ViralCC retrieves complete viral genomes and virus-host pairs from metagenomic Hi-C data

Yuxuan Du, Jed A. Fuhrman and Fengzhu Sun ()
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Yuxuan Du: University of Southern California
Jed A. Fuhrman: University of Southern California
Fengzhu Sun: University of Southern California

Nature Communications, 2023, vol. 14, issue 1, 1-11

Abstract: Abstract The introduction of high-throughput chromosome conformation capture (Hi-C) into metagenomics enables reconstructing high-quality metagenome-assembled genomes (MAGs) from microbial communities. Despite recent advances in recovering eukaryotic, bacterial, and archaeal genomes using Hi-C contact maps, few of Hi-C-based methods are designed to retrieve viral genomes. Here we introduce ViralCC, a publicly available tool to recover complete viral genomes and detect virus-host pairs using Hi-C data. Compared to other Hi-C-based methods, ViralCC leverages the virus-host proximity structure as a complementary information source for the Hi-C interactions. Using mock and real metagenomic Hi-C datasets from several different microbial ecosystems, including the human gut, cow fecal, and wastewater, we demonstrate that ViralCC outperforms existing Hi-C-based binning methods as well as state-of-the-art tools specifically dedicated to metagenomic viral binning. ViralCC can also reveal the taxonomic structure of viruses and virus-host pairs in microbial communities. When applied to a real wastewater metagenomic Hi-C dataset, ViralCC constructs a phage-host network, which is further validated using CRISPR spacer analyses. ViralCC is an open-source pipeline available at https://github.com/dyxstat/ViralCC .

Date: 2023
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DOI: 10.1038/s41467-023-35945-y

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