Evolution of Relative Synonymous Codon Usage in Human Immunodeficiency Virus Type 1

Mutation in HIV-1 is extremely rapid, a consequence of a low-fidelity viral reverse transcription process. The envelope gene has been shown to accumulate substitutions at a rate of approximately 1% per year and can frequently spend a long time in the host (approximately 10 years). The relative synonymous codon usage (RSCU) in HIV-1 is known to be different from that of the human host. However, by reengineering the protein coding sequences of HIV-1 to reflect the RSCU patterns observed in humans, a large increase in protein expression is observed. It is reasonable to suggest that within a host there may be a selective drive for change in the RSCU of HIV-1 towards human RSCU. To test this hypothesis we analysed HIV-1 partial envelope sequences from 8 patients sampled serially in time. For each sequence, an RSCU table was constructed. Sequences were labelled as "early" or "late" depending on whether they were sampled before or after the mid-point of the study. Using t...

• Type: Conference
• Year: 2004
• Where: APBC
• Authors: Peter L. Meintjes, Allen G. Rodrigo
• Keywords: APBC 2004, APBC 2007, HIV-1, Human Rscu, Viral Rscus