A project funded by São Paulo Research Foundation (FAPESP) combines molecular biology, genetic sequencing, and ecological surveillance to map emerging viruses in urban rodents.
The Institut Pasteur de São Paulo (IPSP) has just established the Urban Rodent Virology Laboratory, a new research group dedicated to identifying and characterizing zoonotic viruses present in rodent populations inhabiting large urban centers. The laboratory is coordinated by researcher Robert Andreata Santos, with an initial focus on the city of São Paulo.
The project is based on an integrated approach combining molecular, serological, and ecological surveillance, aiming to understand which viruses circulate among urban rodents—especially rats (Rattus norvegicus and Rattus rattus)—assess their zoonotic potential, and identify environmental factors that favor their spread. The data generated may support prevention strategies, surveillance, and zoonosis control, in coordination with the public health system.
The initiative is funded by FAPESP under the Young Investigator program and will be developed over five years at IPSP.
Active surveillance in an underexplored scenario
Although the presence of rodents in urban areas is widely recognized, studies on the viruses circulating in these animals remain scarce, both in Brazil and internationally. In general, attention tends to focus on well-established bacterial diseases such as leptospirosis. However, according to Santos, there is a significant gap in the systematic monitoring of potentially emerging viruses.
“Active surveillance of viruses in urban rodents is still underdeveloped worldwide. In many cases, we simply do not know what is circulating in these animals, nor whether these viruses may be associated with underreported human clinical conditions or confused with other common viral infections,” the researcher explains.
Viruses already identified in rodents include hantaviruses, arenaviruses, coronaviruses, rotaviruses, hepatitis E, and orthopoxviruses, among others. In the case of hantaviruses, for example, although reported cases in Brazil are not numerous, lethality can exceed 40% depending on the viral variant, reinforcing the importance of monitoring and active surveillance of zoonotic viruses in the country.
Partnership with municipal health surveillance
The project foresees a partnership with the Health Surveillance Coordination Office (COVISA/SMS) of the São Paulo Municipal Government. The collaboration, currently in the process of formalization, will allow access to areas with recorded rodent infestations and integration with ongoing public health actions.
In the initial phase, the work will be mainly based on the collection of fecal samples and dead animals found during routine population control activities carried out by the municipality. Samples will be sent to the IPSP laboratory, where researchers will analyze feces and different organs to identify the presence of viruses and understand their tropism—that is, which tissues are preferentially infected.
“By analyzing specific organs, we can infer possible transmission routes and assess risks associated with human exposure, such as aerosols or environmental contact,” Santos explains.
Sampling is expected to occur monthly or biweekly, following technical and biosafety criteria. Future stages of the project may include more complex studies, such as capturing live animals, depending on logistical feasibility and necessary authorizations.
Molecular biology, sequencing, and biosafety
The Urban Rodent Virology Laboratory will use advanced molecular biology techniques, such as real-time PCR and genetic sequencing, to broadly track viruses present in samples. In positive cases, it will be possible to precisely identify viral agents and compare variants found in different regions of the city.
When feasible, researchers may also perform viral isolation in the laboratory, enabling the study of genetic and functional characteristics of viruses, such as mutations associated with adaptation or pathogenic potential.
The choice of IPSP as the project’s host institution was strategic. The institute has robust biosafety infrastructure, including BSL-2 and BSL-3 laboratories, as well as consolidated experience in the surveillance of emerging and re-emerging pathogens.
“Working with viruses of environmental and animal origin requires not only equipment, but also an institutional culture focused on biosafety and rapid response to health risks. Pasteur brings these conditions together,” the researcher states.
Scientific and public health impact
In addition to generating unprecedented scientific knowledge on virus circulation in urban rodents, the project has the potential to directly contribute to public health. By providing qualified data to health authorities, the laboratory may support decision-making regarding control actions, monitoring of risk areas, and preparedness for potential localized outbreaks.
The group also intends to establish international collaborations, including partnerships with researchers from urban centers in the United States and Europe, enabling comparisons of viral diversity associated with rodents across different geographic and environmental contexts.
Robert Andreata Santos is a biomedical scientist with a PhD in Sciences from the University of São Paulo (USP), working in the field of virology and infectious diseases. He holds a degree in Biomedicine from the State University of Santa Cruz (UESC) and completed part of his training abroad, including an academic period at the University of Aveiro, in Portugal, through the Science Without Borders program.
He completed his master’s and PhD at USP, focusing on vaccines and diagnostic methods for arboviruses such as dengue and Zika. He also carried out a scientific internship at the Institut Pasteur in Paris, integrating the Biological Emergency Intervention Unit (CIBU), and worked as a postdoctoral researcher at the Federal University of São Paulo (Unifesp), studying immune responses to COVID-19 vaccination. Between 2023 and 2024, he conducted research in New York, where he had direct contact with studies on viral surveillance in urban rodents—an experience that contributed to the conception of his current project.