The new algorithm will quickly identify mutations of the COVID-19 coronavirus and determine the genetic subtype of the pathogen that a particular patient is infected with. This will help in the development of drugs and vaccines, as well as in assessing the effectiveness of quarantine.
The development is described in a reprint of a scientific article published on the bioRxiv website by a group led by Gail Rosen of the University of Drexel in the USA. The source code of the algorithm is in the public domain.
Viruses easily mutate. So the culprit of the current pandemic has already been divided into several subtypes. Meanwhile, mutations can affect the virulence (contagiousness) of the pathogen and the course of the disease, as well as protect the coronavirus from the effects of drugs and vaccines.
Therefore, it is so important to monitor changes in its RNA (recall that it is in RNA, and not in DNA, that coronaviruses store hereditary information).
At the beginning of April, COVID-19 genomes obtained from more than four thousand patients were contained in public databases. However, the complete RNA molecule of the virus contains more than thirty thousand bases. Analyzing such a volume of data is not easy.
The authors of a new study identified sections of one nucleotide in the coronavirus genome that are the most informative in terms of its mutations. It turned out that there are only 17 such fragments. Together they form a kind of passport of the genetic subtype of the virus. Biologists have called it an informative subtype marker (ISM).
That is, in order to recognize a particular pathogen, it is enough for scientists to study these 17 fragments. Thanks to this approach, it is not necessary to study the complete COVID-19 genome to say whether it belongs to one of the already known genetic subtypes or has undergone significant mutations. It is enough to analyze only a part. Rosen compares this to a quick barcode scan of a product in a supermarket.
As the scientist explains, at least six or even ten genetic subtypes of coronavirus have already spread in the United States. Some of them were imported from different countries of Europe, others from Asia, and at least one stood out as a result of mutations that occurred with the pathogen already on the American continent.
ISM technology allows you to quickly track the spread of coronavirus from different geographical sources and thereby determine the effectiveness of quarantine measures. In addition, subsequently, doctors will have the opportunity to analyze the course of the disease and the effectiveness of a particular treatment and prevention, taking into account the specific subtype of the virus that spreads in the study region.
The study gave another important result: it helped identify areas of the coronavirus genome that are the same in all its varieties.