Viral metagenomics of fecal samples from zoo mammals in China: 4-20-175-Alpaca
In May to September 2022, a total of 1,145 fecal samples was collected from various animals across 8 animals orders kept in different zoos in the Southwest, Northeast and North China. The animals include: kangaroo, wallaby, capuchin, monkey, baboon, gibbon, lemur, macaque, mandrill, chimpanzee, wolf, hyaena, bear, otter, lynx, lion, tiger, leopard, raccoon, meerkat, fox, panda, takin, camel, giraffe, hippopotamus, waterbuck, llama, alpaca, oryx, eland, vicuna, pony, kiang, zebra, rhinoceros, tapir, folivore, anteater, elephant, guineapig and porcupine. The samples were grouped into 130 sample pools depending on the animal species. Samples were re-suspended in ten volumes of phosphate-buffered saline (PBS) and vigorously vortexed for 5 min, following frozen and thawed three times on dry ice. The supernatants were then collected after centrifugation (10 min, 15,000g). Totally, 500 uL of each supernatant was filtered through a 0.45 um filter (Millipore) to remove eukaryotic and bacterial cell-sized particles. The filtrates enriched in viral particles were treated with DNase and RNase to digest unprotected nucleic acid. Remaining total nucleic acid was then isolated using QIAamp MinElute Virus Spin Kit (Qiagen) according to manufacturer's protocol. Six libraries were then constructed using Nextera XT DNA Sample Preparation Kit (Illumina) and sequenced using the NovaSeq 6000 platform with 250 bases paired ends and dual barcoding for each pool. For bioinformatics analysis, paired-end reads of 250 bp generated by NovaSeq were debarcoded using vendor software from Illumina.