Biomathematics Emphasis Program at San Diego State University


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Matthew Hagen

Detection and visualization of HIV-1 sequences in the human genome

Matthew Hagen%, Rob Edwards, and Roland Wolkowicz§.

Department of Biology§ and Computer Science%, San Diego State University

The retroviral life cycle involves the relatively random integration of a DNA copy of the virus genome into host cell DNA. Once integrated, retroviruses remain in the genomes of their hosts; there are no known viral mechanisms for their excision. Over evolutionary time scales, the retroviral genomes may disappear or change by deletions and mutations, but their footprints may remain and be detected as sequences that are identical with known viral sequences. The DNA sequence of HIV-1 was compared with the human genome to detect possible remains of past integration events. Identical matches were found in all of the human chromosomes, with lengths that are longer than predicted to occur by chance. In some cases, the occurrences are clustered. The distribution of these matches is being analyzed to detect which viral genes have “survived”, and whether there is a preference for which genes have been deleted and which maintained. A tool for the visualization of the matches between the viral genome and the human genome has also been developed. In light of the high mutation rate of retroviruses, the analysis is being repeated with other HIV-1 sequences.