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Chronic infection by oncogenic Human papillomaviruses (HPVs) leads to cancers. Public health interventions, such as cancer screening and mass vaccination, radically change the ecological conditions encountered by circulating viruses. It is currently unclear how HPVs communities may respond to these environmental changes, because little is known about their ecology. Predicting the impact on viral diversity by the introduction of HPV vaccines requires answering the unresolved question of how HPVs interact. Although it is commonly believed that they do not interact (neutral theory), there are suggestions that HPV types may compete for resources or via the immune response (niche-based or non-neutral theory). Here, we applied for the first time established biodiversity measures and methods to epidemiological data in order to assess whether niche-partitioning or neutral processes are shaping HPV diversity patterns at the population level. We find that as infections progress toward cancer, HPVs communities become more uneven and a few HPVs play a stronger dominance role. By fitting species abundance distributions, we found that neutral models were always out-performed by non-neutral distributions, both in asymptomatic infections and in cancers. Our results suggest that temporally moving from a more even to a less even community implies an increase in competition, probably due to environmental changes linked to infection progression. More ecological thinking will be required to understand present-day interactions and to anticipate the future of the long lasting interactions between HPVs and humans.SIGNIFICANCE STATEMENTHuman papillomaviruses (HPVs) are very diverse. Infections by HPVs are very common and chronic infections may lead to cancers. The more oncogenic HPVs are now targetted by effective vaccines, and this has raised the question of whether there may be a viral replacement if these dominant types were removed. This is a medical version of a classical ecological controversy, namely how much biodiversity distributions and community dynamics are explained by neutral theory plays out across ecosystems. For HPVs, epidemiologic studies before and after the vaccination have led to the widespread belief that these viruses do not interact. Here, we apply different methods developed in macroecology to the best available epidemiologic data to address this issue. Consistently, we find that HPVs form non-neutral communities. Instead, competitive niche-partitioning process and dominance explain best HPVs communities. We also find that the vaccine might not change such competitive niche processes. Beyond clinical implications, this garners support that niche processes often best explain biodiversity patterns, even in human viral communities.