COVID-19 pandemic is clear wake-up call to monitor for novel infectious agents, scientists warn | AGÊNCIA FAPESP

COVID-19 pandemic is clear wake-up call to monitor for novel infectious agents, scientists warn In an online seminar held by FAPESP, experts stressed that deforestation favors pathogen spillover from wild animals to humans, and that zoonotic disease surveillance urgently needs to be upgraded (image: webinar screenshot/FAPESP)

COVID-19 pandemic is clear wake-up call to monitor for novel infectious agents, scientists warn

September 29, 2021

By Maria Fernanda Ziegler  |  Agência FAPESP – Among the loudest alarms sounded in Brazil by the COVID-19 pandemic was the urgent need to enhance zoonotic disease surveillance. Zoonoses are infectious diseases transmitted from animals to humans. Advancing deforestation is known to favor what scientists call spillover events in which pathogens are transmitted from species living in the wild to our own. HIV/AIDS, Ebola, Lyme disease, malaria, rabies and very probably COVID-19 are all thought to have spilled over in this sense.

The importance of more comprehensive monitoring and other strategies to prevent the emergence of fresh pandemics was discussed in the fourth and last webinar of the series Health and Environment in the Amazon in the Context of COVID-19, held on August 26, 2021.

The discussion was proposed by researchers who are working on the project After hydropower dams: social and environmental processes occurring since the construction of Belo Monte, Jirau and Santo Antônio in the Brazilian Amazon, supported by FAPESP under the auspices of the São Paulo Excellence Chair (SPEC) program. 

“One may well wonder why no pandemics have started in Brazil so far. Tropical regions with a great many species of mammals are considered hotspots for the emergence of zoonotic diseases. The fact is that we’re still importing more than exporting infectious agents. Nevertheless, the pace of deforestation has accelerated, especially in the Amazon, Pantanal and Cerrado [Brazilian savanna], so one can imagine what this may mean,” said Márcia Chame, a researcher at Oswaldo Cruz Foundation (FIOCRUZ), an arm of Brazil’s Ministry of Health.

According to Chame, who heads the Center for Information on Wildlife Health (CISS) at FIOCRUZ, environmental destruction makes it even more urgent to increase surveillance in parks and nature reserves, especially with regard to animals considered sentinels of zoonotic diseases, as in the case of monkeys for yellow fever.

“Brazil doesn’t do enough monitoring or have good enough models to predict where outbreaks of diseases are likely,” she said. “This is extremely necessary but hard to do because it requires multidisciplinary teams of researchers as well as the involvement of government and the general public.”

The FIOCRUZ group developed a software application called SISS-Geo (short for Wildlife Health Information System), an online tool for recording field observations of animals using mobile communications devices. It was used to monitor the 2018 yellow fever outbreak and predict future disease hotspots. Almost 3,000 people died from yellow fever in the Southeast alone that year.

“Our monitoring work enabled us to understand the paths of the disease,” Chame said. “We transposed these corridors to Paraná and Santa Catarina states, and with the app used by municipal governments [to track monkey deaths], it was possible to classify areas according to the degree of risk. Vaccine rollout was planned on this basis, identifying priority areas and organizing crews to go out into the remoter rural areas.”

Direct correlation

Marcus Barros, a former head of the National Amazon Research Institute (INPA) and of IBAMA, Brazil’s main environmental law enforcement agency, stressed the direct correlation between deforestation and successive outbreaks of old and new diseases in the Amazon.

“I’m alarmed by news of the dismantling of environmental policies in the Amazon and the disastrous consequences for the environment and human health,” Barros said. “We know deforestation is the main cause of the spread of disease, and that the environment and health are closely linked.”

According to Barros, history points to a link between outbreaks of malaria and gold prospecting or large infrastructure projects in the Amazon. “Another example is Chagas disease, which used not to occur in the Amazon but then appeared well upstream among riverine communities who grow cabbage palm [açaí] and Cattley guava [araçá],” he said.

Barros went on to note a link between deforestation and cases of leishmaniasis back in the 1970s and 1980s when he had a teaching job. “The more forest was cleared, the more new cases of the disease there were. We realized this when the São José Operário neighborhood [in eastern Manaus, capital of Amazonas state] was built in the 1980s. The number of cases of cutaneous leishmaniasis jumped from 30 to 200 in a matter of days, pointing to a direct correlation between the disease, deforestation, and unplanned settlement of the area,” he said.

In his 50-year career as a physician and professor of infectious diseases, Barros has also observed the emergence of new diseases in the region. “An example is Altamira hemorrhagic fever [in Pará state, North Brazil], also known as Lazarus black fever. Visceral leishmaniasis and Chagas disease are also new to the region,” he said.

Health policy should be different in the Amazon and the rest of the country owing to the region’s characteristics, he added, especially climate, population density, and ethnic diversity. “COVID-19 came to the Amazon in the context of this government’s encouragement of deforestation. In principle, local authorities minimized the risks. The necessary preventive care was neglected. Not even the region’s characteristics were taken into account, such as low resistance to viral diseases among Indigenous peoples, a well-known fact. There has been no planning or improvement of the medical infrastructure. On the contrary, central government has preferred a totally anti-scientific strategy, including distribution of medications without any efficacy against COVID-19,” he said.

For Ester Sabino, a professor at the University of São Paulo’s Medical School (FM-USP) and principal investigator for the Brazil-UK Center for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE), strategies must urgently be implemented to detect the risk of epidemics before they occur, and this can be done by monitoring viruses, host animals and reservoirs.

“This is nice on paper but difficult in practice, not least because the technologies capable of detecting these viruses are very expensive and hard to offer on a large scale to the general public,” Sabino said. “Also, it’s hard to import materials for the study of pathogens. A primer for PCR [a laboratory technique used to identify pathogens from their genetic makeup] takes more than 30 days to reach Brazil, for example. All this research technology needs to be available to scientists.”

The COVID-19 pandemic has shown the importance of monitoring for pathogens. “It’s interesting to observe how China detected the first case of COVID-19 because it makes one wonder whether we would have been prepared if such a case of pneumonia had been detected in a São Paulo market, for example,” Sabino said. “If the etiological agent of a pneumonia isn’t constantly monitored, it appears to be a viral disease like any other and no one notices the kind of case correlations that characterize an epidemic for a long time.”

The absence of systematic diagnosis results in a long gap between the circulation of novel viruses and detection of the first cases. “A recent study based on zika virus sequencing enabled us to infer that zika entered Brazil almost 18 months before the first case was notified,” she said. “This evidences the need to reduce the cost of tests in order to increase our capacity to detect pathogens. After all, a novel virus can enter the country and we can continue to think it’s dengue, as happened with the zika epidemic.”

According to Sabino, HIV is a striking example of the lag between circulation and detection. Research has shown that this virus has been circulating since the 1920s, but AIDS was not diagnosed until the 1980s. “The AIDS epidemic also teaches us about the consequences of denialism,” she said. “At the turn of the century South Africa had a denialist president and now, 20 years later, the main cause of death in that country is HIV/AIDS, not COVID-19. This is the clearest possible confirmation that failure to take the right measures can have a long-term impact on the progress of an epidemic.”

Sabino recalled that she has conducted several studies on the dissemination of COVID-19 in Brazil, showing that it spread very differently in the various states and regions. The explosion of cases in Manaus was atypical in her view. A study by her group involving blood donors showed that SARS-CoV-2 was highly prevalent in the city and that levels of antibodies against COVID-19 fell rapidly over time.

“Our study pointed to an attack rate of at least 70% among donors and a rapid loss of immunity, at least in terms of antibodies against the virus. This showed in the middle of last year that if a second wave occurred [as was indeed the case a little later], immunity among that population was dangerously low following the first wave. This can be seen in several parts of the world. Even populations with high attack rates suffered the consequences of a second wave, as well as the spread of novel variants,” Sabino said.

The webinar series on “Health and Environment in the Amazon in the Context of COVID-19” is a collaborative initiative involving FAPESP, the University of Campinas (UNICAMP), the University of São Paulo (USP), the Federal University of Pará (UFPA), the National Space Research Institute (INPE), the Federal University of Rondônia (UNIR), the Federal University of Santa Catarina (UFSC), and Michigan State University (MSU) in the United States.

A recording of this webinar, the fourth in the series, is at: The first webinar in the series can be watched at: The second is at:, and the third:




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