Leveraging AI and Genomics to Uncover Thousands of New Viruses

Leveraging AI and Genomics to Uncover Thousands of New Viruses

Sub: Sci

Sec: Awareness in AI and Computer

Why in News

Recent advancements in artificial intelligence (AI) combined with genomics have led to the discovery of thousands of new viruses. Researchers are utilizing deep learning methods and genome sequencing to uncover viral species, enhancing our understanding of viral diversity and its impact on public health. These innovations mark a critical step forward in pandemic preparedness.

What Are Viruses?

• Non-cellular entities consisting of genetic material (DNA or RNA) enclosed in a protein coat called capsid.
• Viruses rely on host cells for replication, making them obligate parasites.
• Lack ribosomes and energy-producing mechanisms, depending entirely on the host’s cellular machinery for protein synthesis and energy.
• Exhibit immense diversity in structure, size, and composition.

Structural Features of Viruses:

• Genetic Material: Can be single- or double-stranded DNA/RNA. Genome size varies from a few thousand bases to over a million.
• Capsid: Protein coat protecting viral genome, composed of capsomere subunits. Can exhibit helical, icosahedral, or complex
• Envelope: Some viruses possess a lipid envelope acquired from host cell membranes, aiding in immune evasion and cell entry.
• Glycoprotein spikes on the envelope (e.g., in influenza and HIV) help in attaching to host cells.

Virus Classification:

Based on Structure:

• Helical: e.g., Influenza virus.
• Icosahedral: e.g., Poliovirus.
• Enveloped: e.g., HIV, Coronavirus.
• Complex: e.g., Bacteriophages.

Based on Host Organism:

• Animal Viruses
• Plant Viruses
• Bacteriophages (infect bacteria).

Based on Nucleic Acid:

• DNA Viruses: e.g., Adenovirus, Herpesvirus.
• RNA Viruses: e.g., Picornavirus, Rhabdovirus.

Viral Reproduction Mechanisms:

Lytic Cycle:

• Attachment: Virus binds to host cell receptors.
• Penetration: Viral genome enters the cell.
• Replication: Virus hijacks host machinery to produce viral components.
• Assembly: New viral particles are assembled.
• Release: Host cell is lysed, releasing new viruses.

Lysogenic Cycle:

• Viral genome integrates into host DNA, remaining dormant as a prophage.
• May enter the lytic cycle later due to environmental triggers.
• Seen in latent infections like herpes or in retroviruses like HIV, where the viral genome integrates into host DNA.

The Ecological and Medical Significance of Viruses

Viruses are found everywhere—from soil and water to extreme environments like hydrothermal vents. Despite this, only a small fraction of the estimated 100 million to a trillion viral species has been identified.

Viruses are increasingly recognized not only as agents of disease but also as contributors to ecosystems. However, their role in emerging infectious diseases poses significant threats, with studies estimating around 300,000 mammalian viruses yet to be discovered, many of which could have zoonotic potential (transmitting from animals to humans).

Rise of Metagenomics in Viral Research:

The reduction in costs and improvements in genome-sequencing technologies have led to widespread adoption of metagenomics. This approach allows researchers to analyse genetic material from environmental samples directly, bypassing the need for culturing.

About Metagenomics:

Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, Eco genomics, community genomics or microbiomics.

Metagenomics is the study of the structure and function of entire nucleotide sequences isolated and analysed from all the organisms (typically microbes) in a bulk sample. Metagenomics is often used to study a specific community of microorganisms, such as those residing on human skin, in the soil or in a water sample.

About Serratus: A Breakthrough Tool

In 2022, Canadian researchers led by Artem Babaian developed Serratus, an open-source tool that matches sequencing data with known viral RNA-dependent RNA polymerase (RdRP) sequences. With over 5.7 million sequencing libraries, Serratus helped discover more than 100,000 new viruses.

AI’s Transformative Role in Viral Research

Traditional metagenomic approaches are limited as they often miss evolved proteins. However, recent studies combining genomics with transformers (a type of deep-learning model) have revolutionized virus detection.

Chinese researchers utilized a transformer, combined with genome-sequencing and the ESMFold model, to analyse metagenomic data. This resulted in the identification of over 160,000 new RNA viruses, with many species described for the first time from extreme environments like hot springs and salt lakes.

About ESM (Evolutionary Scale Modelling) Fold model:

It is a state-of-the-art deep learning model developed by Meta AI for predicting the 3D structures of proteins based on their amino acid sequences. It is a transformer-based model, leveraging advancements in natural language processing (NLP) to understand protein sequences and predict their folding patterns.

ESM Fold has been shown to be highly accurate in predicting protein structures, rivalling other state-of-the-art methods like AlphaFold (developed by DeepMind).