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| HIV and Forensic Uses of Phylogenetics |
Phylogenetic methods have been used to solve practical problems, including determining the sources of infection from HIV. This retrovirus evolves at an extremely rapid rate, owing to its exceptionally high mutation rate. In fact, sequences of HIV genes taken from the same infected individual can be as different as sequences from some homologous genes in humans and birds. Its rapidity of evolution works to HIV's advantage as it wreaks havoc on the immune system. On the other hand, scientists can take advantage of that rapid evolution to study the relationships between HIV and other similar viruses.
Researchers at the Centers for Disease Control and Prevention (CDC) used phylogenetic systematics of HIV for forensic purposes. During the early 1990s a Florida dentist was suspected of transmitting HIV to several of his patients. After the first case of probable transmission surfaced, the dentist wrote an open letter to his patients suggesting that they be tested for HIV. At least ten of the patients tested positive for HIV. However, a few of the infected individuals had other risk factors; therefore, there was the distinct possibility that they had not been infected by the dentist. The CDC researchers sequenced the HIV gp120 gene from several viral isolates taken from the dentist, his infected patients, and non-patients who were also infected. From the phylogeny constructed based on the HIV sequence data, they first denoted what they called the "dentist clade." This monophyletic group contained sequences from the HIV sequences collected from the dentist but not from the non-patients. Five of the patients had viral sequences that were contained in the dentist clade. These patients also lacked other risk factors. Thus, by strong inference, the CDC researchers determined that the dentist had infected these five patients.
There was some controversy over whether or not the dentist clade identified in the CDC study was reliable. Nucleotides in the HIV gp120 gene do not evolve in same way as in other genes. Instead of transitions being universally more prevalent than transversions, as is the case in most genes, A to C transversions are more frequent than transitions of C to T. There was also concern about the types of algorithms used. To address these concerns, David Hillis, John Huelsenbeck, and Cliff Cunningham re-analyzed the data of the CDC study. They found that, under nearly all circumstances, the same dental clade was obtained.4 Thus, the results were statistically reliable. Investigators are using similar studies to determine the source of the anthrax used in the attacks of October 2001.