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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2020. Genomic Epidemiology Data Infrastructure Needs for SARS-CoV-2: Modernizing Pandemic Response Strategies. Washington, DC: The National Academies Press. doi: 10.17226/25879.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2020. Genomic Epidemiology Data Infrastructure Needs for SARS-CoV-2: Modernizing Pandemic Response Strategies. Washington, DC: The National Academies Press. doi: 10.17226/25879.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2020. Genomic Epidemiology Data Infrastructure Needs for SARS-CoV-2: Modernizing Pandemic Response Strategies. Washington, DC: The National Academies Press. doi: 10.17226/25879.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2020. Genomic Epidemiology Data Infrastructure Needs for SARS-CoV-2: Modernizing Pandemic Response Strategies. Washington, DC: The National Academies Press. doi: 10.17226/25879.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2020. Genomic Epidemiology Data Infrastructure Needs for SARS-CoV-2: Modernizing Pandemic Response Strategies. Washington, DC: The National Academies Press. doi: 10.17226/25879.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2020. Genomic Epidemiology Data Infrastructure Needs for SARS-CoV-2: Modernizing Pandemic Response Strategies. Washington, DC: The National Academies Press. doi: 10.17226/25879.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2020. Genomic Epidemiology Data Infrastructure Needs for SARS-CoV-2: Modernizing Pandemic Response Strategies. Washington, DC: The National Academies Press. doi: 10.17226/25879.
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Page viii Cite
Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2020. Genomic Epidemiology Data Infrastructure Needs for SARS-CoV-2: Modernizing Pandemic Response Strategies. Washington, DC: The National Academies Press. doi: 10.17226/25879.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2020. Genomic Epidemiology Data Infrastructure Needs for SARS-CoV-2: Modernizing Pandemic Response Strategies. Washington, DC: The National Academies Press. doi: 10.17226/25879.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2020. Genomic Epidemiology Data Infrastructure Needs for SARS-CoV-2: Modernizing Pandemic Response Strategies. Washington, DC: The National Academies Press. doi: 10.17226/25879.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2020. Genomic Epidemiology Data Infrastructure Needs for SARS-CoV-2: Modernizing Pandemic Response Strategies. Washington, DC: The National Academies Press. doi: 10.17226/25879.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2020. Genomic Epidemiology Data Infrastructure Needs for SARS-CoV-2: Modernizing Pandemic Response Strategies. Washington, DC: The National Academies Press. doi: 10.17226/25879.
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Page xiii Cite
Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2020. Genomic Epidemiology Data Infrastructure Needs for SARS-CoV-2: Modernizing Pandemic Response Strategies. Washington, DC: The National Academies Press. doi: 10.17226/25879.
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Suggested Citation:"Front Matter." National Academies of Sciences, Engineering, and Medicine. 2020. Genomic Epidemiology Data Infrastructure Needs for SARS-CoV-2: Modernizing Pandemic Response Strategies. Washington, DC: The National Academies Press. doi: 10.17226/25879.
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Below is the uncorrected machine-read text of this chapter, intended to provide our own search engines and external engines with highly rich, chapter-representative searchable text of each book. Because it is UNCORRECTED material, please consider the following text as a useful but insufficient proxy for the authoritative book pages.

Genomic Epidemiology Data Infrastructure Needs for SARS-CoV-2 Modernizing Pandemic Response Strategies Committee on Data Needs to Monitor the Evolution of SARS-CoV-2 Board on Health Sciences Policy Health and Medicine Division Board on Life Sciences Division on Earth and Life Studies A Consensus Study Report of i PREPUBLICATION COPY: UNCORRECTED PROOFS

THE NATIONAL ACADEMIES PRESS 500 Fifth Street, NW Washington, DC 20001 This activity was supported by a contract between the National Academy of Sciences and the U.S. Department of Health and Human Services’ Office of the Assistant Secretary for Preparedness and Response (75A50120G00002). Any opinions, findings, conclusions, or recommendations expressed in this publication do not necessarily reflect the views of any organization or agency that provided support for the project. International Standard Book Number-13: 978-0-309-XXXXX-X International Standard Book Number-10: 0-309-XXXXX-X Digital Object Identifier: https://doi.org/10.17226/25879 Additional copies of this publication are available from the National Academies Press, 500 Fifth Street, NW, Keck 360, Washington, DC 20001; (800) 624-6242 or (202) 334-3313; http://www.nap.edu. Copyright 2020 by the National Academy of Sciences. All rights reserved. Printed in the United States of America Suggested citation: National Academies of Sciences, Engineering, and Medicine. 2020. Genomic epidemiology data infrastructure needs for SARS-CoV-2: Modernizing pandemic response strategies. Washington, DC: The National Academies Press. https://doi.org/10.17226/25879. PREPUBLICATION COPY: UNCORRECTED PROOFS ii

The National Academy of Sciences was established in 1863 by an Act of Congress, signed by President Lincoln, as a private, nongovernmental institution to advise the nation on issues related to science and technology. Members are elected by their peers for outstanding contributions to research. Dr. Marcia McNutt is president. The National Academy of Engineering was established in 1964 under the charter of the National Academy of Sciences to bring the practices of engineering to advising the nation. Members are elected by their peers for extraordinary contributions to engineering. Dr. John L. Anderson is president. The National Academy of Medicine (formerly the Institute of Medicine) was established in 1970 under the charter of the National Academy of Sciences to advise the nation on medical and health issues. Members are elected by their peers for distinguished contributions to medicine and health. Dr. Victor J. Dzau is president. The three Academies work together as the National Academies of Sciences, Engineering, and Medicine to provide independent, objective analysis and advice to the nation and conduct other activities to solve complex problems and inform public policy decisions. The National Academies also encourage education and research, recognize outstanding contributions to knowledge, and increase public understanding in matters of science, engineering, and medicine. Learn more about the National Academies of Sciences, Engineering, and Medicine at www.nationalacademies.org. PREPUBLICATION COPY: UNCORRECTED PROOFS iii

Consensus Study Reports published by the National Academies of Sciences, Engineering, and Medicine document the evidence-based consensus on the study’s statement of task by an authoring committee of experts. Reports typically include findings, conclusions, and recommendations based on information gathered by the committee and the committee’s deliberations. Each report has been subjected to a rigorous and independent peer-review process and it represents the position of the National Academies on the statement of task. Proceedings published by the National Academies of Sciences, Engineering, and Medicine chronicle the presentations and discussions at a workshop, symposium, or other event convened by the National Academies. The statements and opinions contained in proceedings are those of the participants and are not endorsed by other participants, the planning committee, or the National Academies. For information about other products and activities of the National Academies, please visit www.nationalacademies.org/about/whatwedo. PREPUBLICATION COPY: UNCORRECTED PROOFS iv

COMMITTEE ON DATA NEEDS TO MONITOR THE EVOLUTION OF SARS-CoV-2 DIANE GRIFFIN (Chair), Distinguished University Service Professor, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health RALPH BARIC, William R. Kenan, Jr. Distinguished Professor, University of North Carolina at Chapel Hill KENT KESTER, Vice President and Head, Translational Sciences and Biomarkers, Sanofi Pasteur DEVEN MCGRAW, Chief Regulatory Officer, Ciitizen Corporation ALEXANDRA PHELAN, Assistant Professor, Center for Global Health Science and Security, Georgetown University SASKIA POPESCU, Senior Infection Preventionist, HonorHealth; Affiliate Faculty, George Mason University; Adjunct Professor, University of Arizona STUART RAY, Professor of Medicine and Vice Chair of Medicine for Data Integrity and Analytics, Johns Hopkins University School of Medicine DAVID RELMAN, Thomas C. and Joan M. Merigan Professor Medicine, and of Microbiology and Immunology; Co-Director, Center for International Security and Cooperation, Stanford University; Chief of Infectious Diseases, Veterans Affairs Palo Alto Health Care System JULIE SEGRE, Chief and Senior Investigator, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health MARK SMOLINSKI, President, Ending Pandemics PAUL TURNER, Rachel Carson Professor of Ecology and Evolutionary Biology, Yale University DEBORAH ZARIN, Program Director, Multi-Regional Clinical Trials Center of Brigham and Women’s Hospital and Harvard Liaison to the Standing Committee on Emerging Infectious Diseases and 21st Century Health Threats HARVEY FINEBERG, President, Gordon and Betty Moore Foundation; Chair, Standing Committee on Emerging Infectious Diseases and 21st Century Health Threats Study Staff LISA BROWN, Study Director EMMA FINE, Associate Program Officer BENJAMIN KAHN, Associate Program Officer STEVEN MOSS, Associate Program Officer ANDREW M. POPE, Senior Director, Board on Health Sciences Policy Science Writer ANNA NICHOLSON PREPUBLICATION COPY: UNCORRECTED PROOFS v

Reviewers This Consensus Study Report was reviewed in draft form by individuals chosen for their diverse perspectives and technical expertise. The purpose of this independent review is to provide candid and critical comments that will assist the National Academies of Sciences, Engineering, and Medicine in making each published report as sound as possible and to ensure that it meets the institutional standards for quality, objectivity, evidence, and responsiveness to the study charge. The review comments and draft manuscript remain confidential to protect the integrity of the deliberative process. We thank the following individuals for their review of this report: ARAYINDA CHAKRAVARTI, New York University MARK R. DENISON, Vanderbilt University Medical Center KATHLEEN M. NEUZIL, University of Maryland School of Medicine MARK A. ROTHSTEIN, University of Louisville JOSHUA M. SHARFSTEIN, Johns Hopkins Bloomberg School of Public Health Although the reviewers listed above provided many constructive comments and suggestions, they were not asked to endorse the conclusions or recommendations of this report nor did they see the final draft before its release. The review of this report was overseen by SUSAN J. CURRY, The University of Iowa, and BOBBIE BERKOWITZ, University of Washington. They were responsible for making certain that an independent examination of this report was carried out in accordance with the standards of the National Academies and that all review comments were carefully considered. Responsibility for the final content rests entirely with the authoring committee and the National Academies. PREPUBLICATION COPY: UNCORRECTED PROOFS vii

Contents ACRONYMS AND ABBREVIATIONS xix SUMMARY 1 1 INTRODUCTION 7 Coronavirus Evolution and SARS-CoV-2, 8 The Power of Genomics in Understanding SARS-CoV-2, 9 Study Charge, 11 About This Report, 12 References, 13 2 APPLICATION OF GENOMIC EPIDEMIOLOGY IN PREVIOUS INFECTIOUS DISEASE OUTBREAKS 15 Previous Efforts to Integrate Analyses of Genomic, Clinical, and Epidemiological Data, 15 Best Practices and Keys to Future Success, 20 References, 21 3 CURRENT GENOMIC EPIDEMIOLOGY EFFORTS RELATED TO SARS-CoV-2 27 Current SARS-CoV-2 Data Sources, 27 Current Efforts to Integrate SARS-CoV-2 Genome Sequence Data with Clinical and Epidemiological Data, 33 Concluding Remarks, 35 References, 36 4 FRAMEWORK TO TRACK AND CORRELATE VIRAL GENOME SEQUENCE DATA WITH CLINICAL AND EPIDEMIOLOGICAL DATA 39 Considerations for Transmission, Evolution, and Clinical Disease, 39 Opportunities to Support Data Integration, 46 Infrastructure Needs, 47 Partnership, Coordination, and Capacity Considerations, 50 Concluding Remarks, 51 References, 52 5 GOVERNANCE AND REGULATORY CONSIDERATIONS 57 Federalism Barriers and Opportunities, 58 International Sharing Barriers, 58 Perceived Versus Actual Domestic Legal Barriers, 59 ix PREPUBLICATION COPY: UNCORRECTED PROOFS

The Health Insurance Portability and Accountability Act (HIPAA), 59 Common Rule, 62 Governance, 66 Concluding Remarks, 67 References, 68 APPENDIXES A COMMITTEE BIOSKETCHES 71 B PUBLIC COMMITTEE MEETING AGENDAS 79 x PREPUBLICATION COPY: UNCORRECTED PROOFS

Boxes, Figures, and Tables BOXES 1-1 Defining Genomic Epidemiology, 10 1-2 Statement of Task, 12 FIGURES 1-1 Pathogen sequencing during infectious disease outbreaks can inform precise interventions, 11 2-1 Customized database for the Antimicrobial Resistance Monitoring and Research Program, 19 3-1 A radial phylogenetic tree of a global set of 10,000 SARS-CoV-2 genomes available on GISAID, 30 TABLES S-1 Summary Table of Considerations for Transmission, Evolution, and Clinical Disease, 3 4-1 Summary Table of Considerations for Transmission, Evolution, and Clinical Disease, 40 xi PREPUBLICATION COPY: UNCORRECTED PROOFS

Acronyms and Abbreviations ACE2 angiotensin-converting enzyme 2 APHL Association of Public Health Laboratories ARMoR Antimicrobial Resistance Monitoring and Research Program ASPR Office of the Assistant Secretary for Preparedness and Response (HHS) CanCOGeN Canadian COVID Genomics Network CARB Combating Antibiotic-Resistant Bacteria National Action Plan CDC U.S. Centers for Disease Control and Prevention CLIA Clinical Laboratory Improvement Amendments COG-UK COVID-19 Genomics UK CoV coronavirus COVID-19 coronavirus disease 2019 DNA deoxyribonucleic acid DoD U.S. Department of Defense ECMO extracorporeal membrane oxygenation EUA Emergency Use Authorization ExoN exoribonuclease FDA U.S. Food and Drug Administration FluSury-NET Influenza Hospitalization Surveillance Network GDP gross domestic product GISAID Global Initiative on Sharing All Influenza Data HHS U.S. Department of Health and Human Services HIE Health Information Exchange HIPAA Health Insurance Portability and Accountability Act HITECH Health Information Technology for Economic and Clinical Health Act PREPUBLICATION COPY: UNCORRECTED PROOFS xiii

ICU intensive care unit IHR International Health Regulations ILI influenza-like illness ILINet Influenza-like Illness Surveillance Network IRB Institutional Review Board MAVEN Massachusetts Viral Epidemiologic Network MERS Middle East respiratory syndrome MIS-C multisystem inflammatory syndrome in children N3C National COVID Cohort Collaborative NCBI National Center for Biotechnology Information NIH National Institutes of Health NIST National Institute of Standards and Technology NLM National Library of Medicine NREVSS National Respiratory and Enteric Virus Surveillance System NYC New York City OCR Office for Civil Rights OSTP Office of Science and Technology Policy PCR polymerase chain reaction PDCoV porcine epidemic diarrhea virus PEDV porcine delta coronavirus PHA4GE Public Health Alliance for Genomic Epidemiology PHI protected health information RdrP RNA-dependent polymerase RNA ribonucleic acid RT-PCR reverse transcription polymerase chain reaction S S spike protein SADS-CoV severe acute diarrhea disease virus SARI severe acute respiratory infection SARS severe acute respiratory syndrome SARS-CoV severe acute respiratory syndrome coronavirus SARS-CoV-2 SARS coronavirus 2 SPHERES Sequencing for Public Health Emergency Response, Epidemiology, and Surveillance VA U.S. Department of Veterans Affairs WGS whole genome sequencing WHO World Health Organization xiv PREPUBLICATION COPY: UNCORRECTED PROOFS

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In December 2019, new cases of severe pneumonia were first detected in Wuhan, China, and the cause was determined to be a novel beta coronavirus related to the severe acute respiratory syndrome (SARS) coronavirus that emerged from a bat reservoir in 2002. Within six months, this new virus—SARS coronavirus 2 (SARS-CoV-2)—has spread worldwide, infecting at least 10 million people with an estimated 500,000 deaths. COVID-19, the disease caused by SARS-CoV-2, was declared a public health emergency of international concern on January 30, 2020 by the World Health Organization (WHO) and a pandemic on March 11, 2020. To date, there is no approved effective treatment or vaccine for COVID-19, and it continues to spread in many countries.

Genomic Epidemiology Data Infrastructure Needs for SARS-CoV-2: Modernizing Pandemic Response Strategies lays out a framework to define and describe the data needs for a system to track and correlate viral genome sequences with clinical and epidemiological data. Such a system would help ensure the integration of data on viral evolution with detection, diagnostic, and countermeasure efforts. This report also explores data collection mechanisms to ensure a representative global sample set of all relevant extant sequences and considers challenges and opportunities for coordination across existing domestic, global, and regional data sources.

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