Comprehensive Evaluation of RNA and DNA Viromic Methods Based on Species Richness and Abundance Analyses Using Marmot Rectal Samples

Abstract

Viral metagenomics can be roughly divided into species richness-based studies and species abundance-based analyses. Viromic methods with different principles have been developed, but rational selection of these techniques according to different purposes requires comprehensive understanding of their properties.

Virome Analysis of Normal and Growth Retardation Disease-Affected Macrobrachiumrosenbergii

“…The virome has proven helpful for understanding viral diversity and describing novel viruses in new diseases ( 1 ). A viromic method based on metatranscriptomic sequencing not only could detect DNA and RNA viruses with excellent sensitivity but also could show high tolerance to stochastic errors to the relative abundance of viromic taxa ( 2 , 3 ). This approach has played an important role in discovering novel viruses in various tissue and fecal samples from humans and animals ( 4 – 6 ).…”

Virome Profiling of an Eastern Roe Deer Reveals Spillover of Viruses from Domestic Animals to Wildlife

“…In particular, BoV was detected in almost all sampled tissues except the liver. This discrepancy should be ascribed to how viromic analysis at such sequencing depth is less sensitive than the conventional PCR method, which can be improved by ultra-deep sequencing [ 15 ].…”

“…Here we report the viromic profiling of a rescue-failed roe deer followed by PCR/RT-PCR validation. In order to obtain the complete spectrum of viruses harbored by this animal, we employed a combination of MDA and MTT methods, which has been proven be robust to capture the whole virome [ 15 ]. Although we generated more than 60 Gb of data for the animal, very limited known eukaryotic viruses were uncovered, which should undoubtedly be attributed to the small sample size and the inability of the viromic annotation method used here to identify those remote viruses.…”

Elimination of Foreign Sequences in Eukaryotic Viral Reference Genomes Improves the Accuracy of Virome Analysis

“…The quality of assemblies should be seriously considered in contig annotation. There are many means to improve the assembly quality, such as choosing suitable software ( 46 ), employing a rational sample treatment protocol ( 47 ), and reducing the bias induced by random amplification ( 48 ). A classification of host and other microorganism reads prior to de novo assembly could help reduce chimeric contigs ( 47 ).…”

“…There are many means to improve the assembly quality, such as choosing suitable software ( 46 ), employing a rational sample treatment protocol ( 47 ), and reducing the bias induced by random amplification ( 48 ). A classification of host and other microorganism reads prior to de novo assembly could help reduce chimeric contigs ( 47 ). Besides, a final check provides an additional guarantee for high-quality annotation ( 49 ), e.g., host contamination should be checked and eliminated as much as possible.…”