References
- Zhu N, Zhang D, Wang W, et al. A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med. 2020;382(8):727–733.
- Lu R, Zhao X, Li J, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. The Lancet. 2020;395(10224):565–574.
- Wu F, Zhao S, Yu B, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579(7798):265–269.
- Zhou P, Yang XL, Wang XG, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020;579(7798):270–273.
- Zhou H, Chen X, Hu T, et al. 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. 2020;30(11):2196–2203.
- Lam TT, Jia N, Zhang YW, et al. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature. 2020;583(7815):282–285.
- Xiao K, Zhai J, Feng Y, et al. Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins. Nature. 2020;583(7815):286–289.
- Murakami S, Kitamura T, Suzuki J, et al. Detection and characterization of Bat sarbecovirus phylogenetically related to SARS-CoV-2, Japan. Emerg Infect Dis. 2020;26(12):3025–3029.
- Zhou H, Ji J, Chen X, et al. Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses. Cell. 2021;184(17):4380–4391.
- [Preprint] Sarah T, Khamsing V, Eduard Baquero S, et al. Coronaviruses with a SARS-CoV-2-like receptor-binding domain allowing ACE2-mediated entry into human cells isolated from bats of Indochinese peninsula. Nature Portfolio. 2021. doi:10.21203/rs.3.rs-871965/v1
- Zhang S, Qiao S, Yu J, et al. Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution. Nat Commun. 2021;12(1):1607.
- Chen S, Zhou Y, Chen Y, et al.. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34(17):ii884–iii90.
- Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–359.
- Grabherr MG, Haas BJ, Yassour M, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29(7):644–652.
- Hung JH, Weng Z. Sequence alignment and homology search with BLAST and ClustalW. Cold Spring Harb Protoc. 2016;2016(11):10.1101.
- [Preprint] Honko AN, Storm N, Bean DJ, et al. Rapid quantification and neutralization assays for novel coronavirus SARS-CoV-2 using Avicel RC-591 semi-solid overlay. 2020. doi:10.20944/preprints202005.0264.v1
- Seitz M, Beineke A, Seele J, et al. A novel intranasal mouse model for mucosal colonization by Streptococcus suis serotype 2. J Med Microbiol. 2012;61(Pt 9):1311–1318.
- Nie J, Li Q, Wu J, et al. Quantification of SARS-CoV-2 neutralizing antibody by a pseudotyped virus-based assay. Nat Protoc. 2020;15(11):3699–3715.
- Züst R, Miller TB, Goebel SJ, et al. Genetic interactions between an essential 3′cis-acting RNA pseudoknot, replicase gene products, and the extreme 3′ End of the mouse coronavirus genome. J Virol. 2008;82(3):1214–1228.
- Kaye M. SARS-associated coronavirus replication in cell lines. Emerg Infect Dis. 2006;12(1):128–133.
- Xie X, Muruato A, Lokugamage KG, et al. An infectious cDNA clone of SARS-CoV-2. Cell Host Microbe. 2020;27(5):841–848.
- Sia SF, Yan L-M, Chin AWH, et al. Pathogenesis and transmission of SARS-CoV-2 in golden hamsters. Nature. 2020;583(7818):834–838.
- Imai M, Iwatsuki-Horimoto K, Hatta M, et al. Syrian hamsters as a small animal model for SARS-CoV-2 infection and countermeasure development. Proc Natl Acad Sci USA. 2020;117(28):16587–16595.
- Chan JF, Zhang AJ, Yuan S, et al. Simulation of the clinical and pathological manifestations of coronavirus disease 2019 (COVID-19) in a golden Syrian hamster model: implications for disease pathogenesis and transmissibility. Clin Infect Dis. 2020;71(9):2428–2446.
- Rokkas T. Gastrointestinal involvement in COVID-19: a systematic review and meta-analysis. Ann Gastroenterol. 2020;33(4):355–365.
- Lee AC, Zhang AJ, Chan JF, et al. Oral SARS-CoV-2 inoculation establishes subclinical respiratory infection with virus shedding in golden Syrian hamsters. Cell Rep Med. 2020;1(7):100121.
- Zhang Y, Huang K, Wang T, et al. SARS-CoV-2 rapidly adapts in aged BALB/c mice and induces typical pneumonia. J Virol. 2021;95(11):e02477-20.
- Gu H, Chen Q, Yang G, et al. Adaptation of SARS-CoV-2 in BALB/c mice for testing vaccine efficacy. Science. 2020;369(6511):1603–1607.
- Ogando NS, Dalebout TJ, Zevenhoven-Dobbe JC, et al. SARS-coronavirus-2 replication in vero E6 cells: replication kinetics, rapid adaptation and cytopathology. J Gen Virol. 2020;101(9):925–940.
- Goebel SJ, Miller TB, Bennett CJ, et al. A hypervariable region within the 3′cis-acting element of the murine coronavirus genome Is nonessential for RNA synthesis but affects pathogenesis. J Virol. 2007;81(3):1274–1287.
- Goh GK, Dunker AK, Foster JA, et al. Shell disorder analysis suggests that pangolins offered a window for a silent spread of an attenuated SARS-CoV-2 precursor among humans. J Proteome Res. 2020;19(11):4543–4552.
- Roberts A, Vogel L, Guarner J, et al. Severe acute respiratory syndrome coronavirus infection of golden Syrian hamsters. J Virol. 2005;79(1):503–511.
- Roberts A, Lamirande EW, Vogel L, et al. Animal models and vaccines for SARS-CoV infection. Virus Res. 2008;133(1):20–32.
- Song Z, Bao L, Yu P, et al. SARS-CoV-2 causes a systemically multiple organs damages and dissemination in hamsters. Front Microbiol. 2021;11:618891.
- Wang Y, Yang C, Song Y, et al. Scalable live-attenuated SARS-CoV-2 vaccine candidate demonstrates preclinical safety and efficacy. Proc Natl Acad Sci USA. 2021;118(29):e2102775118.
- Trimpert J, Dietert K, Firsching TC, et al. Development of safe and highly protective live-attenuated SARS-CoV-2 vaccine candidates by genome recoding. Cell Rep. 2021;36(5):109493.