Novel Virus Identification through Metagenomics: A Systematic Review
Abstract
:1. Introduction
2. Material and Methods
2.1. Search Strategy and Selection Criteria
2.2. Data Extraction and Analysis
3. Results
3.1. Literature Search and General Characteristics of the Included Studies
3.2. Enrichment Strategies, Nucleic Acid Purificationand Sequencing Platforms
3.3. Overview of the Extracted Characteristics
3.4. Viral Genomes and Viral Families in Different Sample Types
3.5. Novel Viruses Found by mNGS Studies
3.6. Bioinformatics Pipelines
3.6.1. Quality Control (QC) Check, Sequence Trimming and Filtering
3.6.2. Viral Genome Identification
3.6.3. Analysis of the Results
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Sample Type | Novel Viruses Found in mNGS Studies | References |
---|---|---|
Animal | Flavivirus | [45,67,85,147,212,213] |
Coronanvirus | [25,214,215] | |
Circovirus | [63,120,159,216,217] | |
Bocaparvovirus | [121,124,200] | |
Siphoviridae, Myoviridae, Podoviridae, crAss-like viruses | [195] | |
Sapovirus | [44,95,218]. | |
Plant | Prunus Geminivirus | [207] |
Mastrevirus | [219,220,221] | |
Begomovirus | [132,209] | |
Genomovirus | [222] | |
Narnavirus | [223] | |
Tepovirus | [224] | |
Environment | Phycodnavirus | [210,225] |
Picornavirus | [50,226] | |
PA-SR01 | [163] | |
Picobirnaviridae | [40] | |
Epatitis E virus | [171] | |
Methanosarcina virus MV (MetMV) | [227] | |
Halovirus | [42,228] | |
SAR11 phage | [185] |
Software | Reference | Available at |
---|---|---|
FastQC | [230] | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (accessed on 28 June 2022) |
Trimmomatic | [231] | |
Trim Galore | [232] | https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ (accessed on 28 June 2022) |
Cutadapt | [233] | https://journal.embnet.org/index.php/embnetjournal/article/view/200/479 (accessed on 28 June 2022) |
CLC Genomics Workbench (Qiagen) | [234] | https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/qiagen-clc-genomics/ (accessed on 28 June 2022) |
BBDuk (part of BBTools/BBMap package) | [235] | https://jgi.doe.gov/data-and-tools/software-tools/bbtools/ (accessed on 28 June 2022) |
Software | Reference |
---|---|
SPAdes | [31] |
MetaSPAdes | [244] |
Megahit | [245] |
Velvet | [246] |
Trinity | [247] |
SOAPdenovo2 | [248] |
Ensemble Assembler | [249] |
MIRA | [250] |
PRICE | [251] |
Codon Code Aligner | [252]; https://www.codoncode.com/aligner/ (accessed on 28 June 2022) |
ABySS | [253] |
Ray Meta | [254] |
CAP3 | [255] |
CLC Genomics Workbench (Qiagen) | [234] |
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Bassi, C.; Guerriero, P.; Pierantoni, M.; Callegari, E.; Sabbioni, S. Novel Virus Identification through Metagenomics: A Systematic Review. Life 2022, 12, 2048. https://doi.org/10.3390/life12122048
Bassi C, Guerriero P, Pierantoni M, Callegari E, Sabbioni S. Novel Virus Identification through Metagenomics: A Systematic Review. Life. 2022; 12(12):2048. https://doi.org/10.3390/life12122048
Chicago/Turabian StyleBassi, Cristian, Paola Guerriero, Marina Pierantoni, Elisa Callegari, and Silvia Sabbioni. 2022. "Novel Virus Identification through Metagenomics: A Systematic Review" Life 12, no. 12: 2048. https://doi.org/10.3390/life12122048
APA StyleBassi, C., Guerriero, P., Pierantoni, M., Callegari, E., & Sabbioni, S. (2022). Novel Virus Identification through Metagenomics: A Systematic Review. Life, 12(12), 2048. https://doi.org/10.3390/life12122048