**Abstract**

Humanity's history contains many pandemic reports and now the scientific community has the possibility to identify the pathogens before the disease emergency. In this perspective, it is essential to carry out large-scale epidemiological studies in key animals that are in constant contact with humans. For this, the next generation sequencing (NGS) by the metagenomic approach—genetic material recovered directly from samples without previous amplification—is able to reveal the hidden microbial diversity. Metagenomes' work aims to contribute to the facilitation of epidemiological studies through the adoption of simple effective strategies for the pathogens' identification, understanding the evolutionary dynamic of them before the pandemic time. Here, we have presented some examples related to the successful metagenomic approaches and the continuous advice of the researchers to identify viruses and other possible pandemic pathogens.

**Keywords:** environmental genetic material, phylogenetic network, biogeography, one health

### **1. Introduction**

Emerging pathogens (those that have recently been introduced, discovered, or recognized; that have recently evolved; or that have increased in incidence through geographic expansion or adaptation to a greater diversity of hosts—spillover; or that have shown changes in their pathogenic properties), especially viral agents, present a unique challenge for science and medicine because little is known about them before they cause epidemics from zoonotic sources. Zoonotic transmission can occur through an overflow event from one animal species to another, eventually causing infections in humans as well. For most of these viruses, therapies and/or vaccination strategies have not been developed, and therefore, clinical treatment options for infected patients are limited to nonspecific supportive therapy (adapted from [1]).

In general, the epidemiological studies are conducted passively, after the establishing horizontal transmission of each viral infectious disease or after spillover events. Such a conduct will certainly not be sufficient to meet the new demands for infectious diseases. Therefore, one health, a science that promotes ecological health through the interaction between human, animal, and environmental health, arises with the proposal that all health should be thought together so that it has a sustainable condition of existence.

In this perspective, it is essential to carry out large-scale epidemiological studies in key animals such as bats and rodents in general. For this, the next generation sequencing (NGS) by the metagenomic approach—genetic material recovered

directly from samples without previous amplification—is able to reveal the hidden microbial diversity. Metagenomes' work aims to contribute to the facilitation of epidemiological studies through the adoption of simple effective strategies for the pathogens' identification, understanding the evolutionary dynamic of them before the pandemic time.
