ArticlemSystems2022
Comprehensive Evaluation of RNA and DNA Viromic Methods Based on Species Richness and Abundance Analyses Using Marmot Rectal Samples.
Article in mSystems, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 26 citations in OpenAlex.
- Neglected kingdoms: the gut virome, mycobiome and their role in inflammatory bowel disease.Gut microbes · 2026Review
- Diversity Patterns of Domestic Herbivore Viruses in China Reveal Transmission Dynamics with Disease Management Implications.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Ecological Factors and Host Community Characteristics as Potential Drivers of Bat RNA Virus Spillover.Biology · 2026Article
- Virome profiling of long-tailed marmots reveals tissue tropism and cross-species transmission of a diversity of uncharacterized mammalian viruses.Microbiome · 2025Article
- Metagenomic Sequencing Reveals the Viral Diversity of Bactrian Camels in China.Microorganisms · 2025Article
- Report of the fourth conference on next-generation sequencing (NGS) for adventitious virus detection in biologics for humans and animals: Validation and implementation of NGS.Biologicals : journal of the International Association of Biological Standardization · 2025Article
- Node role of wild boars in virus circulation among wildlife and domestic animals.Nature communications · 2025Article
- Meta-transcriptomics characterization of individualMicrobiology spectrum · 2025Article
- Isolation and characterization of goose astrovirus genotype 1 causing enteritis in goslings from Sichuan Province, China.BMC veterinary research · 2025Article
- Identification and genetic analysis of new ephemeroviruses in wild boars in China.Virologica Sinica · 2025Article
- Natural fatal infection of Tembusu virus in bottlenose dolphins in Thailand.Scientific reports · 2025Article
- Geographical distribution and characterization of Jingmen tick virus in wild boars in China.Virologica Sinica · 2025Article
- A compendium of 8,176 bat RNA viral metagenomes reveals ecological drivers and circulation dynamics.Nature microbiology · 2025Article
- Complexity of Diarrhea-Associated Viruses in Stunted Pigs Identified by Viral Metagenomics.Transboundary and emerging diseases · 2025Article
- Viromics-based precision diagnosis of reproductive abnormalities in cows reveals a reassortant Akabane disease virus.BMC veterinary research · 2024Article
- The links between dietary diversity and RNA virus diversity harbored by the great evening bat (Ia io).Microbiome · 2024Article
- Unveiling bat-borne viruses: a comprehensive classification and analysis of virome evolution.Microbiome · 2024Article
- First complete genomic sequence analysis of canine distemper virus in wild boar.Virologica Sinica · 2024Article
- The tissue virome of black-spotted frogs reveals a diversity of uncharacterized viruses.Virus evolution · 2024Article
- Isolation and Identification of Severe Fever with Thrombocytopenia Syndrome Virus from Farmed Mink in Shandong, China.Transboundary and emerging diseases · 2024Article
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Authors and funding
10 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Viral metagenomics is the most powerful tool to profile viromic composition for a given sample. Different viromic methods, including amplification-free ones, have been developed, but choosing them for different purposes requires comprehensive benchmarks. Here, we assessed the performance of four routinely used methods, i.e., multiple displacement amplification (MDA), direct metagenomic sequencing (MTG), sequence-independent single-primer amplification (SIA), and metatranscriptomic sequencing (MTT), using marmot rectal samples as the templates spiked with five known viruses of different genome types. The obtained clean data were differently contaminated by host and bacterial genomes, resulting in MDA having the most, with ~72.1%, but MTT had only ~7.5% data, useful for follow-up viromic analysis. MDA showed a broader spectrum with higher efficiency to profile the DNA virome, and MTT captured almost all RNA viruses with extraordinary sensitivity; hence, they are advisable in richness-based viromic studies. MTG was weak in capturing single-stranded DNA viruses, and SIA could detect both RNA and DNA viruses but with high randomness. Due to biases to certain types of viruses, the four methods caused different alterations to species abundance compared to the initial virus composition. SIA and MDA introduced greater stochastic errors to relative abundances of species, genus, and family taxa, whereas the two amplification-free methods were more tolerant toward such errors and thus are recommendable in abundance-based analyses. In addition, genus taxon is a compromising analytic level that ensures technically supported and biologically and/or ecologically meaningful viromic conclusions.
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