Novel Virus Identification through Metagenomics: A Systematic Review

Area of Science:

• Virology
• Genomics
• Bioinformatics

Background:

• Metagenomic Next Generation Sequencing (mNGS) offers a culture-independent approach to study microbial communities.
• It is crucial for characterizing complex viromes and discovering novel viruses from various sources.
• mNGS bypasses the need for prior knowledge of microbial sequences in a sample.

Purpose of the Study:

• To systematically review studies identifying novel viruses using mNGS across different sample origins (plant, animal, environment).
• To describe current experimental and analytical protocols employed in mNGS-based virus discovery.
• To provide insights into methods, platforms, and bioinformatics pipelines used in the field.

Main Methods:

• Systematic literature review of publications describing novel virus identification via mNGS.
• Search criteria included studies from plant, animal, and environmental samples without time limitations.
• Data extraction focused on sample types, geographical origin, enrichment, nucleic acid extraction, sequencing platforms, bioinformatics, and identified viral families.

Main Results:

• 379 publications were identified that met the search criteria.
• The review details diverse sample types, geographical origins, and methodologies used in mNGS studies.
• Commonly used commercial kits for nucleic acid purification and various bioinformatics pipelines were documented.

Conclusions:

• mNGS is a powerful and feasible method for discovering novel viruses from diverse sample origins.
• The review highlights the heterogeneity in experimental and analytical protocols currently in use.
• This work offers a valuable resource on mNGS applications for virus discovery and associated methodologies.