Viral host assignment across the tree of life with VHAMSTeR

[bioRxiv] Grigson, Neri, Roux and colleagues propose a viral host prediction framework, VHAMSTeR, which can classify viral sequences into five host categories: prokaryotes, animals, plants, fungi and protists. The paper states that the method combines fine-tuned genomic language model embeddings with explicit biological features such as genomic structure and protein homology, and significantly outperforms existing host prediction methods on both DNA viruses (MCC>0.91) and RNA viruses (MCC>0.69). The authors applied it to the global metagenomic catalog, resolving host associations in the RNA virome and identifying 175 cryptic RNA phages; analysis of marine viral genomes showed enrichment of protist viruses in polar oceans; comparison of human gut viromes along an urbanization gradient in Africa showed that symbiotic protist viruses detected in rural cohorts decrease in industrialized populations. The code has been made public.