Metagenomics: innovation in the diagnosis and surveillance of emerging viruses

With each passing day, the efficiency and suitability of molecular tests in the diagnosis of infectious diseases has become more evident, especially those caused by viruses, such as the current pandemic of COVID-19.

Molecular tests are able to detect the genetic material of the pathogen, directly attesting its presence in the sample.

Putting it in perspective, the different tests available for the diagnosis of COVID-19 have their utility well defined. The molecular test of RT-qPCR is especially important to identify individuals with viral load, allowing restriction measures such as quarantine to be applied in order to block viral spread. Immunological tests, on the other hand, can be used to identify individuals who have already been exposed to the pathogen and can be used to check “Immune passports”, in order to attest their immunity to the disease. However, none of these tests proved to be adequate for the initial diagnosis in outbreaks, that is, for the identification of new viral pathogens at the time they are emerging.

The new coronavirus, later named SARS-CoV-2, was quickly identified in the city of Wuhan by a research and diagnostic technique called “Metagenomics”. It is a molecular technique that is also capable of directly identifying the genetic material of the virus, but unlike the RT-qPCR technique, metagenomics is not a targeted technique, that is, with a specific target. Instead, the technique makes use of the total extraction of genetic material from the sample, followed by massive parallel sequencing (also known as Next-Generation Sequencing, NGS) and bioinformatics analysis to search the genome and identify the pathogen in a precise way.

From the moment of identification of the pathogen associated with the outbreak of acute respiratory syndrome in Wuhan until the end of January 2020, the diagnosis of patients was possible only through metagenomics. From the deposit of the genome in public banks, RT-qPCR assays began to be developed in the world through detailed studies of the regions of the viral genome.

Meanwhile, the first suspected cases of COVID-19 broke out in Brazil, being discarded one by one by the metagenomics technique developed internally at Hospital Israelita Albert Einstein. Because it is a technique that does not have a specific viral pathogen as a target, it is able to diagnose arboviruses, viral hepatitis and respiratory syndrome from a myriad of different viruses, including all viruses of the Coronaviridae family.

In addition to metagenomics being a multipurpose technique for the diagnosis of viral infections, it has an interesting advantage arising from the collateral data generated by the exam. Unlike RT-qPCR, several virus genome fragments are read by the sequencing equipment, generating complete genomes after analysis. With the genome in hand, the laboratories carrying out these tests are able to generate data for highly sophisticated studies on the molecular epidemiology of several viruses.

These laboratories, together with health authorities, can, for example, carry out a survey of which etiologic agents are most associated with specific syndromes or clinical manifestations, which strains and genotypes circulate of certain viruses, identification of mutations associated with virulence and response to drugs, etc. The possibilities are many.

As an illustrative example of the usefulness of tests based on metagenomics, we can mention a case that occurred in early January 2020 of a patient residing in Sorocaba. This patient had typical symptoms of yellow fever, with hepatic and hemorrhagic manifestations. After performing serological and molecular tests for different agents, all results were negative. There were no known arboviruses (Zika, Dengue, Chikungunya, Yellow fever), viral hepatitis (A, B, C, D and E) or even viruses such as herpesvirus, parvovirus or HIV.

The RT-qPCR test for yellow fever in this patient was repeated twice, both with negative results. It was then that the team at the Special Techniques Laboratory at Hospital Israelita Albert Einstein decided to test the exam based on metagenomics. The result came positive for an Arenavirus from the Sabiá virus group that had not been identified for more than twenty years in Brazilian territory. It was a highly lethal virus transmitted by rodent faeces known to cause a type of hemorrhagic fever. Solved and conclusive diagnosis thanks to metagenomics. 

Therefore, here is our record that molecular tests based on metagenomics can take the field of infectious disease diagnosis to a new paradigm of precision medicine. Providing exceptional benefits to patients and also to laboratories that are willing to practice cutting-edge and innovative diagnostic medicine.

About the authors:

Fernanda Malta, PhD is a biomedical specialist in molecular biology applied to viral diseases with Doctorate and Post-doctorate from the Faculty of Medicine of the University of São Paulo. She is currently linked to the clinical laboratory of Albert Einstein Hospital.

Deyvid Amgarten is a bioinformatics specialist in viral genomics with a bachelor’s and master’s degree from the University of São Paulo. He is currently linked to the Albert Einstein Hospital clinical laboratory.

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