Genomic evidence of the blood virome and bacteriome provides insights into prevalence, evolution, and susceptibility-related genes across Eurasian pigs

Abstract

Abstract Background Infectious diseases are among the primary constraints to pig production, and the globalization of the pig industry has contributed to the emergence and spread of pathogens. However, there is a lack of comprehensive genomic surveillance on the Eurasian scale, resulting in the prevalence and evolution of pig pathogenic viruses and bacteria are still unknown. Results In this study, we proposed a protocol to identify viral and bacterial sequences and estimate the abundance accurately based on the whole-genome sequencing data of the blood samples. Through whole-genome analysis of 685 Eurasian pigs, we constructed the blood virome and bacteriome landscape. There were a total of 15 pathogenic bacteria, 12 pathogenic viruses, and porcine endogenous retrovirus were identified. We divided 685 Eurasian pigs into three subgroups and discovered significant differences in the viral and bacterial composition, prevalence, and abundance among subgroups. Besides, we performed the quantitative Polymerase Chain Reaction experiment to quantify the copy number of porcine endogenous retrovirus and confirm the reliability of the proposed protocol. Furthermore, we constructed the phylogenetic tree of porcine parvovirus 6 and the results suggested that large-scale transportation across China provides viral connectivity between geographically distinct localities, potentially facilitating the spread of viruses. We also discovered the ADAM28 and ADAMDEC1 genes that may relate to porcine lymphotropic herpesvirus, and the ATF4 gene that may correlate with porcine cytomegalovirus. Conclusions Our study provides new insights into the genomic investigation and epidemiology of viruses and bacteria, in turn helping to prevent viral and bacterial infectious diseases in pigs.

Keywords

• Blood
• Virome and bacteriome
• Whole genome sequencing
• Eurasian pigs