Metagenomic investigation of co-infections of Ebola virus disease and Lassa fever patients

Sequencing followed by metagenomic analysis is an extremely promising method for broad, unbiased disease profiling of patients for disease surveillance and diagnosis. Here, we use two popular metagenomics tools in union, k-mer-based Kraken with reads and BLAST- and LCAbased MEGAN with assembled contiguous sequence. We analyze sequence from 463 febrile and afebrile patients from Sierra Leone before and during the 2014 Ebola virus outbreak. We find that co-infection with malaria is correlated with increased survival of Ebola virus patients, from 18% survival rate to 53%. We also explore the utility of and emphasize the need for both positive and negative controls to distinguish and remove noise and contaminants from real signal, especially to keep up with increasing sensitivity in sequencing.

Department dc:contributor.department

Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2016

Author dc:creator

• Krasilnikova, Lydia A

Advisor dc:contributor.advisor

• Pardis Sabeti and Daniel Park

• Electrical Engineering and Computer Science.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about 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/1721.1/106113

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/106113