Brazilian Researchers Develop Tool for Differential Diagnosis of All Tropical Viruses

Brazilian researchers have built a tool to help identify and observe viruses transmitted by “small mammals and arthropods,” such as the Zika virus, Dengue, and Chikungunya.

In a recent study, published in PLOS Neglected Tropical Diseases, the authors stated that because vaccines or treatments are not yet available for these viruses [exceptions being Yellow fever virus, Japanese encephalitis virus, Tick-borne encephalitis virus, and Junin virus], early diagnosis is critical in order to properly manage and contain infection. According to the study, DNA microarray technology is the optimum solution for differential diagnosis of these arboviruses. Two alternate options are polymerase chain reaction (PCR) and high-throughput nucleic acid sequencing; however, PCR cannot be used to test a blood sample against several viruses simultaneously, and high-throughput nucleic acid sequencing is expensive and extremely slow. Therefore, the researchers set out to develop a DNA microarray test that can screen 416 tropical viruses.

Using the “complete and partial nucleotide sequences of all viruses transmitted by small mammals and arthropods that can be found in GenBank,” the research team created a DNA microchip platform diagnostic tool, which they dubbed SMAvirusChip. This new diagnostic tool can detect viremia early after initial infection, using 15,000 probes to differentiate between approximately 9000 “viral target sequences.” According to the researchers, SMAvirusChip can detect both pathogenic and nonpathogenic viruses alike.

Most importantly, the researchers hope to use SMAvirusChip to be able to identify viruses that have the capacity to cause epidemics. With this information, small outbreaks can be contained, preventing epidemics before they happen. However, the authors noted that it is necessary to regularly update the SMAvirusChip probes, so as to include new viruses added to the GenBank database.

To test SMAvirusChip’s ability to detect infection and co-infection, the researchers examined its ability to detect the following, using just one blood sample: “1) viruses from different families, including [Bussuquara virus] (Flaviviridae), [Mayaro virus] (Togaviridae) and [Piry virus] (Rhabdoviridae); 2) viruses of the Flavivirus genus, including [Dengue virus]-2, [Rocio virus], and [St. Louis encephalitis virus]; 3) the four [Dengue virus] serotypes; and 4) viruses that have caused epidemics in Brazil, including [Chikungunya virus], [Dengue virus]-1 and [Zika virus].”

According to the study authors, SMAvirusChip successfully detected all of the aforementioned viruses. The authors noted that detection of the viruses that have caused recent epidemics in Brazil—Zika virus, Chikungunya virus, and Dengue virus—was successful. Furthermore, the platform was also able to detect these viruses when co-infection occurred. The authors wrote, “This suggests that the SMAvirusChip platform could be used as a surveillance system to detect individuals infected with either a single or multiple virus[es].”

Study author, Victor Hugo Aquino, PhD, from the University of São Paulo's Ribeirão Preto Pharmaceutical School, stated in a press release, “Initially, the test will not be for the entire population because of high cost. It will be used on patients with suspected Dengue, Zika or other febrile diseases whose diagnosis isn't confirmed by conventional methods.”

The authors concluded, “Although real-time PCR is becoming the gold standard method for diagnosis of viral infections, [we] still face problems for high-throughput screening of multiple viruses. To date, the cost of performing real-time PCR, when a high number of viruses needs to be screened in a single sample, is becoming similar to the cost of the DNA microarray. Therefore, DNA microarray could be a cost-effective method for virus surveillance programs that would help in the identification of newly introduced viruses that can then be detected with conventional methods, thus reducing the costs of diagnosis.”