Genomic Epidemiology Data Infrastructure Needs for SARS-CoV-2: Modernizing Pandemic Response Strategies

by National Academies of Sciences, Engineering, and Medicine, Division on Earth and Life Studies, Board on Life Sciences, Health and Medicine Division, Board on Health Sciences Policy

Overview

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.

Product Details

ISBN-13:	9780309680912
Publisher:	National Academies Press
Publication date:	10/29/2020
Pages:	110
Product dimensions:	6.00(w) x 9.00(h) x (d)

Table of Contents

Acronyms and Abbreviations xiii

Summary 1

1 Introduction 9

Coronavirus Evolution and SARS-CoV-2 10

The Power of Genomics in Understanding SARS-CoV-2 11

Study Charge 14

About This Report 16

References 16

2 Application of Genomic Epidemiology in Previous Infectious Disease Outbreaks 19

Previous Efforts to Integrate Analyses of Genomic, Clinical, and Epidemiological Data 19

Best Practices and Keys to Future Success 25

References 27

3 Current Genomic Epidemiology Efforts Related to SARS-CoV-2 33

Current SARS-CoV-2 Data Sources 33

Current Efforts to Integrate SARS-CoV-2 Genome Sequence Data with Clinical and Epidemiological Data 41

Concluding Remarks 43

References 44

4 Framework to Track and Correlate Viral Genome Sequences with Clinical and Epidemiological Data 47

Considerations for Transmission, Evolution, and Clinical Disease 47

Opportunities to Support Data Integration 56

Infrastructure Needs 57

Partnerships, Coordination, and Capacity Considerations 62

Concluding Remarks 63

References 64

5 Governance and Regulatory Considerations 69

Federalism Barriers and Opportunities 70

International Sharing Barriers 70

Perceived Versus Actual Domestic Legal Barriers 72

The Health Insurance Portability and Accountability Act (HIPAA) 72

Common Rule 76

Governance 80

Concluding Remarks 81

References 83

Appendixes

A Committee Biosketches 85

B Public Committee Meeting Agendas 93