The 2016 Summer Olympic Games are expected to attract about 500,000 visitors to Rio de Janeiro, Brasil. Yet, until this year’s Olympics, there has never been an infrastructure to monitor the impact of such a large-scale human event on the city’s genetic profile.  As a part of a global consortium to monitor cities, we will pioneer the first-ever, city-scale collection and measure of the Olympics, dubbed the Olympiome.  We will track the localization, transit, and persistence of these visitors’ metagenomes and determine where they colonize and change the local urban metagenome of the host city, including the presence and the fluctuations of medically relevant entities such as anti-microbial resistance markers (AMRs) and phages.

For this, the nine busiest metro stations of Rio are being sampled before, during (3 times a week), and after for those sites recovering DNA and RNA. The swabbing plan, which will also cover non-touristic areas, will cover most geographical areas of Rio and will be continued for another 3 months after the games. Each one of the 1364 samples will be sequenced for DNA and RNA (>5 million reads) using a shotgun strategy allowing the coverage of a huge diversity of virus, fungi and bacteria present in urban microbiomes (Afshinnekoo et al., 2015). In parallel we will also collect geolocated Aedes mosquitoes from 9 different sites (at least 30 female mosquitoes/point), which will be investigated by the same shotgun sequencing approach for DNA and RNA viruses (including dengue, Zika and Chikungunya). Data produced here will be evaluated in the context of microbiota of another >50 urban environments from all 6 main continents, which has the potential of tracing back the origin of some organisms.

Whereas mass events have a role in spreading diseases around the globe, we believe that NGS-based surveillance approaches can be a powerful tool to detect the presence and emergence of microorganisms of potential health interest. The Zika flavirus, which was confined to some regions in the Pacific Ocean and Africa and caused no significant disease, is rapidly spreading. Of relevance, it is believed that it has arrived in Brazil during the 2014 World Cup that brought close 1-million visitors to the country. This project will be repeated during the 2020 Summer Olympic Games (Tokyo), and it could maybe be later used as a model for the surveillance of large cities and during other large-scale human events.