Impacts and shortcomings of genetic clustering methods for infectious disease outbreaks.

ABSTRACT: For infectious diseases, a genetic cluster is a group of closely related infections that is usually interpreted as representing a recent outbreak of transmission. Genetic clustering methods are becoming increasingly popular for molecular epidemiology, especially in the context of HIV where there is now considerable interest in applying these methods to prioritize groups for public health resources such as pre-exposure prophylaxis. To date, genetic clustering has generally been performed with ad hoc algorithms, only some of which have since been encoded and distributed as free software. These algorithms have seldom been validated on simulated data where clusters are known, and their interpretation and similarities are not transparent to users outside of the field. Here, I provide a b

SUBMITTER: Poon AF 

PROVIDER: S-EPMC5210024 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature