Single-cell screening of SARS-CoV-2 target cells in pets, livestock, poultry and wildlife

Chen, Dongsheng; Sun, Jian; Zhu, Jiacheng; Ding, Xiangning; Lan, Tianming; Zhu, Linnan; Xiang, Rong; Ding, Peiwen; Wang, Haoyu; Wang, Xiaoling; Wu, Weiying; Qiu, Jiaying; Wang, Shiyou; Li, Haimeng; An, Fuyu; Bao, Heng; Zhang, Le; Han, Lei; Zhu, Yixin; Wang, Xiran; Wang, Feiyue; Yuan, Yuting; Wu, Wendi; Sun, Chengcheng; Lu, Haorong; Wu, Jihong; Sun, Xinghuai; Zhang, Shenghai; Sahu, Sunil Kumar; Chen, Haixia; Fang, Dongming; Luo, Lihua; Zeng, Yuying; Wu, Yiquan; Cui, ZeHua; He, Qian; Jiang, Sanjie; Ma, Xiaoyan; Feng, Weimin; Xu, Yan; Li, Fang; Liu, Zhongmin; Chen, Lei; Chen, Fang; Jin, Xin; Qiu, Wei; Yang, Huanming; Wang, Jian; Hua, Yan; Liu, Yahong; Liu, Huan; Xu, Xun

A few animals have been suspected to be intermediate hosts of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, a large-scale single-cell screening of SARS-CoV-2 target cells on a wide variety of animals is missing. Here, we constructed the single-cell atlas for 11 representative species in pets, livestock, poultry, and wildlife. Notably, the proportion of SARS-CoV-2 target cells in cat was found considerably higher than other species we investigated and SARS-CoV-2 target cells were detected in multiple cell types of domestic pig, implying the necessity to carefully evaluate the risk of cats during the current COVID-19 pandemic and keep pigs under surveillance for the possibility of becoming intermediate hosts in future coronavirus outbreak. Furthermore, we screened the expression patterns of receptors for 144 viruses, resulting in a comprehensive atlas of virus target cells. Taken together, our work provides a novel and fundamental strategy to screen virus target cells and susceptible species, based on single-cell transcriptomes we generated for domesticated animals and wildlife, which could function as a valuable resource for controlling current pandemics and serve as an early warning system for coping with future infectious disease threats.