4th International Workshop on HIV Drug Resistance & Treatment Strategies Sitges, Spain, 12–16 June 2000

COMPARISON OF EVOLUTIONARY DISTANCES BETWEEN DNA POLYMERASE AND RNASE H DOMAINS OF HIV-1 REVERSE TRANSCRIPTASE IN PATIENTS TREATED WITH ZIDOVUDINE AND LAMIVUDINE

Antivir Ther. 2000 Jun 12-16; 5 (Suppl. 3):16 (Abstract 19

TC Stoeckli, CY Duan, D Shugarts and DR Kuritzkes
Division of Infectious Diseases, University of Colorado Health Sciences Center, Denver, Col., USA

OBJECTIVES: To study the selection pressure of nucleoside RT inhibitors on the DNA polymerase and RNase H domains of HIV-1 RT, by comparing non- synonymous and synonymous distances (rooted in the subtype B consensus sequence) of the DNA polymerase and RNase H coding regions of pol genes, from HIV-1 isolates obtained from patients treated with zidovudine and lamivudine.

METHODS: Thirteen isolates of HIV-1 were cultured from PBMC of 10 patients after prolonged treatment with nucleoside analogue therapy that included zidovudine and lamivudine. One to three biological clones were isolated from each primary isolate by limiting dilution culture. Three full-length molecular clones of RT were sequenced from each biological clone to derive consensus sequences. The non-synonymous (En), synonymous (Es) and total evolutionary distances [E(n+s)] between the consensus sequence of each of the 24 biological clones and the subtype B consensus sequence, were calculated separately for the DNA polymerase and the RNase H coding regions.

RESULTS: Mean (±SD) evolutionary distances for DNA polymerase and RNase H domains, respectively, were: En=0.0238 (±0.0077) and 0.0133 (±0.0076); Es=0.0971 (±0.0171) and 0.1104 (±0.0427); E(n+s)=0.0383 (±0.0076) and 0.0367 (±0.0087). The mean En for the DNA polymerase domain of these isolates compared to B consensus was significantly greater than the mean En for the RNase H domains (P<0.001). Differences for Es and E(n+s) between the two domains were not significant. After excluding mutations in the DNA polymerase coding region known to be associated with drug resistance, mean En for the DNA polymerase region was still significantly higher than mean En for RNase H (En: 0.0188±0.0054; P<0.01).

CONCLUSION: Significantly higher non-synonymous evolutionary distances of the DNA polymerase domain of RT suggest higher selection pressure by treatment with nucleoside RT inhibitors on the DNA polymerase domain than on the RNase H domain of HIV-1 RT. This difference was still significant after excluding positions from the alignment at which resistance mutations occur, suggesting the selection of additional, possibly compensatory mutations in the DNA polymerase domain.

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2000-06-12
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