Researchers in São Paulo have developed a tool that can analyse clinical samples from patients and diagnose infection by 416 different tropical diseases.
The team at University of São Paulo (USP) at Ribeirão Preto in Brazil hope it can be used by Brazil’s reference laboratories such as Adolfo Lutz Institute, Oswaldo Cruz Foundation (Fiocruz) and Evandro Chagas Institute to assist epidemiological surveillance and detect pathogens with the potential to cause epidemics in humans.
The USP is Brazil’s largest research institution, and the results come from its leading Ribeirão Preto Pharmaceutical School (FCFRP-USP), with support from FAPESP, the São Paulo Research Foundation. The development underscores a core of leading research in tropical disease in the state, which is also home to the São Paulo-Minas Gerais Tropical Medicine Research Center (SaMi-Trop).
Professor Victor Hugo Aquino said: “The number of patients with suspected dengue, Zika or chikungunya infection will increase when summer arrives. Conventional methods are frequently unable to confirm diagnosis of these diseases, so we don’t know which viruses are circulating.”
In his view, if a tool like this had been available when Zika began circulating in Brazil, it might have been possible to restrict its spread to the initial outbreak location: “We took a long time to realise an epidemic was under way because no one was thinking of Zika at the time.”
The platform is designed foremost to detect pathogens transmitted by arthropods such as mosquitoes and ticks, though it can also diagnose infectious agents transmitted by small mammals, like hantavirus. It can also detect a number of viruses which haven’t yet caused problems in humans but may do so one day if they evolve and spread, such as Mayaro, an alphavirus related to chikungunya that is transmitted by wild mosquitoes; and Oropouche, which to date has caused epidemics confined to riverine communities in the Amazon region.
The test encompasses all viruses occurring in tropical regions with DNA sequences deposited in GenBank, a public database maintained by the National Center for Biotechnology Information (NCBI).
A device – the same as that used in microarray assays for the analysis of gene expression – reads a DNA microarray slide with eight identical sub-arrays containing viral probes replicated at least three times to complete the array with 15,000 probes. Each probe contains the sequences for 60 nucleotides that are complementary to the genomes of the viruses.
“If a blood sample contains one of the 416 viruses included on the microchip, the pathogen’s genome will bind with one of the probes to produce a marker that can be detected by a scanner,” Aquino said.
The methodology was validated using 20 viruses available at FCFRP-USP’s Virology Laboratory. It also proved effective in diagnosing cases of co-infection, such as when the same patient has been infected by both Zika and dengue.
High costs will mean the test is not initially available for the general population, but it will be used on patients with suspected dengue, Zika or other febrile diseases when diagnosis isn’t confirmed by conventional methods.