Abstract
The human immunodeficiency virus (HIV) epidemic in Fiji has progressed from a low prevalence state to a more generalized public health issue, characterized by rising transmission and nascent drug resistance. This thesis reports the first molecular epidemiological analysis of HIV-1 in Fiji, with the aim to describe viral subtypes and determine phylogenetic clustering in HIV-positive individuals. A total of 222 samples were collected from both antiretroviral-naïve and antiretroviral experienced HIV-1-positive Fijian individuals. RNA was extracted, purified and sequenced using the Illumina MiSeq platform, generating polymerase sequences for phylogenetic analyses. Phylodynamic analysis revealed an overwhelming dominance of HIV-1 subtype C (87%), with the rest being subtype B and minor recombinant forms. Phylogeographic modelling traced the origin of Fiji's epidemic to at least six separate introductions from foreign sources-primarily Africa and North America-between the 1980s and 2000s. Phylodynamic modelling estimated a peak effective reproductive number (Re) of 2.4 prior to 2015 and posterior means below 1.0 after 2017. However, the 95% credible interval for 2019-2021 included 1.0. The temporal association with expanded contact tracing and antiretroviral therapy is compatible with a beneficial effect but does not establish causality. Demographic analysis revealed a median age of 35 years among infected individuals, with 56% of the sequenced cohort being women and heterosexual contact being the predominant transmission route. Notably, drug resistance mutations were observed which justifies the need for the continued genomic surveillance in the country. The study also identified the emergence of injecting drug use–associated practices, including secondary blood exposure (“bluetoothing”), in which blood from an individual who has recently injected drugs is transferred to another person. This practice represents a high-risk route for HIV transmission, particularly among younger populations. The findings suggest the immediate need for the systematic integration of molecular surveillance into national HIV programs specifically targeting HIV patients, the implementation of targeted harm reduction strategies, and the improvement of antiretroviral therapy guidelines according to regional resistance patterns. This study addresses a dire knowledge gap concerning HIV in the Pacific, particularly in Fiji. It also offers necessary real i world data to inform public health decision-making, plan future activities, and facilitate continued control of the epidemic in Fiji and across the broader Pacific region.