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Fiocruz presents the results of pathogen surveillance work at WHO workshop


Fiocruz Amazônia


Researchers from the Leônidas & Maria Deane Institute (ILMD/Fiocruz Amazônia) presented on Thursday (7/20) the results obtained from the surveillance work on emerging and re-emerging pathogens circulating in wild fauna and in human cases, carried out by the unit. The research can contribute to effective monitoring and faster responses to future epidemics and pandemics. The work was presented during the Technical Workshop on Regional Surveillance of Emerging and Zoonotic Pathogens with Epidemic and Pandemic Potential, in Manaus, organized by the World Health Organization (WHO) and the Pan American Health Organization (PAHO), in partnership with the Ministry of Health and Fiocruz, and with the presence of the head of the WHO Department of Epidemic and Pandemic Preparedness and Prevention, Maria Van Kerkhove, and the coordinator of the PAHO Technical Unit for Surveillance, Preparedness and Responses to Emergencies and Disasters in Brazil, Alexander Rosewell.

Felipe Naveca, Maria Van Kerkhove and Alessandra Nava during the event, in Manaus (photo: Fiocruz Amazônia)

The event was attended by representatives of institutions from different Brazilian states and countries connected by the Amazon such as Suriname, Colombia, Peru, Ecuador, Panama, and Venezuela, as well as Argentina and the United States. The objectives of the workshop were to map ongoing or planned field research activities on emerging pathogens, discuss possible strategies to coordinate and strengthen actions related to prevention, surveillance, timely detection, notification, preparedness and response in public health with a view to protecting the human population; and propose plans to coordinate applied research in order to fill knowledge gaps about said pathogens. Together, the experts hope, at the end of the meeting, to outline a collaboration plan for the surveillance and investigation of pathogens with epidemic and pandemic potential in wildlife reservoirs, hosts and vectors in the Amazon region.

The panel with researchers from Fiocruz Amazônia had the participation of Maria Van Kerkove. Virologist Felipe Naveca, the coordinator of the Center for Surveillance of Emerging, Re-emerging or Neglected Viruses at Fiocruz Amazônia, highlighted the importance of genomic surveillance in the post-pandemic scenario, mentioning the discoveries made from the work carried out by Fiocruz Amazônia in partnership with public reference laboratories in Amazonas, Roraima, Acre and Rondônia. “We were only able to move forward with strong partnerships, several committed institutions. In this sense, we have been working with other Fiocruz units, the Rosemary Costa Pinto Health Surveillance Foundation (FVS-RCP), PAHO, as well as counting on investments from international agencies to carry out studies”, he highlighted.

According to Naveca, Amazonas is the Brazilian state with the highest number of sequenced Sars-CoV-2 genomes based on the number of confirmed cases. “We have made huge efforts since the beginning of the pandemic, which has enabled us, among other points, to know that the main variant circulating in the country at the moment is the XBB.1.5, and which previously led us to the discovery of the Gamma variant, in 2021, allowing us to follow its evolution, in a population with high hybrid immunity, such as that of Amazonas. And, more recently, it was possible to show how the expansion of the Delta and Omicron variants took place. It was and continues to be an important work, especially in a region as severely affected as the Amazon”, said Naveca.

From the genomic studies carried out by Fiocruz Amazônia for the Gamma, Delta and Omicron variants, it was also possible to attest that the main dissemination hub was from Manaus to other municipalities. “There was also a smaller dissemination of lineages that were introduced, for example, by the Triple Frontier (Brazil/Colombia/Peru) and others from other borders of the State, but Manaus was invariably the main dissemination hub”, he observed.

Among the lessons learned from the pandemic, Naveca highlights the need to train health teams locally and in all surveillance areas. “We had the opportunity to work not only in Amazonas, but in three other states in the Northern Region, in the so-called Western Amazon – Roraima, Acre and Rondônia. We did this training for the teams from the Lacens [Central Public Health Laboratories] of Rondônia, Roraima and Acre, not only in the laboratory part, but also for the analysis of data in the central laboratories of each state, so that these teams can continue carrying out the work regardless of whether we are there or not”, he said.

The emergence of monkeypox and the increase in dengue cases with the introduction of genotypes in the region also generated demands for Fiocruz Amazônia, as highlighted by Naveca. “We were asked by the Ministry of Health to take over as a regional reference laboratory for monkeypox, for the states of Amazonas, Rondônia and Roraima. With regard to arboviruses, from 2019 to 2021, the dengue virus serotype 1 was the most prevalent. However, in November 2022, the team from Lafron Amazonas reported an unexpected increase in dengue cases at a time when this high number of cases were not expected to be occurring, and we immediately received the samples, performed the sequencing and identified an introduction of genotype 2 (cosmopolitan) of the dengue virus serotype 2 in that region. This result, including the genomes, was immediately shared on public databases. We did a space-time reconstruction analysis showing that it was a second introduction in Brazil, coming from Peru. The epidemiology of dengue in the Amazon has changed and, since that introduction, dengue 2 quickly replaced dengue 1, as per data available in the report for the Ministry of Health, as well as in the pre-print”, he recalled.

Naveca also mentioned a similar situation that occurred in Roraima, when the team from the local Lacen identified the introduction of the dengue virus serotype 3. “This data surprised us, since this serotype has not caused epidemics for 15 years and our genomic analyses, in collaboration with the CDC/USA, not only confirmed the result of the Lacen-RR, but also showed that it was a strain for the Americas, originating from the Indian subcontinent”, he said. Finally, the virologist recalled the emergence of cases of the oropouche virus in Roraima, Amazonas, Rondônia and Acre, confirmed by the Lacens of each state, using the protocol developed by the ILMD/Fiocruz Amazônia, highlighting the need for continuous research for the identification of new viruses, such as the new phlebovirus (virus transmitted by phlebotomine), recently found in a rural area of the municipality of Presidente Figueiredo (AM).


In her lecture, veterinarian Alessandra Nava characterized the surveillance of circulating pathogens in wild fauna, specifically in populations of bats and primates, warning about the risks of deforestation in urban areas. “We have beautiful and wonderful forests, with endangered species, which turn into a mall overnight. This is a dynamic that is constant and the speed with which it happens is very serious, especially with the loosening of environmental protection in the last four years, leading to an increase in the frequency of human contact with wild and domestic animals, which could possibly be a triggering factor of zoonotic emergencies”, she exemplified, showing the image of an area of anthropic forest in a neighborhood in the North Zone of Manaus, which extends over an environmental protection area in the city.

In partnership with the Center for Surveillance of Emerging, Re-emerging or Neglected Viruses, headed by Naveca, Alessandra said that it has been possible to develop a project that aims to map the diversity of coronaviruses in bats and primates, among other species, in the Amazon. “In addition to viruses, we work with other neglected diseases such as filariasis, parasitic diseases and rabies monitoring through bite records more constant in the region. Our strategy is to try to understand and have material for the next emergencies, which is why we started a biobank, in partnership with Cetas/Ibama, where we collect material from species from all over the state and make the samples available to other researchers”, she explains, adding that much more than finding emerging viruses, the proposal intends to understand the relationships and frequencies of contacts between humans and animals as triggers for emergency situations, which is in line with what the WHO One Health High-Level Expert Panel recommends.

Nava highlighted the importance of partnerships, mentioning the letter-commitment signed between the Leônidas & Maria Deane Institute (ILMD/Fiocruz Amazônia), Fiocruz Ceará and the International Platform for Science, Technology and Innovation in Health (PICTIS) of Fiocruz, headquartered in Portugal, for the creation of the first Surveillance Network in the North and Northeast of Brazil for Monitoring Circulating Pathogens in Wild Fauna. The objective is to lay the foundations for the systematization of Fiocruz activities within the scope of One Health – which is based on the understanding that animal and human diseases are associated –, strengthening the surveillance and research of zoonotic pathogens and the ability to provide better monitoring and responses to epidemics. The letter is signed by the directors of Fiocruz Amazônia and Fiocruz Ceará, Adele Schwartz Benzaken and Antônio Carlile Holanda de Lavor, respectively, and the PICTIS coordinator, José Luiz Passos Cordeiro.

The workshop ended on Friday (7/21). Throughout the day, participants were involved in panel discussions, with leading questions about national/subnational capacities for public health surveillance and detection of emerging pathogens, existing gaps in the Amazon region, integration of surveillance in livestock, wildlife and the environment with public health surveillance and innovations being tested. There will also be a panel on research initiatives and activities in the Brazilian Amazon region, presented by the vice president of Research and Biological Collections at Fiocruz, Lourdes Oliveira, and the researcher in Public Health at the Evandro Chagas Institute, Lívia Carício Martins.

From the workshop, WHO/PAHO intends to catalog ongoing and planned applied research activities in the Amazon region related to surveillance, early detection, diagnosis and response to emerging and zoonotic pathogens with epidemic and pandemic potential, in addition to preparing an executive summary for Brazilian national authorities to be presented at the Meeting of Presidents of the Amazon Basin Countries in August 2023, reporting the identification of the main gaps in surveillance, diagnosis and applied/field research, as well as proposing necessary activities to fill these gaps and, finally, preparing proposals for priority actions and activities needed to improve prevention, surveillance, early detection, notification, preparedness and response to pathogens with epidemic and pandemic potential in the Amazon region.

PAHO/WHO organized the technical workshop in close collaboration with the Ministry of Health, Fiocruz and other Brazilian partners. Building on a similar workshop held in Panama in April 2022 – jointly organized by the Rockefeller Foundation, Instituto Conmemorativo Gorgas, and the PAHO Infectious Hazards Management Unit – as well as a series of technical workshops organized by the WHO Emerging Diseases and Zoonoses Unit at its headquarters, it seeks to broaden the understanding of current research and surveillance activities on emerging and zoonotic pathogens with epidemic and pandemic potential in wildlife worldwide.

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