Evaluation of deep sequencing in determination of genotypic resistance and detection of multiple HIV infections in treatment-experienced HIV-infected patients in Taiwan

• Main Authors: Zong-Yu Yang, 楊宗諭
• Other Authors: Sui-Yuan Chang
• Format: Others
• Language: zh-TW
• Published: 2013
• Online Access: http://ndltd.ncl.edu.tw/handle/99978360278823942824

碩士 === 國立臺灣大學 === 醫學檢驗暨生物技術學研究所 === 101 === In Taiwan, the major transmisstion routes for HIV infection are men who have sex with men (MSM), injecting drug use (IDU), and hetersexual sexual contact. The major HIV subtypes in these three populations are subtype B, CRF07_BC, and subtypeB/CRF07_BC/CRF01_AE, respectively. The cocirculation of different subtypes in Taiwan has raised the concern of super-infection or co-infection by different HIV subtypes. In the past, due to the technical limitations of Sanger sequencing, co-infection or super-infection patients were difficult to be identified. Here we used the deep sequencing to investigate the presence of super-infection or co-infection in Taiwan and to evaluate its application in the genotypic drug resistance testing. First, we evaluated the applicability of next generation sequencing (NGS) primers in different subtypes from the database and the epidemic strains amplified in Taiwan. We selected three patients whose protease and reverse transcriptase sequences were previously defined as different genotypes to evaluate whether they were infected by different HIV subtypes. Nine patients infected with dominant HIV-1 subtypes in Taiwan were selected for comparison. We used Roche 454 NGS to investigate whether these patients had super-infection, and we determined the genotypic resistance of a patient with super-infection in a longitudinal follow-up study. Our data showed that the primers designed for NGS might not be suitable for all HIV subtypes. Super-infection (or co-infection) was observed in some cases. Because of multiple infections with HIV, recombinant strains did exist. Some undetected drug resistance mutants appeared in a minor viral population. In the longitudinal study, we observed the shift of different virus population, the rise and fall of recombinant strains, and the replacement of wild type by resistance strains. In conclusion, the NGS can be applied to detect the genetypic drug resistance and super-infection. Furthermore, the rate of super-infection in Taiwan may have been underestimated.