Data Infrastructure Needs
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
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
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.
Coronavirus Evolution and SARS-CoV-2
The Power of Genomics in Understanding SARS-CoV-2
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
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
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
Partnerships, Coordination, and Capacity Considerations
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)
Boxes, Figures, and Tables
1-1 Defining Genomic Epidemiology
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
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
|ARMoR||Antimicrobial Resistance Monitoring and Research [Program]|
Combating Antibiotic-Resistant Bacteria National Action Plan
U.S. Centers for Disease Control and Prevention
COVID-19 Genomics UK
coronavirus disease 2019
U.S. Department of Defense
department of public health
Global Initiative on Sharing All Influenza Data
U.S. Department of Health and Human Services
health information exchange
Health Insurance Portability and Accountability Act
intensive care unit
International Health Regulations
Influenza-like Illness Surveillance Network
Institutional Review Board
Middle East respiratory syndrome
multisystem inflammatory syndrome in children
National COVID Cohort Collaborative
National Center for Biotechnology Information
National Institutes of Health
New York City
Office for Civil Rights
protected health information
reverse transcription polymerase chain reaction
severe acute respiratory syndrome
severe acute respiratory syndrome coronavirus
severe acute respiratory syndrome coronavirus 2
Sequencing for Public Health Emergency Response, Epidemiology, and Surveillance
whole genome sequencing
World Health Organization