• Almagro Armenteros JJ, Tsirigos KD, Sønderby CK, Petersen TN, Winther O, Brunak S, von Heijne G, Nielsen H (2019) SignalP 5.0 improves signal peptide predictions using deep neural networks. Nat Biotechnol 37:420-423

  • Buchfink B, Xie C, Huson DH (2015) Fast and sensitive protein alignment using DIAMOND. Nat Methods 12:59-60

  • Burgin CJ, Colella JP, Kahn PL, Upham NS (2018) How many species of mammals are there? Journal of Mammalogy 99:1-14

  • Chen L, Liu B, Yang J, Jin Q (2014) DBatVir:the database of bat-associated viruses. Database (Oxford) 2014:bau021

  • Coutard B, Valle C, de Lamballerie X, Canard B, Seidah NG, Decroly E (2020) The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade. Antiviral Res 176:104742

  • Duckert P, Brunak S, Blom N (2004) Prediction of proprotein convertase cleavage sites. Protein Eng Des Sel 17:107-112

  • Frutos R, Serra-Cobo J, Pinault L, Lopez Roig M, Devaux CA (2021) Emergence of Bat-Related Betacoronaviruses:Hazard and Risks. Front Microbiol 12:591535

  • Ge XY, Wang N, Zhang W, Hu B, Li B, Zhang YZ, Zhou JH, Luo CM, Yang XL, Wu LJ, Wang B, Zhang Y, Li ZX, Shi ZL (2016) Coexistence of multiple coronaviruses in several bat colonies in an abandoned mineshaft. Virol Sin 31:31-40

  • Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature biotechnology 29:644-652

  • Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies:assessing the performance of PhyML 3.0. Syst Biol 59:307-321

  • Hu B, Guo H, Zhou P, Shi ZL (2021) Characteristics of SARS-CoV-2 and COVID-19. Nat Rev Microbiol 19:141-154

  • Hu D, Zhu C, Ai L, He T, Wang Y, Ye F, Yang L, Ding C, Zhu X, Lv R, Zhu J, Hassan B, Feng Y, Tan W, Wang C (2018) Genomic characterization and infectivity of a novel SARS-like coronavirus in Chinese bats. Emerg Microbes Infect 7:154

  • Jiang S, Shi ZL (2020) The First Disease X is Caused by a Highly Transmissible Acute Respiratory Syndrome Coronavirus. Virol Sin 35:263-265

  • Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS (2017) ModelFinder:fast model selection for accurate phylogenetic estimates. Nat Methods 14:587-589

  • Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7:improvements in performance and usability. Mol Biol Evol 30:772-780

  • Kido H, Okumura Y, Takahashi E, Pan HY, Wang S, Yao D, Yao M, Chida J, Yano M (2012) Role of host cellular proteases in the pathogenesis of influenza and influenza-induced multiple organ failure. Biochim Biophys Acta 1824:186-194

  • Lam TT, Jia N, Zhang YW, Shum MH, Jiang JF, Zhu HC, Tong YG, Shi YX, Ni XB, Liao YS, Li WJ, Jiang BG, Wei W, Yuan TT, Zheng K, Cui XM, Li J, Pei GQ, Qiang X, Cheung WY, Li LF, Sun FF, Qin S, Huang JC, Leung GM, Holmes EC, Hu YL, Guan Y, Cao WC (2020) Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature 583:282-285

  • Lau SK, Li KS, Tsang AK, Shek CT, Wang M, Choi GK, Guo R, Wong BH, Poon RW, Lam CS, Wang SY, Fan RY, Chan KH, Zheng BJ, Woo PC, Yuen KY (2012) Recent transmission of a novel alphacoronavirus, bat coronavirus HKU10, from Leschenault's rousettes to pomona leaf-nosed bats:first evidence of interspecies transmission of coronavirus between bats of different suborders. J Virol 86:11906-11918

  • Letko M, Marzi A, Munster V (2020a) Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses. Nat Microbiol 5:562-569

  • Letko M, Seifert SN, Olival KJ, Plowright RK, Munster VJ (2020b) Bat-borne virus diversity, spillover and emergence. Nat Rev Microbiol 18:461-471

  • Letunic I, Bork P (2016) Interactive tree of life (iTOL) v3:an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 44:W242-245

  • Li B, Si HR, Zhu Y, Yang XL, Anderson DE, Shi ZL, Wang LF, Zhou P (2020) Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation Sequencing. mSphere 5:e00807-19

  • Li LL, Wang JL, Ma XH, Sun XM, Li JS, Yang XF, Shi WF, Duan ZJ (2021) A novel SARS-CoV-2 related coronavirus with complex recombination isolated from bats in Yunnan province, China. Emerg Microbes Infect 10:1683-1690

  • Li MY, Li L, Zhang Y, Wang XS (2020) Expression of the SARS-CoV-2 cell receptor gene ACE2 in a wide variety of human tissues. Infect Dis Poverty 9:45

  • Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005) InterProScan:protein domains identifier. Nucleic Acids Res 33:W116-120

  • Scialo F, Daniele A, Amato F, Pastore L, Matera MG, Cazzola M, Castaldo G, Bianco A (2020) ACE2:The Major Cell Entry Receptor for SARS-CoV-2. Lung 198:867-877

  • Singh A, Singh RS, Sarma P, Batra G, Joshi R, Kaur H, Sharma AR, Prakash A, Medhi B (2020) A Comprehensive Review of Animal Models for Coronaviruses:SARS-CoV-2, SARS-CoV, and MERS-CoV. Virol Sin 35:290-304

  • Sun X, Tse LV, Ferguson AD, Whittaker GR (2010) Modifications to the hemagglutinin cleavage site control the virulence of a neurotropic H1N1 influenza virus. J Virol 84:8683-8690

  • Temmam S, Vongphayloth K, Baquero E, Munier S, Bonomi M, Regnault B, Douangboubpha B, Karami Y, Chrétien D, Sanamxay D, Xayaphet V, Paphaphanh P, Lacoste V, Somlor S, Lakeomany K, Phommavanh N, Pérot P, Dehan O, Amara F, Donati F, Bigot T, Nilges M, Rey FA, van der Werf S, Brey PT, Eloit M (2022) Bat coronaviruses related to SARS-CoV-2 and infectious for human cells. Nature 604:330-336

  • Wan Y, Shang J, Graham R, Baric RS, Li F (2020) Receptor Recognition by the Novel Coronavirus from Wuhan:an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus. J Virol 94:e00127-20

  • Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, Heer FT, de Beer TAP, Rempfer C, Bordoli L, Lepore R, Schwede T (2018) SWISS-MODEL:homology modelling of protein structures and complexes. Nucleic Acids Res 46:W296-w303

  • Yang Y, Zheng M, Liu Y, Wang Y, Xu Y, Zhou Y, Sun D, Chen L, Li H (2021) Analysis of Intermediate Hosts and Susceptible Animals of SARS-CoV-2 by Computational Methods. Zoonoses https://doi.org/10.15212/ZOONOSES-2021-0010

  • Zhou H, Chen X, Hu T, Li J, Song H, Liu Y, Wang P, Liu D, Yang J, Holmes EC, Hughes AC, Bi Y, Shi W (2020) A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein. Curr Biol 30:2196-2203.e2193

  • Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, Si HR, Zhu Y, Li B, Huang CL, Chen HD, Chen J, Luo Y, Guo H, Jiang RD, Liu MQ, Chen Y, Shen XR, Wang X, Zheng XS, Zhao K, Chen QJ, Deng F, Liu LL, Yan B, Zhan FX, Wang YY, Xiao GF, Shi ZL (2020) A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579:270-273

  • Zhu W, Huang Y, Yu X, Chen H, Li D, Zhou L, Huang Q, Liu L, Yang J, Lu S (2022) Discovery and Evolutionary Analysis of a Novel Bat-Borne Paramyxovirus. Viruses 14:288

  • Zhu W, Song W, Fan G, Yang J, Lu S, Jin D, Luo XL, Pu J, Chen H, Xu J (2021a) Genomic Characterization of a New Coronavirus from Migratory Birds in Jiangxi Province of China. Virol Sin 36:1656-1659

  • Zhu W, Yang J, Lu S, Jin D, Wu S, Pu J, Luo XL, Liu L, Li Z, Xu J (2021b) Discovery and Evolution of a Divergent Coronavirus in the Plateau Pika From China That Extends the Host Range of Alphacoronaviruses. Front Microbiol 12:755599

  • Zhu W, Yang J, Lu S, Lan R, Jin D, Luo XL, Pu J, Wu S, Xu J (2021c) Beta- and Novel Delta-Coronaviruses Are Identified from Wild Animals in the Qinghai-Tibetan Plateau, China. Virol Sin 36:402-411