In many nations it is a crime to infect someone with HIV by intention or non-disclosure. As phylogenetic experts who advise courts worldwide, we are calling for guidelines on how phylogenetics should be used in criminal HIV investigations. The inappropriate use of such evidence in suspected transmission cases can have dire legal and social ramifications.

The scientist's job is not to argue for or against a defendant's guilt: that is a task for lawyers. Phylogenetic investigators should limit themselves to an expert opinion on what information about viral transmission can be deduced from their analysis. This must be derived impartially, for example by blinding the identities of case subjects.

Scientists must explain to courts that phylogenetic analysis cannot 'prove' any particular hypothesis, such as 'person A infected person B'. Rather, results may be compatible with several hypotheses, or support one over another.

An a priori hypothesis should be formulated by different, independent epidemiological experts, based on contact possibilities between the purported victim(s) and the defendant, and on any additional contacts or risk factors.

Phylogenetic analysis alone cannot exclude the possibility that HIV was transmitted from A to B through unsampled persons. Although the direction of viral transmission can sometimes be supported, it does not prove direct transmission.