Researchers developed a new diagnostic method and identified infection in 2 patients who died
By André Julião
The thrush virus (SABV), which causes an acute hemorrhagic and neurological syndrome with 4 fatal cases recorded since 1990 in the State of São Paulo, has been circulating for 142 years in Brazil. Recent analyzes of 2 cases recorded in 2019 and 2020 reveal that the virus presents genetic variation over time, and was therefore not identified by existing tests.
The results are part of a study in the journal PLOS Neglected Tropical Diseases by researchers from (CADDE), supported by Fapesp, based at the Faculty of Medicine of the University of São Paulo and Imperial College, in the United Kingdom. The group developed primerssmall fragments of DNA used to detect the virus in laboratory tests. The material was sent to the Adolpho Lutz Institute, in São Paulo, a reference in the State for this type of test.
“The reference strain of the thrush virus is from 1990, from a case in Cotia. The diagnostic method was developed from this genome. As more than 30 years have passed, it was even likely that the virus had changed. We don’t have so many occurrences to be able to carry out new validations of this method, but it can be used for future suspected cases with more precision than the tests used until then”he stated, that he carried out the work during his doctorate with Fapesp at FM-USP and is currently undertaking a post-doctorate at the University of Kentucky, in the United States.
The genomes recovered from the thrush showed 89% genetic identity compared to strains previously described in 1999, when the second case in history was recorded. “By analyzing the genome of new cases, we identified mutations in target regions of the primers that prevented detection by existing diagnostic tests. We modified these regions and it is now possible to identify the circulating strains”said Claro.
CADDE is coordinated in Brazil by , professor at FM-USP responsible for the 1st sequencing of SARS-CoV-2 in the country, in March 2020 (read and ), and of the mpox virus, in 2022 (read ).. In the United Kingdom, the center is coordinated by , from Imperial College.
Faria’s team coordinated the project, which deals with the Zika virus, the yellow fever outbreak and its spread in Brazil and São Paulo, in addition to having, together with Sabino, the first characterization of the gamma variant of SARS-CoV-2 in Manaus.
How the virus interacts with human cells
The 2020 case of SABV infection was identified through metagenomic analysis, a technique that allows different microorganisms to be detected directly in a sample, without having to know in advance which virus to look for. The thrush was present in the blood of a 52-year-old patient from Sorocaba, in the interior of São Paulo. The method used was a rapid metagenomics approach during Claro’s doctorate, allowing the rapid detection of emerging pathogens in clinical samples.
With a history of walking through forested areas, the man sought care at a basic health unit on December 30, 2019, was transferred to the Hospital das Clínicas de São Paulo with suspected yellow fever and ended up dying on January 11, 2020. Initial tests were negative for yellow fever and thrush.
After detecting the virus in the Sorocaba patient’s sample, the researchers decided to analyze blood samples from seven other previous cases of acute hemorrhagic and neurological syndrome who had tested negative for yellow fever. It was then that they found the case of a 63-year-old rural worker from Assis, admitted to Hospital das Clínicas on December 10, 2019 and dead two days later.
In both cases, the researchers observed changes in the virus’ binding protein with the human cell. Phylogenetic analyses, which allow us to reconstruct the evolutionary history of the pathogen, indicated that it has been circulating for decades in Brazil and is possibly not a recent introduction.
“There were probably other cases in the past that were not identified. It is important to know the virus, develop tests and study the changes that occur in its genome in order to anticipate future new cases and even outbreaks of the disease”said Sabino.
Unknown reservoir
The species that serves as a reservoir for SABV is not yet known, but it is believed that they are wild rodents. Infections occurred in rural areas, where there may be interaction between animals and humans.
“In this context, metagenomics approaches have proven to be essential tools for the detection of rare or unexpected pathogens, especially when targeted diagnostic tests fail. This strategy has been fundamental in both the identification of fatal cases of thrush in humans and wild animals and highlights the essential role of genomic surveillance in detecting risks to public health”declared Faria, from Imperial College, giving as an example a recent one from the group on the evolution and transmission dynamics of yellow fever in Brazil.
SABV is considered one of the Brazilian viruses with the highest risk of transmission by aerosols in a laboratory environment, which requires the maximum level of biosafety to handle it, something that still does not exist in South America.
The inauguration of Orion is scheduled for 2030, the first laboratory in the country capable of storing and manipulating the active virus, under construction at the National Center for Research in Energy and Materials (CNPEM), in Campinas. Currently, the reference strain of thrush is in the United States.
The article Genomic characterization of sabiá virus in Brazil, 2019-2020: Implications for diagnostics, virus evolution, and receptor binding can be read.
This text was originally published by Agência Fapesp, on May 27, 2026. The content is free for republication, with the source cited, and was adapted to the standard of Poder360.
