Scientists have recently sequenced the Indian Cobra’s genome, which helps in understanding the evolution of snakes and their venoms.

Genome sequence is an important first step in searching for designing effective antivenoms.

Research into venoms can further aid the development of new drugs.

Researchers have for the first time mapped the Indian cobra’s genome and identified 19 important toxin genes that together form the recipe for the lethal venom brewed in its venom glands. The study was published in the January issue of Nature Genetics and involves a team of international scientists, including many from India.

Toxins in snake venoms are classified based on the way they act. Neurotoxins lead to neuromuscular paralysis; hemotoxic proteins block blood clotting or help bleed excessively; the cytotoxic compounds kill cells and myotoxic compounds affect muscles.

Genome mapping could pave the way in making antivenom for snake-bite victims. “Our hypothesis is that targeting the most abundantly present toxins in the venom is the key to quickly neutralise the systemic effects of the venom,” said Kushal Suryamohan, first author of the study.

The researchers hope to catalogue the most potent toxins across different venomous snakes.

“Once we have this knowledge, we can synthesise the toxins using recombinant technologies and develop antibodies specific to each of these toxins,” added Suryamohan. “A cocktail containing these specific antibodies can then be used to rapidly and safely treat victims.”

The Naja naja species of the snake has different names: spectacled cobra, the Indian cobra, or the common cobra. It is part of the ‘Big Four’ group, known for their venomous properties across India — the common krait, Russel viper and the saw-scaled viper being the other three. The Big Four account for majority of snake bites in India.

An estimated five million people suffer snake bites every year, according to the World Health Organisation (WHO), and around 100,000 people die from it. India alone accounts for 50,000 of these deaths. There is a vast difference in estimates of cases of snakebites and deaths from various sources.

The ‘venom-ome’

Using advanced genomic technologies such as long read single molecule sequencing, short read sequencing, optical maps and single chromosome sequencing, the researchers first assembled a male individual’s genome. Using specialised algorithms, they identified 23,248 genes that are responsible for producing proteins.

For the next step, the team wanted to understand how these genes are being expressed; that is, how instructions embedded in the genome are being made into other molecules like RNA and proteins. When they sequenced RNA from different tissues, including the venom gland, they found that 12,346 of the 23,348 protein-producing genes were expressed in the venom gland. They called this set the “venom-ome” – the part of the genome that is actively interpreted in venom.

They then searched the proteins encoded by the venom-ome for toxin-like signatures by comparing it to a database of toxins. This allowed them to identify 139 protein coding genes that belong to 33 toxin families. They further narrowed down the list of the 139 to 19 ‘venom-ome-specific toxins’ (VSTs), that likely form the key lethal components of the venom cocktail, based on their venom gland-specific expression. These are the proteins that maim and/or kill the victims of snakebite.

“Targeting these 19 specific toxins using synthetic human antibodies should lead to a safe and effective antivenom for treating Indian cobra bites” said Sekar Seshagiri, President, SciGenom Research Foundation (SGRF), India and former Staff Scientist at Genentech, U.S.A. and lead study author.

“This sequenced genome would be invaluable for understanding the genomic adaptations, and the evolution of snakes and their venoms. For example, a sequenced genome is indispensable for gaining insights into the origin and diversification of venom proteins from non-toxic physiological proteins,” said Kartik Sunagar, assistant professor at Evolutionary Venmics Lab at Indian Institute of Science. Sunagar is not involved in the research.

The genome sequence information can be used to identify evolutionarily conserved regions in venom proteins, for example, continued Sunagar. This, in turn, “can be useful for designing highly targeted recombinant antibodies,” he added.

“Sequencing of the genome, however, is the first step towards making efficacious antivenoms, and there is a lot more that needs to be done,” said Sunagar.

How are antivenoms made?

Currently, antivenom is produced by vaccinating horses with venom milked from snakes. It is based on a method over a hundred years old and is far from perfect. Antibodies produced by the horse are purified from its blood and used as antivenom. The catch is the horse blood also contains other antibodies that the horse has made in response to its own infections.

The snakebite victim treated with the horse derived antivenom gets a lot of irrelevant horse antibodies, which lead to “serum sickness”, a set of reactions to the foreign antibodies that involves allergic reactions and kidney failure. In treating the snakebite, the current antivenom puts the snakebite victim at risk of serum sickness, that on its own can be fatal.

“Using the genomic information and leveraging recombinant protein expression technologies and phage display for antibody production we can produce an affordable, safe, defined, effective antivenom. The recombinant antibodies can be made to look like human antibodies thus avoiding the risk of serum sickens,” added Seshagiri.

Recombinant protein expression technology has been around now for over 40 years. Insulin, widely used to treat diabetes, was recombinantly produced in bacteria. The insulin gene, contains the instruction to make insulin protein. This instruction when inserted into the bacterium Escherichia coli, transforms it into an insulin-producing factory. Similarly, if the code for the venom toxins is inserted into the right cells, it can result in recombinant toxin and raise antibodies against it. These antibodies will function as antivenom as they will help clear the toxins from the snakebite victim’s body.

Read more: New antivenom could be a gamechanger in treatment of snakebites.

As a next step, besides the work on the cobra antivenom, the team is working on sequencing the genomes of other three remaining snakes from the ‘Big Four’ to identify the key toxin genes that constitute the venom from these animals. They aim to create a broad spectrum antivenom (an universal antivenom) that works against an array of toxins from different snake species.

CITATION:

Suryamohan, K., Krishnankutty, S. P., Guillory, J., Jevit, M., Schröder, M. S., Wu, M., … & Goldstein, L. D. (2020). The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins. Nature Genetics, 1-12.

Banner image: The Indian king cobra. Photo by Eric Kilby / Flickr.