Virology By The Numbers: A Quantitative Exploration of Viral Energetics, Genomics, and Ecology

• Main Author: Mahmoudabadi, Gita
• Format: Others
• Published: 2018
• Online Access: https://thesis.library.caltech.edu/10812/1/GitaMahmoudabadiThesis-postProofFinal.pdf; Mahmoudabadi, Gita (2018) Virology By The Numbers: A Quantitative Exploration of Viral Energetics, Genomics, and Ecology. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z9Q81B91. https://resolver.caltech.edu/CaltechTHESIS:04172018-174233725 <https://resolver.caltech.edu/CaltechTHESIS:04172018-174233725>

<p>Over the past couple of decades, technological advancements in sequencing and imaging have unequivocally proven that the world of viruses is far bigger and more consequential than previously imagined. There are 10³¹ viruses estimated to inhabit our planet, outnumbering even bacteria. Despite their astronomical numbers and staggering sequence diversity, environmental viruses are poorly characterized. In this thesis we will demonstrate our three-pronged exploration of viruses through the lenses of energetics (Chapters 2 and 3), genomics (Chapter 4) and ecology (Chapter 5). We will first focus on one of the defining features of viruses, namely their reliance on their host for energy, and demonstrate the energetic cost of building a virus and mounting an infection. In our second study, we present one of the largest surveys of complete viral genomes, providing a comprehensive and quantitative snapshot of viral genomic trends for thousands of viruses. In our third study, we shift our focus towards ecological questions surrounding the large number of commensal phages inhabiting the human body. We discovered that phage community composition could serve as a fingerprint, or a "phageprint" – highly personal and stable over time. To our knowledge, this study is one of the largest studies of human phages and the first to demonstrate the feasibility of human identification based on phage sequences.</p>