The curious case of Genome Sequencing against Covid19

Genomics is an interdisciplinary field of biology focusing on the function, evolution, editing and mapping of genomes. It is the process of determining nearly the entirety of the DNA sequence of an organism’s genome at a single time which helps find out the order of DNA bases or nucleotides in a genome - the order of As, Cs, Gs, and Ts that make up an organism’s DNA. The first sequence was obtained in the early 1970s by the academic researchers using laborious and substantial methods dependent on two-dimensional chromatography.

Currently, Genome Sequencing can be seen in various fields including mutation frequencies, diagnostic use, genome-wide association studies and rare variant association study. There are many benefits to sequence an entire genome; for example – it represents a valuable shortcut, which helps researchers and scientists detect genes much more quickly and smoothly. It also helps in clearly understanding the working of genome as a whole - how genes work together to direct the development, maintenance and growth of an entire organism. With sequencing, scientists can know the entire genome sequence which helps them study the parts of the genome outside the genes.

Use of AI-ML and analytics to decode a DNA

AI has two main applications in genetics: treatment of diseases and identification of harmful genes. For the first use case, a big argument in favor of gene editing is the ability to cut out disease-causing genes. However, the technologies like CRISPR have travelled a long path, the risk of error remains important and safety must be held as the first priority for gene editing to progress. Machine learning algorithms are beneficial in identifying where the alteration must be made and how to ensure that the DNA strand is repaired properly afterwards, decreasing potential for mistakes throughout the whole process.AI is useful in personalized medicine too, which needs treatments to be specified to one patient’s needs versus another. Further, using 3D imaging, AI is used to identify genetic mutations within tumors.

For example, a research from 2017, stated that technology could monitor the presence of a glioma using brain scans of a patient with a high rate of accuracy (over 97%). Now, using techniques such as neural networks, deep-learning, machines can detect the presence of a mutation.

Genome Sequencing and AI Against Covid-19

The healthcare systems worldwide are being provoked by accelerating demand for care of COVID-19 patients. Thus, it is critical to maintain curative and preventive services, especially for the most vulnerable populations, such as older persons, children, minorities and people living with disabilities and people living with chronic health conditions.

Unprecedented momentum of efforts to address the COVID-19 pandemic situation is leveraged by artificial intelligence and big data worldwide. Applications of Artificial Intelligence are accumulating a lot of hope and interest in the fight against COVID-19 - in evolution of therapeutics, in protein structure prediction, to reduce burden on healthcare staff and medical practitioners, in strict monitoring of COVID-19 cases and in tracking and predicting

Apart from preventive health care, the mutations in of the Coronavirus has proved to be a neck breaking event across the pandemic. Thus, it is necessary for researchers and medical practitioners to understand these genetic variations that occur over time and can lead to the emergence of new variants that may have different characteristics.

“Sequencing enabled the world to rapidly identify SARS-CoV-2 and develop diagnostic tests and other tools for outbreak management. Continued genome sequencing supports the monitoring of the disease’s spread and evolution of the virus,” stated a WHO report from January 2021. Thus, it is the need-of-the-hour to increase the pace of Genome Sequencing to understand the COVID-19 variants.

The Genome India Project

The Genome India Project is a collaboration of 20 institutions including some IITs and the Indian Institute of Science that aims at enabling new efficiencies in agriculture, life science and medicine field. Its focus is to form a grid of the Indian “reference genome”, to fully understand the nature and the type of diseases and its traits that comprise the diverse population of India.

This mega project aims to form a grid after collecting 10,000 samples in its first phase across different parts of India, to reach at the representative genome of India. But the slow pace of country’s genetic sequencing capacity is a major global concern.

For example, to detect new variants of the coronavirus, genome sequencing is extremely relevant. The first data on the Delta variant was detected in Maharashtra. The data on the Delta variant emerged from the UK, because the private Indian labs have been barred from genome sequencing. Thus, it is safe to state that despite the enormous insufficiency in its efforts, India is not fully utilising existing sequencing capacity specially in the private sector.

From Nepal and Sri Lanka, scientists and researchers with limited resources are working to discover which variants through genome sequencing. And India must focus on increasing its genome sequencing capacity to manage the rising Covid crisis.

The author is Tanisha Gupta.