In March 1998 six foreign medics (five Bulgarian nurses and a doctor from Palestine) joined the medical staff at Al-Fateh Children’s Hospital (AFH) in Benghazi, Libya. Two months later, several hundred child patients tested positive for HIV. The rash of HIV infections prompted many to suspect that the children were purposely infected by their caregivers. Not surprisingly, one year later, the six foreign medics were accused of purposefully infecting more than 400 children with HIV. Several scientific reports and papers have been published to show that the HIV strains isolated from the infected children are close to the locale HIV isolate and that the HIV infection started in the hospital prior to the arrival of Bulgarian medic workers (VISCO-COMANDINI et al., 2002; DE OLIVEIRA et al., 2006).
In this case study, students will collect the Libya Benghazi HIV sequences and other HIV reference sequences from Genbank, constructing phylogeny using various methods, and evaluate the validity of different arguments based on phylogeny.
Data set: About 80 nucleotide sequences of the gag protein gene isolated from the HIV-infected children at Banghazi, Libya are available at Genbank (VISCO-COMANDINI et al., 2002).
Software: R scripts based on the APE package (Analyses of Phylogenetics and Evolution), complemented by CLUSTALW, MEGA and MrBayes.
Learning outcomes: Quantitative reasoning based on molecular evolution and phylogeny. Critical reasoning by designing studies using proper controls. Students will also learn how to do bootstrap, an important concept in simulation and permutation.
References:
- HIV trial in Libya
Sequences for exercise: