Novel Virus Identification through Metagenomics: A Systematic Review

Abstract

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.

Discovery of two novel tilapia lake virus‐like virus isolates in the transcriptomic data of guppy fish (Poecilia reticulata)

“…Next‐generation sequencing technology has revolutionized the era of modern microbiology by identifying novel viruses without prior knowledge of the nucleotide sequences present in the clinical samples (Bassi et al, 2022). Transcriptomic and metagenomic raw data deposited in public depositories such as the Sequence Read Archive (SRA) database (https://www.ncbi.nlm.nih.gov/sra) of the National Center for Biotechnology Information (NCBI) have been reanalysed by researchers in order to expand the current knowledge of viruses across different kingdoms (Edgar et al, 2022; Mifsud et al, 2022), including fish species (Mercer et al, 2022).…”

Direct genome sequencing of respiratory viruses from low viral load clinical specimens using target capture sequencing technology

“…The thresholds of minimum number of reads on a reference, minimum coverage, and minimum fraction of reference covered were set to be 100, 10, and 0.5, respectively. 2 The BioFire FilmArray Respiratory Panel 2.1 detected adenovirus, human metapneumovirus, parainfluenza virus 3, and human rhinovirus/enterovirus in addition to SARS-CoV-2 in this specimen.…”

“…Next-generation sequencing (NGS) techniques have proven to be an indispensable tool for monitoring and controlling emerging pathogens, as demonstrated by the SARS-CoV-2 pandemic (1). In addition, high-throughput and parallel nucleotide sequence analysis by NGS is enabling metagenomic sequencing, which could provide comprehensive genome sequences present in specimens (2). However, metagenomic sequencing has a lower detection sensitivity for viral genomes than traditional diagnostic methods such as PCR because the copy number of viral genomes is much lower than that of host and bacterial genomes in clinical specimens (3).…”

The Metagenomic Analysis of Viral Diversity in Colorado Potato Beetle Public NGS Data

“…The metagenomic approach has proven to be a highly efficient way of detecting viruses in a variety of environments [ 1 , 2 ]. Unlike traditional cultural and diagnostic methods, viral metagenomics uses high-throughput next-generation sequencing, which makes it possible to identify rare and new viruses and to establish ecological links between microorganisms and their natural habitat [ 3 ].…”