March 03, 2021

Sorting by Strains / Gorodskoy Ritm

Geneticists from the ReadSense Troitsk company, a member of the TechnoSpark Group of Companies, have created the first Russian system for rapid diagnostics of coronavirus strains. This is a set of reagents and a cloud service that allows to completely decode the virus genome 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. There was one line on the graph in December 2019, now there is a whole range of strains, up to 40 changes in the genome. They differ in the contagiousness level, mortality rate and can ‘escape’ from vaccines. Knowing the virus version a patient has helps in selecting the 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: ‘yes/no’ result. But here the researcher, knowing that there is a virus, must determine the entire genome in order to compare it with the base of strains. The sequencing device is engaged in decoding the genome. “The development is aimed at the reagents that allow to quickly read the virus genome,” 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 the use of the test system would be impossible.”

Photo by Vladimir Milovidov

Diagnostics begins, as usual, with a smear. First, PCR analysis is done. If it gives a positive result, a part of the specimen undergoes sample preparation using a test system created in ReadSense. The SARS-CoV2 RNA molecule is being isolated, converted into DNA, divided into blocks of about 1,000 ‘letters’ each. The codes individual for each sample are added to the end, and the genome is multiplied (amplified) and decoded (sequenced). The third generation method is used—monomolecular nanopore sequencing. Oxford Nanopore, UK, manufactures these sequencing devices. They are available in Russian laboratories as well. MinION is the smallest of them, it is on the table. It is almost a flash drive in size and connects to a computer the same way. A sample is dropped inside. There is a membrane on which protein molecules (nanopore channels through which DNA passes under electric current) are fixed. Different nucleotides cause different fluctuations in the ion current in the membrane. Decoding these data allows to get the genome (up to 96 samples at the same time). The processing takes place in the ReadSense cloud service hosted at the facilities of Yandex (Yandex Cloud) in Russia. “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. “Analyzing raw data in the cloud takes a few minutes, and it takes half a day on a PC.”

Similar test systems are already being dealt with in the world. But, according to Gleb, Western solutions sacrifice efficiency and accuracy for the sake of velocity. TechnoSpark uses the MinION’s advantage (the ability to process long chains) to the maximum.

8x12 cells hold 96 samples analyzed simultaneously

Photo by Vladimir Milovidov

“We used the original SMART amplification technology which allows to obtain the longest possible DNA fragments,” Speshilov clarifies. “The method 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 it was forgotten and we revived it in order to ‘extract’ target RNA in the presence of a huge number of other matrices.”

Test kits for analysis are boxes of reagents for 96 samples. TechnoSpark has production facilities, so it is possible to produce up to 5,000 kits per month. “Our method is practically universal,” Gleb Speshilov concludes. “The reagent kit and cloud platform can be easily optimized for other tasks. For example, the detection of bacterial infections.” But this is for the future. Now the main task is to fight off COVID.

Source: Gorodskoy Ritm

This website uses cookies to improve its performance. For more information please refer to our Privacy policy.

I accept