Leveraging genomic and genetic diversity to gain insights into viral evolution and spread Open Access

Martin, Michael (Summer 2022)

Permanent URL: https://etd.library.emory.edu/concern/etds/1z40kv14t?locale=en


As viral pathogens replicate within host species, errors by the viral polyermase introduce differences between the original and replicated genomes. Even when these errors do not alter viral function, their accumulation over time leaves characteristic patterns representative of the biological context in which they arose. Fitting quantitative models to these data provides a way for researchers to interrogate these patterns. Here, we analyze influenza A and SARS- CoV-2 sequence data to better understand the dynamics of these pathogens across biological scales. We show that the within- ost evolution of influenza genomic diversity is highly stochastic, that transmission bottlenecks of SARS-CoV-2 between hosts are extremely small, and that population level SARS-CoV-2 transmission is characterized by rapid undetected geographic dispersion and a high degree of transmission heterogeneity between infected hosts. Our results as a whole add to the growing body of literature regarding the ecology and evolution of human RNA viruses and in particular highlight how these populations are shaped by cross-scale dynamics.

Table of Contents

1 Introduction

1.1 Generation of viral diversity 1.2 Processes which shape viral diversity 1.3 Characterizing viral diversity 1.4 Cross-scales analysis of acute viral diversity

2 Leveraging genomic diversity to gain insights into within host influenza dynamics

2.1 Abstract 2.2 Introduction 2.3 Materials and methods 2.3.1 Data source 2.3.2 Transmission analyses 2.3.3 DVG identification 2.3.4 DVG quality filtering 2.3.5 BlastN analysis 2.3.6 Statistical analyses and visualization 2.4 Results 2.4.1 Limited DVGs in plasmid controls 2.4.2 DVGs observed readily in clinical samples 2.4.3 Nearly ubiquitous NS DVG 2.4.4 DVG populations are dynamic 2.4.5 Limited evidence for the transmission of DVGs 2.5 Discussion 2.6 Supplementary 2.6.1 Supplementary Figures 2.6.2 SupplementaryTables 3 Insights from SARS-CoV-2 sequences 3.1 M.A.M Contributions 3.2 Published Manuscript 4 Comment on “Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2” 4.1 M.A.M Contributions 4.2 Published Manuscript 4.3 Supplement 5 Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel 5.1 M.A.M. Contributions 5.2 PublishedManuscript 5.3 Supplement 6 Unrecognized introductions of SARS-CoV-2 into the US state of Georgia shaped the early epidemic 6.1 M.A.M. Contributions 6.2 Published Manuscript 6.3 Supplement

7 Discussion

About this Dissertation

Rights statement
  • Permission granted by the author to include this thesis or dissertation in this repository. All rights reserved by the author. Please contact the author for information regarding the reproduction and use of this thesis or dissertation.
Subfield / Discipline
  • English
Research Field
Committee Chair / Thesis Advisor
Committee Members
Last modified

Primary PDF

Supplemental Files