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Screening of cell-virus, cell-cell, gene-gene interactions among kingdoms of life at single cell resolution

By Dongsheng Chen, Zhihua Ou, Jiacheng Zhu, Peiwen Ding, Haoyu Wang, Lihua Luo, Xiangning Ding, Tianming Lan, Weiying Wu, Yuting Yuan, Wendi Wu, Jiaying Qiu, Yixin Zhu, Yi Jia, Yanan Wei, Qiuyu Qin, Runchu Li, Chengcheng Sun, Wandong Zhao, Zhiyuan Lv, Mingyi Pu, Shangchen Yang, Ashley Chang, Xiaofeng Wei, Fengzhen Chen, Tao Yang, Zhenyong Wei, Fan Yang, Yuejiao Li, Yan Hua, Huan Liu

Posted 13 Aug 2021
bioRxiv DOI: 10.1101/2021.08.13.456190

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) issued a significant and urgent threat to global health. The exact animal origin of SARS-CoV-2 remains obscure and understanding its host range is vital for preventing interspecies transmission of this virus. Previously, we have assessed the target cell profiles of SARS-CoV-2 in pets, livestock, poultry and wild animals. With the reverse zoonotic transmission of SARS-CoV-2 to farm animals. Herein, we expand this investigation to a wider range of animal species and viruses to provide it is urgent to expand the a comprehensive source for large-scale susceptible host screening of potential virus hosts to a larger scale. Therefore, we constructed the single cell atlas for several representative mammalian species (alpaca, hamster, hedgehog, chinchilla etc.), as well as comparative atlas for lung, brain and peripheral blood mononuclear cells (PBMC) for various lineages of animals were constructed, from which we systemically analyzed the virus entry factors for SARS-CoV-2 to identify potential host species. Moreover, to fully apply these resources to the prevention of other infectious diseases, we further evaluated the target cells for 113 viruses over 10 million single cells covering 102 species from mammalians, birds, reptiles, amphibians and invertebrates. Conserved cellular connectomes and regulomes were also identified, with great implication for revealing the fundamental cell-cell and gene-gene cross-talks between these species. Overall, our study could help understand the transmission identify the potential host range and tissue tropism of SARS-CoV-2 and, as well as many other diverse set of viruses and, revealing the host-virus co-evolution footprints and throw light upon the control and prevention of current and future pandemics.

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