Central regions | Technology & innovation

System for rapid COVID type identification rolled out

4 Mar '21
Genetics from the Trinity firm ReadSense, part of the TechnoSpark group of companies, have created the first system for rapid diagnosis of coronavirus strains in Russia. This is a set of reagents and a cloud service that allows you to completely decipher the genome of the virus and determine its version in three to four hours.

Gleb Speshilov, head of the ReadSense genomic center, shows an online diagram. It is an open database where laboratories around the world upload their latest results. In December 2019, there was one line on the graph, now a whole forest of strains - up to 40 changes in the genome. They differ in the level of infectiousness, lethality, and can “escape” from vaccines. Knowing which variant of the virus a patient has will help in the selection of therapy and understanding how a pandemic is spreading. PCR is not enough, new methods are needed.

In PCR, a fragment of the genome that is present in all strains is selected as a sample for detection: the result is yes/no. But here the researcher, knowing that there is a virus, must determine the genome as a whole in order to compare it with the base of strains. The sequencing device is engaged in decoding the genome.
“The essence of the development is reagents that allow you to quickly read the genome of the virus,” says Gleb Speshilov. “The analysis is done in three to four hours, this is comparable to PCR, alternative methods take several days. The development also includes a cloud service for data interpretation, without which it would be impossible to use the test system. ”
Diagnostics begins, as usual, with a smear. First, a PCR analysis is done, if it gave a positive result, a part of the preparation undergoes sample preparation using a test system created in ReadSense. The SARS-CoV2 RNA molecule is isolated, converted into DNA, divided into blocks of about 1,000 “letters” each, codes are added to the end, which are individual for each sample, and the genome is multiplied (amplified) and deciphered (sequencing). The third generation method is used - monomolecular nanopore sequencing. Devices for it are produced by the British company Oxford Nanopore, they are also in Russian laboratories. On the table is the smallest of them - MinION. It's almost like a flash drive in size and connects to a computer in the same way. A sample is buried in it, inside a membrane on which protein molecules are fixed - nanopore channels through which DNA passes under the action of an electric current. In this case, different nucleotides cause different fluctuations in the ion current in the membrane; decrypting these data, you can get the genome (up to 96 samples at the same time). The processing takes place in the ReadSense cloud service hosted in Russia at the facilities of Yandex (Yandex Cloud).
“There is a set of ready-made software solutions, we have optimized it for our purposes, in the correct order and with the correct settings,” Speshilov explains. “Analysis of an array of raw data in the cloud takes a few minutes, and on a PC it takes half a day.”
Similar test systems are already being dealt with in the world, but, according to Gleb, Western solutions sacrifice for speed efficiency and accuracy. TechnoSpark uses the MinION's advantage to the maximum - the ability to process long chains.
“We used the original SMART amplification technology, which allows us to obtain the longest possible DNA fragments,” Speshilov clarifies. “The technique was created in the late 1990s - early 2000s by scientists from Russia, who then worked in the United States, I personally know its authors. It was relevant for the first generation sequencing technologies, then they forgot about it, and we reanimated it in order to “pull out” target RNAs in the presence of a huge number of other templates. ”
Test systems for analysis - These are boxes with reagents for 96 samples. TechnoSpark has production facilities; it is possible to produce up to 5,000 such sets per month.
“Our method is practically universal,” concludes Gleb Speshilov. “The reagent kit and cloud platform can be easily optimized for other tasks. For example, the detection of bacterial infections.”
But this is in the future, now the main thing is to overcome covid.
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