Identification of reassortant influenza viruses at scale : algorithm and applications
Author(s)Ma, Eric J. (Eric Jinglong)
Massachusetts Institute of Technology. Department of Biological Engineering.
Jonathan A. Runstadler.
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Reassortment is a reticulate evolutionary process that results in genome shuffling; the most prominent virus known to reassort is the influenza A virus. Methods to identify reassortant influenza viruses do not scale well beyond hundreds of isolates at a time, because they rely on phylogenetic reconstruction, a computationally expensive method. This thus hampers our ability to test systematically whether reassortment is associated with host switching events. In this thesis, I use phylogenetic heuristics to develop a new reassortment detection algorithm capable of finding reassortant viruses in tens of thousands viral isolates. Together with colleagues, we then use the algorithm to test whether reassortment events are over-represented in host switching events and whether reassortment is an alternative 'transmission strategy' for viral persistence.
Thesis: Sc. D., Massachusetts Institute of Technology, Department of Biological Engineering, 2017.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student-submitted PDF version of thesis.Includes bibliographical references (pages 75-83).
DepartmentMassachusetts Institute of Technology. Department of Biological Engineering.
Massachusetts Institute of Technology