B. Levine and D. Klionsky, Development by self-digestion: molecular mechanisms and biological functions of autophagy, Dev. Cell, vol.6, issue.4, pp.463-477, 2004.

P. Codogno, M. Mehrpour, and T. Proikas-cezanne, Canonical and noncanonical autophagy: variations on a common theme of self-eating?, Nat. Rev. Mol. Cell Biol, vol.13, issue.1, pp.7-12, 2011.

T. Saitoh and S. Akira, Regulation of innate immune responses by autophagy-related proteins, J. Cell Biol, vol.189, issue.6, pp.925-935, 2010.

M. Komatsu, S. Waguri, T. Chiba, S. Murata, J. Iwata et al., Loss of autophagy in the central nervous system causes neurodegeneration in mice, Nature, vol.441, issue.7095, pp.880-884, 2006.

S. Chakradeo, K. Sharma, A. Alhaddad, D. Bakhshwin, N. Le et al., Yet another function of p53: the switch that determines whether radiation-induced autophagy will be cytoprotective or nonprotective. Implications for autophagy inhibition as a therapeutic strategy, Mol. Pharmacol, vol.114, p.95273, 2015.

A. Chiramel, N. R. Brady, and R. Bartenschlager, Divergent roles of autophagy in virus infection, Cells, vol.2, issue.1, pp.83-104, 2013.

P. Gobeil and D. Leib, Herpes simplex virus c34.5 interferes with autophagosome maturation and antigen presentation in dendritic cells, MBio, vol.3, issue.5, pp.267-279, 2012.

M. Gannage, D. Schmid, R. Albrecht, J. Dengjel, T. Torossi et al., Matrix protein 2 of influenza A virus blocks autophagosome fusion with lysosomes, Cell Host Microbe, vol.6, issue.4, pp.367-380, 2009.

D. Zhou and S. A. Spector, Human immunodeficiency virus type-1 infection inhibits autophagy, AIDS, vol.22, issue.6, p.22, 2008.
DOI : 10.1097/qad.0b013e3282f4a836
URL : http://europepmc.org/articles/pmc2764485?pdf=render

X. Chen, K. Wang, Y. Xing, J. Tu, X. Yang et al., Coronavirus membrane-associated papain-like proteases induce autophagy through interacting with Beclin1 to negatively regulate antiviral innate immunity, Protein Cell, vol.5, issue.12, pp.912-927, 2014.
DOI : 10.1007/s13238-014-0104-6
URL : https://link.springer.com/content/pdf/10.1007%2Fs13238-014-0104-6.pdf

M. Granato, V. Lacconi, M. Peddis, L. D. Renzo, S. Valia et al., Hepatitis C virus present in the sera of infected patients interferes with the autophagic process of monocytes impairing their in-vitro differentiation into dendritic cells, Biochim. Biophys. Acta, vol.1843, issue.7, pp.1348-1355, 2014.

Z. Yang and D. J. Klionsky, Mammalian autophagy: core molecular machinery and signaling regulation, Curr. Opin. Cell Biol, vol.22, issue.2, pp.124-131, 2010.
DOI : 10.1016/j.ceb.2009.11.014
URL : http://europepmc.org/articles/pmc2854249?pdf=render

V. Deretic, Autophagy as an innate immunity paradigm: expanding the scope and repertoire of pattern recognition receptors, Curr. Opin. Immunol, vol.24, issue.1, pp.21-31, 2012.

M. Laplante and D. M. Sabatini, MTOR signaling in growth control and disease, Cell, vol.149, issue.2, pp.274-293, 2012.
DOI : 10.1016/j.cell.2012.03.017
URL : https://doi.org/10.1016/j.cell.2012.03.017

N. Hosokawa, T. Hara, T. Kaizuka, C. Kishi, A. Takamura et al., Nutrient-dependent mTORC1 association with the ULK1-Atg13-FIP200 complex required for autophagy, Mol. Biol. Cell, vol.20, issue.7, p.20, 2009.

B. Hu, Y. Zhang, L. Jia, H. Wu, C. Fan et al., Binding of the pathogen receptor HSP90AA1 to avibirnavirus VP2 induces autophagy by inactivating the AKT-MTOR pathway, Autophagy, 2015.

J. Zhao, Z. Li, M. Wang, Z. Zhang, H. Ma et al., Manipulation of autophagy by HCMV infection is involved in mTOR and influences the replication of virus, Acta Biochim. Biophys. Sin. (Shanghai), issue.11, pp.979-981, 2013.

Y. Ohsumi and N. Mizushima, Two ubiquitin-like conjugation systems essential for autophagy, Semin. Cell Dev. Biol, vol.15, pp.231-236, 2004.
DOI : 10.1016/j.semcdb.2003.12.004

M. Hayashi-nishino, N. Fujita, T. Noda, A. Yamaguchi, T. Yoshimori et al., A subdomain of the endoplasmic reticulum forms a cradle for autophagosome formation, Nat. Cell Biol, vol.11, pp.1433-1437, 2009.

D. W. Hailey, A. S. Rambold, P. Satpute-krishnan, K. Mitra, R. Sougrat et al., Mitochondria supply membranes for autophagosome biogenesis during starvation, Cell, vol.141, pp.656-667, 2010.
DOI : 10.1016/j.cell.2010.04.009
URL : https://doi.org/10.1016/j.cell.2010.04.009

J. Geng, U. Nair, K. Yasumura-yorimitsu, and D. J. Klionsky, Post-Golgi Sec proteins are required for autophagy in Saccharomyces cerevisiae, Mol. Biol. Cell, vol.21, pp.2257-2269, 2010.

N. C. Mcknight and Y. Zhenyu, Beclin 1, an essential component and master regulator of PI3K-III in health and disease, Curr. Pathobiol. Rep, vol.1, issue.4, pp.231-238, 2013.

C. Liang, P. Feng, B. Ku, I. Dotan, D. Canaani et al., Autophagic and tumour suppressor activity of a novel Beclin1-binding protein UVRAG, Nat. Cell Biol, vol.8, issue.7, pp.688-699, 2006.
DOI : 10.1038/ncb1426

S. He, D. Ni, B. Ma, J. H. Lee, T. Zhang et al., PtdIns(3)P-bound UVRAG coordinates Golgi-ER retrograde and Atg9 transport by differential interactions with the ER tether and the beclin 1 complex, Nat. Cell Biol, vol.15, issue.10, pp.1206-1219, 2013.

M. Jin and D. J. Klionsky, Transcriptional regulation of ATG9 by the Pho23-Rpd3 complex modulates the frequency of autophagosome formation, Autophagy, vol.10, issue.9, pp.1681-1682, 2014.

T. Proikas-cezanne, Z. Takacs, P. Donnes, and O. Kohlbacher, WIPI proteins: essential PtdIns3P effectors at the nascent autophagosome, J. Cell Sci, vol.128, issue.2, pp.207-217, 2015.
DOI : 10.1242/jcs.146258
URL : http://jcs.biologists.org/content/128/2/207.full.pdf

T. Hanada, N. N. Noda, Y. Satomi, Y. Ichimura, Y. Fujioka et al., The Atg12-Atg5 conjugate has a novel E3-like activity for protein lipidation in autophagy, J. Biol. Chem, vol.282, pp.37298-37302, 2007.

M. Walczak and S. Martens, Dissecting the role of the Atg12-Atg5-Atg16 complex during autophagosome formation, Autophagy, vol.9, issue.3, pp.424-425, 2013.

Y. Kabeya, N. Mizushima, A. Yamamoto, S. Oshitani-okamoto, Y. Ohsumi et al., ) LC3, GABARAP and GATE16 localize to autophagosomal membrane depending on form-II formation, J. Cell Sci, vol.117, pp.2805-2812, 2004.
DOI : 10.1242/jcs.01131
URL : http://jcs.biologists.org/content/117/13/2805.full.pdf

N. Martinez-lopez, D. Athonvarangkul, P. Mishall, S. Sahu, and R. Singh, Autophagy proteins regulate ERK phosphorylation, Nat. Commun, vol.4, p.2799, 2013.
DOI : 10.1038/ncomms3799
URL : https://www.nature.com/articles/ncomms3799.pdf

Y. Ichimura, T. Kirisako, T. Takao, Y. Satomi, Y. Shimonishi et al., A ubiquitin-like system mediates protein lipidation, Nature, vol.488, issue.6811, pp.488-492, 2000.
DOI : 10.1038/35044114

N. Fujita, T. Itoh, H. Omori, M. Fukuda, T. Noda et al., The Atg16L complex specifies the site of LC3 lipidation for membrane biogenesis in autophagy, Mol. Biol. Cell, vol.19, issue.5, pp.2092-2100, 2008.

T. Shpilka, H. Weidberg, S. Pietrokovski, and Z. Elazar, Atg8: an autophagy-related ubiquitin-like protein family, Genome Biol, vol.12, p.226, 2011.
DOI : 10.1186/gb-2011-12-7-226
URL : https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2011-12-7-226

G. Bjørkøy, T. Lamark, A. Brech, H. Outzen, M. Perander et al., P62/SQSTM1 forms protein aggregates degraded by autophagy and has a protective effect on huntingtin-induced cell death, J. Cell Biol, vol.171, issue.4, pp.603-614, 2005.

Y. Takahashi, D. Coppola, N. Matsushita, H. D. Cualing, M. Sun et al., , 2007.

, Bif-1 interacts with Beclin 1 through UVRAG and regulates autophagy and tumorigenesis, Nat. Cell Biol, vol.9, issue.10, pp.1142-1151

M. Chaumorcel, M. Lussignol, L. Mouna, Y. Cavignac, K. Fahie et al., The human cytomegalovirus protein TRS1 inhibits autophagy via its interaction with Beclin 1, J. Virol, vol.86, issue.5, pp.2571-2584, 2012.
DOI : 10.1128/jvi.05746-11
URL : https://jvi.asm.org/content/86/5/2571.full.pdf

S. Mcfarlane, J. Aitken, J. S. Sutherland, M. J. Nicholl, V. G. Preston et al., Early induction of autophagy in human fibroblasts after infection with human cytomegalovirus or herpes simplex virus 1, J. Virol, vol.85, issue.9, pp.4212-4221, 2011.

J. Zhao, Z. Li, M. Wang, Z. Zhang, H. Ma et al., Manipulation of autophagy by HCMV infection is involved in mTOR and influences the replication of virus, Acta Biochim. Biophys. Sin, vol.45, issue.11, pp.979-981, 2013.

R. Beale, H. Wise, A. Stuart, B. J. Ravenhill, P. Digard et al., A LC3-interacting motif in the influenza A virus M2 protein is required to subvert autophagy and maintain virion stability, Cell Host Microbe, vol.15, issue.2, pp.239-247, 2014.

P. Mehrbod, M. Hair-bejo, T. A. Ibrahim, A. R. Omar, M. E. Zowalaty et al., Simvastatin modulates cellular components in influenza A virus-infected cells, Int. J. Mol. Med, vol.34, issue.1, pp.61-73, 2014.

H. S. Lee, B. H. Daniels, E. Salas, A. W. Bollen, J. Debnath et al., Clinical utility of LC3 and p62 immunohistochemistry in diagnosis of drug-induced autophagic vacuolar myopathies: a case-control study, PLoS One, vol.7, issue.4, p.36221, 2012.

K. Hegedus, S. Takats, A. L. Kovacs, and G. Juhasz, Evolutionarily conserved role and physiological relevance of a STX17/Syx17 (syntaxin 17)-containing SNARE complex in autophagosome fusion with endosomes and lysosomes, Autophagy, vol.9, issue.10, pp.1642-1646, 2013.

P. Jiang, T. Nishimura, Y. Sakamaki, E. Itakura, T. Hatta et al., The HOPS complex mediates autophagosomelysosome fusion through interaction with syntaxin 17, Mol. Biol. Cell, vol.25, issue.8, pp.1327-1337, 2014.

X. Ao, L. Zou, and Y. Wu, Regulation of autophagy by the Rab GTPase network, Cell Death Differ, vol.21, issue.3, pp.348-358, 2014.

H. Liu, M. Cao, Y. Wang, L. Li, L. Zhu et al., Endoplasmic reticulum stress is involved in the connection between inflammation and autophagy in type 2 diabetes, Gen. Comp. Endocrinol, vol.210, pp.124-129, 2014.

R. Zeng, Y. Cui, Y. Hai, and Y. Liu, Pattern recognition receptors for respiratory syncytial virus infection and design of vaccines, Virus Res, vol.167, pp.138-145, 2011.

F. Heil, P. Ahmad-nejad, H. Hemmi, H. Hochrein, F. Ampenberger et al., The Toll-like receptor 7 (TLR7)-specific stimulus loxoribine uncovers a strong relationship within the TLR7, 8 and 9 subfamily, Eur. J. Immunol, vol.33, issue.11, pp.2987-2997, 2003.

M. Matsumoto, K. Funami, M. Tanabe, H. Oshiumi, M. Shingai et al., Subcellular localization of Toll-like receptor 3 in human dendritic cells, J. Immunol, vol.171, issue.6, pp.3154-3162, 2003.

K. J. Brandt, C. Fickentscher, E. K. Kruithof, and P. D. Moerloose, TLR2 ligands induce NF-jB activation from endosomal compartments of human monocytes, PLoS One, vol.8, issue.12, p.80743, 2013.

T. Demoor, B. C. Petersen, S. Morris, S. Mukherjee, C. Ptaschinski et al., IPS-1 signaling has a nonredundant role in mediating antiviral responses and the clearance of respiratory syncytial virus, J. Immunol, vol.189, issue.12, pp.5942-5953, 2012.

M. A. Sanjuan, C. P. Dillon, S. W. Tait, S. Moshiach, F. Dorsey et al., Toll-like receptor signalling in macrophages links the autophagy pathway to phagocytosis, Nature, vol.450, pp.1253-1257, 2007.

M. Wu, S. Chen, and S. Hsieh, Distinct regulation of dengue virus-induced inflammasome activation in human macrophage subsets, J. Biomed. Sci, vol.20, issue.36, 2013.

A. Szabo and E. Rajnavolgyi, Collaboration of Toll-like and RIG-I-like receptors in human dendritic cells: tRIGgering antiviral innate immune responses, Am. J. Clin. Exp. Immunol, vol.2, issue.3, pp.195-207, 2013.

M. A. Mandell, A. Jain, J. Arko-mensah, S. Chauhan, T. Kimura et al., TRIM proteins regulate autophagy and can target autophagic substrates by direct recognition, Dev. Cell, vol.30, issue.4, pp.394-409, 2014.

K. Yang, H. X. Shi, X. Y. Liu, Y. F. Shan, B. Wei et al., TRIM21 is essential to sustain IFN regulatory factor 3 activation during antiviral response, J. Immunol, vol.182, issue.6, pp.3782-3792, 2009.

M. Mandell, T. Kimura, A. Jain, T. Johansen, and V. Deretic, TRIM proteins regulate autophagy: TRIM5 is a selective autophagy receptor mediating HIV-1 restriction, Autophagy, vol.10, issue.12, pp.2387-2388, 2014.

N. Jounai, F. Takeshita, K. Kobiyama, A. Sawano, A. Miyawaki et al., The Atg5-Atg12 conjugate associates with innate antiviral immune responses, Proc. Natl. Acad. Sci. USA, vol.104, issue.35, pp.14050-14055, 2007.

X. H. Liang, L. K. Kleeman, H. H. Jiang, G. Gordon, J. E. Goldman et al., Protection against fatal Sindbis virus encephalitis by beclin, a novel Bcl-2-interacting protein, J. Virol, vol.72, issue.11, pp.8586-8596, 1998.

A. Orvedahl, S. Macpherson, R. Sumpter, Z. Talloczy, Z. Zou et al., Autophagy protects against Sindbis virus infection of the central nervous system, Cell Host Microbe, vol.7, issue.2, pp.115-127, 2010.

Y. Lei, H. Wen, Y. Yu, D. J. Taxman, L. Zhang et al., The mitochondrial proteins NLRX1 and TUFM form a complex that regulates type 1 interferon and autophagy, Immunity, vol.36, issue.6, pp.933-946, 2012.

M. M. Desai, B. Gong, T. Chan, R. A. Davey, L. Soong et al., Differential, type I interferon-mediated autophagic trafficking of hepatitis C virus proteins in mouse liver, Gastroenterology, vol.141, issue.2, pp.674-685, 2011.

M. T. Sorbara, L. K. Ellison, M. Ramjeet, L. H. Travassos, N. L. Jones et al., The protein ATG16L1 suppresses inflammatory cytokines induced by the intracellular sensors Nod1 and Nod2 in an autophagy-independent manner, Immunity, vol.39, issue.5, pp.858-873, 2013.

L. H. Travassos, L. A. Carneiro, M. Ramjeet, S. Hussey, Y. G. Kim et al., Nod1 and Nod2 direct autophagy by recruiting ATG16L1 to the plasma membrane at the site of bacterial entry, Nat. Immunol, vol.11, issue.1, pp.55-62, 2010.

C. S. Shi and J. H. Kehrl, Traf6 and A20 differentially regulate TLR4-induced autophagy by affecting the ubiquitination of Beclin 1, Autophagy, vol.6, issue.7, pp.986-987, 2010.

H. K. Lee, L. M. Mattei, B. E. Steinberg, P. Alberts, Y. H. Lee et al., In vivo requirement for Atg5 in antigen presentation by dendritic cells, J. Immunol, vol.191, issue.5, pp.2526-2537, 2013.

S. Morris, M. S. Swanson, A. Lieberman, M. Reed, Z. Yue et al., Autophagy-mediated DC activation is essential for innate cytokine production and APC function with respiratory syncytial virus responses, J. Immunol, vol.187, issue.8, pp.3953-396, 2011.

M. Reed, S. H. Morris, S. Jang, S. Mukherjee, Z. Yue et al., Autophagy-inducing protein beclin-1 in dendritic cells regulates CD4 T cell responses and disease severity during respiratory syncytial virus infection, J. Immunol, vol.191, issue.5, pp.2526-2537, 2013.

H. Pan, Y. Zhang, Z. Luo, P. Li, L. Liu et al., Autophagy mediates avian influenza H5N1 pseudotyped particleinduced lung inflammation through NF-jB and p38 MAPK signaling pathways, Am. J. Physiol. Lung Cell. Mol. Physiol, vol.306, issue.2, pp.183-195, 2014.
DOI : 10.1152/ajplung.00147.2013

F. P. Blanchet, A. Moris, D. S. Nikolic, M. Lehmann, S. Cardinaud et al., Human immunodeficiency virus-1 inhibition of immunoamphisomes in dendritic cells impairs early innate and adaptive immune responses, Immunity, vol.32, issue.5, pp.654-669, 2010.
URL : https://hal.archives-ouvertes.fr/pasteur-00488629

V. Deretic, T. Saitoh, and S. Akira, Autophagy in infection, inflammation and immunity, Nat. Rev. Immunol, vol.13, issue.10, pp.722-737, 2013.
DOI : 10.1038/nri3532
URL : http://europepmc.org/articles/pmc5340150?pdf=render

J. D. Mintern, C. Macri, and J. A. Villadangos, Modulation of antigen presentation by intracellular trafficking, Curr. Opin. Immunol, vol.34, pp.16-21, 2015.

L. English, M. Chemali, J. Duron, C. Rondeau, A. Laplante et al., Autophagy enhances the presentation of endogenous viral antigens on MHC class I molecules during HSV-1 infection, Nat. Immunol, vol.10, pp.480-487, 2009.

R. Ravindran, N. Khan, H. I. Nakaya, S. Li, J. Loebbermann et al., Vaccine activation of the nutrient sensor GCN2 in dendritic cells enhances antigen presentation, Science, vol.343, issue.6168, pp.313-317, 2014.

Y. Li, L. X. Wang, G. Yang, F. Hao, W. J. Urba et al., Efficient cross-presentation depends on autophagy in tumor cells, Cancer Res, vol.68, pp.6889-6895, 2008.

F. Wiede, A. Ziegler, D. Zehn, and T. Tiganis, PTPN2 restrains CD8 + T cell responses after antigen cross-presentation for the maintenance of peripheral tolerance in mice, J. Autoimmun, vol.53, pp.105-114, 2014.

H. Kim, B. Mazumdara, S. K. Bosea, K. Meyera, A. M. Biscegliea et al., Hepatitis C virus-mediated inhibition of cathepsin S increases invariant-chain expression on hepatocyte surface, J. Virol, vol.86, issue.18, pp.9919-9928, 2012.

C. Paludan, D. Schmid, M. Landthaler, M. Vockerodt, D. Kube et al., Endogenous MHC class II processing of a viral nuclear antigen after autophagy, Science, vol.307, issue.5709, pp.593-596, 2005.

S. Romao, N. Gasser, A. C. Becker, B. Guhl, M. Bajagic et al., Autophagy proteins stabilize pathogen-containing phagosomes for prolonged MHC II antigen processing, J. Cell Biol, vol.203, issue.5, pp.757-766, 2013.
DOI : 10.1084/jem.21013oia64
URL : http://europepmc.org/articles/pmc3857489?pdf=render

D. H. Barouch, Novel adenovirus vector-based vaccines for HIV-1, Curr. Opin. HIV AIDS, vol.5, pp.386-390, 2010.

M. J. Mcelrath, S. C. Rosa, Z. Moodie, S. Dubey, L. Kierstead et al., HIV-1 vaccine-induced immunity in the test-of-concept Step Study: a case-cohort analysis, Lancet, vol.372, issue.9653, pp.1894-1905, 2008.

Y. Jin, C. Sun, L. Feng, P. Li, L. Xiao et al., Regulation of SIV antigen-specific CD4+ T cellular immunity via autophagosome-mediated MHC II molecule-targeting antigen presentation in mice, PLoS One, vol.9, issue.3, p.93143, 2014.

X. Fu, L. Tao, and X. Zhang, A short polypeptide from the herpes simplex virus type 2 ICP10 gene can induce antigen aggregation and autophagosomal degradation for enhanced immune presentation, Hum. Gene Ther, vol.21, issue.12, pp.1687-1696, 2010.

M. Salio, D. J. Puleston, T. S. Mathan, D. Shepherd, A. J. Stranks et al., Essential role for autophagy during invariant NKT cell development, Proc. Natl. Acad. Sci. USA, vol.111, issue.52, pp.5678-87, 2014.

W. Beron, M. G. Gutierrez, M. Rabinovitch, and M. I. Colombo, Coxiella burnetii localizes in a Rab7-labeled compartment with autophagic characteristics, Infect Immunol, vol.70, pp.5816-5821, 2002.

I. Nakagawa, A. Amano, N. Mizushima, A. Yamamoto, H. Yamaguchi et al., Autophagy defends cells against invading group A Streptococcus. Science, vol.306, issue.5698, pp.1037-1040, 2004.

M. Cemma and J. H. Brumell, Interactions of pathogenic bacteria with autophagy systems, Curr. Biol, vol.22, issue.13, pp.540-545, 2012.

S. C. Corr and L. A. Neill, Listeria monocytogenes infection in the face of innate immunity, Cell. Microbiol, vol.11, issue.5, pp.703-709, 2009.

S. Santana, I. Sastre, M. Recuero, M. J. Bullido, and J. Aldudo, Oxidative stress enhances neurodegeneration markers induced by herpes simplex virus type 1 infection in human neuroblastoma cells, PLoS One, vol.8, issue.10, p.75842, 2013.

D. R. Wilcox, N. R. Wadhwani, R. Longnecker, and W. J. Muller, Differential reliance on autophagy for protection from HSV encephalitis between newborns and adults, PLoS Pathog, 2015.

M. Ait-goughoulte, T. Kanda, K. Meyer, J. S. Ryerse, R. B. Ray et al., Hepatitis C virus genotype 1a growth and induction of autophagy, J. Virol, vol.82, issue.5, pp.2241-2249, 2008.

D. Sir, W. Chen, J. Choi, T. Wakita, B. Yen et al., Induction of incomplete autophagic response by hepatitis C virus via the unfolded protein response, Hepatology, vol.48, issue.4, pp.1054-1061, 2008.

E. M. Buckingham, J. E. Carpenter, W. Jackson, and C. Grose, Autophagy and the effects of its inhibition on varicella-zoster virus glycoprotein biosynthesis and infectivity, J. Virol, vol.88, issue.2, pp.890-902, 2014.

C. Richetta, I. P. Gregoire, P. Verlhac, O. Azocar, J. Baguet et al., Sustained autophagy contributes to measles virus infectivity, PLoS Pathog, vol.9, issue.9, p.1003599, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00965032

E. Delorme-axford, S. Morosky, J. Bomberger, D. B. Stolz, W. T. Jackson et al., BPIFB3 regulates autophagy and coxsackievirus B replication through a noncanonical pathway independent of the core initiation machinery, MBio, vol.5, issue.6, p.2147, 2014.

S. E. Crawford, J. M. Hyser, B. Utama, and M. K. Estes, Autophagy hijacked through viroporin-activated calcium/calmodulin-dependent kinase kinase-P signaling is required for rotavirus replication, Proc. Natl. Acad. Sci. USA 09, pp.3405-3418, 2012.

C. C. Kemball, M. Alirezaei, C. T. Flynn, M. R. Wood, S. Harkins et al., Coxsackievirus infection induces autophagy-like vesicles and megaphagosomes in pancreatic acinar cells in vivo, J. Virol, vol.23, issue.84, p.23, 2010.

X. Zeng and C. R. Carlin, Host cell autophagy modulates early stages of adenovirus infections in airway epithelial cells, J. Virol, vol.87, issue.4, pp.2307-2319, 2013.

A. Nakashima, N. Tanakaa, K. Tamaia, M. Kyuumaa, Y. Ishikawaa et al., Survival of parvovirus B19-infected cells by cellular autophagy, Virology, vol.349, issue.2, pp.254-263, 2006.

L. W. Chu, Y. L. Huang, J. H. Lee, L. Y. Huang, W. J. Chen et al., Single-virus tracking approach to reveal the interaction of Dengue virus with autophagy during the early stage of infection, J. Biomed. Opt, vol.19, issue.1, p.11018, 2014.

I. P. Gregoire, C. Richetta, L. Meyniel-schicklin, S. Borel, F. Pradezynski et al., IRGM is a common target of RNA viruses that subvert the autophagy network, PLoS Pathog, vol.7, issue.12, p.1002422, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00965402

G. B. Kyei, C. Dinkins, A. S. Davis, E. Roberts, S. B. Singh et al., Autophagy pathway intersects with HIV-1 biosynthesis and regulates viral yields in macrophages, J. Cell Biol, vol.86, issue.2, pp.255-268, 2009.

S. Shoji-kawata, R. Sumpter, M. Leveno, G. Campbell, Z. Zou et al., Identification of a candidate therapeutic autophagy-inducing peptide, Nature, vol.494, issue.7436, pp.201-206, 2013.

E. Prentice, W. G. Jerome, T. Yoshimori, N. Mizushima, and M. R. Denison, Coronavirus replication complex formation utilizes components of cellular autophagy, J. Biol. Chem, vol.279, issue.11, pp.10136-10141, 2004.

Z. Zhao, L. B. Thackray, B. C. Miller, T. M. Lynn, M. M. Becker et al., Coronavirus replication does not require the autophagy gene ATG5, Autophagy, vol.3, issue.6, pp.581-585, 2007.
DOI : 10.4161/auto.4782
URL : https://www.tandfonline.com/doi/pdf/10.4161/auto.4782?needAccess=true

E. M. Cottam, H. J. Maier, M. Manifava, L. C. Vaux, P. Chandra-schoenfelder et al., Coronavirus nsp6 proteins generate autophagosomes from the endoplasmic reticulum via an omegasome intermediate, Autophagy, vol.7, issue.11, pp.1335-1347, 2011.

H. Y. Zhu, L. Han, X. L. Shi, B. L. Wang, H. Huang et al., Baicalin inhibits autophagy induced by influenza A virus H3N2, Antiviral Res, vol.113, pp.62-70, 2015.

B. S. Zha, X. Wan, X. Zhang, W. Zha, J. Zhou et al., HIV protease inhibitors disrupt lipid metabolism by activating endoplasmic reticulum stress and inhibiting autophagy activity in adipocytes, PLoS One, vol.8, issue.3, p.59514, 2013.

M. Laforge, S. Limou, F. Harper, N. Casartelli, V. Rodrigues et al., DRAM triggers lysosomal membrane permeabilization and cell death in CD4, 2013.

, + T cells infected with HIV. PLoS Pathog, vol.9, issue.5, p.1003328

M. Alirezaei, W. B. Kiosses, C. T. Flynn, N. R. Brady, and H. S. Fox, Disruption of neuronal autophagy by infected microglia results in neurodegeneration, PLoS One, vol.3, issue.8, p.2906, 2008.

X. H. Liang, S. Jackson, M. Seaman, K. Brown, B. Kempkes et al., Induction of autophagy and inhibition of tumorigenesis by beclin 1, Nature, vol.402, issue.6762, pp.672-676, 1999.

M. J. Raftery, E. Wolter, S. Fillatreau, H. Meisel, S. H. Kaufmann et al., NKT cells determine titer and subtype profile of virusspecific IgG antibodies during herpes simplex virus infection, J. Immunol, vol.192, issue.9, pp.4294-4302, 2014.

A. A. Ashkar and K. L. Rosenthal, Interleukin-15 and natural killer and NKT cells play a critical role in innate protection against genital herpes simplex virus type 2 infection, J. Virol, vol.77, issue.18, pp.10168-10171, 2003.

P. O. Ilyinskii, R. Wang, S. P. Balk, and M. A. Exley, CD1d mediates Tcell-dependent resistance to secondary infection with encephalomyocarditis virus (EMCV) in vitro and immune response to EMCV infection in vivo, J. Virol, vol.80, issue.14, pp.7146-7158, 2006.

T. R. Johnson, S. Hong, L. V. Kaer, Y. Koezuka, and B. S. Graham, NK T cells contribute to expansion of CD8(+) T cells and amplification of antiviral immune responses to respiratory syncytial virus, J. Virol, vol.76, issue.9, pp.4294-4303, 2002.

J. Li, Y. Liu, Z. Wang, K. Liu, Y. Wang et al., Subversion of cellular autophagy machinery by hepatitis B virus for viral envelopment, J. Virol, vol.85, issue.13, pp.6319-6333, 2011.

D. Sir, Y. Tian, W. Chen, D. K. Ann, T. B. Yen et al., The early autophagic pathway is activated by hepatitis B virus and required for viral DNA replication, Proc. Natl. Acad. Sci. USA, vol.107, issue.9, pp.4383-4388, 2010.

T. Doring and R. Prange, Rab33B and its autophagic Atg5/12/16L1 effector assist in hepatitis B virus naked capsid formation and release, Cell Microbiol, 2014.

C. C. Huang, K. L. Chen, C. H. Cheung, and J. Y. Chang, Autophagy induced by cathepsin S inhibition induces early ROS production, oxidative DNA damage, and cell death via xanthine oxidase. Free Radic, Biol. Med, vol.65, pp.1473-1486, 2013.