HIV-1 Genotyping and Resistance Analysis

Plasma HIV-1 RNA load was detected using the Roche COBAS-TaqMan Assay (HIV-1 Test, version 2.0, Indianapolis, IN, United states). The target fragment for the subgenotyping includes 99 amino acid coding codons from the protease (PR) region, and resistance analysis consists of approximately 300 amino acid coding codons from the reverse transcriptase region (primer sequences listed in Supplementary Table S1). The subgenotype of HIV-1 was tested using Bioedit and MEGA5 software with the standard strains selected from the Los Alamos HIV database, and mutation sites were identified using the Stanford HIV-resistant database (Rhee et al., 2017 (link); Zhang et al., 2017 (link)).

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Guo P.L., He H.L., Chen X.J., Chen J.F., Chen X.T., Lan Y., Wang J., Du P.S., Zhong H.L., Li H., Liu C., Li L.Y., Hu F.Y., Tang X.P., Cai W.P, & Li L.H. (2021). Antiretroviral Long-Term Efficacy and Resistance of Lopinavir/Ritonavir Plus Lamivudine in HIV-1-Infected Treatment-Naïve Patients (ALTERLL): 144-Week Results of a Randomized, Open-Label, Non-Inferiority Study From Guangdong, China. Frontiers in Pharmacology, 11, 569766.

Publication 2020

COBAS-TaqMan Assay (HIV-1 Test, version 2.0

Amino acid Assay Codons Hiv 1 Hiv test Mutation Plasma Primer Protease Reverse transcriptase Strains

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Variable analysis

independent variables

Plasma HIV-1 RNA load detection using the Roche COBAS-TaqMan Assay (HIV-1 Test, version 2.0)
Subgenotyping of HIV-1 using Bioedit and MEGA5 software with standard strains selected from the Los Alamos HIV database
Mutation sites identification using the Stanford HIV-resistant database

dependent variables

HIV-1 subgenotype
Mutation sites in the reverse transcriptase region

control variables

Target fragment for the subgenotyping includes 99 amino acid coding codons from the protease (PR) region
Resistance analysis consists of approximately 300 amino acid coding codons from the reverse transcriptase region

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