A drop in the sea of threats
MIPT scientists explained why it is so difficult to detect new dangerous viruses
In a recently published fundamental review devoted to methods of diagnosing viral infections, a team of Russian scientists, including MIPT employees, for the first time systematically described and summarized the current technologies of the rapidly developing field of biological science. In recent years, a number of new effective methods for detecting viruses have appeared, including in patients with infections of unknown etiology (unknown origin). Researchers consider the so-called high-performance sequencing (NGS) to be one of the promising technologies in this area. The method promises a revolution in the field of detection and research of new pathogenic viruses, but it is separated from the introduction into mass medical practice by at least several years.
During the rapid development of the COVID-19 coronavirus pandemic, the monthly magazine Viruses, one of the world's authoritative scientific publications in the field of virology, published a fundamental review on the problem of detecting new pathogenic microorganisms, including viruses of unknown etiology – such as the notorious coronavirus (Kiselev et al., Current Trends in Diagnostics of Viral Infections of Unknown Etiology).
"According to various statistical estimates, there are more than 320 thousand different viruses parasitizing mammals on our planet," says one of the authors of the review, an employee of the Laboratory of Historical Genetics, radiocarbon Analysis and Applied physics Kamil Hafizov. "But out of such a gigantic variety, man has so far managed to more or less study less than one percent of these mysterious organisms."
Most viruses, including those that cause respiratory, intestinal and other pathologies in humans, remain unexplored and therefore practically unrecognizable. The fact is that the test systems currently used in everyday medical practice are able to detect only specific, fairly well-studied strains of the virus.
"In fact, people are trying to see a huge sea of threats through the eye of a needle," the authors write in their paper. It analyzes, in particular, the disadvantages of the polymerase chain reaction method (PCR diagnostics). This method of molecular testing of microorganisms, which is the main one for modern medicine, practically does not allow detecting poorly studied viruses, which is one of the main problems of modern virology.
But, fortunately, methods are already emerging that can potentially solve the problem of identifying and identifying new microorganisms, and they are given the main place in the published review. The authors of the work call the most promising of such technologies NGS (from the English – Next Generation Sequencing), or sequencing of a new generation. In Russian, it is also often called high-performance sequencing, because it allows you to read a very large number of DNA sections at the same time.
"An integral part of the method is effective mathematical algorithms," explains the co–author of the review, graduate student at MIPT Alina Matsvai. "They allow, in the process of reading the genome of an unknown virus or other microorganism, to "punch" it through all the huge genomic libraries available, predicting all kinds of properties of the new virus, including its pathogenic potential."
The main disadvantage of NGS is the high cost of equipment and reagents for conducting research using this method, as well as rather lengthy processes of sample preparation, sequencing and data analysis. These restrictions, along with strict requirements for the qualification of laboratory personnel, prevent the introduction of the method into mass medical practice. However, every year the cost of technology is steadily decreasing, and speed, accuracy and productivity are increasing.
According to Kamil Hafizov, the coronavirus pandemic has clearly demonstrated the importance of NGS methods in identifying new pathogens in clinical samples, as well as for studying the molecular mechanisms of transmission of the virus from animals to humans. Perhaps the technology will be certified for use in healthcare in the coming years.
Along with scientists from the Moscow Institute of Physics and Technology, the authors' team of the fundamental work included representatives of the Center for Strategic Planning of the Ministry of Health of Russia, Moscow Sechenov University and the Pasteur Institute in St. Petersburg.
The work was carried out with the support of the Russian Science Foundation.
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