How one of India’s premier research institutes is tracking new SARS-COV2 variants

Genome sequencing helps us understand the evolution and spread of the virus and its variants. It has enabled us to look closely at the mutations that arise in the virus during replication inside the human body after infection. Looking at such mutations helps determine if a different lineage or ‘variant’ of SARS-CoV-2 has emerged in a region.

Identification of virus lineages is important from a public health point of view since particular mutations may lend additional advantages to the virus in terms of its ability to transmit better from person-to-person, or in terms of its ability to decrease the efficacy of vaccines, as we have seen for the Alpha, Beta and now Delta variants.

Additionally, tracking such mutations can also allow the tracing of the origin and spread of a specific variant of the virus especially as variants spread across geographical areas. For example, we have seen that the Delta variant predominated during the second wave in India and its prevalence corresponded to the increase in cases seen in the country. Multiple studies subsequently suggested that Delta is more transmissible as compared to other previous lineages of SARS-CoV-2.

What exactly is a gene sequence?

The SARS-CoV-2 virus has certain genetic instructions that it uses to generate copies of itself. These instructions are coded in a sequence of 29,903 letters of RNA (ribonucleic acid bases – A, U, G, C) which make up what is known as the ‘genome’ of the virus. Sequencing the genome of the virus essentially means that we determine the sequence of the 29,903 letters of the virus. Approximately 50,000 genome sequences of SARS-CoV-2 have been assembled in India and more than 2.5 million genome sequences are available publicly from world over.

How are the variants named?

Since the beginning of the pandemic, researchers have emphasized the need to have a uniform naming system for different variants. PANGO is a system of assigning names to different lineages of SARS-CoV-2 genomes, which was developed by virologists in the UK and Australia early in 2020. It is a hierarchical system of naming lineages. For example, the B.1.1.7 lineage, more commonly known as the Alpha variant, emerged from the lineage B.1.1 which had emerged from the lineage B.1, which is a direct descendant of the lineage B.

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The system is designed to assign lineages in a dynamic manner. A group of genomes will be given a new lineage name according to the system if they have a defined set of characteristics, such as having a common ancestor, having a group of common mutations, or being linked to an important epidemiological event such as a large outbreak of the disease. The Pango nomenclature and the tool that can be used to assign lineages to genomes was initially developed by virologists at the University of Edinburgh, the University of Sydney and the University of Oxford.

AY.3, a new sub-lineage of Delta is being found in some parts of US. Do we need to worry about this in India?

Since the emergence of Delta, it was expected that sub-lineages of Delta with additional mutations will also emerge. Not all mutations are of significance as they arise as a natural process of evolution. Currently, AY.3 is being reported in significant numbers from the US. However, the Pango system of assignment of lineages works better and more accurately if it processes more sequences that represent a particular lineage. Since currently, AY.3 numbers are small, the lineage assignment for AY.3 may not be accurate. For instance, the small number of genomes from India currently assigned as AY.3 lack the mutations that have been reported in the cluster of genomes from the USA. Although the number of such lineages is small, we will be continuously tracking the genome sequences of the virus to see if AY.3 or any other Delta sub-lineage emerged in India or elsewhere.