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Annu Rev Virol. 2016 Sep 29;3(1):173-195. Epub 2016 Aug 3.

Genomic Analysis of Viral Outbreaks.

Wohl S1,2, Schaffner SF1,2,3, Sabeti PC1,2,3.

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FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138.
Broad Institute, Cambridge, Massachusetts 02142; email: ,
Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115.


Genomic analysis is a powerful tool for understanding viral disease outbreaks. Sequencing of viral samples is now easier and cheaper than ever before and can supplement epidemiological methods by providing nucleotide-level resolution of outbreak-causing pathogens. In this review, we describe methods used to answer crucial questions about outbreaks, such as how they began and how a disease is transmitted. More specifically, we explain current techniques for viral sequencing, phylogenetic analysis, transmission reconstruction, and evolutionary investigation of viral pathogens. By detailing the ways in which genomic data can help us understand viral disease outbreaks, we aim to provide a resource that will facilitate the response to future outbreaks.


evolution; infectious disease; phylogeny; sequencing; transmission

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