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This article examines the profound impact of HIV molecular epidemiology on public health strategies, shedding light on its pivotal role in understanding transmission dynamics, guiding prevention efforts, monitoring drug resistance, and optimizing treatment protocols. Through advanced sequencing techniques and phylogenetic analysis, researchers can reconstruct transmission networks, identify high-risk groups, and pinpoint geographic hotspots [1]. This molecular insight informs targeted prevention strategies and allows for early outbreak identification. Additionally, molecular epidemiology aids in detecting drug-resistant mutations, enabling tailored treatment plans and preventing treatment failure. However, ethical considerations and legal implications must be carefully navigated. The integration of molecular epidemiology into public health practices offers a transformative approach to combating the HIV/AIDS pandemic [2].