Simultaneous Identification of DNA and RNA Viruses Present in Pig Faeces Using Process-Controlled Deep Sequencing

摘要: Background: Animal faeces comprise a community of many different microorganisms including bacteria and viruses. Only scarce information is available about the diversity viruses present in pigs. Here we describe protocol, which was optimized for purification total fraction viral particles from pig faeces. The genomes purified DNA RNA were simultaneously amplified by PCR subjected to deep sequencing followed bioinformatic analyses. efficiency method monitored using process control consisting three bacteriophages (T4, M13 MS2) with morphology genome types. Defined amounts added sample their abundance assessed quantitative during preparation procedure. Results: procedure applied pooled faecal five From this sample, 69,613 sequence reads generated. All identified analysis reads. In total, 7.7% showed significant identities published sequences. They mainly originated (73.9%) mammalian (23.9%); 0.8% sequences plant most abundant detected porcine kobuvirus, rotavirus C, astrovirus, enterovirus B, sapovirus picobirnavirus. addition, chimpanzee stool-associated circular ssDNA virus identified. Whole indicates that virus, tentatively designated as (PigSCV), represents novel virus. Conclusion: established protocol enables simultaneous detection identification so far unknown It may be studies investigating aetiology, epidemiology ecology diseases. implemented serves quality control, ensures comparability used further optimization.