Purpose of review: The purpose of this study is to summarize recent advances in public health applications of comparative methods for HIV-1 sequence analysis in real time, including genetic clustering methods.
Recent findings: Over the past 2 years, several groups have reported the deployment of established genetic clustering methods to guide public health decisions for HIV prevention in 'near real time'. However, it remains unresolved how well the readouts of comparative methods like clusters translate to events that are actionable for public health. A small number of recent studies have begun to elucidate the linkage between clusters and HIV-1 incidence, whereas others continue to refine and develop new comparative methods for such applications.
Summary: Although the use of established methods to cluster HIV-1 sequence databases has become a widespread activity, there remains a critical gap between clusters and public health value.