Abstract
Nigeria has been reported to have the highest number of AIDS-related deaths in the world. In this study, we aimed to use molecular epidemiology to investigate the HIV-1 diversity and phylodynamics in Nigeria. We analyzed 1,442 HIV-1 pol sequences collected from 1999 to 2014 from seven geopolitical zones in Nigeria. The main circulating strains, CRF02_AG (44.1% of the analyzed sequences), Subtype G (8.3%), and CRF43_02G (16.4%), were introduced to Nigeria in the 1960s, 1970s, and 1980s, respectively. The number of effective infections decreased in Nigeria after the introduction of free antiretroviral treatment in 2006. We also found a significant number of unique recombinant forms (22.7%), the majority of which were recombinants between the two or three of the main circulating strains described above. In addition, phylogeographic analysis indicates multiple occasions of HIV-1 transmission between Lagos and Abuja (two of the main cities in Nigeria). Our results may be relevant for HIV-1 intervention and contribute in making informed decisions in strategies aiming at reducing further spread of HIV-1 in Nigeria.