New Delhi: The whole world is currently facing the corona epidemic and the concern about new variants of the virus is increasing even more. In such a situation, the technique of genome sequencing has become an essential tool to identify different variants and mutants of the virus. Genome sequencing is a technique that helps to understand and identify the changing nature of viruses in common people. In view of the possibility of third wave of corona in the country and the danger of delta plus variant, genome sequencing lab has been opened in the capital Delhi.
The first step is to extract RNA from the sample. Talking about this process, Dr. Ekta Gupta said that all the Kovid positive samples from Delhi, first come to the RTPCR lab. Precautions with BSL-3 (Bio Safety Level-3) are taken in this lab. In this lab, RNA is extracted from the sample and after that it is applied for sequencing. Extraction of RNA is carried out with great care, as it is highly infectious, so it is performed at the BSL-3 lab facility.
Sample Preparation Area
After RNA extraction, the sample is brought to the ‘Sample Preparation Area’. Describing the sample preparation area, Dr Chhagan Bihari, in-charge of the Genome Sequencing Lab Facility, said that there is an RNA isolation area in the sample preparation area. This is followed by the phase of library preparation in which there are several steps such as cDNA synthesis in which DNA is made from RNA and amplified it. This is followed by the process of tegmentation, PCR clean up, library pooling, quantification and normalization. The entire process of library preparation takes 2-3 days.
Genome Sequencing Area
This is the most sensitive and critical part of the lab where samples are applied for sequencing. Dr Chhagan Bihari said that there are 2 platforms in this part of the ILBS Genome Sequencing Lab. The first is NextSeq 550 in which 384 samples can be run in 1 week. This process also takes 2-3 days. That is, the entire process of genome sequencing takes about 1 week. Which we say that our capacity is 384 samples. The second sequencing machine in the lab is of low-throughput, in which 96 samples can be run simultaneously. This is called MiSeq. In this also it takes about 2 days to run the sample. At present, samples have been used for sequencing in the lab and it will take about 1 week to get their results. The readings of the machine in running samples and the quality of the sample are also visible in the display. Regarding this, doctors say that the genome is made up of 4 nucleotides A, T, C and G. 4 of them are visible in the color display graph.
The last step of the process is analysis. Evaluating the data that comes after the completion of the sequencing run, it is known which variant or a new mutant is there in the sample. Dr Chhagan Bihari told that this next step is called analysis which bioinformatician does. All the raw data that comes after sequencing is analyzed by the software. We can tell the mutations which we know, those which we do not know are then further analyzed.
How Genome Sequencing Will Help
- Doctors will be helped in designing the strategy.
- Mapping can be done at district level by taking samples from each district.
- If any abnormal variant comes, the doctor immediately They send their reports to the IDSP (infectious disease survivability program) Delhi State and Health Authority. After this, it can be decided that the infected person and the contact can be isolated, so that the variant can be prevented from spreading.
- According to the doctors, the variants will keep coming but they will not spread. They will be easier to track and isolate with the help of genome sequencing.
- It will help to identify the strains that spread the infection faster and are more life threatening.
- >This will help in timely identification of any new variants in the city.
- Genomic data will also help in classification of new strains and variants.