title: Analysis of Variability in HIV-1 Subtype A Strains in Russia Suggests a Combination of Deep Sequencing and Multitarget RNA Interference for Silencing of the Virus.
abstract: Any method for silencing the activity of the HIV-1 retrovirus should tackle the extremely high variability of HIV-1 sequences and mutational escape. We studied sequence variability in the vicinity of selected RNA interference (RNAi) targets from isolates of HIV-1 subtype A in Russia, and we propose that using artificial RNAi is a potential alternative to traditional antiretroviral therapy. We prove that using multiple RNAi targets overcomes the variability in HIV-1 isolates. The optimal number of targets critically depends on the conservation of the target sequences. The total number of targets that are conserved with a probability of 0.7-0.8 should exceed at least 2. Combining deep sequencing and multitarget RNAi may provide an efficient approach to cure HIV/AIDS.
authors.affiliation: Engelhardt Institute of Molecular Biology , Russian Academy of Sciences, Moscow, Russia .
authors.forename: Olga V
authors.initials: OV
authors.lastname: Kretova
authors.affiliation: Engelhardt Institute of Molecular Biology , Russian Academy of Sciences, Moscow, Russia .
authors.forename: Vladimir R
authors.initials: VR
authors.lastname: Chechetkin
authors.affiliation: Engelhardt Institute of Molecular Biology , Russian Academy of Sciences, Moscow, Russia .
authors.forename: Daria M
authors.initials: DM
authors.lastname: Fedoseeva
authors.affiliation: Engelhardt Institute of Molecular Biology , Russian Academy of Sciences, Moscow, Russia .
authors.forename: Yuri V
authors.initials: YV
authors.lastname: Kravatsky
authors.affiliation: Engelhardt Institute of Molecular Biology , Russian Academy of Sciences, Moscow, Russia .
authors.forename: Dmitri V
authors.initials: DV
authors.lastname: Sosin
authors.affiliation: Engelhardt Institute of Molecular Biology , Russian Academy of Sciences, Moscow, Russia .
authors.forename: Ildar R
authors.initials: IR
authors.lastname: Alembekov
authors.affiliation: Engelhardt Institute of Molecular Biology , Russian Academy of Sciences, Moscow, Russia .
authors.forename: Maria A
authors.initials: MA
authors.lastname: Gorbacheva
authors.affiliation: Engelhardt Institute of Molecular Biology , Russian Academy of Sciences, Moscow, Russia .
authors.forename: Natalya M
authors.initials: NM
authors.lastname: Gashnikova
authors.affiliation: Engelhardt Institute of Molecular Biology , Russian Academy of Sciences, Moscow, Russia .
authors.forename: Nickolai A
authors.initials: NA
authors.lastname: Tchurikov
mesh_terms: D000998:Antiviral Agents / Q000378:metabolism*; D014644:Genetic Variation / Q000187:drug effects*; D005838:Genotype; D057809:HEK293 Cells; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000187:drug effects* / Q000235:genetics / Q000302:isolation & purification; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008081:Liposomes / Q000378:metabolism; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000378:metabolism; D012426:Russia
chemical_list: D000998:Antiviral Agents; D008081:Liposomes; D034741:RNA, Small Interfering
keywords: HIV-1 in Russia; RNAi; deep sequencing; multiple targeting