Viral Ecology of Major Herbivorous livestock in Western China

To elucidate the virome and ecological features of herbivorous livestock in China,this study analyzed 5,679 healthy herbivorous livestock from 128 surveillance sites. From 2021 to 2023, a total of 13,124 nasopharyngeal, anal and vaginal swabs, serum, and Oesophagus-pharyngeal samples were collected from 2,587 cattle, 398 yaks, 1,907 sheep, 408 goats, 259 camels, and 120 horses in Inner Mongolia, Qinghai, Ningxia, Shaanxi, and Gansu, China.Total of 482 pools were constructed, and MTT and MDA libraries were constructed respectively. For MTT, RNA was extracted using Trizol reagent  (Invitrogen, Carlsbad, California, USA) and rRNA depletion was performed using Ribo-ZeroTM Magnetic Gold Kit (Epicentra Biotechnologies, Madison,, USA), RNA sequencing was performed on an Illumina NovaSeq sequencer using NEBNext Super-Directed RNA Library Prep Reagents cassette (New England Biolabs, Ipswich,USA). For MDA, DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany) and amplified using the illustra GenomiPhi V2 DNA Amplification Kit (GE, Fairfield,, USA). Products were purified using the QIAquick PCR purification Kit (Qiagen, Hilden, Germany), followed by paired-end sequencing (150 bp) on an Illumina NovaSeq 6000 sequencer or on an DNBSEQ-T7 sequencer. There are individual data losses, and the lost clean data is replaced with data removing hosts and other microorganisms (with the suffix .useqs)