RNA viruses are of great medical importance. Evolution of sequencing technologies has made it increasingly common to undertake large scale sequencing strategies to investigate infected populations to gain insigths into basic epidemiological, investigate individuals to gain insights into disease progression and evolutionary parameters of the infecting virus. The purpose of my current research is to investigate the human immunodeficiency virus (HIV) and hepatitis C virus (HCV) genetic diversity, transmission dynamics and drug resistance. I am combining a strong global health component (with active projects in sub-Saharan Africa) with laboratory investigations and state-of-art computational approaches. Most-at-risk-populations (MARPs) are a core group and pool for spread into the general population, and for this reason close surveillance of such populations are critical in order to address the epidemics of these viruses in an effective way. Advances in population genetic methods have integrated epidemiological models to accommodate viral sequence data in computational approaches and represent powerful and well established tools for hypothesis testing, estimating evolutionary rates of viruses both within an infected individual and in a population, associate transmissions clusters with sociodemographic data of the hosts and estimate population sizes. The use of these powerful techniques has greatly improved our understanding of the complex virus-host-population interactions and represents an invaluable asset in studies of viral genetic variability and evolution, and the link to disease progression and drug resistance development. Monitoring of these epidemics, through genetic characterization of the virus, drug resistance prevalence and the dynamics of the molecular epidemiology will be instrumental for designing novel diagnostic, prevention and treatment interventions, which will be important in the implementation of improved of public health policies.