Near real-time monitoring of HIV transmission hotspots from routine HIV genotyping: an implementation case study.

ABSTRACT:

Background

HIV evolves rapidly and therefore infections with similar genetic sequences are likely linked by recent transmission events. Clusters of related infections can represent subpopulations with high rates of transmission. We describe the implementation of an automated near real-time system to monitor and characterise HIV transmission hotspots in British Columbia, Canada.

Methods

In this implementation case study, we applied a monitoring system to the British Columbia drug treatment database, which holds more than 32 000 anonymised HIV genotypes for nearly 9000 residents of British Columbia living with HIV. On average, five to six new HIV genotypes are deposited in the database every day, which triggers an automated reanalysis of the entire database. We extracted clust

SUBMITTER: Poon AF 

PROVIDER: S-EPMC4853759 | biostudies-literature | 2016 May

REPOSITORIES: biostudies-literature