All 46 records catalogued during the review (IDs E01-E46), with the stage reached, the decision and the exclusion criterion. Criterion codes are defined in protocol.md.
| ID | Authors (year) | Title / tool | Stage | Decision | Criterion | Reason |
|---|---|---|---|---|---|---|
| E01 | Liu et al. (2022) | RNN-VirSeeker: A Deep Learning Method for Identification of Short Viral Sequences From Metagenomes | Full text | Included | — | Meets CI1-CI4 |
| E02 | Sukhorukov et al. (2022) | VirHunter: A Deep Learning-Based Method for Detection of Novel RNA Viruses in Plant Sequencing Data | Full text | Included | — | Meets CI1-CI4 |
| E03 | Jiang et al. (2023) | Virus classification for viral genomic fragments using PhaGCN2 | Full text | Included | — | Meets CI1-CI4 |
| E04 | Camargo et al. (2023) | Identification of mobile genetic elements with geNomad | Full text | Excluded | CE6 | Classifies viruses and plasmids jointly |
| E05 | Wu et al. (2024) | Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes | Full text | Included | — | Meets CI1-CI4 |
| E06 | Dong, Chen & Zhao (2024) | VirRep: a hybrid language representation learning framework for identifying viruses from human gut metagenomes | Full text | Included | — | Meets CI1-CI4 |
| E07 | Zhou et al. (2024) | GCN-LSTM: A Graph-Based Deep Learning Method for Metagenomic Virus Classification | Full text | Excluded | CE4 | Conference proceedings without journal extension |
| E08 | Xia et al. (2026) | PhaGCN_Cluster: A Scalable and Robust Framework for Automated Classification and Discovery of Viral Dark Matter from Metagenomes | Full text | Excluded | CI4 | Full text not accessible |
| E09 | Santiago-Rodriguez & Hollister (2022) | Unraveling the viral dark matter through viral metagenomics | Full text | Excluded | CE3 | Literature review without primary data |
| E10 | Galeeva et al. (2025) | Bioinformatics Tools and Approaches for Virus Discovery in Genomic Data: A Systematic Review | Full text | Excluded | CE3 | Systematic review without primary data; cited as the main related work |
| E11 | Jiang et al. (2025) | Illuminating the Virosphere's Dark Matter using Hierarchical Deep Learning | Full text | Excluded | CE4 | Preprint, pending peer review |
| E12 | Staple et al. (2025) | The respiratory tract virome: unravelling the role of viral dark matter in respiratory health and disease | Full text | Excluded | CE3 | Literature review without primary data |
| E13 | Vasconcelos et al. (2024) | Predicting novel mosquito-associated viruses from metatranscriptomic dark matter | Screening | Excluded | — | Focus on mosquito-associated viruses only |
| E14 | Montenegro de Campos (2025) | Aplicação de algoritmos de aprendizagem de máquina para identificação de vírus em dados provenientes da matéria escura de sequenciamento de última geração | Full text | Excluded | CE4 | Master's dissertation |
| E15 | Amgarten (2022) | Machine learning prediction in genomic sequences of prokaryotic viruses from metagenomic datasets | Full text | Excluded | CE4 | Not peer-reviewed; also flagged as a duplicate |
| E16 | Roev et al. (2023) | Unlocking the Viral Universe: Metagenomic Analysis of Bat Samples Using Next-Generation Sequencing | Screening | Excluded | — | Focus on bat samples only |
| E17 | Modha (2022) | Sequence data mining and characterisation of unclassified microbial diversity | Screening | Excluded | — | Excluded at title/keyword screening |
| E18 | Modha et al. (2022) | Quantifying and Cataloguing Unknown Sequences within Human Microbiomes | Full text | Excluded | CE1/CE5 | Characterisation study without original algorithm |
| E19 | Parekh (2026) | Viral dark matter and immune calibration: Metagenomic frontiers in host–virome interactions | Full text | Excluded | CE3 | Literature review without primary data |
| E20 | Cissell & McCoy (2023) | Top-heavy trophic structure within benthic viral dark matter | Full text | Excluded | CE1/CE5 | Ecological study without original algorithm |
| E21 | Gregory et al. (2026) | Evolving strategies for virus discovery | Full text | Excluded | CE3 | Literature review without primary data |
| E22 | Herbold (2024) | EnVhogDB: an extended view of the viral protein families on Earth through a vast collection of HMM profiles | Full text | Excluded | CE4 | Open-review preprint |
| E23 | Camargo et al. (2023) | IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata | Full text | Excluded | CE7 | Database without its own classifier |
| E24 | Krishnamurthy & Wang (2017) | Origins and challenges of viral dark matter | Full text | Excluded | CE3 | Seminal review without primary data; used in the background |
| E25 | Sinno et al. (2025) | Charting the virosphere: computational synergies of AI and bioinformatics in viral discovery and evolution | Full text | Excluded | CE3 | Review without primary data; used in the background |
| E26 | Fiamenghi et al. (2026) | Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes | Full text | Excluded | CE7 | Database without its own classifier |
| E27 | Ren et al. (2017) | VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data | Full text | Excluded | CI2 | Published in 2017; used as historical baseline |
| E28 | Ren et al. (2020) | Identifying viruses from metagenomic data using deep learning (DeepVirFinder) | Full text | Excluded | CI2 | Published in 2020; used as historical baseline |
| E29 | Guo et al. (2021) | VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses | Full text | Included | — | Meets CI1-CI4 |
| E30 | Richardson et al. (2023) | MGnify: the microbiome sequence data analysis resource in 2023 | Full text | Excluded | CE7 | Database without its own classifier |
| E31 | Robertson, Consul & Vikalo (2025) | NextVir: Enabling classification of tumor-causing viruses with genomic foundation models | Full text | Included | — | Meets CI1-CI4 |
| E32 | Ye et al. (2026) | ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks | Full text | Excluded | CE4 | Preprint |
| E33 | Zhou et al. (2023) | DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome | Full text | Excluded | CE6 | General multi-species genomic model without viral focus |
| E34 | Palukaitis & Murphy (2025) | Tobamoviruses: Molecular Aspects and Resistance Regulation—A Special Issue Commemorating 125 Years of Research on Tobamoviruses | Full text | Excluded | CE2 | Tobamoviruses only; no generalisable algorithm; used for context in the Introduction |
| E35 | Koonin et al. (2021) | Viruses Defined by the Position of the Virosphere within the Replicator Space | Screening | Excluded | — | Background reference; not a computational method |
| E36 | Wang et al. (2022) | A Game of Infection – Song of Respiratory Viruses and Interferons | Screening | Excluded | — | Background reference; not a computational method |
| E37 | Klimina et al. (2026) | Bacteriophages in gut metagenomes: from analysis to application | Screening | Excluded | — | Excluded at title/keyword screening |
| E38 | Yin et al. (2024) | IPEV: identification of prokaryotic and eukaryotic virus-derived sequences in virome using deep learning | Full text | Included | — | Meets CI1-CI4 |
| E39 | Sullivan et al. (2023) | Interrogating the viral dark matter of the rumen ecosystem with a global virome database | Full text | Excluded | CE7 | Catalogue without its own classifier |
| E40 | Azzedin et al. (2025) | A Hybrid GCN–BERT Model for Read-Level Viral Classification with Potential Threat Detection | Full text | Excluded | CE4 | Conference proceedings without journal extension |
| E41 | Li (2026) | Transformer-based deep learning for multiclass viral classification in metagenomic sequencing | Full text | Excluded | CE4 | Single-author preprint, not peer-reviewed |
| E42 | Chakulya et al. (2026) | AI-powered analysis of viral metagenomic sequencing data for rapid outbreak investigation and novel pathogen discovery | Full text | Excluded | CE3 | Review without primary data |
| E43 | Khoury et al. (2025) | Charting the virosphere: computational synergies of AI and bioinformatics in viral discovery and evolution | Full text | Excluded | CE3 | Review without primary data; same title as E25 |
| E44 | Bejerman & Debat (2025) | An Update on RNA Virus Discovery: Current Challenges and Future Perspectives | Full text | Excluded | CE3 | Literature review without primary data |
| E45 | Liu et al. (2026) | A global atlas of deep-sea cold seep viruses uncovers extensive genomic novelty and biotechnological potential | Screening | Excluded | — | Excluded at title/keyword screening |
| E46 | Wang et al. (2026) | Diversity and distinctive characteristics of the global RNA virome in urban and peri-urban environments | Full text | Excluded | CE1/CE5 | Environmental virome characterisation without original algorithm |
Totals: 46 records, 7 excluded at screening, 39 assessed in full text, 31 excluded, 8 included.