Bioinformatics Education Dissemination: Reaching Out, Connecting and Knitting-together


HIV Problem Space

Markham RB, Wang WC, Weisstein AE, Wang Z, Munoz A, Templeton A, Margolick J, Vlahov D, Quinn T, Farzadegan H, Yu X-F. 1998. Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proc. Natl. Acad. Sci. USA 95: 12568-12573. The original paper presenting and analyzing the data on which this problem space is based.

Bailes E., Gao F., Bibollet-Ruche F., Courgnaud V., Peeters M., Marx P. A., Hahn B. H., Sharp P. M. 2003. Hybrid origin of SIV in chimpanzees. Science 300: 1713-???
Presents evidence that SIVcpz, the ancestor of HIV-1, was formed by recombination between SIVrcm (from red-capped mangabeys) and SIVgsn (from greater spot-nosed monkeys).

Cornelissen M, Mulder-Kampinga G, Veenstra J, Zorgdrager F, Kuiken C, Hartman S, Dekker J, van der Hoek L, Sol C, Coutinho R, et al. 1995. Syncytium-inducing (SI) phenotype suppression at seroconversion after intramuscular inoculation of a non-syncytium-inducing/SI phenotypically mixed human immunodeficiency virus population. J. Virol. 69: 1810-1818.
Discusses two cases of health-care workers accidentally infected with mixed populations of SI and NSI strains. SI strains were most common immediately after infection, but NSI strains predominated after serocoversion.

Hahn MW, Rausher MD, and Cunningham CW. 2002. Distinguishing between selection and population expansion in an experimental lineage of bacteriophage T7. Genetics 161: 11-20.
Refines standard neutrality tests to discriminate between the effects of selection and demography by examining synonymous and nonsynonymous substitutions separately.

Koot M, Keet IP, Vos AH, de Goede RE, Roos MT, Coutinho RA, Miedema F, Schellekens PT, Tersmette M. 1993. Prognostic value of HIV-1 syncytium-inducing phenotype for rate of CD4+ cell depletion and progression to AIDS. Ann. Intern. Med. 118: 681-688.
Studies the association between within-host evolution of HIV and host immunological function. The appearance of SI strains was found to correlate with subsequent increases in the rate of CD4 decline.

Vlahov D., Anthony J.C., Munoz A., Margolick J., Nelson K.E., Celentano D.D., Solomon L., Polk B.F. 1991. The ALIVE study: A longitudinal study of HIV-1 infection in intravenous drug users: Description of methods. NIDA Res. Monogr. 109: 75-100.
A comprehensive description of the ALIVE study. Available online at

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