This dissertation, "Molecular Epidemiology of HIV-1 and Characterization of Drug ResistantHIV-1 in Hong Kong" by H K, Jonathan, Chen, 陳漢坤, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. Abstract: Abstract of thesis entitled Molecular Epidemiology of HIV-1 and Characterization of Drug Resistant HIV-1 in Hong Kong submitted by Jonathan H.K. Chen for the degree of Doctor of Philosophy at the University of Hong Kong in August 2007 Human immunodeficiency virus type 1 (HIV-1) pandemic has spread throughout all civilized continents in last 20 years. The first HIV-1 case in Hong Kong was reported in 1984. Subsequently, HIV-1 infections in Hong Kong increased gradually and drug resistant mutants were identified in recent years. In this study, an in-house genotyping resistance test (GRT) was evaluated and the developed protocol was extended to investigate our HIV-1 epidemic history and drug resistance mutations among diverse HIV-1 genotypes. The end point detection of this in-house GRT reached 400 copies/mL on HIV-1 plasma samples with diverse genotypes. It showed high concordance to the TM FDA-approved ViroSeq GRT on drug resistance mutation detection. A total of 771 HIV-1 positive patients were recruited between 1994 and 2006. The prevalent genotypes in Hong Kong were subtype B and CRF01_AE. Other genotypes including subtype A1, C, D, G, CRF02_AG, CRF06_cpx, CRF07_BC, CRF08_BC and some new recombinants were also detected. Phylogenetic analyses identified 6 local transmission clusters, mainly in the Chinese men who have sex with men and injecting drug users in Hong Kong. The subtype B viruses were responsible for the first HIV-1 epidemic in Hong Kong starting from late 1980s. CRF01_AE viruses were subsequently detected during early 1990s. For HIV-1 detected among 771 patients, amino acid insertions at protease (PR) codon 35 were identified in 13 subtype B and 1 CRF01_AE isolates. The prevalence of this insertion in Hong Kong was 9 times higher than that reported in the western countries. Novel insertion patterns E35E_D, E35E_E and E35D_ID were detected among our samples. The E35E_E and E35E_D inserted samples were estimated to exhibit divergence time in 1994 and 2006 respectively. Through the pseudo-typed phenotyping test, viral strains with the insertion in the PR could decrease the IC 50 towards IDV and NFV comparing to the wildtype virus. The structural differences between the 3-dimentional protein models of the wildtype and inserted PRs further illustrated the association between the PR codon 35 insertions and PI resistance. In Hong Kong, mutations leading to primary resistance were found in 6.7% of treatment naive HIV-1 samples since 1996. Baseline GRT may be essential before initiating antiretroviral therapy. Among treatment failure samples, significant differences in the prevalence of some major drug resistance mutations were observed between subtype B and CRF01_AE isolates. Secondary mutations at PR codon 10 and 20 apparently associated with clinical failure cases with subtype B viruses. Among the natural polymorphisms of CRF01_AE strains, potential resistance related mutations V179D and R211K were found in high frequencies. In future, large scale screening of resistance related natural polymorphisms among non-B viruses should be initiated. In conclusion, our findings shed light to the potential applications of in-house GRT on HIV-1 epidemiology investigation and drug resistance monitoring. This study also highlights the differential prevalence of drug resistance mutation development in HIV-1 CRF01_AE, which is relevant to other prevailing regions