Using molecular epidemiology to investigate HIV transmission and prevention efforts

The Human Immunodeficiency Virus (HIV) is a retrovirus that causes HIV infection and, if untreated, leads to Acquired Immunodeficiency Syndrome (AIDS) and death. An estimated 36.7 million people in the world are HIV-infected; around 10% of them live in Europe. In this thesis I use molecular epidemiology in combination with mathematical modelling and traditional epidemiological analysis to describe HIV transmission dynamics and to assess various HIV prevention strategies, which might help to inform public health decisions. I start by characterizing the explosive HIV growth in people who inject drugs (PWID) in Russia and Ukraine in the 1990s in Chapter 2. I chose those settings as a model system in which to study HIV transmission in PWID in the absence of prevention. I then use my estimates to build a mathematical model that can be used to evaluate preventive measures during HIV outbreaks in PWID. In Chapter 3 I analyse newly-generated HIV-1 subtype A genetic sequences from Ukraine and apply a novel method to show how HIV spread among Ukrainian regions shifted after the initiation of war on the country’s eastern borders. I show that, since 2014, HIV is moving westwards, carried by large-scale human migration. In Chapter 4 I created the largest Ukrainian subtype B (the second most prevalent HIV-1 subtype in Ukraine) dataset to date, and show how the virus distribution changed in the country over the last 15 years. I then simulated phylogenies under scenarios similar to the Ukrainian subtype A and subtype B epidemics, to study the performance of various phylodynamic models that are used to estimate changes in HIV population size and transmission dynamics from virus gene sequences. Finally, Chapter 5 describes the molecular epidemiological profiles of the two most prevalent HIV-1 subtypes in Portugal, subtypes B and G. I use novel phylodynamic approaches to trace and compare the effect of various public health interventions on the transmission dynamics of these subtypes, given their different transmission group composition.