NextVir: Enabling classification of tumor-causing viruses with genomic foundation models

by John Robertson, Shorya Consul, Haris Vikalo

Motivation: Oncoviruses, pathogens known to cause or increase the risk of cancer, include both common viruses such as human papillomaviruses and rarer pathogens such as human T-lymphotropic viruses. Computational methods for detecting viral DNA from data acquired by modern DNA sequencing technologies have enabled studies of the association between oncoviruses and cancers. Those studies are rendered particularly challenging when multiple species of oncovirus are present in a tumor sample. In such scenarios, merely detecting the presence of a sequencing read of viral origin is insufficiently informative—instead, a more precise characterization of the viral content in the sample is required. Results: We address this need with NextVir, to our knowledge the first multi-class viral classification framework that adapts genomic foundation models to detecting and classifying sequencing reads of oncoviral origin. Specifically, NextVir explores several foundation models—DNABERT-S, Nucelotide Transformer, and HyenaDNA—and efficiently fine-tunes them to enable accurate identification of the sequencing reads’ origin. The results demonstrate superior performance of the proposed framework over existing deep learning methods and suggest downstream potential for foundational models in genomics.