Viral Metagenome-Based Precision Surveillance of Pig Population at Large Scale Reveals Viromic Signatures of Sample Types and Influence of Farming Management on Pig Virome

Abstract

Pigs are deeply involved in human lives; hence, their viruses are associated with public health. Here, we established the most comprehensive virome of healthy piglets to date, which provides a viromic baseline of weaned pigs for disease prevention and control, highlighting that longitudinal viromic monitoring is needed to better understand the dynamics of the virome in pig development and disease occurrence.

De-heterogeneity of the eukaryotic viral reference database (EVRD) improves the accuracy and efficiency of viromic analysis

“…But of special note is that, besides 622 reads in dataset AH annotated to porcine reproductive and respiratory syndrome virus (PRRSV) field strains, there were another 1,193 reads annotated to PRRSV vaccine strain in the dataset (Fig. 6F), indicating co-circulation of field viruses and vaccine strains in the farm, which should be especially concerning, since new viruses could be generated through recombination between field viruses and vaccine strains, resulting in vaccine failure (16). Viromic annotation is quite time- and computing resource-consuming.…”

“…The blastn hit of a contig to a subject with one alignment of evalue ≤ 10e-10 and length ≥ 450 or ≥ two alignments of evalue ≤ 10e-5 and length ≥ 150 was considered positive, and the blastx hit to a subject was recognized positive if it had one alignment of evalue ≤ 10e-10 and length ≥ 150 or ≥ two alignments of evalue ≤ 10e-5 and length ≥50. The positive reads and contigs were further verified by blastn/x search against nt/nr databases (16). All blast searches were performed using 12 x86_64 CPUs of an Inter® Xeon® Gold 2.660 GHz processor.…”

“…The copyright holder for this preprint this version posted March 3, 2022. ; https://doi.org/10.1101/2022.03.03.482774 doi: bioRxiv preprint (14), xenotropic murine leukemia virus-related virus (15) and human endogenous retrovirus H (16), are technically viral, but often carried by nucleic acid extraction spin columns, biologicals or experimental performers, and are very easy to contaminate samples, resulting in wrong conclusion in analyses (14)(15)(16)(17)(18). For example, parvovirus was erroneously diagnosed in dairy cattle with fever and diarrhea, but which was found to be a contaminant originating from Qiagen extraction columns (17).…”

“…Based on our experiences of viromic studies over the past decade, those HGSs are mainly related to laboratory components and nonviral organisms or artefacts. The laboratory component-derived sequences (LCDs), such as those of parvovirus-like hybrid virus (14), xenotropic murine leukemia virus-related virus (15) and human endogenous retrovirus H (16), are technically viral, but often carried by nucleic acid extraction spin columns, biologicals or experimental performers, and are very easy to contaminate samples, resulting in wrong conclusion in analyses (14)(15)(16)(17)(18). For example, parvovirus was erroneously diagnosed in dairy cattle with fever and diarrhea, but which was found to be a contaminant originating from Qiagen extraction columns (17).…”

A variety of highly divergent eukaryotic ssDNA viruses in sera of pigs

“…In pigs, CRESS DNA viruses have been frequently detected in faeces [22][23][24][25][26]. However, studies focusing on the investigation of viral genomes in serum of these animals are scarce [27][28][29][30]. Additionally, characterization of novel viral genomes enhances viral database information, increasing the power of future studies to identify more viruses [31,32].…”