Identification of reassortant influenza viruses at scale : algorithm and applications

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.

Department dc:contributor.department

Massachusetts Institute of Technology. Department of Biological Engineering.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2017

Author dc:creator

• Ma, Eric J. (Eric Jinglong)

Advisor dc:contributor.advisor

• Jonathan A. Runstadler.

• Biological Engineering.

Statement dc:rights

• MIT theses are protected by copyright. They may be viewed, downloaded, or printed from this source but further reproduction or distribution in any format is prohibited without written permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/112387

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/112387