ArticleNature communications2023
ViralCC retrieves complete viral genomes and virus-host pairs from metagenomic Hi-C data.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
30 citing papers in PubMed.
- Why did some viruses evolve to be giants while others did not?Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Insights Gained by High-throughput Chromosome Conformation Capture (Hi-C) into the Viral Modulation of Methane Production in Anaerobic Digestion.Environmental science & technology · 2026Article
- VirBinn improves viral genome binning from metagenomic Hi-C through graph diffusion.Bioinformatics (Oxford, England) · 2026Article
- Review
- The human skin virome: Ecological dynamics, aberrant profiles, and therapeutic opportunities.Cell host & microbe · 2026Review
- Gut virome-microbiome interactions across hosts and environments.NPJ biofilms and microbiomes · 2026Article
- Tools and approaches to study the human gut virome: from the bench to bioinformatics.mSystems · 2026Review
- Metagenomic Hi‑C Protocols for Viral Genome Binning, Taxonomic Annotation, and Interaction Network Visualization.Current protocols · 2026Article
- Viromics approaches for the study of viral diversity and ecology in microbiomes.Nature reviews. Genetics · 2026Review
- Computational Microbial and Viral Ecology Analysis.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Prophages and their interactions with lytic phages in the human gut microbiota and their impact on microbial diversity, gut health, and disease.Applied and environmental microbiology · 2025Review
- Single cell viral tagging ofGut microbes · 2025Article
- Benchmarking with synthetic communities provides a baseline for virus-host inferences from Hi-C proximity linking.PLoS biology · 2025Article
- Phages with a broad host range are common across ecosystems.Nature microbiology · 2025Article
- Synthetic community Hi-C benchmarking provides a baseline for virus-host inferences.bioRxiv : the preprint server for biology · 2025Article
- MetaHiCNet: a web server for normalizing and visualizing microbial Hi-C interaction networks.Nucleic acids research · 2025Article
- Gut phages and their interactions with bacterial and mammalian hosts.Journal of bacteriology · 2025Review
- Review
- Evaluating phage lytic activity: from plaque assays to single-cell technologies.Frontiers in microbiology · 2025Review
- Contrasting defense strategies of oligotrophs and copiotrophs revealed by single-cell-resolved virus-host pairing of freshwater bacteria.ISME communications · 2025Article
Corrections and comments
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Authors and funding
3 authors.
Funding
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 .
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.