, * Publications that have not been peer-reviewed and are available on pre-publication servers

, WHO. WHO Coronavirus Disease (COVID-19) Dashboard, 2020.

M. Hoffmann, SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor, Cell, vol.181, pp.271-280, 2020.

S. Matsuyama, Enhanced isolation of SARS-CoV-2 by TMPRSS2-expressing cells, Proc. Natl Acad. Sci. USA, vol.117, pp.7001-7003, 2020.

D. A. Berlin, R. M. Gulick, and F. J. Martinez, Severe Covid-19, N. Engl. J. Med, 2020.

E. Z. Ong, A dynamic immune response shapes COVID-19 progression, Cell Host Microbe, vol.27, pp.879-882, 2020.

P. G. Gibson, L. Qin, and S. H. Puah, COVID-19 acute respiratory distress syndrome (ARDS): clinical features and differences from typical pre-COVID-19 ARDS, Med. J. Aust, vol.213, pp.54-56, 2020.

P. M. George, A. U. Wells, and R. G. Jenkins, Pulmonary fibrosis and COVID-19: the potential role for antifibrotic therapy, Lancet Resp. Med, vol.8, pp.807-815, 2020.

P. Gautret, Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical trial, Int. J. Antimicrob. Agents, p.105949, 2020.
URL : https://hal.archives-ouvertes.fr/hal-02525126

P. Horby, Dexamethasone in Hospitalized Patients with Covid-19 -Preliminary Report, N. Engl. J. Med, 2020.

N. Zhu, A novel coronavirus from patients with pneumonia in China, N. Engl. J. Med, vol.382, pp.727-733, 2019.

H. Chu, Comparative tropism, replication kinetics, and cell damage profiling of SARS-CoV-2 and SARS-CoV with implications for clinical manifestations, transmissibility, and laboratory studies of COVID-19: an observational study, Lancet Microbe, vol.1, pp.14-23, 2020.

P. Zhou, A pneumonia outbreak associated with a new coronavirus of probable bat origin, Nature, vol.579, pp.270-273, 2020.

X. Ou, Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV, Nat. Commun, vol.11, p.1620, 2020.

H. Xu, High expression of ACE2 receptor of 2019-nCoV on the epithelial cells of oral mucosa, Int. J. Oral Sci, vol.12, 2020.

Y. Wang, M. Liu, and J. Gao, Enhanced receptor binding of SARS-CoV-2 through networks of hydrogen-bonding and hydrophobic interactions, Proc. Natl Acad. Sci. USA, vol.117, pp.13967-13974, 2020.

S. A. Lauer, The incubation period of coronavirus disease 2019 (COVID-19) from publicly reported confirmed cases: estimation and application, Ann. Intern. Med, vol.172, pp.577-582, 2020.

W. Guan, Clinical characteristics of coronavirus disease 2019 in China, N. Engl. J. Med, vol.382, pp.1708-1720, 2020.

C. Wu, Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China, JAMA Intern. Med, vol.180, pp.934-943, 2020.

T. Chen, Clinical characteristics of 113 deceased patients with coronavirus disease 2019: retrospective study, BMJ, vol.368, p.1091, 2020.

R. Du, Predictors of mortality for patients with COVID-19 pneumonia caused by SARS-CoV-2: a prospective cohort study, Eur. Respiratory J, vol.55, 2020.

E. J. Williamson, OpenSAFELY: factors associated with COVID-19 death in 17 million patients, Nature

W. Sungnak, SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes, Nat. Med, vol.26, pp.681-687, 2020.

Z. Xu, Pathological findings of COVID-19 associated with acute respiratory distress syndrome, Lancet Respir. Med, vol.8, pp.420-422, 2020.

L. M. Buja, The emerging spectrum of cardiopulmonary pathology of the coronavirus disease 2019 (COVID-19): report of 3 autopsies from Houston, Texas, and review of autopsy findings from other United States cities, Cardiovasc. Pathol, vol.48, pp.107233-107233, 2020.

M. Ackermann, Pulmonary vascular endothelialitis, thrombosis, and angiogenesis in Covid-19, N. Engl. J. Med, vol.383, pp.120-128, 2020.

C. Li, IL-17 response mediates acute lung injury induced by the 2009 pandemic influenza A (H1N1) virus, Cell Res, vol.22, pp.528-538, 2012.

W. H. Mahallawi, O. F. Khabour, Q. Zhang, H. M. Makhdoum, and B. A. Suliman, MERS-CoV infection in humans is associated with a pro-inflammatory Th1 and Th17 cytokine profile, Cytokine, vol.104, pp.8-13, 2018.

L. Tan, Lymphopenia predicts disease severity of COVID-19: a descriptive and predictive study, Signal Transduct. Tar. Ther, vol.5, p.33, 2020.

B. Diao, Reduction and functional exhaustion of T cells in patients with coronavirus disease 2019 (COVID-19), Front. Immunol, vol.11, p.827, 2020.

J. Hadjadj, Impaired type I interferon activity and inflammatory responses in severe COVID-19 patients, Science, p.6027, 2020.
URL : https://hal.archives-ouvertes.fr/pasteur-02900830

C. Qin, Dysregulation of immune response in patients with COVID-19 in Wuhan, China, Clin. Infect. Dis, vol.71, pp.762-768, 2020.

O. Pacha, M. A. Sallman, and S. E. Evans, COVID-19: a case for inhibiting IL-17?, Nat. Rev. Immunol, vol.20, pp.345-346, 2020.

K. Subbarao, Prior infection and passive transfer of neutralizing antibody prevent replication of severe acute respiratory syndrome coronavirus in the respiratory tract of mice, J. Virol, vol.78, pp.3572-3577, 2004.

W. G. Glass, K. Subbarao, B. Murphy, and P. M. Murphy, Mechanisms of host defense following severe acute respiratory syndrome-coronavirus (SARS-CoV) pulmonary infection of mice, J. Immunol, vol.173, pp.4030-4039, 2004.

R. J. Hogan, Resolution of primary severe acute respiratory syndromeassociated coronavirus infection requires Stat1, J. Virol, vol.78, pp.11416-11421, 2004.

M. B. Frieman, SARS-CoV pathogenesis is regulated by a STAT1 dependent but a type I, II and III interferon receptor independent mechanism, PLOS Pathog, vol.6, p.1000849, 2010.

L. M. Gretebeck and K. Subbarao, Animal models for SARS and MERS coronaviruses, Curr. Opin. Virol, vol.13, pp.123-129, 2015.

W. Li, Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus, Nature, vol.426, pp.450-454, 2003.

P. B. Mccray, Lethal infection of K18-hACE2 mice infected with severe acute respiratory syndrome coronavirus, J. Virol, vol.81, pp.813-821, 2007.

J. Netland, D. K. Meyerholz, S. Moore, M. Cassell, and S. Perlman, Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2, J. Virol, vol.82, pp.7264-7275, 2008.

X. H. Yang, Mice transgenic for human angiotensin-converting enzyme 2 provide a model for SARS coronavirus infection, Comp. Med, vol.57, pp.450-459, 2007.

C. M. Coleman and M. B. Frieman, Coronaviruses: important emerging human pathogens, J. Virol, vol.88, pp.5209-5212, 2014.

A. S. Agrawal, Generation of a transgenic mouse model of Middle East respiratory syndrome coronavirus infection and disease, J. Virol, vol.89, pp.3659-3670, 2015.

A. Barlan, Receptor variation and susceptibility to Middle East respiratory syndrome coronavirus infection, J. Virol, vol.88, pp.4953-4961, 2014.

A. S. Cockrell, Mouse dipeptidyl peptidase 4 is not a functional receptor for Middle East Respiratory syndrome coronavirus infection, J. Virol, vol.88, pp.5195-5199, 2014.

N. Van-doremalen, Host species restriction of Middle East respiratory syndrome coronavirus through its receptor, dipeptidyl peptidase 4, J. Virol, vol.88, pp.9220-9232, 2014.

A. S. Cockrell, A mouse model for MERS coronavirus-induced acute respiratory distress syndrome, Nat. Microbiol, vol.2, p.16226, 2016.

K. Li, Mouse-adapted MERS coronavirus causes lethal lung disease in human DPP4 knockin mice, Proc. Natl Acad. Sci. USA, vol.114, pp.3119-3128, 2017.

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

L. Bao, The pathogenicity of SARS-CoV-2 in hACE2 transgenic mice, Nature, vol.583, pp.830-833, 2020.

R. Jiang, Pathogenesis of SARS-CoV-2 in transgenic mice expressing human angiotensin-converting enzyme 2, Cell, vol.182, pp.50-58, 2020.

V. D. Menachery, SARS-like WIV1-CoV poised for human emergence, Proc. Natl Acad. Sci. USA, vol.113, pp.3048-3053, 2016.

G. B. Moreau, Evaluation of K18-hACE2 Mice as a Model of SARS-CoV-2 Infection, Am. J. Tropical Med. Hygiene, ajtmh, pp.20-0762, 2020.

E. S. Winkler, SARS-CoV-2 infection in the lungs of human ACE2 transgenic mice causes severe inflammation, immune cell infiltration, and compromised respiratory function, 2020.

F. S. Oladunni, Lethality of SARS-CoV-2 infection in K18 human angiotensin converting enzyme 2 transgenic mice, vol.18, p.210179, 2020.

J. W. Golden, Human angiotensin-converting enzyme 2 transgenic mice infected with SARS-CoV-2 develop severe and fatal respiratory disease, 2020.

S. *perlman and P. Mccray, K18-hACE2 mice develop dose-dependent disease, 2020.

J. Zhao, Rapid generation of a mouse model for Middle East respiratory syndrome, Proc. Natl Acad. Sci. USA, vol.111, pp.4970-4975, 2014.

A. O. Hassan, A SARS-CoV-2 infection model in mice demonstrates protection by neutralizing antibodies, Cell, vol.182, pp.744-753, 2020.

S. H. Sun, A mouse model of SARS-CoV-2 infection and pathogenesis, Cell Host Microbe, vol.28, pp.124-133, 2020.

, Animal and translational models of SARS-CoV-2 infection and COVID-19

. Md-johansen,

A. Roberts, A mouse-adapted SARS-coronavirus causes disease and mortality in BALB/c mice, PLoS Pathog, vol.3, p.5, 2007.

C. W. Day, A new mouse-adapted strain of SARS-CoV as a lethal model for evaluating antiviral agents in vitro and in vivo, Virology, vol.395, pp.210-222, 2009.

C. Fett, M. L. Dediego, J. A. Regla-nava, L. Enjuanes, and S. Perlman, Complete protection against severe acute respiratory syndrome coronavirus-mediated lethal respiratory disease in aged mice by immunization with a mouse-adapted virus lacking E protein, J. Virol, vol.87, pp.6551-6559, 2013.

J. Netland, Immunization with an attenuated severe acute respiratory syndrome coronavirus deleted in E protein protects against lethal respiratory disease, Virology, vol.399, pp.120-128, 2010.

H. Gu, Rapid adaptation of SARS-CoV-2 in BALB/c mice: Novel mouse model for vaccine efficacy, 2020.

K. H. *dinnon, A mouse-adapted SARS-CoV-2 model for the evaluation of COVID-19 medical countermeasures, 2020.

N. N. Pettit, Obesity is associated with increased risk for mortality among hospitalized patients with COVID-19, Obesity

Z. H. Wu, Y. Tang, and Q. Cheng, Diabetes increases the mortality of patients with COVID-19: a meta-analysis, Acta Diabetol

J. Casanova and H. C. Su, & COVID Human Genetic Effort. A global effort to define the human genetics of protective immunity to SARS-CoV-2 infection, Cell, vol.181, pp.1194-1199, 2020.

C. C. Genetics, The genome architecture of the collaborative cross mouse genetic reference population, Genetics, vol.190, pp.389-401, 2012.

T. M. Keane, Mouse genomic variation and its effect on phenotypes and gene regulation, Nature, vol.477, pp.289-294, 2011.

K. E. Noll, M. T. Ferris, and M. T. Heise, The collaborative cross: a systems genetics resource for studying host-pathogen interactions, Cell Host Microbe, vol.25, pp.484-498, 2019.

L. E. Gralinski, Genome wide identification of SARS-CoV susceptibility loci using the collaborative cross, PLOS Genet, vol.11, p.1005504, 2015.

L. E. Gralinski, Allelic variation in the toll-like receptor adaptor protein Ticam2 contributes to SARS-coronavirus pathogenesis in mice, Bethesda), vol.3, pp.1653-1663, 2017.

R. E. Jordan, P. Adab, and K. K. Cheng, Covid-19: risk factors for severe disease and death, BMJ, vol.368, p.1198, 2020.

J. Yang, Prevalence of comorbidities and its effects in patients infected with SARS-CoV-2: a systematic review and meta-analysis, Int. J. Infect. Dis, vol.94, pp.91-95, 2020.

M. R. Mehra, S. S. Desai, S. R. Kuy, T. D. Henry, and A. N. Patel, Cardiovascular disease, drug therapy, and mortality in Covid-19, N. Engl. J. Med, vol.382, p.102, 2020.

F. Rubino, New-Onset Diabetes in Covid-19, N. Engl. J. Med, 2020.

A. Clark, Global, regional, and national estimates of the population at increased risk of severe COVID-19 due to underlying health conditions in 2020: a modelling study, Lancet Glob. Health, vol.8, pp.1003-1017, 2020.

A. C. Hsu, Targeting PI3K-p110alpha suppresses influenza virus infection in chronic obstructive pulmonary disease, Am. J. Respir. Crit. Care Med, vol.191, pp.1012-1023, 2015.

A. C. Hsu, MicroRNA-125a and -b inhibit A20 and MAVS to promote inflammation and impair antiviral response in COPD, JCI Insight, vol.2, p.90443, 2017.

J. S. Alqahtani, Prevalence, severity and mortality associated with COPD and smoking in patients with COVID-19: a rapid systematic review and meta-analysis, PLoS ONE, vol.15, p.233147, 2020.

J. C. Smith, Cigarette smoke exposure and inflammatory signaling increase the expression of the SARS-CoV-2 receptor ACE2 in the respiratory tract, Dev. Cell, vol.53, pp.514-529, 2020.

E. L. Beckett, A new short-term mouse model of chronic obstructive pulmonary disease identifies a role for mast cell tryptase in pathogenesis, J. Allergy Clin. Immunol, vol.131, pp.752-762, 2013.

B. Jones, Animal models of COPD: what do they tell us?, Respirology, vol.22, pp.21-32, 2017.

G. Liu, Fibulin-1 regulates the pathogenesis of tissue remodeling in respiratory diseases, JCI Insight, vol.1, p.86380, 2016.

P. M. Hansbro, Importance of mast cell Prss31/transmembrane tryptase/ tryptase-? in lung function and experimental chronic obstructive pulmonary disease and colitis, J. Biol. Chem, vol.289, pp.18214-18227, 2014.

H. L. Tay, Antagonism of miR-328 increases the antimicrobial function of macrophages and neutrophils and rapid clearance of non-typeable haemophilus influenzae (NTHi) from infected lung, PLOS Pathog, vol.11, p.1004549, 2015.

X. Li, Risk factors for severity and mortality in adult COVID-19 inpatients in Wuhan, J. Allergy Clin. Immunol, vol.146, pp.110-118, 2020.

S. Garg, Hospitalization rates and characteristics of patients hospitalized with laboratory-confirmed coronavirus disease 2019-COVID-NET, 14 States, Morbidity Mortal. Wkly. Rep. (MMWR), vol.69, pp.458-464, 2020.

P. M. Hansbro, Mechanisms and treatments for severe, steroid-resistant allergic airway disease and asthma, Immunol. Rev, vol.278, pp.41-62, 2017.

R. Y. Kim, MicroRNA-21 drives severe, steroid-insensitive experimental asthma by amplifying phosphoinositide 3-kinase-mediated suppression of histone deacetylase 2, J. Allergy Clin. Immunol, vol.139, pp.519-532, 2017.

R. Y. Kim, Role for NLRP3 Inflammasome-mediated, IL-1beta-Dependent Responses in Severe, Steroid-Resistant Asthma, Am. J. Respir. Crit. Care Med, vol.196, pp.283-297, 2017.

D. S. Hui, Impact of severe acute respiratory syndrome (SARS) on pulmonary function, functional capacity and quality of life in a cohort of survivors, Thorax, vol.60, pp.401-409, 2005.

T. Venkataraman and M. B. Frieman, The role of epidermal growth factor receptor (EGFR) signaling in SARS coronavirus-induced pulmonary fibrosis, Antivir. Res, vol.143, pp.142-150, 2017.

L. Xie, Follow-up study on pulmonary function and lung radiographic changes in rehabilitating severe acute respiratory syndrome patients after discharge, Chest, vol.127, pp.2119-2124, 2005.

P. Zhang, Long-term bone and lung consequences associated with hospitalacquired severe acute respiratory syndrome: a 15-year follow-up from a prospective cohort study, Bone Res, vol.8, 2020.

R. Xu, SARS-CoV-2 induced transcriptional signatures in human lung epithelial cells that promote lung fibrosis, Respiratory Res, vol.21, p.182, 2020.

G. Liu, Fibulin-1c regulates transforming growth factor-? activation in pulmonary tissue fibrosis, JCI Insight, vol.5, p.124529, 2019.

P. Camacho, H. Fan, Z. Liu, and J. Q. He, Small mammalian animal models of heart disease, Am. J. Cardiovasc Dis, vol.6, pp.70-80, 2016.

M. Kleinert, Animal models of obesity and diabetes mellitus, Nat. Rev. Endocrinol, vol.14, pp.140-162, 2018.

R. S. Surwit, C. M. Kuhn, C. Cochrane, J. A. Mccubbin, and M. N. Feinglos, Dietinduced type II diabetes in C57BL/6J mice, Diabetes, vol.37, pp.1163-1167, 1988.

M. S. Winzell and B. Ahrén, The high-fat diet-fed mouse: a model for studying mechanisms and treatment of impaired glucose tolerance and type 2 diabetes, Diabetes, vol.53, pp.215-219, 2004.

L. Chen, X. Li, M. Chen, Y. Feng, and C. Xiong, The ACE2 expression in human heart indicates new potential mechanism of heart injury among patients infected with SARS-CoV-2, Cardiovasc. Res, vol.116, pp.1097-1100, 2020.

C. Cristelo, C. Azevedo, J. M. Marques, R. Nunes, and B. Sarmento, SARS-CoV-2 and diabetes: New challenges for the disease, Diabetes Res Clin. Pr, vol.164, p.108228, 2020.

H. Roca-ho, M. Riera, V. Palau, J. Pascual, and M. J. Soler, Characterization of ACE and ACE2 Expression within Different Organs of the NOD Mouse, Int. J. Mol. Sci, vol.18, p.563, 2017.

K. D. Hulme, L. A. Gallo, and K. R. Short, Influenza virus and glycemic variability in diabetes: a killer combination?, Front. Microbiol, vol.8, p.861, 2017.

C. M. Petrilli, Factors associated with hospital admission and critical illness among 5279 people with coronavirus disease 2019 in New York City: prospective cohort study, BMJ, vol.369, p.1966, 2020.

A. L. Mueller, M. S. Mcnamara, and D. A. Sinclair, Why does COVID-19 disproportionately affect older people?, Aging, vol.12, pp.9959-9981, 2020.

K. Bilinska, P. Jakubowska, C. S. Von-bartheld, and R. Butowt, Expression of the SARS-CoV-2 entry proteins, ACE2 and TMPRSS2, in cells of the olfactory epithelium: identification of cell types and trends with age, ACS Chem. Neurosci, vol.11, pp.1555-1562, 2020.

A. Roberts, Severe acute respiratory syndrome coronavirus infection of golden Syrian hamsters, J. Virol, vol.79, pp.503-511, 2005.

A. S. Booeshaghi and L. Pachter, Decrease in ACE2 mRNA expression in aged mouse lung, 2020.

D. Deming, Vaccine efficacy in senescent mice challenged with recombinant SARS-CoV bearing epidemic and zoonotic spike variants, PLoS Med, vol.3, p.525, 2006.

T. Enkirch and V. Von-messling, Ferret models of viral pathogenesis, Virology, vol.479, pp.259-270, 2015.

J. M. Van-den-brand, Pathology of experimental SARS coronavirus infection in cats and ferrets, Vet. Pathol, vol.45, pp.551-562, 2008.

Y. K. Chu, The SARS-CoV ferret model in an infection-challenge study, Virology, vol.374, pp.151-163, 2008.

B. E. Martina, Virology: SARS virus infection of cats and ferrets, Nature, vol.425, p.915, 2003.

Y. Wan, J. Shang, R. Graham, R. S. Baric, and F. Li, Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus, J. Virol, vol.94, pp.127-00120, 2020.

. Md-johansen, Animal and translational models of SARS-CoV-2 infection and COVID-19

Y. I. Kim, Infection and rapid transmission of SARS-CoV-2 in ferrets, Cell Host Microbe, vol.27, pp.704-709, 2020.

J. Shi, Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS-coronavirus 2, Science, vol.368, pp.1016-1020, 2020.

S. J. Park, Antiviral efficacies of FDA-approved drugs against SARS-CoV-2 infection in ferrets, vol.11, pp.1114-01120, 2020.

D. Blanco-melo, Imbalanced host response to SARS-CoV-2 drives development of COVID-19, Cell, vol.181, 2020.

J. Miao, L. S. Chard, Z. Wang, and Y. Wang, Syrian hamster as an animal model for the study on infectious diseases, Front Immunol, vol.10, p.2329, 2019.

R. Li, Production of genetically engineered golden Syrian hamsters by pronuclear injection of the CRISPR/Cas9 complex, J. Vis. Exp, vol.131, p.56263, 2018.

J. Miao, Characterization of an N-terminal non-core domain of RAG1 gene disrupted Syrian Hamster model generated by CRISPR Cas9, Viruses, vol.10, p.243, 2018.

K. Toth, STAT2 knockout Syrian hamsters support enhanced replication and pathogenicity of human adenovirus, revealing an important role of type I interferon response in viral control, PLoS Pathog, vol.11, p.1005084, 2015.

A. Roberts, Therapy with a severe acute respiratory syndrome-associated coronavirus-neutralizing human monoclonal antibody reduces disease severity and viral burden in golden Syrian hamsters, J. Infect. Dis, vol.193, pp.685-692, 2006.

S. R. Schaecher, An immunosuppressed Syrian golden hamster model for SARS-CoV infection, Virology, vol.380, pp.312-321, 2008.

J. F. Chan, Simulation of the clinical and pathological manifestations of Coronavirus Disease 2019 (COVID-19) in golden Syrian hamster model: implications for disease pathogenesis and transmissibility, Clin. Infect. Dis

J. Luan, Y. Lu, X. Jin, and L. Zhang, Spike protein recognition of mammalian ACE2 predicts the host range and an optimized ACE2 for SARS-CoV-2 infection, Biochem. Biophys. Res. Commun, vol.526, pp.165-169, 2020.

(. Fda) and F. A. , Product development under the animal rule: Guidance for Industry, 2015.

T. Kuiken, Newly discovered coronavirus as the primary cause of severe acute respiratory syndrome, Lancet, vol.362, pp.263-270, 2003.
URL : https://hal.archives-ouvertes.fr/pasteur-00167032

R. A. Fouchier, Aetiology: Koch's postulates fulfilled for SARS virus, Nature, vol.423, p.240, 2003.

J. V. Lawler, Cynomolgus macaque as an animal model for severe acute respiratory syndrome, PLoS Med, vol.3, p.149, 2006.

J. Mcauliffe, Replication of SARS coronavirus administered into the respiratory tract of African Green, rhesus and cynomolgus monkeys, Virology, vol.330, pp.8-15, 2004.

T. Rowe, Macaque model for severe acute respiratory syndrome, J. Virol, vol.78, pp.11401-11404, 2004.

B. L. Haagmans, Pegylated interferon-alpha protects type 1 pneumocytes against SARS coronavirus infection in macaques, Nat. Med, vol.10, pp.290-293, 2004.

S. L. Smits, Exacerbated innate host response to SARS-CoV in aged nonhuman primates, PLoS Pathog, vol.6, p.1000756, 2010.

B. Rockx, Comparative pathogenesis of three human and zoonotic SARS-CoV strains in cynomolgus macaques, PLoS ONE, vol.6, p.18558, 2011.

C. Qin, An animal model of SARS produced by infection of Macaca mulatta with SARS coronavirus, J. Pathol, vol.206, pp.251-259, 2005.

T. C. Greenough, Pneumonitis and multi-organ system disease in common marmosets (Callithrix jacchus) infected with the severe acute respiratory syndrome-associated coronavirus, Am. J. Pathol, vol.167, pp.455-463, 2005.

E. De-wit, Middle East respiratory syndrome coronavirus (MERS-CoV) causes transient lower respiratory tract infection in rhesus macaques, Proc. Natl Acad. Sci. USA, vol.110, pp.16598-16603, 2013.

V. J. Munster, E. De-wit, and H. Feldmann, Pneumonia from human coronavirus in a macaque model, N. Engl. J. Med, vol.368, pp.1560-1562, 2013.

Y. Yao, An animal model of MERS produced by infection of rhesus macaques with MERS coronavirus, J. Infect. Dis, vol.209, pp.236-242, 2014.

E. De-wit, Prophylactic and therapeutic efficacy of mAb treatment against MERS-CoV in common marmosets, Antivir. Res, vol.156, pp.64-71, 2018.

D. Falzarano, Infection with MERS-CoV causes lethal pneumonia in the common marmoset, PLoS Pathog, vol.10, p.1004250, 2014.

V. J. Munster, Respiratory disease and virus shedding in rhesus macaques inoculated with SARS-CoV-2, 2020.

P. Yu, Age-related rhesus macaque models of COVID-19, Anim. Model Exp. Med, vol.3, pp.93-97, 2020.

S. Lu, Comparison of SARS-CoV-2 infections among 3 species of nonhuman primates, 2020.

A. D. *melin, M. C. Janiak, F. Marrone, P. S. Arora, and J. P. Higham, Comparative ACE2 variation and primate COVID-19 risk, 2020.

A. Chandrashekar, SARS-CoV-2 infection protects against rechallenge in rhesus macaques, Science, p.4776, 2020.

J. Yu, DNA vaccine protection against SARS-CoV-2 in rhesus macaques, Science, vol.369, pp.806-811, 2020.

N. Van-doremalen, ChAdOx1 nCoV-19 vaccination prevents SARS-CoV-2 pneumonia in rhesus macaques, Nature

N. I. Health, COVID-19 vaccine (ChAdOx1 nCoV-19) trial in South African adults with and without HIV-infection, 2020.

M. F. Boni, Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic, Nat. Microbiol

K. Schlottau, SARS-CoV-2 in fruit bats, ferrets, pigs, and chickens: an experimental transmission study. Lancet Microbe, pp.30089-30095, 2020.

S. J. Anthony, Global patterns in coronavirus diversity, Virus Evolution, vol.3, p.12, 2017.

V. J. Munster, Replication and shedding of MERS-CoV in Jamaican fruit bats (Artibeus jamaicensis), Sci. Rep, vol.6, p.21878, 2016.

S. Watanabe, Bat coronaviruses and experimental infection of bats, the Philippines, Emerg. Infect. Dis, vol.16, pp.1217-1223, 2010.

J. Zhou, Infection of bat and human intestinal organoids by SARS-CoV-2, Nat. Med, vol.26, pp.1077-1083, 2020.

T. I. Shaw, Transcriptome Sequencing and Annotation for the Jamaican Fruit Bat (Artibeus jamaicensis), PLOS ONE, vol.7, p.48472, 2012.

W. H. , Consensus document on the epidemiology of severe acute respiratory syndrome (SARS). Department of Communicable Disease Surveillance and Response, pp.1-44, 2003.

P. J. Halfmann, Transmission of SARS-CoV-2 in Domestic Cats, N. Engl. J. Med, 2020.

C. Sailleau, First detection and genome sequencing of SARS-CoV-2 in an infected cat in France, Transbound Emerg. Dis
URL : https://hal.archives-ouvertes.fr/hal-02874788

A. Newman, First Reported Cases of SARS-CoV-2 Infection in Companion Animals, MMWR Morb. Mortal. Wkly Rep, vol.69, pp.710-713, 2020.

. Idexx, Leading Veterinary Diagnostic Company Sees No COVID-19 Cases in Pets, 2020.

Q. Zhang, SARS-CoV-2 neutralizing serum antibodies in cats: a serological investigation, 2020.

T. H. Sit, Infection of dogs with SARS-CoV-2. Nature, 2020.

K. L. Macmahon, Protecting poultry workers from exposure to avian influenza viruses, Public Health Rep, vol.123, pp.316-322, 2008.

Y. Yang, M. E. Halloran, J. D. Sugimoto, and I. M. Longini, Detecting human-tohuman transmission of avian influenza A (H5N1), Emerg. Infect. Dis, vol.13, pp.1348-1353, 2007.

R. Brauer and P. Chen, Influenza virus propagation in embryonated chicken eggs, J. Vis. Exp, p.52421, 2015.

H. M. Weingartl, Susceptibility of pigs and chickens to SARS coronavirus, Emerg. Infect. Dis, vol.10, pp.179-184, 2004.

D. E. Swayne, Domestic poultry and SARS coronavirus, southern China, Emerg. Infect. Dis, vol.10, pp.914-916, 2004.

Y. Zhao, Susceptibility of tree shrew to SARS-CoV-2 infection, 2020.

P. M. Hansbro, Surveillance and analysis of avian influenza viruses, Australia, Emerg. Infect. Dis, vol.16, pp.1896-1904, 2010.

W. C. Society, Bronx Zoo Tigers and Lions Recovering from COVID-19, 2020.

N. Oreshkova, SARS-CoV-2 infection in farmed minks, the Netherlands, Eurosurveillance, vol.25, p.2001005, 2020.

N. Geographic, Seven more big cats test positive for coronavirus at Bronx Zoo, 2020.

L. Wang, Complete genome sequence of SARS-CoV-2 in a tiger from a U, S. zoological collection. Microbiol. Resour. Announcements, vol.9, pp.468-00420, 2020.

W. Li, Bats are natural reservoirs of SARS-like coronaviruses, Science, vol.310, pp.676-679, 2005.

L. Wahba, An extensive meta-metagenomic search identifies SARS-CoV-2-homologous sequences in pangolin lung viromes, vol.5, pp.160-00120, 2020.

M. C. Wong, S. J. Javornik-cregeen, N. J. Ajami, and J. F. Petrosino, Evidence of recombination in coronaviruses implicating pangolin origins of nCoV-2019, 2020.

, Animal and translational models of SARS-CoV-2 infection and COVID-19

. Md-johansen,

J. Zhao, Detection of SARS-coronavirus in both human and animals by RT-PCR, Wei Sheng Yan Jiu, vol.34, pp.412-415, 2005.

H. Zhou, 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, vol.30, pp.2196-2203, 2020.

D. J. Mciver, Coronavirus surveillance of wildlife in the Lao People's Democratic Republic detects viral RNA in rodents, Arch. Virol, vol.165, pp.1869-1875, 2020.

P. Liu, W. Chen, and J. Chen, Viral Metagenomics revealed sendai virus and coronavirus infection of Malayan Pangolins (Manis javanica), Viruses, vol.11, p.979, 2019.

N. C. Ammerman, M. Beier-sexton, and A. F. Azad, Growth and maintenance of Vero cell lines, Curr. Protoc. Microbiol. Appendix, vol.4, p.4, 2008.

H. P. Jia, ACE2 receptor expression and severe acute respiratory syndrome coronavirus infection depend on differentiation of human airway epithelia, J. Virol, vol.79, pp.14614-14621, 2005.

E. C. Mossel, Exogenous ACE2 expression allows refractory cell lines to support severe acute respiratory syndrome coronavirus replication, J. Virol, vol.79, pp.3846-3850, 2005.

J. Harcourt, Severe acute respiratory syndrome coronavirus 2 from patient with 2019 novel coronavirus disease, United States, Emerg. Infect. Dis, vol.26, pp.1266-1273, 2020.

A. C. Hsu, Critical role of constitutive type I interferon response in bronchial epithelial cell to influenza infection, PLoS ONE, vol.7, p.32947, 2012.

I. H. Heijink, D. S. Postma, J. A. Noordhoek, M. Broekema, and A. Kapus, House dust mite-promoted epithelial-to-mesenchymal transition in human bronchial epithelium, Am. J. Respir. Cell Mol. Biol, vol.42, pp.69-79, 2010.

A. Faiz, Effect of long-term corticosteroid treatment on microRNA and gene-expression profiles in Chronic Obstructive Pulmonary Disease, Eur. Resp. J, p.1801202, 2019.

M. Hu, Respiratory syncytial virus co-opts host mitochondrial function to favour infectious virus production, Elife, vol.8, p.42448, 2019.

L. Kedzierski, Suppressor of cytokine signaling (SOCS)5 ameliorates influenza infection via inhibition of EGFR signaling, Elife, vol.6, p.20444, 2017.

A. Mulay, SARS-CoV-2 infection of primary human lung epithelium for COVID-19 modeling and drug discovery, 2020.

A. Horani, A. Nath, M. G. Wasserman, T. Huang, and S. L. Brody, Rho-associated protein kinase inhibition enhances airway epithelial basal-cell proliferation and lentivirus transduction, Am. J. Resp. Cell Mol. Biol, vol.49, pp.341-347, 2013.

I. Huang and R. Pranata, Lymphopenia in severe coronavirus disease-2019 (COVID-19): systematic review and meta-analysis, J. Intensive Care, vol.8, p.36, 2020.

Q. Zhao, Lymphopenia is associated with severe coronavirus disease 2019 (COVID-19) infections: a systemic review and meta-analysis, Int J. Infect. Dis, vol.96, pp.131-135, 2020.

Y. T. Yen, Modeling the early events of severe acute respiratory syndrome coronavirus infection in vitro, J. Virol, vol.80, pp.2684-2693, 2006.

L. F. Ng, A human in vitro model system for investigating genome-wide host responses to SARS coronavirus infection, BMC Infect. Dis, vol.4, p.34, 2004.

A. Banerjee, Isolation, sequence, infectivity and replication kinetics of SARS-CoV-2. Emerg Infect Dis. eid2609, 2020.

Y. Chen, The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) directly decimates human spleens and lymph nodes, 2020.

X. Wang, SARS-CoV-2 infects T lymphocytes through its spike proteinmediated membrane fusion, Cell. Mol. Immunol, 2020.

H. Chu, Middle East respiratory syndrome coronavirus efficiently infects human primary T lymphocytes and activates the extrinsic and intrinsic apoptosis pathways, J. Infect. Dis, vol.213, pp.904-914, 2015.

I. Ragan, L. Hartson, H. Pidcoke, R. Bowen, and R. Goodrich, Pathogen reduction of SARS-CoV-2 virus in plasma and whole blood using riboflavin and UV light, PLOS ONE, vol.15, p.233947, 2020.

M. A. Lancaster, Cerebral organoids model human brain development and microcephaly, Nature, vol.501, pp.373-379, 2013.

R. A. Wimmer, Human blood vessel organoids as a model of diabetic vasculopathy, Nature, vol.565, pp.505-510, 2019.

T. Sato, Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche, Nature, vol.459, pp.262-265, 2009.

M. Elbadawi and T. Efferth, Organoids of human airways to study infectivity and cytopathy of SARS-CoV-2, Lancet Resp. Med, pp.30238-30231, 2020.

B. R. Dye, In vitro generation of human pluripotent stem cell derived lung organoids, Elife, vol.4, p.5098, 2015.

A. J. Miller, Generation of lung organoids from human pluripotent stem cells in vitro, Nat. Protoc, vol.14, pp.518-540, 2019.

Y. Li, Q. Wu, X. Sun, J. Shen, and H. Chen, Organoids as a powerful model for respiratory diseases, Stem Cells Int, vol.2020, p.5847876, 2020.

Y. Han, Identification of candidate COVID-19 therapeutics using hPSCderived lung organoids, 2020.

Z. Varga, Endothelial cell infection and endotheliitis in COVID-19, Lancet, vol.395, pp.1417-1418, 2020.

X. Yang, Prevalence and impact of acute renal impairment on COVID-19: a systematic review and meta-analysis, Crit. Care, vol.24, p.356, 2020.

C. Huang, Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet, vol.395, pp.497-506, 2020.

J. Helms, Neurologic Features in Severe SARS-CoV-2 Infection, N. Engl. J. Med, vol.382, pp.2268-2270, 2020.

M. M. Lamers, SARS-CoV-2 productively infects human gut enterocytes, Science, vol.369, pp.50-54, 2020.

V. Monteil, Inhibition of SARS-CoV-2 infections in engineered human tissues using clinical-grade soluble human ACE2, Cell, vol.181, pp.905-913, 2020.

R. Zang, TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes, Sci. Immunol, vol.5, p.3582, 2020.

B. Zhao, Recapitulation of SARS-CoV-2 infection and cholangiocyte damage with human liver ductal organoids, Protein Cell

N. I. Health, Recombinant Human Angiotensin-converting Enzyme 2 (rhACE2) as a Treatment for Patients With COVID-19 (APN01-COVID-19, 2020.

M. L. Stanifer, Critical role of type III interferon in controlling SARS-CoV-2 infection in human intestinal epithelial cells, Cell Rep, p.107863, 2020.

A. *ramani, SARS-CoV-2 targets cortical neurons of 3D human brain organoids and shows neurodegeneration-like effects, 2020.

C. K. Bullen, Infectability of human BrainSphere neurons suggests neurotropism of SARS-CoV-2, Altex. altex, 2020.

R. Prihandoko, Pathophysiological regulation of lung function by the free fatty acid receptor FFA4, 2020.

J. P. Joad, K. S. Kott, J. M. Bric, J. L. Peake, and K. E. Pinkerton, Effect of perinatal secondhand tobacco smoke exposure on in vivo and intrinsic airway structure/ function in non-human primates, Toxicol. Appl. Pharm, vol.234, pp.339-344, 2009.

M. Schlepütz, Neurally mediated airway constriction in human and other species: a comparative study using precision-cut lung slices (PCLS), PLOS ONE, vol.7, p.47344, 2012.

M. K. Ali, Critical role for iron accumulation in the pathogenesis of fibrotic lung disease, J. Pathol, vol.251, pp.49-62, 2020.

C. Donovan, H. J. Seow, J. E. Bourke, and R. Vlahos, Influenza A virus infection and cigarette smoke impair bronchodilator responsiveness to ?-adrenoceptor agonists in mouse lung, Clin. Sci, vol.130, pp.829-837, 2016.

G. Liu, Airway remodelling and inflammation in asthma are dependent on the extracellular matrix protein fibulin-1c, J. Pathol, vol.243, pp.510-523, 2017.

J. L. Booth, K. M. Coggeshall, B. E. Gordon, and J. P. Metcalf, Adenovirus type 7 induces interleukin-8 in a lung slice model and requires activation of Erk, J. Virol, vol.78, pp.4156-4164, 2004.

F. Meng, Replication characteristics of swine influenza viruses in precisioncut lung slices reflect the virulence properties of the viruses, Vet. Res, vol.44, pp.110-110, 2013.

M. Ebsen, Infection of murine precision cut lung slices (PCLS) with respiratory syncytial virus (RSV) and chlamydophila pneumoniae using the Krumdieck technique, Pathol. Res. Pr, vol.198, pp.747-753, 2002.

T. P. Sheahan, Broad-spectrum antiviral GS-5734 inhibits both epidemic and zoonotic coronaviruses, Sci. Transl. Med, vol.9, p.3653, 2017.

J. H. Beigel, Remdesivir for the Treatment of Covid-19 -Preliminary Report, N. Engl. J. Med, 2020.

Y. Cao, Potent neutralizing antibodies against SARS-CoV-2 identified by high-throughput single-cell sequencing of convalescent patients' B cells, Cell, vol.182, pp.73-84, 2020.

T. F. Rogers, Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model, Science, p.7520, 2020.

S. Reagan-shaw, M. Nihal, and N. Ahmad, Dose translation from animal to human studies revisited, Faseb j, vol.22, pp.659-661, 2008.

J. H. Erasmus, Single-dose replicating RNA vaccine induces neutralizing antibodies against SARS-CoV-2 in nonhuman primates, 2020.

N. K. Routhu, Modified vaccinia Ankara based SARS-CoV-2 vaccine expressing full-length spike induces strong neutralizing antibody response, 2020.

,. *tian, SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 elicits immunogenicity in baboons and protection in mice, 2020.

*. Yahalom-ronen and Y. , A single dose of recombinant VSV-?G-spike vaccine provides protection against SARS-CoV-2 challenge, 2020.

Y. Jiang, Blockade of the C5a-C5aR axis alleviates lung damage in hDPP4-transgenic mice infected with MERS-CoV, Emerg. Microbes Infect, vol.7, p.77, 2018.

C. H. Von-weyhern, I. Kaufmann, F. Neff, and M. Kremer, Early evidence of pronounced brain involvement in fatal COVID-19 outcomes, Lancet, vol.395, p.109, 2020.

, Animal and translational models of SARS-CoV-2 infection and COVID-19

. Md-johansen,