HIV phylogenetics

The recent flurry of criminal cases brought against people in the United Kingdom accused of infecting their sexual partner(s) with HIV has resulted in several convictions. This has caused concern among health professionals and community groups about the detrimental effect such cases may have on disclosure of HIV infection and uptake of voluntary HIV testing, which contrasts with the move to normalise HIV testing and clinical care. The potential negative effect of this on the public health programme to reduce transmission of HIV has been widely discussed in these pages1 2 and elsewhere.3

Virological evidence, specifically HIV gene sequence data obtained from the defendant and complainant, has been used in these cases because a prerequisite for establishing criminal liability is that the defendant caused the complainant's infection. Because HIV-1, like other RNA viruses, evolves rapidly, the virus isolated from independently infected people is typically distinct. The extent of similarity between viruses from different people is associated with the likelihood of a common source of infection.

Within infected people, viral populations expand from a small initial population, and the viral genome can change during chronic infection by up to 1% each year. Thus, an onward transmission, if it occurred some time after initial infection, is likely to involve a strain distinguishable …