Lytras, Spyros and Lamb, Kieran D. and Ito, Jumpei and Grove, Joe and Yuan, Ke and Sato, Kei and Hughes, Joseph and Robertson, David L. (2025) Pathogen genomic surveillance and the AI revolution. Journal of Virology, 99 (2): e0160124. ISSN 0022-538X

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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.

Information
Title Pathogen genomic surveillance and the AI revolution
Creators Lytras, Spyros and Lamb, Kieran D. and Ito, Jumpei and Grove, Joe and Yuan, Ke and Sato, Kei and Hughes, Joseph and Robertson, David L.
Identification Number 10.1128/jvi.01601-24
Date February 2025
Divisions College of Medical Veterinary and Life Sciences > School of Cancer Sciences
College of Medical Veterinary and Life Sciences > School of Infection & Immunity
Publisher American Society for Microbiology
Additional Information We acknowledge funding from the UK Medical Research Council (MRC, MC_UU_12014/12, MC_UU_00034/5, MR/V01157X/1, and a Doctoral Training Programme in Precision Medicine studentship for KDL, MR/N013166/1) and the UK Research and Innovation (UKRI) to the G2P2 consortium (MR/Y004205/1). J.I. is supported by grants from Japan Science and Technology Agency PRESTO (JPMJPR22R1), JSPS KAKENHI Grant-in-Aid for Early-Career Scientists (JP23K14526), and Mitsubishi UFJ Financial Group Vaccine Development Research Support. J.G. is supported by the Wellcome Trust and Royal Society through a Sir Henry Dale Fellowship (107653/Z/15/Z). K.S. is supported by the Agency for Medical Research and Development (AMED) Adopting Sustainable Partnerships for Innovative Research Ecosystem (ASPIRE) Program (JP24jf0126002), AMED Strategic Center of Biomedical Advanced Vaccine Research and Development for Preparedness and Response (SCARDA) Japan Initiative for World-leading Vaccine Research and Development Centers “UTOPIA” (JP243fa627001), AMED SCARDA Program on R&amp;D of new generation vaccine including new modality application (JP243fa727002), AMED Research Program on Emerging and Re-emerging Infectious Diseases (JP24fk0108690), Japan Society for the Promotion of Science (JSPS) Grant-in-Aid for Scientific Research (KAKENHI) (JP24H00607), and Mitsubishi UFJ Financial Group Vaccine Development Research Support.
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URI https://pub.demo35.eprints-hosting.org/id/eprint/58
Item Type Article
Depositing User Unnamed user with email ejo1f20@soton.ac.uk
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Date Deposited 11 Jun 2025 16:34
Revision 18
Last Modified 12 Jun 2025 13:01
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