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Vol 52(2018) N 3 p. 393-397; DOI 10.1134/S002689331803007X Full Text

O.V. Kretova, M.A. Gorbacheva, D.M. Fedoseeva, Y.V. Kravatsky, V.R. Chechetkin, N.A. Tchurikov*

Mutation Frequencies in HIV-1 Genome in Regions Containing Efficient RNAi Targets As Calculated from Ultra-Deep Sequencing Data

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia

*tchurikov@eimb.ru
Received - 2017-06-07; Accepted - 2017-08-28

HIV-1 is one of the most variable viruses. The development of gene therapy technology using RNAi for AIDS/HIV-1 treatment is a potential alternative for traditional anti-retroviral therapy. Anti-HIV-1 siRNA should aim to exploit the most conserved viral targets. Using the deep sequencing of potential RNAi targets in 100-nt HIV-1 genome fragments from the clinical HIV-1 subtype A isolates in Russia, we found that the frequencies of all possible transversions and transitions in certain RNAi targets are 3-38 times lower than in adjacent sequences. Therefore, these targets are conserved. We propose the development of these RNAi targets for AIDS/HIV-1 treatment. Deep sequencing also enables the detection of the characteristic mutational bias of RT during the replication of viral RNA.

gene therapy, HIV-1, RNAi, mutations, RT, transversions, transitions, gene therapy, deep sequencing



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