The applied genomic epidemiology handbook : a practical guide to leveraging pathogen genomic data in public health / Allison Black and Gytis Dudas.

Format:

Book

Author/Creator:

Black, Allison, author.

Dudas, Gytis, author.

Contributor:

Taylor & Francis eBooks

Dr. D. Sergeant Pepper Memorial Fund.

Series:

Computational biology series

Language:

English

Subjects (All):

Epidemiology.

Medical Subjects:

Epidemiology.

Physical Description:

1 online resource (xx, 144 pages).

Edition:

First edition.

Place of Publication:

Boca Raton : CRC Press, Taylor & Francis Group, 2024.

Biography/History:

Allison Black is a genomic epidemiologist passionate about strengthening public health's ability to use pathogen genomic data for outbreak response, disease surveillance, and decision-making. While she trained as an academic genomic epidemiologist, she now leads molecular epidemiology activities at the Washington State Department of Health. Gytis Dudas is an evolutionary biologist at Vilnius University's Life Sciences Center working on RNA virus evolution at both long- and short-term scales. Most of Gytis' PhD and postdoctoral work focused on the genomic epidemiology of Ebola virus in West Africa and MERS coronavirus in the Arabian Peninsula.

Contents:

Cover

Half Title

Series Page

Title Page

Copyright Page

Dedication

Contents

Preface

About the Authors

Contributors

CHAPTER 1: The Value of Pathogen Genomics in Applied Epidemiology

1.1. THE VALUE OF GENOMIC EPIDEMIOLOGY FOR SURVEILLANCE

1.2. THE VALUE OF GENOMIC EPIDEMIOLOGY FOR OUTBREAK RESPONSE

1.3. THE VALUE OF RETROSPECTIVE DATA

CHAPTER 2: Fundamental Theory in Genomic Epidemiology

2.1. THE OVERLAPPING TIMESCALES OF PATHOGEN EVOLUTION AND PATHOGEN TRANSMISSION

2.1.1. Viral Diversity Accumulates Over the Course of a Single Individual's Infection

2.1.2. Stochasticity and Selection Influence Variant Frequency Within an Infection

2.1.3. When a Transmission Event Occurs, the Within-Host Viral Diversity of the Infector is Sampled and Transmitted to the Recipient

2.1.4. Consensus Genomes Provide a Summary of the Within-Host Diversity

2.2. TERMINOLOGY FOR DESCRIBING CHANGES IN GENETIC SEQUENCES

2.3. MUTATION RATES, EVOLUTIONARY RATES, AND THE MOLECULAR CLOCK

2.4. MULTIPLE SEQUENCE ALIGNMENT

2.5. PHYLOGENETIC TREES

2.5.1. What is a Phylogenetic Tree?

2.5.2. Assessing and Reading a Phylogenetic Tree

2.5.3. Temporally Resolved Phylogenetic Trees

2.6. THE TRANSMISSION TREE DOES NOT EQUATE THE PHYLOGENETIC TREE

2.7. WHY IS SEQUENCING BETTER AT DISMISSING LINKS THAN CONFIRMING THEM?

2.7.1. How Many Mutations are Enough to Rule Linkage Out?

CHAPTER 3: Sample Selection

3.1. REPRESENTATIVE SAMPLING

3.2. TARGETED SAMPLING

3.3. CONTEXTUAL DATA

3.3.1. Contextual Data as a Backdrop

3.3.2. Contextual Data as Controls

CHAPTER 4: Public Health Use Cases of Genomic Epidemiology

4.1. ASSESSING EPIDEMIOLOGIC LINKAGE BETWEEN CASES

4.1.1. Fundamental Principles to Draw Upon

4.1.2. How Should You Sample?

4.1.3. Tools and Approaches You Can Use to Explore the Question

4.1.4. Caveats, Limitations, and Ways Things Go Wrong

4.1.5. Relevant Case Studies

4.2. EXPLORING RELATIONSHIPS BETWEEN CASES OF INTEREST AND OTHER SEQUENCED INFECTIONS

4.2.1. Fundamental Principles to Draw Upon

4.2.2. How Should You Sample?

4.2.3. Tools and Approaches You Can Use to Explore the Question

4.2.4. Caveats, Limitations, and Ways Things Go Wrong

4.2.5. Relevant Case Studies

4.3. ESTIMATING THE START AND DURATION OF AN OUTBREAK

4.3.1. Fundamental Principles to Draw Upon

4.3.2. How Should You Sample?

4.3.3. Tools and Approaches You Can Use to Explore the Question

4.3.4. Caveats, Limitations, and Ways Things Go Wrong

4.3.5. Relevant Case Studies

4.4. ASSESSING HOW DEMOGRAPHIC, EXPOSURE, AND OTHER EPIDEMIOLOGICAL DATA RELATE TO A GENOMICALLY DEFINED OUTBREAK

4.4.1. Fundamental Principles to Draw Upon

4.4.2. How Should You Sample?

4.4.3. Tools and Approaches You Can Use to Explore the Question

Notes:

Includes bibliographical references and index.

Electronic reproduction. London Available via World Wide Web.

Online resource; title from PDF title page (Taylor & Francis, viewed February 1, 2024).

Local Notes:

Acquired for the Penn Libraries with assistance from the Dr. D. Sergeant Pepper Memorial Fund.

ISBN:

9781003409809

1003409806

9781003853848

1003853846

9781003853824

100385382X

Publisher Number:

99996110968

Access Restriction:

Restricted for use by site license.