Cross-species transmission risks in farmed and wild mammals

Surveillance of viruses and other microorganisms in non-traditional farmed mammals is sparse compared with traditional livestock species. Now, a study by Shi et al. uncovers uncharted diversity of potential pathogens and mobile antibiotic resistance genes (ARGs) in samples from wild mammals and non-traditional farmed mammals. Faecal, intestinal and lung samples were collected from 973 mammals across 29 provinces in China between 2022 and 2024. Viral diversity was explored using short-read metatranscriptomic sequencing, whereas the diversity of the microbiome (bacteria, fungi and parasites) and resistome (putative ARGs) was assessed using short-read metagenomic sequencing. The authors identified 128 viruses (30 novel), as well as a new coronavirus genus (Etacoronavirus).