摘要Background: Four Integrase Strand Transfer Inhibitors (INSTIs) have been approved for HIV-1 by the Food and Drug Administration (FDA). Recently, resistance against these INSTIs drugs and cross-resistance among them have been reported. The aim of the current study was to evaluate INSTIs drug resistant patterns in patients having virology failure to INSTIs and mutation analysis in the Nef gene.Methods: Samples were collected from individuals who had treatment failure to INSTIs. DNA and RNA were extracted by QIAamp RNA and DNA extraction kit. The PCR reaction was performed by using Qiagen one step master mix and in-house developed primers. PCR products were sequenced by Sanger method and after performing the quality control in Recall web (http://pssm.cfenet.ubc.ca/home/process_data), drug resistant mutation was analyzed by Stanford database and phylogenetic analysis was performed by MEGA5 software. Results: The phylogenetic analysis was done by 42 reference subtypes and result revealed that our sequences are in subtype CRF-35AD. The integrase major and minor mutations, T66AY143R, Y143R and T97A, showed high to intermediate resistance level to Raltegravir and Elvitegravir, respectively. The analysis of RT-RNA and proviruses revealed that pattern of drug resistance was similar in these two patients in RNA and proviruses, respectively. Moreover, analysis of the Nef sequence by codon software revealed that there were no deletion and mutation in Nef gene. Conclusion: It is the first report regarding integrase inhibitor drug resistance in Iran. Considering the wide use of antiretroviral drugs, it is necessary to determine subtype-dependent resistance in Iranian society. It is also recommended that integrase inhibitor resistance should be evaluated in naive patients, and it needs more considerations in relation to the resistance to out locate integrase.