Human immunodeficiency virus type 1 (HIV-1) infection is a life-long threat which cannot be prevented by vaccination or completely cured by antiretroviral (ARV) treatment. The establishment of genotypic resistant testing (GRT) greatly improved the infection management and provided further guidelines on ARV strategies. The current study aimed to utilize the accumulated GRT data to investigate the HIV-1 molecular epidemiology, trends of drug resistance mutations (DRMs) among local patients and intra-host viral evolution. In order to maximize the therapeutic options for HIV-1 patients, the genotypic study also extended to two relatively new ARV classes for determination of integrase polymorphisms and tropism prevalence. From 1994 through 2013, a total of 3,108 plasma samples were available from 2,475 HIV-1 positive patients for epidemiological and viral investigations. The predominant genotypes in Hong Kong were subtype B (42.1%) and CRF01_AE (39.7%). Other genotypes including subtypes A1, C, D, F1, G, CRF02_AG, CRF06_cpx, CRF07_BC, CRF08_BC and CRF12_BF were also identified. Though the phylogenetic studies of subtype B and CRF01_AE identified several sporadic distinct clusters, their transmissions had been widely established between all local risk groups. In contrast, most of the non-B and non-AE cases were infected outside Hong Kong or circulated within non-Chinese population. However, one of the clusters in CRF07_BC suggested that this genotype might have been established quite well among local Chinese men-who-have-sex-with-men community. Routine GRT also provided valuable longitudinal data to study intra-host viral evolution. The observed intra-host evolutionary rates in CRF01_AE variants (11.68 x 〖10〗^(-4), IQR: 8.87 – 20.54 x 〖10〗^(-4) substitutions per site per year) was significantly higher than subtype B variants (5.27 x 〖10〗^(-4), IQR: 3.32 – 8.01 x 〖10〗^(-4) substitutions per site per year). Of 2,157 treatment-naïve patients included in this study, 4.4% of them were found carrying surveillance protease (PR) or reverse transcriptase (RT) DRMs. More importantly, half of the GRT data from 407 treatment-failure patients were potentially resistant to PR or RT inhibitors. The introduction of integrase inhibitors and CCR5 antagonists provided new insights and era for treating HIV-1 patients who were resistant to PR or RT inhibitors. The integrase GRT results showed that there were no major DRMs observed in integrase inhibitors-naïve patients. The distribution of integrase polymorphic sites between subtype B and CRF01_AE was significantly differed. On the other hand, the prevalence of X4/Dual-Mixed tropism in CRF01_AE variants was always significantly higher than subtype B, regardless of the interpretation algorithms and treatment history. In conclusion, this study demonstrated the HIV-1 molecular epidemiology and intra-host viral evolution of Hong Kong in the last two decades by utilizing the GRT data obtained from the ARV surveillance program. The in-house integrase GRT and genotypic tropism test were as well evaluated. The high prevalence of X4/Dual-Mixed tropism in CRF01_AE isolates would definitely limit the salvage therapeutic options for CRF01_AE-infected patients. Summarizing these findings, it is possible to project that CRF01_AE virus has unique characteristics from subtype B and should be investigated further in terms of disease progression and replicative capacity. / published_or_final_version / Microbiology / Doctoral / Doctor of Philosophy