Introduction Phylogenetic information provides new horizons for clinical case finding in HIV, but raises issues of acceptability, privacy and even criminalisation. We reviewed studies describing use of phylogenetics to directly inform case finding in community acquired stigmatised infectious diseases.

Methods A search in MEDLINE, Embase, CINAHL and PsychINFO for articles where phylogenetics have been used to facilitate case finding in sexually transmitted infections, TB, HBV or HCV, published until July 2016 in English.

Results 26 of 6042 papers screened met the inclusion criteria; 17 TB, 9 HIV. 19 studies reported using phylogenetics to identify and investigate HIV outbreaks but did not report its role in case finding. Case finding strategies included confirming the source of an outbreak to prompt wider investigation (HIV); investigation of phylogenetically clustered cases (TB, HIV); combined cluster and geographical information to target screening (TB); screening informed by discrepancies between genotypic and epidemiological data (TB); phylogenetic characterisation to inform a screening intervention (HIV); epidemiological data to identify of a source (HIV); and contact tracing with genotype matching to a phenotype (HIV). Facilitators included sharing molecular surveillance data to establish community support in targeted TB screening. Barriers included delayed results, time lapse between cases and refusal of access to premises for screening. However patient barriers were rarely reported. Ethical issues included media coverage of an HIV sources identity.

Conclusion Phylogenetics-informed approaches to case finding are feasible in stigmatised infections. However studies reporting their use in clinical and public health practice provide limited information on patient related barriers, acceptability, or on ethical challenges such as identification of “core” transmitters or criminalisation. Research into patient views on acceptability, risks and preferred approaches to using phylogenetic information for case finding in HIV is needed to inform interventions.