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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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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

images

THE NATIONAL ACADEMIES PRESS
Washington, DC
www.nap.edu

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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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: 978-0-309-68091-2
International Standard Book Number-10: 0-309-68091-3
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.

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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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.

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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.

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Learn more about the National Academies of Sciences, Engineering, and Medicine at www.nationalacademies.org.

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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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.

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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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

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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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

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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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

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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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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.

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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Acronyms and Abbreviations

ARMoR Antimicrobial Resistance Monitoring and Research [Program]
CARB

Combating Antibiotic-Resistant Bacteria National Action Plan

CDC

U.S. Centers for Disease Control and Prevention

COG-UK

COVID-19 Genomics UK

CoV

coronavirus

COVID-19

coronavirus disease 2019

DoD

U.S. Department of Defense

DPH

department of public health

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

ICU

intensive care unit

IHR

International Health Regulations

ILI

influenza-like illness

ILINet

Influenza-like Illness Surveillance Network

IRB

Institutional Review Board

MERS

Middle East respiratory syndrome

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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MIS-C

multisystem inflammatory syndrome in children

N3C

National COVID Cohort Collaborative

NCBI

National Center for Biotechnology Information

NIH

National Institutes of Health

NYC

New York City

OCR

Office for Civil Rights

PHI

protected health information

RdRp

RNA-dependent polymerase

RT-PCR

reverse transcription polymerase chain reaction

SARS

severe acute respiratory syndrome

SARS-CoV

severe acute respiratory syndrome coronavirus

SARS-CoV-2

severe acute respiratory syndrome coronavirus 2

SPHERES

Sequencing for Public Health Emergency Response, Epidemiology, and Surveillance

WGS

whole genome sequencing

WHO

World Health Organization

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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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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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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