pośpiech, Agata Jarosz, Adrianna Klajmon, Kamila Marszałek, Katarzyna Pancer, Magdalena ViroGenetics - BSL3 Laboratory of ViroGenetics - BSL3 Laboratory of Rzeczkowska, Tomasz Wołkowicz, Virology; Human Genome Variation Virology; Human Genome Variation Katarzyna Zacharczuk, Agnieszka Research Group & Genomics Centre Research Group & Genomics Centre Kołakowska-Kulesza, Natalia Wolaniuk, hCoV- MCB; Bioinformatics Research Group MCB; Bioinformatics Research Group Ewelina Hallman-Szelińska, Paweł P Łabaj, 45 EPI_ISL_416488 GISAID Europe / Poland / Zielonogorskie 19/Poland/PL_P1/2020 2020-03-03 Department of Virology Department of Virology Wojciech Branicki, Krzysztof Pyrć Claudio Tavares Sacchi, Claudia Regina Gonçalves, Carlos Henrique Camargo, Erica Valessa Ramos Gomes, Fabiana Cristina Pereira dos Santos, Daniela Bernardes Borges da Silva, Simone Guadagnucci Morillo, Adriano Abbud, Adriana Bugno, Maria do Carmo Sampaio South America / Brazil / Sao hCoV-19/Brazil/SPBR- Instituto Adolfo Lutz, Interdiciplinary Tavares Timenetsky, Terezinha Maria de 46 EPI_ISL_416033 GISAID Paulo / Sao Paulo 11/2020 2020-03-03 Hospital Israelita Albert Einstein Procedures Center, Strategic Laboratory Paiva Yan Li, Krista Queen, Clinton R. Paden, Pathogen Discovery, Respiratory Rachel Marine, Anna Uehara, Ying Tao, Viruses Branch, Division of Viral Jing Zhang, Haibin Wang, Mary S. Keckler, hCoV- Diseases, Centers for Disease Control Alison S. Laufer Halpin, Christopher A. 47 EPI_ISL_424874 GISAID North America / USA / Nebraska 19/USA/NE_6605/2020 2020-03-05 NE Public Health Laboratory and Prevention Elkins, Suxiang Tong

Asia / China / Zhejiang / hCoV- Hangzhou Center for Disease Control Inspection Center of Hangzhou Center Yu hua, Wang haoqiu, Li jun, Yu xinfeng, 48 EPI_ISL_418509 GISAID Hangzhou 19/Hangzhou/HZ178/2020 2020-01-23 and Prevention for Disease Control and Prevention Pan jingcao National Institute for Communicable National Institute for Communicable Allam M, Kwenda S, van Heusden P, hCoV-19/South Diseases of the National Health Diseases of the National Health Khumalo Z, Mohale T, Subramoney K, von 49 EPI_ISL_430297 GISAID Africa / South Africa / GP Africa/R02827-20/2020 2020-03-06 Laboratory Service Laboratory Service Gottberg, A, Ismail A, Bhiman JN Wu,F., Zhao,S., Yu,B., Chen,Y.-M., Wang,W., Hu,Y., Song,Z.-G., Tao,Z.-W., Asia / China / Hubei / 2019-12-30 Wuhan Jinyintan Hospital Hubei Provincial Center for Disease ControlTian,J.-H., and Prevention Pei,Y.-Y., Yuan,M.L., Zhang,Y.- Wuhan L., Dai,F.-H., Liu,Y., Wang,Q.-M., Zheng,J.- J., Xu,L., Holmes,E.C. and Zhang,Y.-Z 50 NC 045512.2 GenBank Wuhan Changtai Wang, Zhongping Liua, Zixiang Second Hospital of Anhui Medical Second Hospital of Anhui Medical Chen, Xin Huang, Mengyuan Xua, Tengfei 51 EPI_ISL_412026 GISAID Asia / China / Anhui / Hefei hCoV-19/Hefei/2/2020 2020-02-23 University University He, Mengji Lu, Zhenhua Zhang NHC Key laboratory of Enteric Lunbiao Cui,Kangchen Zhao,Xiaojuan hCoV- Pathogenic Microbiology, Institute of Jiangsu Provincial Center for Disease Zhu,Yiyue Ge,Tao Wu,Bin Wu,Yin 52 EPI_ISL_411950 GISAID Asia / China / Jiangsu 19/Jiangsu/JS01/2020 2020-01-23 Pathogenic Microbiology Control & Prevention Chen,Fengcai Zhu,Baoli Zhu,Ming Wu

Krista Queen, Anna Uehara, Jing Zhang, Yan Li, Ying Tao, Clinton R. Paden, Haibin Wang, Shifaq Kamili, Xiaoyan Lu, Brian Pathogen Discovery, Respiratory Lynch, Senthil Kumar K. Sakthivel, Brett L. Viruses Branch, Division of Viral Whitaker, Lijuan Wang, Janna' R. Murray, North America / USA / Diseases, Centers for Disease Control Jasmine Padilla, Justin Lee, Susan I. 53 EPI_ISL_412862 GISAID California / Solano hCoV-19/USA/CA9/2020 2020-02-23 California Department of Public Health and Prevention Gerber, Stephen Lindstrom, Suxiang Tong Xianding Deng, Scot Federman, Chao-Yang North America / USA / hCoV-19/USA/CA-CDPH- Chiu Laboratory, University of California, Pan, Hugo Guevara,Wei Gu, Debra A. 54 EPI_ISL_413559 GISAID California / Solano County UC3/2020 2020-02-27 California Department of Public Health San Francisco Wadford, and Charles Y. Chiu North America / USA / hCoV-19/USA/WI- University of Wisconsin-Madison AIDS University of Wisconsin-Madison AIDS 55 EPI_ISL_428324 GISAID Wisconsin / Greenfield 228/2020 2020-03-26 Vaccine Research Laboratories Vaccine Research Laboratories Gage Moreno and Katarina Braun, et al.

Sadsad R, Draper J, Sim E, Bachmann N, Rockett R, Lam C, Gray K, Timms V, Gall M, Arnott A, Carter I, Holmes EC, NSW Health Pathology - Institute of O’Sullivan MV, Byun R, Sintchenko V, Chen Clinical Pathology and Medical SC, Eden JS, Maddocks S, Kok J, Oceania / Australia / New South hCoV- Centre for Infectious Diseases and Research; Westmead Hospital; Propenko M, Sorrell T, Chang S, Basile K, 56 EPI_ISL_427779 GISAID Wales / Sydney 19/Australia/NSW169/2020 2020-03-24 Microbiology Public Health University of Sydney Dwyer DE for the 2019-nCoV Study Group North America / USA / hCoV-19/USA/WI- University of Wisconsin-Madison AIDS University of Wisconsin-Madison AIDS 57 EPI_ISL_428333 GISAID Wisconsin / Whitefish 237/2020 2020-03-27 Vaccine Research Laboratories Vaccine Research Laboratories Gage Moreno and Katarina Braun, et al. Guangdong Provincial Center for Bosheng Li, Haogao Gu, Lijun Liang, hCoV- Diseases Control and Zhencui Li, Hui-Ling Yen, Yao Hu, Yingchao Asia / China / Guangdong / 19/Guangdong/20SF812/20 Prevention;Guangdong Provincial School of Public Health, The University Song , Hanri Zeng, Tie Song, Jie Wu, Leo 58 EPI_ISL_428475 GISAID Huizhou 20 2020-01-28 Institute of Public Health of Hong Kong L.M. Poon hCoV-19/Belgium/UM- KU Leuven, Clinical and Epidemiological KU Leuven, Clinical and Epidemiological Joan Marti-Carreras, Bert Vanmechelen, 59 EPI_ISL_420359 GISAID Europe / Belgium / Honnelles 0318103/2020 2020-03-18 Virology Virology Tony Wawina, Piet Maes Ivars Silamiķelis, Kaspars Megnis, Monta Ustinova, Ņikita Zrelovs, Vita Rovīte, Mikus Latvian Biomedical Research and Study Gavars, Dmitrijs Perminovs, Uga Dumpis, 60 EPI_ISL_426288 GISAID Europe / Latvia hCoV-19/Latvia/0008/2020 2020-03-30 E. Gulbja Laboratorija Centre Jānis Kloviņš Anna Majer, Shari Tyson, Grace Seo, Kristyn Burak, Philip Mabon, Elsie Grudeski, Rhiannon Huzarewich, Russell Mandes, Jennifer Tanner, Natalie Knox, Morag Graham, Gary Van Domselaar, Richard Garceau, Guillaume Desnoyers, hCoV- Dr. Georges-L.-Dumont University Nathalie Bastien, Yan Li, Timothy Booth, 61 EPI_ISL_429806 GISAID North America / Canada / NB 19/Canada/NB_1/2020 2020-03-09 Hospital Centre National Microbiology Laboratory Matthew Gilmour Bixing Huang, Alyssa Pyke, Amanda De Jong, Andrew Van Den Hurk, Carmel Taylor, David Warrilow, Doris Genge, Elisabeth Gamez, Glen Hewitson, Ian Maxwell Mackay, Inga Sultana, Jamie McMahon, Jean Barcelon, Judy Northill, Mitchell Finger, Natalie Simpson, Neelima Nair, Peter Burtonclay, Peter Moore, Sarah hCoV- Wheatley, Sean Moody, Sonja Hall- Oceania / Australia / 19/Australia/QLDID920/202 Mendelin, Timothy Gardam, and Frederick 62 EPI_ISL_417032 GISAID Queensland / Rockhampton 0 2020-03-11 Rockhampton Base Hospital Public Health Virology Laboratory Moore Alexander Nagy, Oldrich Bartos, Helena The National Institute of Public Health Jirincova, Klara Labska, Ludmila Novakova, Europe / Czech Republic / Usti hCoV-19/Czech Center for Epidemiology and Olga Storkanova, Dusan Trnka, Jaromira 63 EPI_ISL_414477 GISAID nad Labem Republic/951/2020 2020-03-01 Microbiology State Veterinary Institute Prague Vecerova Oleg V. Pyankov, Sergey A. Bodnev, State Research Center of Virology and State Research Center of Virology and Tatyana V. Tregubchak, Alexander N. Europe / Russia / Samara hCoV-19/Russia/Samara- Biotechnology VECTOR, Department of Biotechnology VECTOR, Department of Shvalov, Elena V. Gavrilova, Rinat A. 64 EPI_ISL_428885 GISAID Region 73406/2020 2020-03-20 Collection of Microorganisms Collection of Microorganisms Maksyutov Bas Oude Munnink, David Nieuwenhuijse, Reina Sikkema, Claudia Schapendonk, Irina Chestakova, Anne van der Linden, Theo Bestebroer, Stefan van Nieuwkoop, Mark Pronk, Pascal Lexmond, Corien Swaan, Manon Haverkate, Madelief Mollers, Mart Stein, Sandra Kengne Kamga Mobou, Jeroen van Kampen, Jolanda Voermans, Aura Timen, Corine GeurtsvanKessel, Annemiek van der Eijk, Richard hCoV- Molenkamp, Marion Koopmans, on behalf of 19/Netherlands/Utrecht_20/ the Dutch national COVID-19 response 65 EPI_ISL_422897 GISAID Europe / Netherlands / Utrecht 2020 2020-03-11 Dutch COVID-19 response team Erasmus Medical Center team. Daniel F Gudbjartsson; Agnar Helgason; Hakon Jonsson; Olafur T Magnusson; Pall Melsted; Gudmundur L Norddahl; Jona Saemundsdottir; Asgeir Sigurdsson; Patrick Sulem; Arna B Agustsdottir; Berglind Eiriksdottir; Run Fridriksdottir; Elisabet E Gardarsdottir; Gudmundur Georgsson; Olafia S Gretarsdottir; Kjartan R Gudmundsson; Thora R Gunnarsdottir; Arnaldur Gylfason; Hilma Holm; Brynjar O Jensson; Aslaug Jonasdottir; Kamilla S Josefsdottir; Thordur Kristjansson; Droplaug N Magnusdottir; Louise le Roux; Gudrun Sigmundsdottir; Gardar Sveinbjornsson; Kristin E Sveinsdottir; Maney Sveinsdottir; Emil A Thorarensen; Bjarni Thorbjornsson; Gisli Masson; Ingileif Jonsdottir; Alma Moller; Thorolfur The National University Hospital of Gudnason; Karl G Kristinsson; Unnur 66 EPI_ISL_424614 GISAID Europe / Iceland / Reykjavik hCoV-19/Iceland/594/2020 2020-03-27 Iceland deCODE genetics Thorsteinsdottir; Kari Stefansson Victor M Corman, Julia Schneider, Jörn hCoV- Beheim-Schwarzbach, Talitha Veith, 19/Lithuania/ChVir1632/202 National Public Health Surveillance Charite Universitaetsmedizin Berlin, Barbara Muehlemann, Terry Jones, Ana 67 EPI_ISL_416741 GISAID Europe / Lithuania / Vilnius 0 2020-02 Laboratory, Vilnius, Lithuania Institute of Virology Steponkiene, Christian Drosten Sergey A. Bodnev, Oleg V. Pyankov, hCoV- State Research Center of Virology and State Research Center of Virology and Tatyana V. Tregubchak, Alexander N. Europe / Russia / Sverdlovsk 19/Russia/Sverdlovsk- Biotechnology VECTOR, Department of Biotechnology VECTOR, Department of Shvalov, Elena V. Gavrilova, Rinat A. 68 EPI_ISL_428879 GISAID Region 71905/2020 2020-03-19 Collection of Microorganisms Collection of Microorganisms Maksyutov Ndongo Dia, Ousmane Faye, Amadou 69 EPI_ISL_418213 GISAID Africa / Senegal / Touba hCoV-19/Senegal/094/2020 2020-03-12 Institut Pasteur Dakar Institut Pasteur de Dakar Alpha Sall Sergey A. Bodnev, Oleg V. Pyankov, State Research Center of Virology and State Research Center of Virology and Tatyana V. Tregubchak, Alexander N. Europe / Russia / Republic of hCoV-19/Russia/Buryatia- Biotechnology VECTOR, Department of Biotechnology VECTOR, Department of Shvalov, Elena V. Gavrilova, Rinat A. 70 EPI_ISL_428899 GISAID Buryatia 86204/2020 2020-03-29 Collection of Microorganisms Collection of Microorganisms Maksyutov Sergey A. Bodnev, Oleg V. Pyankov, State Research Center of Virology and State Research Center of Virology and Tatyana V. Tregubchak, Alexander N. Europe / Russia / Republic of hCoV-19/Russia/Crymea- Biotechnology VECTOR, Department of Biotechnology VECTOR, Department of Shvalov, Elena V. Gavrilova, Rinat A. 71 EPI_ISL_428901 GISAID Crymea 80603/2020 2020-03-23 Collection of Microorganisms Collection of Microorganisms Maksyutov

Ramesh Pandit, Tejas Shah, Ankit Hinsu, Pritesh Sabara, Apurvasinh Puvar, Janvi Raval, Monika Gandhi, Pinal Trivedi, Maharshi Pandya, Amit Kanani, Akanksha Verma, Nitin Savaliya, Raghawendra Kumar, Dinesh Kumar, Zubair Saiyed, Dipa Kinariwala, Disha Patel, Binita Aring, Geeta Vaghela, Sonia Barve, Bhavesh Modi, Kairavi Joshi, Nidhi Sood, Pranay Shah, R hCoV- Sir M P Shah Government Medical D Dixit, Snehal Bagatharia, Madhvi Joshi, 72 EPI_ISL_426414 GISAID Asia / India / Gujarat 19/India/GBRC1/2020 2020-04-05 College Gujarat Biotechnology Research Centre Chaitanya Joshi

Gall M, Arnott A, Sadsad R, Draper J, Sim E, Bachmann N, Rockett R, Lam C, Gray K, Timms V, Carter I, Holmes EC, O’Sullivan NSW Health Pathology - Institute of MV, Byun R, Sintchenko V, Chen SC, Eden Clinical Pathology and Medical JS, Maddocks S, Kok J, Propenko M, Oceania / Australia / New South hCoV- Centre for Infectious Diseases and Research; Westmead Hospital; Sorrell T, Chang S, Basile K, Dwyer DE for 73 EPI_ISL_427772 GISAID Wales / Sydney 19/Australia/NSW107/2020 2020-03-22 Microbiology Public Health University of Sydney the 2019-nCoV Study Group Martin Sundqvist, Olov Svartstrom, Maria Lind Karlberg, Anna-Malin Linde, Oskar hCoV-19/Sweden/20- Karlsson Lindsjo, Anna Risberg, Shaman 74 EPI_ISL_429153 GISAID Europe / Sweden / Varmland 50180/2020 2020-03-08 Klinisk mikrobiologi Orebro The Public Health Agency of Sweden Muradrasoli, Karin Tegmark-Wisell Oceania / Australia / Western hCoV- Department of Microbiology, PathWest Department of Microbiology, PathWest Chisha Sikazwe, Jurissa Lang, Avram Levy, 75 EPI_ISL_420532 GISAID Australia / Perth 19/Australia/WA02/2020 2020-03-13 QEII Medical Centre QEII Medical Centre David Speers and David Smith hCoV-19/Belgium/DB- KU Leuven, Clinical and Epidemiological KU Leuven, Clinical and Epidemiological Bert Vanmechelen, Tony Wawina, Joan 76 EPI_ISL_416470 GISAID Europe / Belgium / Couthuin 03023/2020 2020-03-02 Virology Virology Marti-Carreras, Piet Maes Sergey A. Bodnev, Oleg V. Pyankov, State Research Center of Virology and State Research Center of Virology and Tatyana V. Tregubchak, Alexander N. hCoV-19/Russia/Tver- Biotechnology VECTOR, Department of Biotechnology VECTOR, Department of Shvalov, Elena V. Gavrilova, Rinat A. 77 EPI_ISL_428921 GISAID Europe / Russia / Tver Region 72601/2020 2020-03-19 Collection of Microorganisms Collection of Microorganisms Maksyutov North America / USA / Alaska / hCoV-19/USA/AK- 78 EPI_ISL_431018 GISAID Fairbanks PHL052/2020 2020-03-26 Alaska State Virology Laboratory Alaska State Virology Laboratory Jack Chen, Ph.D.

Anna Majer, Shari Tyson, Grace Seo, Kristyn Burak, Philip Mabon, Elsie Grudeski, Rhiannon Huzarewich, Russell Mandes, Jennifer Tanner, Natalie Knox, Morag Graham, Gary Van Domselaar, Ryan McDonald, Amanda Lang, Rachel DePaulo, hCoV- Jessica Minion, Nathalie Bastien, Yan Li, 79 EPI_ISL_429809 GISAID North America / Canada / SK 19/Canada/SK_16/2020 2020-03-13 Roy Romanow Provincial Laboratory National Microbiology Laboratory Timothy Booth, Matthew Gilmour Tsuyoshi Sekizuka, Michiyo Shinohara, Tsuyoshi Kishimoto, Kentaro Itokawa, Rina Saitama Prefectural Institute of Public Pathogen Genomics Center, National Tanaka, Masanori Hashino, Hajime Kamiya, 80 EPI_ISL_419308 GISAID Asia / Japan / Saitama hCoV-19/Japan/P4-8/2020 2020-03-19 Health Institute of Infectious Diseases Motoi Suzuki, Makoto Kuroda Luke W Meredith, M. Estee Torok , Myra Hosmillo, William L. Hamilton, Martin D. Curran, Theresa Feltwell, Anna Yakovleva, Europe / United Kingdom / hCoV-19/England/CAMB- Department of Pathology, University of COVID-19 Genomics UK (COG-UK) Charlotte J. Houldcroft, Aminu S. Jahun, 81 EPI_ISL_425269 GISAID England 73A37/2020 2020-03-31 Cambridge Consortium Sarah L. Caddy, Ian Goodfellow

Michael Carr, Gabriel Gonzalez, Jonathan Dean, Suzie Coughlan, Alison Murphy, hCoV-19/Ireland/Dublin- UCD National Virus Reference UCD National Virus Reference Kevin Byrne, Ken Wolfe, Jeff Connell, 82 EPI_ISL_418580 GISAID Europe / Ireland / Cork 22361/2020 2020-03-08 Laboratory Laboratory Brendan Loftus, Cillian F De Gascun Bixing Huang, Alyssa Pyke, Amanda De Jong, Andrew Van Den Hurk, Carmel Taylor, David Warrilow, Doris Genge, Elisabeth Gamez, Glen Hewitson, Ian Maxwell Mackay, Inga Sultana, Jamie McMahon, Jean Barcelon, Judy Northill, Mitchell Finger, Natalie Simpson, Neelima Nair, Peter Burtonclay, Peter Moore, Sarah hCoV- Wheatley, Sean Moody, Sonja Hall- Oceania / Australia / 19/Australia/QLDID926/202 Mendelin, Timothy Gardam, and Frederick 83 EPI_ISL_418804 GISAID Queensland / Sunshine Coast 0 2020-03-18 Pathology Queensland Public Health Virology Laboratory Moore Paola Resende, Fernando Motta, Luciana Appolinario, Sunando Roy, Aline Mattos, Instituto Oswaldo Cruz FIOCRUZ - Milene Miranda, Cristiana Garcia, Braulia South America / Brazil / hCoV-19/Brazil/AL- LACEN-AL - Laboratorio Central de Laboratory of Respiratory Viruses and Caetano, Maria Ogrzewalska, Priscila Born, 84 EPI_ISL_427292 GISAID Alagoas / Maceio 837/2020 2020-03-18 Alagoas Measles (LVRS) Jonathan Lopes, Marilda Siqueira Sergey A. Bodnev, Oleg V. Pyankov, State Research Center of Virology and State Research Center of Virology and Tatyana V. Tregubchak, Alexander N. hCoV-19/Russia/Perm- Biotechnology VECTOR, Department of Biotechnology VECTOR, Department of Shvalov, Elena V. Gavrilova, Rinat A. 85 EPI_ISL_428895 GISAID Europe / Russia / Perm Region 82707/2020 2020-03-24 Collection of Microorganisms Collection of Microorganisms Maksyutov Victor M Corman, Jörn Beheim- Schwarzbach, Barbara Mühlemann, Talitha Veith, Julia Schneider, Liidia Dotsenko, hCoV- Health Board Laboratory of Charité Universitätsmedizin Berlin, Natalja Kuznetsova, Terry Jones, Christian 86 EPI_ISL_420065 GISAID Europe / Estonia 19/Estonia/ChVir1982/2020 2020-03 Communicable Diseases Institute of Virology Drosten Oleg V. Pyankov, Sergey A. Bodnev, hCoV- State Research Center of Virology and State Research Center of Virology and Tatyana V. Tregubchak, Alexander N. Europe / Russia / Krasnodar 19/Russia/Krasnodar- Biotechnology VECTOR, Department of Biotechnology VECTOR, Department of Shvalov, Elena V. Gavrilova, Rinat A. 87 EPI_ISL_428867 GISAID Region 63401/2020 2020-03-11 Collection of Microorganisms Collection of Microorganisms Maksyutov

FSBSI "Chumakov Federal Scientific Liubov Kozlovskaya, Anastasia Piniaeva, FSBSI "Chumakov Federal Scientific Center for Research and Development Georgy Ignatyev, Anna Shishova, Aydar Center for Research and Development of Immune-and-Biological Products of Ishmukhametov, Mikhail Rychev, Egor hCoV-19/Russia/Moscow- of Immune-and-Biological Products of Russian Academy of Sciences" & NRC Prokhorchuk, Denis Protsenko, Anastasia 88 EPI_ISL_428851 GISAID Europe / Russia / Moscow 25I/2020 2020-04-02 Russian Academy of Sciences" "Kurchatov institute" Berestovskaya Daniel F Gudbjartsson; Agnar Helgason; Hakon Jonsson; Olafur T Magnusson; Pall Melsted; Gudmundur L Norddahl; Jona Saemundsdottir; Asgeir Sigurdsson; Patrick Sulem; Arna B Agustsdottir; Berglind Eiriksdottir; Run Fridriksdottir; Elisabet E Gardarsdottir; Gudmundur Georgsson; Olafia S Gretarsdottir; Kjartan R Gudmundsson; Thora R Gunnarsdottir; Arnaldur Gylfason; Hilma Holm; Brynjar O Jensson; Aslaug Jonasdottir; Kamilla S Josefsdottir; Thordur Kristjansson; Droplaug N Magnusdottir; Louise le Roux; Gudrun Sigmundsdottir; Gardar Sveinbjornsson; Kristin E Sveinsdottir; Maney Sveinsdottir; Emil A Thorarensen; Bjarni Thorbjornsson; Gisli Masson; Ingileif Jonsdottir; Alma Moller; Thorolfur The National University Hospital of Gudnason; Karl G Kristinsson; Unnur 89 EPI_ISL_424530 GISAID Europe / Iceland / Reykjavik hCoV-19/Iceland/508/2020 2020-03-20 Iceland deCODE genetics Thorsteinsdottir; Kari Stefansson Pathogen Discovery, Respiratory Ying Tao, Jing Zhang, Krista Queen, Anna Viruses Branch, Division of Viral Uehara, Clinton R. Paden, Yan Li, Haibin hCoV- GA Department of Public Health Diseases, Centers for Disease Control Wang, Jasmine Padilla, Justin Lee, Suxiang 90 EPI_ISL_419557 GISAID North America / USA / Georgia 19/USA/GA_2742/2020 2020-02-29 Laboratory and Prevention Tong hCoV- 19/Switzerland/VD5615/202 Swiss National Reference Centre for 91 EPI_ISL_414023 GISAID Europe / Switzerland / Vaud 0 2020-03-01 Laboratoire de Virologie, HUG Influenza LAUBSCHER Florian et al. Huolin Tu, Matthew Avenarius, Preeti Panchioli, Sean Caruthers, Joan-Miquel North America / USA / Ohio / hCoV-19/USA/OH- The Ohio State University-James Balada-Llasat, Jason Garee, Matt Hunt, 92 EPI_ISL_421660 GISAID Columbus OSUP0109/2020 2020-04-01 The Ohio State University Molecular Lab at Polaris Xiaokang Pan, Dan Jones

Anna Majer, Shari Tyson, Grace Seo, Philip Mabon, Natalie Knox, Morag Graham, Paul Van Caeseele, Jared Bullard, David hCoV- Alexander, Kerry Dust, Nathalie Bastien, 93 EPI_ISL_418813 GISAID North America / Canada / MB 19/Canada/MB_10/2020 2020-03-13 Cadham Provincial Laboratory National Microbiology Laboratory Yan Li, Matthew Gilmour, Timothy Booth hCoV- 19/Portugal/IGC00010/202 Hospital Prof. Doutor Fernando João Costa, Cathy Paulino, Joao Sobral, 94 EPI_ISL_419387 GISAID Europe / Portugal / Lisbon 0 2020-03-18 Fonseca, EPE Instituto Gulbenkian de Ciência Susana Ladeiro, Ricardo Leite

Maria Aguero-Rosenfeld, Brendan Belovarac, Margaret Black, Ludovic Boytard, John Cadley, Paolo Cotzia, John Chen, Dacia Dimartino, Xiaojun Feng, Tatyana Gindin, Emily Guzman, Adriana Heguy, Megan Hogan, Emily Huang, George Jour, Lawrence H. Lin, Raven Luther, Andrew Lytle, Christian Marier, Matthew T. Maurano, Mark J. Mulligan, Peter Meyn, Raquel Ordonez Ciriza, Iman Osman, Jared Pinnell, Vanessa Raabe, Sitharam Ramaswami, Amy Rapkiewicz, Andre M. Ribeiro-dos-Santos, Marie Samanovic-Golden, Antonio Serrano, Departments of Pathology and Guomiao Shen, Matija Snuderl, Theodore North America / USA / New hCoV-19/USA/NJ- Medicine, New York University School Vougiouklakis, Nick Vulpescu, Gael 95 EPI_ISL_430371 GISAID Jersey / Hudson County NYUMC344/2020 2020-04-08 NYU Langone Health of Medicine Westby, Paul Zappile, Yutong Zhang Oleg V. Pyankov, Sergey A. Bodnev, State Research Center of Virology and State Research Center of Virology and Tatyana V. Tregubchak, Alexander N. Europe / Russia / Republic of hCoV-19/Russia/Yakutia- Biotechnology VECTOR, Department of Biotechnology VECTOR, Department of Shvalov, Elena V. Gavrilova, Rinat A. 96 EPI_ISL_428888 GISAID Sakha (Yakutia) 73703/2020 2020-03-20 Collection of Microorganisms Collection of Microorganisms Maksyutov Luke W Meredith, M. Estee Torok , Myra Hosmillo, William L. Hamilton, Martin D. Curran, Theresa Feltwell, Anna Yakovleva, Europe / United Kingdom / hCoV-19/England/CAMB- Department of Pathology, University of COVID-19 Genomics UK (COG-UK) Charlotte J. Houldcroft, Aminu S. Jahun, 97 EPI_ISL_425440 GISAID England 76F35/2020 2020 Cambridge Consortium Sarah L. Caddy, Ian Goodfellow Bas Oude Munnink, David Nieuwenhuijse, Reina Sikkema, Claudia Schapendonk, Irina Chestakova, Anne van der Linden, Theo Bestebroer, Stefan van Nieuwkoop, Mark Pronk, Pascal Lexmond, Corien Swaan, Manon Haverkate, Madelief Mollers, Mart Stein, Sandra Kengne Kamga Mobou, Jeroen van Kampen, Jolanda Voermans, Aura Timen, Corine GeurtsvanKessel, Annemiek van der Eijk, Richard hCoV- Molenkamp, Marion Koopmans, on behalf of Europe / Netherlands / Zuid 19/Netherlands/ZuidHolland the Dutch national COVID-19 response 98 EPI_ISL_422901 GISAID Holland _102/2020 2020-03-18 Dutch COVID-19 response team Erasmus Medical Center team. hCoV- Alireza Eshaghi, Samir N Patel, Jonathan B North America / Canada / 19/Canada/ON_PHL3536/2 Gubbay, Vanessa G Allen, Christine Frantz, 99 EPI_ISL_418362 GISAID Ontario 020 2020-03-10 Public Health Ontario Laboratories Public Health Ontario Laboratories Aimin Li, Sandeep Nagra Sergey A. Bodnev, Oleg V. Pyankov, hCoV- State Research Center of Virology and State Research Center of Virology and Tatyana V. Tregubchak, Alexander N. Europe / Russia / Primorskiy 19/Russia/Primorskiy- Biotechnology VECTOR, Department of Biotechnology VECTOR, Department of Shvalov, Elena V. Gavrilova, Rinat A. 100 EPI_ISL_428903 GISAID Region 79001/2020 2020-03-22 Collection of Microorganisms Collection of Microorganisms Maksyutov Le Quynh Mai, Taichiro Takemura, Meng Ling Moi, Takeshi Nabeshima, Nguyen Le Khanh Hang, Hoang Vu Mai Phuong, Ung Thi Hong Trang, Le Thi Thanh, Nguyen Vu Son, Vuong Duc Cuong, Pham Thi Hien, National Influenza Center, National National Influenza Center, National Tran Thu Huong, Nguyen Phuong Anh, hCoV- Institute of Hygiene and Epidemiology Institute of Hygiene and Epidemiology Pham Hong Quynh Anh, Kouichi Morita, 101 EPI_ISL_416428 GISAID Asia / Vietnam / Quangning 19/Vietnam/39607/2020 2020-03-07 (NIHE) (NIHE) Futoshi Hasebe, Dang Duc Anh Sergey A. Bodnev, Oleg V. Pyankov, State Research Center of Virology and State Research Center of Virology and Tatyana V. Tregubchak, Alexander N. hCoV-19/Russia/Tatarstan- Biotechnology VECTOR, Department of Biotechnology VECTOR, Department of Shvalov, Elena V. Gavrilova, Rinat A. 102 EPI_ISL_428917 GISAID Europe / Russia / Tatarstan 82208/2020 2020-03-24 Collection of Microorganisms Collection of Microorganisms Maksyutov Virology Department, Royal Infirmary of Edinburgh, NHS Lothian / School of Biological Sciences, University of McHugh M, Dewar R, Rooke S, Gallagher Edinburgh / Institute of Genetics and M, Balcaza C, O'Toole A, Hill V, McCrone Europe / United Kingdom / hCoV- Molecular Medicine, University of COVID-19 Genomics UK (COG-UK) JT, Colquhoun R, Yu X, Jackson B, Scher 103 EPI_ISL_425902 GISAID Scotland 19/Scotland/EDB118/2020 2020-03-23 Edinburgh Consortium E, Rambaut A, Williams TC, Templeton K Sergey A. Bodnev, Oleg V. Pyankov, hCoV- State Research Center of Virology and State Research Center of Virology and Tatyana V. Tregubchak, Alexander N. Europe / Russia / Novosibirsk 19/Russia/Novosibirsk- Biotechnology VECTOR, Department of Biotechnology VECTOR, Department of Shvalov, Elena V. Gavrilova, Rinat A. 104 EPI_ISL_428918 GISAID Region 84101/2020 2020-03-27 Collection of Microorganisms Collection of Microorganisms Maksyutov

Department of Virus and Microbiological Europe / Denmark / hCoV-19/Denmark/SSI- Special diagnostics, Statens Serum Morten Rasmussen, Maiken Worsoe 113 EPI_ISL_416140 GISAID Copenhagen 05/2020 2020-03-02 Institut, Copenhagen, Denmark. Statens Serum Institute Rosenstierne , Anders Fomsgaard Nabaes Jodar, MS; Goya, S; Natale, MI; hCoV- Área de Secuenciación del Laboratorio Lusso, S; Tittarelli, E; Suárez, A; South America / Argentina / Rio 19/Argentina/PAIS_A017/2 Departamento de Biología y genética de Virología del Hospital de Niños Dr. Masciovecchio MV; Streitenberger ER; 114 EPI_ISL_430808 GISAID Negro 020 2020-04-03 molecular, IACA Laboratorios. Ricardo Gutierrez Mistchenko, AS; Valinotto, LE; Viegas, M. South America / Argentina / hCoV- Área de Secuenciación del Laboratorio Nabaes Jodar, MS; Goya, S; Natale, MI; Ciudad Autonoma de Buenos 19/Argentina/PAIS_A018/2 Laboratorio de Virología del Hospital de de Virología del Hospital de Niños Dr. Lusso, S; Gravis, E; Mistchenko, AS; 115 EPI_ISL_430809 GISAID Aires 020 2020-04-04 Niños Dr. Ricardo Gutierrez Ricardo Gutierrez Valinotto, LE; Viegas, M.

Central Public Health Talita Adelino, Joilson Xavier, Marta Laboratory/Octávio Magalhães Institute Giovanetti, Vagner Fonseca, Marcos South America / Brazil / Minas (IOM) from the Ezequiel Dias Instituto Octávio Magalhães / Fundação Vinícius Silva, Luiz Carlos Junior Alcantara, 116 EPI_ISL_429687 GISAID gerais hCoV-19/Brazil/CV31/2020 2020-03-17 Foundation (FUNED) Ezequiel Dias (IOM/Funed) Marluce Aparecida Assunção Oliveira Anna Uehara, Yan Li, Krista Queen, Clinton Pathogen Discovery, Respiratory R. Paden, Rachel Marine, Ying Tao, Jing Viruses Branch, Division of Viral Zhang, Haibin Wang, Mary S. Keckler, hCoV- HI Dept. of Health, State Laboratories Diseases, Centers for Disease Control Alison S. Laufer Halpin, Christopher A. 117 EPI_ISL_426420 GISAID North America / USA / Hawaii 19/USA/HI_4970/2020 2020-03-05 Division and Prevention Elkins, Suxiang Tong Sergey A. Bodnev, Oleg V. Pyankov, State Research Center of Virology and State Research Center of Virology and Tatyana V. Tregubchak, Alexander N. hCoV-19/Russia/Omsk- Biotechnology VECTOR, Department of Biotechnology VECTOR, Department of Shvalov, Elena V. Gavrilova, Rinat A. 118 EPI_ISL_428878 GISAID Europe / Russia / Omsk Region 89001/2020 2020-04-01 Collection of Microorganisms Collection of Microorganisms Maksyutov Oleg V. Pyankov, Sergey A. Bodnev, State Research Center of Virology and State Research Center of Virology and Tatyana V. Tregubchak, Alexander N. hCoV-19/Russia/Pskov- Biotechnology VECTOR, Department of Biotechnology VECTOR, Department of Shvalov, Elena V. Gavrilova, Rinat A. 119 EPI_ISL_428908 GISAID Europe / Russia / Pskov Region 83602/2020 2020-03-25 Collection of Microorganisms Collection of Microorganisms Maksyutov Iglesias-Caballero, M. Molinero Calamita, M. González-Esguevillas, M. Camarero S. hCoV- Pozo F. Casas I. Jiménez, P. Jiménez, M. 19/Spain/Cataluna201397/2 Zaballos, A. Monzón, S. Varona, S. Juliá, 120 EPI_ISL_419707 GISAID Europe / Spain / Catalonia 020 2020 HOSPITAL CLINIC Instituto de Salud Carlos III M. Cuesta, I. Marcos, M.A Krista Queen, Yan Li, Ying Tao, Jing Zhang, Anne Uehara, Clinton R. Paden, Haibin Pathogen Discovery, Respiratory Wang, Rachel Marine, Mary S. Keckler, Viruses Branch, Division of Viral Alison S. Laufer Halpin, Jasmine Padilla, North America / USA / Rhode hCoV- Diseases, Centers for Disease Control Justin Lee, Christopher A. Elkins, Suxiang 121 EPI_ISL_420795 GISAID Island 19/USA/RI_0556/2020 2020-03-01 RI State Health Laboratory and Prevention Tong Virological Research Group, Bioinformatics Research Group, Péter Urbán, Endre Gábor Tóth, Gábor hCoV- Szentágothai Research Centre, Szentágothai Research Centre, Kemenesi, Róbert Herczeg, Attila Gyenesei, 122 EPI_ISL_416426 GISAID Europe / Hungary / Budapest 19/Hungary/mbl1/2020 2020-03-17 University of Pécs University of Pécs Ferenc Jakab hCoV- Europe / Russia / Saint- 19/Russia/StPetersburg- WHO National Influenza Centre WHO National Influenza Centre Russian Andrey Komissarov, Artem Fadeev, Mariia 123 EPI_ISL_427314 GISAID Petersburg RII4546V/2020 2020-04-02 Russian Federation Federation Sergeeva, Anna Ivanova, Daria Danilenko Laurens Lambrechts, Nick Vereecke, Marthe Pauwels, Basiel Cole, Bruno hCoV-19/Belgium/UGent- Verhasselt, Linos Vandekerckhove, Hans 124 EPI_ISL_425050 GISAID Europe / Belgium / Ghent 2/2020 2020-03-24 Lab voor klinische biologie Onderzoeksgroep Virologie Nauwynck, Sebastiaan Theuns Kassela K., Bampali,M., Dovrolis,N., Laboratory of Microbiology, Medical Laboratory of Biology, Department of Gatzidou,E., Froukala,E., Stavropoulou,A., School, National and Kapodistrian Medicine, Democritus University of Veletza,S., Tsakris,A., Spanakis,N. and 125 EPI_ISL_434460 GISAID Europe / Greece / Athens hCoV-19/Greece/38/2020 2020-03-23 University of Athens Thrace Karakasiliotis,I.

Pathogen Discovery, Respiratory Ying Tao, Clinton R. Paden, Jing Zhang, Viruses Branch, Division of Viral Krista Queen, Anna Uehara, Yan Li, Haibin North America / USA / hCoV- Diseases, Centers for Disease Control Wang, Mary S. Keckler, Alison S. Laufer 135 EPI_ISL_424914 GISAID Massachusetts 19/USA/MA_2652/2020 2020-03-06 MA State Public Health Laboratory and Prevention Halpin, Christopher A. Elkins, Suxiang Tong Mélanie Albert, Marion Barbet, Sylvie Behillil, Méline Bizard, Angela Brisebarre, National Reference Center for Viruses of Flora Donati, Etienne Simon-Lorière, Europe / France / Ile de France hCoV- Respiratory Infections, Institut Pasteur, Vincent Enouf, Maud Vanpeene, Sylvie van 136 EPI_ISL_421503 GISAID / Saint Germain en Laye 19/France/IDF2414/2020 2020-03-12 Parc des Dames Paris der Werf Mélanie Albert, Marion Barbet, Sylvie Behillil, Méline Bizard, Angela Brisebarre, hCoV- National Reference Center for Viruses of Flora Donati, Etienne Simon-Lorière, 19/Algeria/G0638_2264/20 NIC Viral Respiratory Unit - Institut Respiratory Infections, Institut Pasteur, Vincent Enouf, Maud Vanpeene, Sylvie van 137 EPI_ISL_418241 GISAID Africa / Algeria / Boufarik 20 2020-03-02 Pasteur of Algeria Paris der Werf, Fawzi Derrar Gilberto A. Santiago, Glenda Gonzalez, Betzabel Flores, Keyla Charriez, Fabiola Cruz, Chaney Kalinich, Joseph Fauver, North America / USA / Puerto hCoV-19/Puerto Rico/CDC- Centers for Disease Control and Jessica I. Falcon, Nathan Grubaugh, Jorge 138 EPI_ISL_434549 GISAID Rico S9/2020 2020-03-23 Puerto Rico Department of Health Prevention, Dengue Branch L. Munoz-Jordan

Tim Holzer, Mayuri Vaidya, Angie Fulford, Sam McNeely, Rachael Redmond, Phil Clinical Diagnostics Laboratory, Clinical Diagnostics Laboratory, Ebert, John Calley, Leslie O’Neill Reising, North America / USA / Indiana / hCoV-19/USA/IN-Lilly- Diagnostic & Experimental Pathology, Diagnostic & Experimental Pathology, Pat Finnegan, Erin Wray, John McElwee, 142 EPI_ISL_421279 GISAID Indianapolis IPB0170-4bc20/2020 2020-03-19 Lilly Research Laboratories Lilly Research Laboratories Jeff Fill, Joe Oakley, Andrew Schade Jeremy P. Kamil, John A. Vanchiere, Rona S. Scott, Martin J. Sapp, Andrew D. hCoV-19/USA/LA- LSUHS Emerging Viral Threat Yurochko, Paul M. Weinberger, Christopher 143 EPI_ISL_435041 GISAID North America / USA / Louisiana EVTL08/2020 2020-04-15 Laboratory Microbial Genome Sequencing Center G. Kevil, Danitoto North America / USA / hCoV-19/USA/MN-MDH- Minnesota Department of Health, Public Minnesota Department of Health, Public 144 EPI_ISL_427284 GISAID Minnesota 145/2020 2020-03-22 Health Laboratory Health Laboratory Matt Plumb, Jacob Garfin and Xiong Wang Microbiological Diagnostic Unit Public Health Laboratory and Victorian Infectious Diseases Reference hCoV- Victorian Infectious Diseases Reference Laboratory, The Peter Doherty Institute Caly L., Seemann T., Sait, M., Schultz M., 145 EPI_ISL_430690 GISAID Oceania / Australia / Victoria 19/Australia/VIC1316/2020 2020-04-11 Laboratory (VIDRL) for Infection and Immunity Druce J., Sherry, N. hCoV-19/USA/ID-UW- Pavitra Roychoudhury, Hong Xie, Keith 146 EPI_ISL_430948 GISAID North America / USA / Idaho 4383/2020 2020-03-29 UW Virology Lab UW Virology Lab Jerome, Alexander Greninger North America / USA / hCoV-19/USA/WI- University of Wisconsin-Madison AIDS University of Wisconsin-Madison AIDS 147 EPI_ISL_428335 GISAID Wisconsin / Mequon 239/2020 2020-03-27 Vaccine Research Laboratories Vaccine Research Laboratories Gage Moreno and Katarina Braun, et al.

Anna Majer, Shari Tyson, Grace Seo, Kristyn Burak, Philip Mabon, Elsie Grudeski, Rhiannon Huzarewich, Russell Mandes, Jennifer Tanner, Natalie Knox, Morag Graham, Gary Van Domselaar, Todd hCoV- Queen Elizabeth II Health Science Hatchette, Jason LeBlanc, Nathalie Bastien, 148 EPI_ISL_429812 GISAID North America / Canada / NS 19/Canada/NS_30/2020 2020-03-14 Centre National Microbiology Laboratory Yan Li, Timothy Booth, Matthew Gilmour North America / USA / hCoV-19/USA/WI-GMF- Gundersen Molecular Diagnostics 149 EPI_ISL_419651 GISAID Minnesota / Winona County 00466/2020 2020-03-29 Laboratory Kabara Cancer Research Institute Craig S. Richmond & Paraic A. Kenny Microbiological Diagnostic Unit Public Health Laboratory and Victorian Infectious Diseases Reference hCoV- Victorian Infectious Diseases Reference Laboratory, The Peter Doherty Institute Caly L., Seemann T., Sait, M., Schultz M., 150 EPI_ISL_430556 GISAID Oceania / Australia / Victoria 19/Australia/VIC990/2020 2020-03-31 Laboratory (VIDRL) for Infection and Immunity Druce J., Sherry, N.

Department of Virus and Microbiological Special Diagnostics, Statens Serum Albertsen lab, Department of Chemistry hCoV-19/Denmark/ALAB- Institut, Copenhagen, Denmark, and Bioscience, Aalborg University, 154 EPI_ISL_429588 GISAID Europe / Denmark / Unknown SSI523/2020 2020-03-26 Artillerivej 5, 2300 Copenahgen S Denmark Rasmus Kirkegaard Sergey A. Bodnev, Oleg V. Pyankov, State Research Center of Virology and State Research Center of Virology and Tatyana V. Tregubchak, Alexander N. Europe / Russia / Orenburg hCoV-19/Russia/Orenburg- Biotechnology VECTOR, Department of Biotechnology VECTOR, Department of Shvalov, Elena V. Gavrilova, Rinat A. 155 EPI_ISL_428902 GISAID Region 80305/2020 2020-03-23 Collection of Microorganisms Collection of Microorganisms Maksyutov Pilailuk,Okada; Siripaporn,Phuygun; Thanutsapa,Thanadachakul; National Institute of Health. Department Sittiporn,Parnmen;Warawan,Wongboot; hCoV-19/Thailand/NIH- of medical Sciences, Ministry of Public Sunthareeya,Waicharoen; 156 EPI_ISL_430842 GISAID Asia / Thailand / Nonthaburi 2982/2020 2020-03-18 Central chest Institute of Thailand Health, Thailand Malinee,Chittaganpitch North America / USA / hCoV-19/USA/WA-UW- Pavitra Roychoudhury, Hong Xie, Keith 157 EPI_ISL_430943 GISAID Washington 4338/2020 2020-03-30 UW Virology Lab UW Virology Lab Jerome, Alexander Greninger North America / USA / hCoV-19/USA/WA-UW- Pavitra Roychoudhury, Hong Xie, Keith 158 EPI_ISL_430902 GISAID Washington 5364/2020 2020-04-05 UW Virology Lab UW Virology Lab Jerome, Alexander Greninger North America / USA / hCoV-19/USA/WA-UW- Pavitra Roychoudhury, Hong Xie, Keith 159 EPI_ISL_430885 GISAID Washington 546/2020 2020-03-12 UW Virology Lab UW Virology Lab Jerome, Alexander Greninger Maria Aguero-Rosenfeld, Brendan Belovarac, Margaret Black, Ludovic Boytard, John Cadley, Paolo Cotzia, John Chen, Dacia Dimartino, Xiaojun Feng, Tatyana Gindin, Emily Guzman, Adriana Heguy, Megan Hogan, Emily Huang, George Jour, Lawrence H. Lin, Raven Luther, Andrew Lytle, Christian Marier, Matthew T. Maurano, Mark J. Mulligan, Peter Meyn, Raquel Ordonez Ciriza, Iman Osman, Jared Pinnell, Vanessa Raabe, Sitharam Ramaswami, Amy Rapkiewicz, Andre M. Ribeiro-dos-Santos, Marie Samanovic-Golden, Antonio Serrano, Departments of Pathology and Guomiao Shen, Matija Snuderl, Theodore North America / USA / New hCoV-19/USA/NY- Medicine, New York University School Vougiouklakis, Nick Vulpescu, Gael 160 EPI_ISL_430380 GISAID York / Queens NYUMC353/2020 2020-04-08 NYU Langone Health of Medicine Westby, Paul Zappile, Yutong Zhang North America / USA / hCoV-19/USA/CT-UW- Pavitra Roychoudhury, Hong Xie, Keith 161 EPI_ISL_429641 GISAID Connecticut 5038/2020 2020-04-06 UW Virology Lab UW Virology Lab Jerome, Alexander Greninger Krista Queen, Yan Li, Ying Tao, Jing Zhang, Anne Uehara, Clinton R. Paden, Haibin Pathogen Discovery, Respiratory Wang, Rachel Marine, Mary S. Keckler, Viruses Branch, Division of Viral Alison S. Laufer Halpin, Jasmine Padilla, North America / USA / New hCoV- NH Department of Health and Human Diseases, Centers for Disease Control Justin Lee, Christopher A. Elkins, Suxiang 162 EPI_ISL_420792 GISAID Hampshire 19/USA/NH_0008/2020 2020-03-02 Services Public Health Labs and Prevention Tong hCoV-19/USA/VA-DCLS- 163 EPI_ISL_434598 GISAID North America / USA / Virginia 0106/2020 2020-04-14 Division of Consolidated Laboratories Division of Consolidated Laboratories Division of Consolidated Laboratories Oceania / Australia / Western hCoV- Department of Microbiology, PathWest Department of Microbiology, PathWest Chisha Sikazwe, Jurissa Lang, Avram Levy, 164 EPI_ISL_420533 GISAID Australia / Perth 19/Australia/WA03/2020 2020-03-14 QEII Medical Centre QEII Medical Centre David Speers and David Smith Oleg V. Pyankov, Sergey A. Bodnev, hCoV- State Research Center of Virology and State Research Center of Virology and Tatyana V. Tregubchak, Alexander N. Europe / Russia / Krasnoyarsk 19/Russia/Krasnoyarsk- Biotechnology VECTOR, Department of Biotechnology VECTOR, Department of Shvalov, Elena V. Gavrilova, Rinat A. 165 EPI_ISL_428871 GISAID Region 66501/2020 2020-03-13 Collection of Microorganisms Collection of Microorganisms Maksyutov

Peter M. Thielen, Thomas Mehoke, Shirlee Wohl, Srividya Ramakrishnan, Melanie Kirsche, Amanda Ernlund, Oluwaseun Falade-Nwulia, Timothy Gilpatrick, Paul Morris, Norah Sadowski, Nídiá Trovao, hCoV-19/USA/MD- Johns Hopkins Hospital Department of Johns Hopkins Hospital Department of Victoria Gniazdowski, Michael Schatz, 176 EPI_ISL_434685 GISAID North America / USA / Maryland HP024/2020 2020-03-20 Pathology Pathology Stuart C. Ray, Winston Timp, Heba Mostafa Table S2: Climatic parameters for each SARS CoV-2 strain Koppen Environment/ Climate Koppen Climate Temp Precipitation Group Strain ID Location Continent Region Latitude zone Climate type (°C) (mm) Seoul South G1 1 Korea Others Coastal 37.5661102 NTZ D Dwa 11.9 1373 Tianmen G1 2 China China Continental 29.0991674 NSTZ C Cfa 17 1399 G1 3 Talca Chile South America Coastal -35.4230921 STZ C Csb 14.7 758 Kabardino- Balkaria G1 4 Russia Russia Coastal 43.3939922 NTZ D Dfb 9.6 724 G1 5 Beijing China China Coastal 39.9123357 NTZ D Dwa 12.8 637.5 G1 6 Tokyo Japan Others Coastal 35.7794225 NTZ C Cfa 16.3 1529.1 Shanghai G1 7 China China Coastal 31.2178806 NTZ C Cfa 16.1 1148.1 G1 8 Niteroi Brazil South America Coastal -22.8881116 TZ A Aw 24.2 1099.8 Valencia G1 9 Spain Europe Coastal 39.4730878 NTZ C Csa 17.2 459.7 Yongchuan G1 10 China China Continental 29.356117 NSTZ C Cfa 18 1082 G1 11 Fujian China China Coastal 26.5063899 NSTZ C Cfa 21.8 1003 British Columbia G1 12 Canada Canada Coastal 53.8443411 NTZ C Cfb 10.4 1188.7 G1 13 Utah USA USA Continental 39.1909424 NTZ D Dfb 11.6 408.9 G1 14 NL Canada Canada Coastal 53.1895204 NTZ D Dfb 5.1 1534.2 Brisbane G1 15 Australia Australia Coastal -27.4644149 SSTZ C Cfa 20.6 1196.3 Mexico city G1 16 Mexico Others Continental 19.4344423 TZ C Cwb 17.2 635 Washington G1 17 USA USA Coastal 47.7604677 NTZ C Cfa 14.6 1008.4 Kuming G1 18 Yunnan China China Continental 24.8825036 NSTZ C Cfa 17.5 1389 G1 19 Chicago USA USA Continental 41.8792517 NTZ D Dfa 9.9 937.3

Chendu G1 20 Sichuan China China Continental 30.572875 NTZ C Cfa 16.7 985.5 South G1 21 Carolina USA USA Coastal 33.8239397 NTZ C Cfa 17.7 1132.8 G1 22 Florida USA USA Coastal 27.726841 NSTZ A Am 25.1 1572.3 Manila G1 23 Philippines Others Coastal 14.6149872 TZ A Af 27.8 1976.1 Riyadh Soudi G1 24 Arabia Middle East Continental 24.7215922 NSTZ B BWh 23.9 109.2

Join Ville G1 25 Santa Catarina South America Coastal -26.2807799 SSTZ C Cfa 24.4 1897.4 Ramat Gan G1 26 Israel Middle East Coastal 32.0688854 NTZ C Csa 19.8 579 G1 27 Texas USA USA Coastal 31.814558 NTZ C Cfa 20.6 774.7 Victoria G1 28 Australia Australia Coastal -37.4806026 STZ C Cfb 14.4 566.4 Dasman G1 29 Kuwait Middle East Coastal 29.3877622 NSTZ B BWh 26.1 110 Kayseri G1 30 Turkey Middle East Coastal 38.7275639 NTZ C Csb 10.6 365.8 Moscow G1 31 Russia Russia Continental 55.7450056 NTZ D Dfb 4.4 599.4 Quingdao Shangdong G1 32 China China Coastal 36.072312 NTZ C Cfa 12.8 688.3 Hong Kong G1 33 China China Coastal 22.329241 TZ C Cfa 23.9 2189.5 Jian Jiangxi G1 34 China China Coastal 27.1290189 NSTZ C Cfa 12.8 1750.1 G1 35 Zhuhai China China Coastal 22.285772 TZ C Cfa 22.5 1757.7 Tibilisi G1 36 Georgia Others Coastal 41.7133957 NTZ C Cfa 12.9 500.4 Libson G1 37 Portugal Europe Coastal 38.7253857 NTZ C Csa 17 726.4 Vila Velha G1 38 Brazil South America Coastal -20.3461726 TZ A Aw 27.8 1673.9 G1 39 Nevada USA USA Coastal 39.358291 NTZ B BSk 9.6 210.8 G1 40 Oregon USA USA Coastal 43.8257313 NTZ C Csb 12.5 914.4 Solvenia G1 41 Europe Europe Coastal 46.1413726 NTZ C Cfb 9.4 782.3 Sao Paulo G1 42 Brazil South America Coastal -23.549261 SSTZ C Cfa 17.8 1409.7 Ketchikan G1 43 Alaska Alaska Coastal 55.3476602 NTZ C Cfb 7.2 3714 Heinsberg G1 44 Germany Europe Coastal 51.0608085 NTZ C Cfb 9.4 566.4

Zielonogorskie G1 45 Poland Europe Coastal 51.1188211 NTZ C Cfb 8.3 548.6 Sao Paulo G1 46 Brazil South America Coastal -23.5681434 SSTZ C Cfb 17.8 1409.7 Nebraska G1 47 USA USA Continental 40.6798977 NTZ D Dfa 10.6 777.2 Hangzhou G1 48 China China Coastal 30.2799057 NTZ C Cfa 16.7 1447.8 GP South G1 49 Africa Africa Continental -26.2666677 SSTZ C Csa 17.2 579.1 G1 50 Wuhan China China Coastal 30.6279532 NTZ C Cfa 17.2 1204 G1 51 Hefei China China Coastal 31.825118 NTZ C Cfa 16.1 1003.3

G1 52 Jiangsu China China Coastal 33.1336901 NTZ C Cfa 15.6 1000.8 Solana SF G1 53 USA USA Coastal -23.6623056 SSTZ C Csb 13.1 508 Salono Country CA G1 54 USA USA Coastal 38.3087664 NTZ C Csb 15.8 579.1 Greenfield G1 55 WI USA USA Coastal 42.9628263 NTZ D Dfb 9.1 861 Wales Sydney G1 56 Australia Australia Coastal -33.6447445 STZ C Cfa 17.8 1130.3 Whitefish WI G1 57 USA USA Coastal 43.1138498 NTZ D Dfb 6.2 551.2 Huizhou G1 58 China China Coastal 23.1060684 TZ C Cfa 22.4 2059.9 Honnelles G2 59 Belgium Europe Coastal 50.3678832 NTZ C Cfb 10.6 812.8 G2 60 Lativa Europe Europe Coastal 56.8831921 NTZ D Dfb 6.7 569 G2 61 NB Canada Canada Coastal 46.6378627 NTZ D Dfb 4.4 1087.1

Rockhampton G2 62 QL Australia Australia Coastal -23.3817042 TZ C Cfa 22.2 850.9 Usti nad G2 63 Labem Europe Coastal 50.6632504 NTZ C Cfb 8.9 668 Samara G2 64 Russia Russia Continental 53.2169256 NTZ D Dfb 4.9 566.4 Utrecht G2 65 Netherlands Europe Coastal 52.0964108 NTZ C Cfb 9.6 810.3 Reykjavik G2 66 Iceland Europe Coastal 64.3931053 NTZ C Cfc 4.4 817.9 Vilnius G2 67 Lithuanian Europe Coastal 54.694523 NTZ D Dfb 5.6 652.8 Sverdlovsk G2 68 Russia Russia Continental 59.0712926 NTZ D Dfb 1.9 424.2 Touba G2 69 Sengal Africa Africa Coastal 14.8575913 TZ A Aw 24.5 1399.5 Buryatia G2 70 Russia Russia Continental 54.845768 NTZ D Dwc -1.3 256.5 Republic of G2 71 Crimea Russia Russia Coastal 44.950759 NTZ C Cfa 10.6 375.9 G2 72 Gujarat India Others Coastal 22.2169736 TZ B BSh 27.3 678.2 Sydney G2 73 Australia Australia Coastal -33.8673267 STZ C Cfa 17.8 1130.3 Vramland G2 74 Sweden Europe Coastal 60.8358155 NTZ D Dfb 4.9 669 Perth G2 75 Australia Australia Coastal -31.8866974 STZ C Csa 18.3 800.1 Couthuin G2 76 Belgium Europe Coastal 50.53167 NTZ C Cfb 10.6 812.8 G2 77 Tver Russia Russia Coastal 56.8606554 NTZ D Dfb 5.1 652.8 Fairbanks G2 78 Alaska Alaska Coastal 64.8394678 NTZ D Dfc -2.4 274.3 G2 79 SK Canada Canada Continental 53.0635209 NTZ D Dfb 1.7 373.4 Saitama G2 80 Japan Others Coastal 35.8643801 NTZ C Cfa 14.9 1395 G2 81 England UK Europe Coastal 52.411119 NTZ C Cfb 10.3 754.4 G2 82 Cork Ireland Europe Coastal 51.9036006 NTZ C Cfb 9.9 1082 Sunshine G2 83 coast Australia Australia Coastal -26.6539932 SSTZ C Cfa 20.7 1740 Maceio G2 84 Alagoas Brazil South America Coastal -9.6286362 TZ A Aw 23.8 731.5 G2 85 Prem Russia Russia Continental 58.0150228 NTZ D Dfb 1.8 574 G2 86 Estonia Europe Coastal 58.7072704 NTZ D Dfb 5.5 693.4 Krasnodar G2 87 Russia Russia Coastal 45.0444288 NTZ C Cfa 11.3 716.3 Moscow G2 88 Russia Russia Continental 55.7573715 NTZ D Dfb 4.4 599.4 Reykjavik G2 89 Iceland Europe Coastal 64.1259139 NTZ C Cfb 4.7 869 G2 90 Georgia USA USA Coastal 32.2543393 NTZ C Cfa 17 1262 Vaud G2 91 Switzerland Europe Coastal 46.5795113 NTZ C Cfb 10.1 1379.2 Columbus G2 92 Ohio USA USA Coastal 39.9761376 NTZ D Dfa 11.9 998.2 G2 93 MB Canada Canada Coastal 53.9780004 NTZ D Dfb 2.8 513.1 Libson G2 94 Portugal Europe Coastal 38.0050753 NTZ C Csa 17 726.4 Hudson Country NJ G2 95 USA USA Coastal 40.7306424 NTZ C Cfa 11.4 1170.9 G2 96 Sakha Russia Russia Coastal 52.7915601 NTZ D Dfc -7.9 271.8 G2 97 England Europe Coastal 52.4245201 NTZ C Cfb 10.3 754.4 Zuid Holland G2 98 Netherlands Europe Coastal 52.1035272 NTZ C Cfb 10 815.3 G2 99 ON Canada Canada Coastal 51.0626315 NTZ D Dfb 7.7 853.4 Primorskiy G2 100 Russia Russia Coastal 45.8731843 NTZ D Dfb 4.4 718.8 Quangning G2 101 Vietnam Others Coastal 15.1229375 TZ A Aw 28.3 1950.7 Tatarstan G2 102 Russia Russia Continental 55.2500342 NTZ D Dfb 3.3 447 G2 103 Scotland UK Europe Coastal 56.7228072 NTZ C Cfb 9.6 901.7 Novosibirsk G2 104 Russia Russia Continental 54.9711658 NTZ D Dfb 0.9 448 Minas Gerias G2 105 Brazil South America Coastal -18.490384 TZ C Cfa 21.1 1585

Buenos Aires G2 106 Argentina South America Coastal -34.6031104 STZ C Cfa 17.7 977.9 G2 107 Brasilia Brazil South America Coastal -15.7988239 TZ A Aw 21.1 1668 G2 108 Missouri USA USA Continental 38.1367026 NTZ C Cfa 12.6 988.1 G2 109 Switzerland Europe Coastal 46.839801 NTZ C Cfb 9.3 1132.8 Sao Paulo G2 110 Brazil South America Coastal -22.910011 TZ C Cfb 18.5 1340 Feira de Santana G2 111 Bahia Brazil South America Coastal -12.2487694 TZ A Aw 23 888 Sao Paulo G2 112 Brazil South America Coastal -23.6587593 SSTZ C Cfb 18.5 1340 Copenhagen G2 113 Denmark Europe Coastal 55.6822612 NTZ C Cfb 8.4 621 Rio Negro G2 114 Argentina South America Coastal -40.8613497 STZ A Am 23.9 1743

Buenos Aries G2 115 Argentina South America Coastal -34.6875632 STZ C Cfa 17.7 977.9 Minas Gerais G2 116 Brazil South America Coastal -15.5071456 TZ C Cfa 21.1 1585 G2 117 Hawaii USA USA Coastal 19.9746957 TZ A As 25.4 434.3 G2 118 Omsk Russia Russia Continental 54.9972502 NTZ D Dfb 2.2 335.3 G2 119 Pskov Russia Russia Coastal 57.8190766 NTZ D Dfb 5.1 665.5 Catalonia G2 120 Spain Europe Coastal 41.5999477 NTZ C Csa 15.5 640.1 G2 121 Rhode Island USA Coastal 41.6749094 NTZ C Cfa 10.5 1163.3 Budapest G2 122 Hungary Europe Coastal 47.5053058 NTZ D Dfb 10.6 619.8 St. Petresburg G2 123 Russia Russia Coastal 59.9377825 NTZ D Dfb 4.1 538.5 Ghent G2 124 Belgium Europe Coastal 51.0599302 NTZ C Cfb 10.2 754 Athens G2 125 Greece Europe Coastal 37.9844781 NTZ C Csa 18.5 365.8 Minas Gerias G2 126 Brazil South America Coastal -14.5946198 TZ C Cfa 21.1 1585 New Taipei G2 127 City Taiwan Others Coastal 25.0690855 NSTZ C Cfa 22.8 2067.6 Chechen Republic G2 128 Russia Russia Coastal 43.9747521 NTZ D Dfa 11.2 491 British Columbia G2 129 Canada Canada Coastal 53.7770392 NTZ C Cfb 10.4 1188.7 Minas Gerias G2 130 Brazil South America Coastal -19.3011286 TZ C Cfa 21.1 1585 Khabarovsk G2 131 Russia Russia Coastal 48.4834817 NTZ D Dwb 1.7 678 G2 132 Kansas USA USA Continental 39.1097552 NTZ C Cfa 12.6 988.1 Pennsylvania G2 133 USA USA Coastal 41.1891509 NTZ D Dfb 10.8 970.3 West Coast Region G2 134 Gambia Africa Coastal 13.2262893 TZ A Aw 26.1 1056.6

Massachussett G2 135 s USA USA Coastal 42.4923287 NTZ D Dfa 10.7 1071.9 Saint Germain en G2 136 Laye France Europe Coastal 48.8996773 NTZ C Cfb 12.4 637.5 Baufarik G2 137 Algeria Africa Africa Coastal 36.5853623 NTZ C Csa 18.3 693.4 Puerto Rico G2 138 USA USA Coastal 18.13749 TZ A Am 26.8 1397 Manhattan G2 139 USA USA Coastal 40.7822804 NTZ C Cfa 13.1 1135.4 G2 140 Virginia USA USA Coastal 37.3997354 NTZ C Cfa 14.9 1107.4 San Francisco CA G2 141 USA USA Coastal 37.7739556 NTZ C Csb 13.1 508 Indianapolis G2 142 USA USA Coastal 39.7676088 NTZ D Dfa 11.1 1011 Louisiana G2 143 USA USA Coastal 30.9542967 NTZ C Cfa 20.4 1551.9 Minnesota G2 144 USA USA Coastal 46.7722818 NTZ D Dfa 8.4 723.9 Victoria G2 145 Australia Australia Coastal -37.6895827 STZ C Cfb 14.4 566.4 G2 146 Idaho USA USA Coastal 43.916449 NTZ C Csb 11.4 297.2 Mequon WI G2 147 USA USA Coastal 43.214458 NTZ D Dfb 8.1 876.3 G2 148 NS Canada Canada Coastal 45.3253253 NTZ D Dfb 6.1 1407 Winona MN G2 149 USA USA Coastal 44.0075959 NTZ D Dfa 8.4 723.9 Victoria G2 150 Australia Australia Coastal -37.6513296 STZ C Cfb 14.4 566.4 Nassau Country NA G2 151 USA USA Coastal 40.6513151 NTZ C Cfa 13.1 1135.4 Compiegene G2 152 France South America Coastal 49.4189327 NTZ C Cfb 12.4 637.5 District of G2 153 Columbia USA USA Coastal 38.9030939 NTZ C Cfa 14.6 1008.4 G2 154 Denmark Europe Coastal 56.2925676 NTZ C Cfb 8.3 645.2 Orenburg G2 155 Russia Russia Continental 51.7711394 NTZ D Dfa 4.1 363.2 Nonthaburi G2 156 Thailand Others Coastal 13.8599208 TZ A Aw 28.9 1450.3 Washington G2 157 USA USA Coastal 43.242699 NTZ C Cfa 14.6 1008.4 Washington G2 158 USA USA Coastal 50.2078972 NTZ C Cfa 14.6 1008.4 Washington G2 159 USA USA Coastal 46.33679 NTZ C Cfa 14.6 1008.4 Queens NY G2 160 USA USA Coastal 40.7334272 NTZ C Cfa 13.1 1135.4 Connecticut G2 161 USA USA Coastal 41.6560961 NTZ D Dfa 10.1 1148.1 New Hampshire G2 162 USA USA Coastal 43.195517 NTZ D Dfb 7.9 1021.1 G2 163 Virginia USA USA Coastal 37.4002883 NTZ C Cfa 15.6 1209 Perth G2 164 Australia Australia Coastal -32.0800587 STZ C Csa 18.3 800.1 Krasnoyarsk G2 165 Russia Russia Continental 56.0236222 NTZ D Dfc 1.1 424.2 NSW G2 166 Australia Australia Coastal -33.3913181 STZ C Cfa 17.8 1130.3 Eielson AFB G2 167 ALaska Alaska Coastal 64.2762858 NTZ D Dfc -2.35 500 Chelyabinsk G2 168 Russia Russia Continental 55.1798514 NTZ D Dfb 3.2 429.3 Noord Barbarant G2 169 Netherlands Europe Coastal 51.4844322 NTZ C Cfb 10 815.3 Sakhalin G2 170 Russia Russia Coastal 50.5295881 NTZ D Dfb 2.8 835.7 Duesseldorf G2 171 Germany Europe Coastal 51.2306631 NTZ C Cfb 10.6 762 Ontario G2 172 Canada Canada Coastal 51.5160937 NTZ D Dfb 6.4 942.3 G2 173 Norway Europe Coastal 60.8940026 NTZ D Dfb 3 894.1 Juneau G2 174 Alaska Alaska Coastal 58.315208 NTZ D Dfc 5.6 1582.4 G2 175 Austria Europe Coastal 47.5739045 NTZ C Cfb 11.4 548.6

G2 176 Maryland USA USA Coastal 39.0973899 NTZ C Cfa 12.8 1064.3