The first few cases of COVID-19 started in the Wuhan City of China sometime in December. From then till now it has spread from China to as many as 190 countries claiming close to 200 hundred thousand lives and still counting. Scientists across the world are making great efforts to respond to this crisis. Research is being conducted to understand the virus so as to develop tests, vaccines, and possible therapies. Long-Read sequencing may well be the technology that helps address many questions plaguing the scientists. Here’s how;
Long-Read Sequencing, LRS
To understand coronavirus better, there is a need to understand basic biology first. When there is detailed information available, it helps the scientists greatly in their research. Until recently, the short-read sequencing was used as the genome of organisms which was too long to be sequenced as a single string. So the DNA was split into short amplified sequences and read. But with this novel virus, such short-reads are challenging to read.
Hence the long-read sequencing of the virus’s genome is one of the most efficient ways of getting in-depth data. It helps to simplify the phases of mutation and detection as all the genomes are in a single sequence. By getting this information about the various phases, researchers get a better understanding of the way mutation happens and other important data like the spread of the virus, the speed of infection, resistance and much more. But for all this to happen, there is a need for high-quality sequencing data so that the test is successful.
There is great optimism that the LRS technique can help address the COVID-19 situation because of its earlier success in HIV research. There are examples of the LRS sequencing giving in-depth data on the way the virus evolved through mutation during the infection. This has helped to reveal useful information that leads to better therapeutic results.
LRS helps in Variant Detection
Coronavirus is a group of viruses that belong to the same family. Some of them cause mild illnesses in humans like cold, while there are deadly ones like the MERS-CoV and SARS-Cov that lead to severe illnesses. There are many viruses of the same family that live in animals that can infect people. It is thus essential to know the variant of the virus to know the features of their genomes. Short-read sequencing poses a challenge as it is difficult to detect the genomes. So instead, scientists have to explore RNA-seq datasets so that long-reads, which span larger regions can happen. It can also help in inserting or deleting repetitive regions, or with low diversity of nucleotides. When it becomes possible to detect more relevant variants it also enhances detection quality.
The need of the hour is faster sequencing and long-read does just that when compared to other types of genome sequencing like SRS. There are certain technologies developed that help in real-time analysis. It helps in quicker data collection and analysis as and when desired by the researcher. It also reduces the need for sequencing in batches which involves multiple samples. That helps in testing specific regions of the genomes and also smaller genomes like the current COVID-19.
It also helps determine why one is more susceptible than other
Though the reason why one person is more prone to this illness than the person next to you may be related to the immune system. But it is equally important to understand which population this virus tends to infect the most. Experts believe that long reads can sequence the IGH locus and the LHA genes along with the BCR, this reduces the challenge to phase and sequence. When the BCR is sequenced, identifying the antibodies that neutralized the virus from patients who have had COVID-19 can then be used as a treatment.
Additionally, the LRS can also avoid the known issues of the SRS techniques and sequence the immune system. When you are examining the sequences of two people, the variant differences between two people’s genes can give a clue as to how the disease progresses and the outcome of it.
Current work of the Scientists on COVID-19
An interactive tool is being used by scientists to study the genetic data of this virus. The genome of the same is posted that has helped scientists to learn about the structure and also ways to contain it. Based on the data available researchers have come up with the 3D atomic-scale map. A study has also found that an immune cell present in the lung can control the inflammation when it is infected. However, more research is essential to prove this. An IV transplantation of mesenchymal stem cells appears to be effective with some patients. But everything is in the early stages.
Hence the many benefits of LRS for reading and analyzing the genomes have become helpful and can help in the diagnosis and treatment of COVID-19.