Pathogen genomic surveillance and the AI revolution

2025/01/29 by Spyros Lytras, Kieran D. Lamb, Jumpei Ito +5 · 1 voice · 14 citations
Biochemistry, Genetics and Molecular Biology · #2019-20 coronavirus outbreak #Biology #Computational biology #Computer science #Coronavirus disease 2019 (COVID-19) #Data science #Disease #Gene #Genetics #Genome #Genomic sequencing #Genomics #Genomics and Phylogenetic Studies #Infectious disease (medical specialty) #Machine Learning in Bioinformatics #Pandemic #Pathogen #RNA and protein synthesis mechanisms #Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) #Virology

paper · doi:10.1128/jvi.01601-24

published in Journal of Virology 99(2), e0160124 (American Society for Microbiology)

openalex publication_date 2025/01/29 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/06

Abstract

The unprecedented sequencing efforts during the COVID-19 pandemic paved the way for genomic surveillance to become a powerful tool for monitoring the evolution of circulating viruses. Herein, we discuss how a state-of-the-art artificial intelligence approach called protein language models (pLMs) can be used for effectively analyzing pathogen genomic data. We highlight examples of pLMs applied to predicting viral properties and evolution and lay out a framework for integrating pLMs into genomic surveillance pipelines.

Citations

• Logan: Planetary-Scale Genome Assembly Surveys Life’s Diversity

Cited by

• Emerging technologies transforming the future of global biosecurity. [europepmc]
• Artificial intelligence and machine learning in the development of vaccines and immunotherapeutics-yesterday, today, and tomorrow. [europepmc]
• Genomics in Epidemiology and Disease Surveillance: An Exploratory Analysis. [europepmc]
• Inferring context-specific site variation with evotuned protein language models. [europepmc]
• Zoon0PredV: Potential Virus Species Crossover Prediction Using Convolutional Neural Networks and Viral Protein Sequence Patterns. [europepmc]
• Beyond the Mutation Abyss: Revisiting SARS-CoV-2 Receptor-Binding Domain Evolution from ACE2 Binding Optimization to Immune Epitope Remodeling. [europepmc]
• Klebsiella pneumoniae Genome Database: A Global Resource for Genomic Surveillance of Dissemination, Pathogenicity, and Antimicrobial Resistance. [europepmc]

Discussions

• Recently we have been doing lots of work on how modern #AI methods can be applied to studying virus evolution, so it felt like great timing to write a perspective about it! Very happy to see our pape [bsky, 32 points, 2 comments]

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