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

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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 (75A50120C00093). 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: 978-0-309-68091-2
International Standard Book Number-10: 0-309-68091-3
Digital Object Identifier: https://doi.org/10.17226/25879

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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.

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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 of Medicine and Professor 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

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:

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.

Contents

ACRONYMS AND ABBREVIATIONS

SUMMARY

1 INTRODUCTION

Coronavirus Evolution and SARS-CoV-2

The Power of Genomics in Understanding SARS-CoV-2

Study Charge

About This Report

References

2 APPLICATION OF GENOMIC EPIDEMIOLOGY IN PREVIOUS INFECTIOUS DISEASE OUTBREAKS

Previous Efforts to Integrate Analyses of Genomic, Clinical, and Epidemiological Data

Best Practices and Keys to Future Success

References

3 CURRENT GENOMIC EPIDEMIOLOGY EFFORTS RELATED TO SARS-CoV-2

Current SARS-CoV-2 Data Sources

Current Efforts to Integrate SARS-CoV-2 Genome Sequence Data with Clinical and Epidemiological Data

Concluding Remarks

References

4 FRAMEWORK TO TRACK AND CORRELATE VIRAL GENOME SEQUENCES WITH CLINICAL AND EPIDEMIOLOGICAL DATA

Considerations for Transmission, Evolution, and Clinical Disease

Opportunities to Support Data Integration

Infrastructure Needs

Partnerships, Coordination, and Capacity Considerations

Concluding Remarks

References

5 GOVERNANCE AND REGULATORY CONSIDERATIONS

Federalism Barriers and Opportunities

International Sharing Barriers

Perceived Versus Actual Domestic Legal Barriers

The Health Insurance Portability and Accountability Act (HIPAA)

Common Rule

Governance

Concluding Remarks

References

APPENDIXES

A COMMITTEE BIOSKETCHES

B PUBLIC COMMITTEE MEETING AGENDAS

Boxes, Figures, and Tables

BOXES

1-1 Defining Genomic Epidemiology

1-2 Statement of Task

FIGURES

1-1 Pathogen sequencing during infectious disease outbreaks can inform precise interventions

2-1 Customized database for the Antimicrobial Resistance Monitoring and Research (ARMoR) Program

3-1 A radial phylogenetic tree of a global set of 10,000 SARS-CoV-2 genomes available on GISAID

TABLES

S-1 Summary Table of Considerations for Transmission, Evolution, and Clinical Disease

4-1 Summary Table of Considerations for Transmission, Evolution, and Clinical Disease

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Acronyms and Abbreviations