**4. Conclusions**

The metagenomic proceeding is fast and highly sensitive to access the genetic diversity on the ecosystem in general. With the use of the metagenomic approach, in a few days, the scientific community has managed to obtain the complete SARS-CoV-2 genome. Because epidemiological studies are still conducted from the onset of diseases, outbreaks are still being worked on, not prevention. From this perspective, this methodology showed to be able to be applied to conduct epidemiological surveys and it should be widely applied to understand, by the genetic diversity, the molecular eco-epidemiology of viral agents before the pandemic time.
