Novel Virus Identification through Metagenomics: A Systematic Review

被引:18
作者
Bassi, Cristian [1 ,2 ]
Guerriero, Paola [1 ,2 ]
Pierantoni, Marina [1 ]
Callegari, Elisa [1 ]
Sabbioni, Silvia [2 ,3 ]
机构
[1] Univ Ferrara, Dept Translat Med, I-44121 Ferrara, Italy
[2] Univ Ferrara, Lab Tecnol Terapie Avanzate LTTA, I-44121 Ferrara, Italy
[3] Univ Ferrara, Dept Life Sci & Biotechnol, I-44121 Ferrara, Italy
来源
LIFE-BASEL | 2022年 / 12卷 / 12期
关键词
viral metagenomics; NGS; novel virus; plant; animal; environment; VIRAL METAGENOMICS; FECAL VIROME; DNA VIRUSES; HUMAN GUT; SHOTGUN METAGENOMICS; MICROBIAL GENOMES; READ ALIGNMENT; CIRCULAR DNA; DIVERSITY; WILD;
D O I
10.3390/life12122048
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
Metagenomic Next Generation Sequencing (mNGS) allows the evaluation of complex microbial communities, avoiding isolation and cultivation of each microbial species, and does not require prior knowledge of the microbial sequences present in the sample. Applications of mNGS include virome characterization, new virus discovery and full-length viral genome reconstruction, either from virus preparations enriched in culture or directly from clinical and environmental specimens. Here, we systematically reviewed studies that describe novel virus identification through mNGS from samples of different origin (plant, animal and environment). Without imposing time limits to the search, 379 publications were identified that met the search parameters. Sample types, geographical origin, enrichment and nucleic acid extraction methods, sequencing platforms, bioinformatic analytical steps and identified viral families were described. The review highlights mNGS as a feasible method for novel virus discovery from samples of different origins, describes which kind of heterogeneous experimental and analytical protocols are currently used and provides useful information such as the different commercial kits used for the purification of nucleic acids and bioinformatics analytical pipelines.
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页数:28
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