African swine fever virus (ASFV) is a member of the large DNA virus family and belongs to the family Asfarviridae (Netherton et al., 2019). The genome is double-stranded linear DNA, encoding more than 150 proteins (Chen et al., 2021). ASFV infection causes a highly contagious and fatal hemorrhagic fever in pigs (Costard et al., 2013). However, there are few studies on autophagy caused by ASFV infection. Hernaez et al. (2013) discovered that the viral protein A179L encoded by ASFV, which is homologous to B-cell lymphoma-2 (Bcl2), interacts with the autophagy regulatory factor beclin-1 to inhibit autophagy (Hernaez et al., 2013). A further study showed that, similar to Bcl-2, A179L inhibits autophagy by binding to beclin-1 through its BH3 binding grooves (Banjara et al., 2019). Moreover, E199L is a viral inner membrane protein necessary for virus entry (Matamoros et al., 2020). E199L interacts with PYCR2 and downregulates the expression of PYCR2, and therefore activates complete autophagy (Chen et al., 2021).

Pseudorabies virus (PRV), also known as Suid herpesvirus 1 (suHV-1), is a double-stranded DNA virus, which belongs to the subfamily α herpesvirus (Muller et al., 2011; Yu et al., 2014). The virus has a wide range of infected hosts, and pigs are the only natural reservoir hosts. PRV causes Aujeszky disease in adult pigs, leading to significant global economic losses (Pomeranz et al., 2005; Sun et al., 2017). The role of autophagy in human herpesvirus has been widely studied. For example, Herpes simplex virus 1 (HSV-1) ICP34.5 binds to autophagy regulatory gene beclin-1, thus inhibiting autophagy (Orvedahl et al., 2007). However, there are few studies on autophagy in PRV. Sun et al. (2017) confirmed the relationship between PRV and autophagy. Their research found that high MOI PRV could activate autophagy without virus replication at the early stage of infection, while with virus replication, the viral envelope protein US3 reduced the level of autophagy by activating the AKT/mTOR pathway to promote virus replication (Sun et al., 2017). By contrast, another report showed that PRV infection of mouse neuro-2a (N2a) cells significantly increased the transformation of LC3-I to LC3-II and the number of autophagosomes (Xu et al., 2018). In addition, the autophagy inducer rapamycin promotes virus replication, while the autophagy inhibitor 3-MA inhibits virus replication, indicating that PRV activates autophagy through the beclin-1-ATG7-ATG5 pathway, thus promoting virus replication (Xu et al., 2018). It was found to vary PRV strains induced the different level of autophagy (Xu et al., 2018). The level of autophagy induced by mutant ZJ01 infection was higher than that of the LA vaccine strain (Xu et al., 2018). In short, whether autophagy is activated or inhibited by PRV infection relates to the type of infected cells and the virus strains.

Porcine parvovirus (PPV) is one of the main pathogens causing reproductive disorders in sow (Cotmore et al., 2014; Zhang et al., 2019c). It belongs to the genus Protoparvovirus of the family Parvoviridae (Mengeling and Cutlip, 1976). The viral genome is a single-stranded linear DNA, encoding four nonstructural proteins (NS1, NS2, NS3, and NS4) and three structural proteins (VP1, VP2, and VP3) (Bergeron et al., 1996; Simpson et al., 2002; Zadori et al., 2005). At present, few studies have investigated the interaction between PPV and autophagy. Zhang et al. (2019c) reported that PPV infection in porcine placental trophoblasts cells can induce autophagy, which promotes virus replication. PPV exploits MAPKs (p38 and ERK1/2), protein kinase C (PKC), and Ca²⁺ to induce incomplete autophagy (Zhao et al., 2021).

Porcine circoviruses (PCVs) are members of the genus circovirus in the family Cycloviridae (Ellis, 2014). The genome of PCV is a single-stranded circular DNA of 1.76 kb. It is, by far, the smallest DNA virus found to infect mammals (Delwart and Li, 2012). There are three types of PCVs: PCV1 (Tischer et al., 1974), PCV2 (Allan et al., 1998), and PCV3 (Phan et al., 2016; Palinski et al., 2017). PCV1 is not pathogenic to pigs and is a contaminant in PK-15 cells (Tischer et al., 1974). PCV2 is a pathogen of porcine circovirus-associated diseases that causes significant economic losses (Ellis, 2014). PCV3 is a new virus found in some pig-raising countries in recent years (Phan et al., 2016; Faccini et al., 2017; Kwon et al., 2017; Franzo et al., 2018; Hayashi et al., 2018; Kedkovid et al., 2018). PCV3 infection induces complete autophagy by inhibiting the phosphorylation of mTORC. Cap protein encoding by PCV3 induces autophagy (Geng et al., 2020). Accumulating evidence has revealed an interaction between PCV2 and autophagy. Zhu et al. (2012) found that PCV2 infection in PK-15 cells induces autophagosome formation, increases autophagy flux, and promotes virus replication. Mechanismly, PCV2 upregulates calcium/calmodulin-dependent protein kinase (CaMK) kinase β (CaMKKβ) by increasing cytoplasmic Ca²⁺ through inositol 1,4,5-triphosphate receptors (IP3R) (Gu et al., 2016). CaMKKβ activates both AMPK and CaMKI, while the activation of AMPK phosphorylates TSC2, thus activating autophagy by mTORC inhibition. The activation of autophagy, in turn, promotes virus replication (Zhu et al., 2012; Gu et al., 2016; Ren et al., 2016). Except for activating autophagy through this pathway, PCV2 activates autophagy by increasing host oxidative stress and inhibiting apoptosis (Qian et al., 2017; Zhai et al., 2019). The inhibition of reactive oxygen species (ROS) production by taurine, selenizing astragalus polysaccharide, and SeMet inhibits autophagy and PCV2 replication (Liu et al., 2018; Qian et al., 2018; Zhai et al., 2018; Zhai et al., 2019). Several PCV2 proteins are involved in autophagy. ORF5 activates autophagy through AMPK-ERK1/2-mTOR and PERK-eIF2α-ATF4 pathways, thus promoting PCV2 replication (Lv et al., 2020). However, another study showed that ORF5 directly binds to host regulatory factor 14-3-3β (YWHAB), which inhibits ERS, ROS, and autophagy, thus inhibiting virus replication (Guo et al., 2020). In addition, PCV2 infection increases the expression of pDNAJB6 in PK-15 cells, and the C-terminal J domain of pDNAJB6 binds to the cap protein, which increases the formation of autophagy and promotes virus replication (Han et al., 2020). Upon PCV2 infection, host microRNAs play an important role in regulating autophagy. PCV2 upregulates miR-30a-5p, which directly targets the 14-3-3 gene, leading to cell cycle arrest at the G2 phase, and thus promoting autophagy and triggering PCV2 replication (Wang et al., 2017b). PCV2 infection induces not only autophagy but also mitophagy. PCV2 infection increases the production of ROS and the phosphorylation of dynamin-related protein 1 (Drp1), upregulates the expression of PTEN-induced kinase 1 (PINK1), and stimulates the recruitment of Parkin to mitochondria, thus inducing mitophagy (Zhang et al., 2020c).

Rabies virus (RABV) is a neurophagic virus that can infect people and animals and cause fatal rabies (Li et al., 2017). It is a member of the Lyssavirus genus of the Rhabdoviridae family (Tu et al., 2018). The genome is a single negative-strand RNA that encodes five viral proteins (Banerjee et al., 1991). Peng et al. (2016) reported that both wild-type (WT) and attenuated strains can trigger autophagy, but compared with attenuated strains, WT strains have a stronger ability to induce autophagy. Notably, the level of LC3-II/LC3-I was upregulated upon RABV infection in both human neuroblastoma cells (SK) and mouse neuroblastoma cells (NA), but whereas SK cells showed complete autophagy, NA cells showed incomplete autophagy (Peng et al., 2016). In addition, the M protein encoded by RABV can cooperate with the virus to increase the occurrence of autophagy (Peng et al., 2016). Except for the role of M protein in autophagy, it was found that the 173-222 amino acid (aa) residues of the P5 protein directly bind to the N-terminal 1-139 residues of beclin-1, thus inducing incomplete autophagy through the activation of CASP2-AMPK-MAPK and CASP2-AMPK-AKT-MTOR pathways and providing a scaffold for virus replication (Liu et al., 2017; Liu et al., 2020). In addition, RABV induced autophagy in BV2 cells in a dose-dependent manner (Wang et al., 2021a).

Foot-and-mouth disease virus (FMDV) is an acute infectious infection virus that can cause more than 70 kinds of foot-and-mouth disease in animals (Grubman and Baxt, 2004; Jamal and Belsham, 2013). FMDV belongs to the Aphthovirus genus of the Picornaviridae family (Mason et al., 2003; Klein, 2009; Tulloch et al., 2014). The genome is a single positive-stranded RNA that can encode four structural proteins and eight nonstructural proteins (Logan et al., 2018). The interaction between FMDV and autophagy has been widely studied. PK15 cells infected with FMDV can rapidly induce LC3 lipidation and GFP-LC3 subcellular redistribution in the early stage, which has been proven to depend on ATG5 in mouse embryonic fibroblasts (Fan et al., 2017). In ATG5-deficient cells, the titer of FMDV decreased (Berryman et al., 2012). Treatment of FMDV-infected PK-15 cells with rapamycin increases the virus titer, while 3-MA inhibits virus replication, indicating that autophagy benefits virus replication (Sun et al., 2018). Autophagy induced by FMDV infection in MEFs is independent of Vps34’s class III PI3K activity because the PI3K inhibitor wortmannin treatment does not affect autophagosome formation (Sun et al., 2018). FMDV can also promote virus replication by activating the stimulator of interferon response cGAMP interactor 1 (STING1) to induce reticulophagy (Zhang et al., 2021b). In addition, accumulating studies have shown that viral proteins encoded by FMDV are involved in autophagy, thus regulating virus replication. Several FMDV viral proteins have been shown to be localized with autophagy-related proteins, such as nonstructural proteins 2B, 2C, and 3A localized with LC3, structural protein VP1 localized with ATG5, LC3, and lysosomal associated membrane protein 1 (LAMP-1) (O’Donnell et al., 2011). The FMDV capsid protein VP2 interacts with the small heat shock protein beta-1 (HSPB1) to activate autophagy through the eukaryotic translation initiation factor 2 subunit alpha (EIF2S1)-activating transcription factor 4 (ATF4) pathway, thus promoting virus replication (Sun et al., 2018). Moreover, UV-FMDV can also induce autophagy through the EIF2S1-ATF4 and AKT-MTOR pathways, indicating that FMDV-induced autophagy is independent of virus replication (Sun et al., 2018). FMDV infection not only activates but also inhibits autophagy to promote replication. In the process of FMDV infection, viral protein 2C binds to beclin-1, thus preventing the fusion of lysosomes and autophagosomes, and resulting in the survival of the virus (Gladue et al., 2012). In macrophages, the 2 C protein activates autophagy depending on WIPI1, WIPI2, ATG5, and ATG7, but not beclin-1 (Liao et al., 2013). Some controversial studies have also reported that autophagy is induced by FMDV infection through the PERK-eIF2α and ATF6 signaling pathways but has no effect on virus replication (Wu et al., 2021). The Seneca valley virus (SVV), another member of the Picornaviridae family, causes neonatal death and vesicular lesions in pigs (Hales et al., 2008). SVV infection also activates autophagy through the PERK and ATF6 unfolded protein reaction (UPR) pathways, thus promoting virus replication (Hou et al., 2019).

Classical swine fever virus (CSFV) is the pathogen of classical swine fever (Kleiboeker, 2002). It is a member of the Pestivirus genus within the Flaviviridae family, and its genome is a single positive-stranded RNA (Becher et al., 2003). CSFV infection causes high fever, multiple hemorrhages, nervous system diseases, and respiratory and gastrointestinal diseases in pigs (Kleiboeker, 2002; Lohse et al., 2012). Growing studies have demonstrated that CSFV activates autophagy to promote virus replication. Pei et al. (2014) discovered that CSFV induced the transformation of LC3-I/LC3-II and the level of the ATG5-ATG12 conjunction system, as well as the formation of autophagosomes. Interfering autophagy regulatory factors inhibits the production of offspring virus (Pei et al., 2014). Subsequently, Zhu et al. (2021) proved that CSFV-infected PK-15 and 3D4/2 cells activated ERS by activating the PERK and IRE1 pathways, thus inducing autophagy to promote virus replication. Gou et al. (2017a) demonstrated that CSFV infection activates the autophagy of splenocytes in vivo for the first time, and 3-MA inhibits CSFV replication in vitro and in vivo. In addition, CSFV infection activates the PINK1 and Parkin pathways to degrade mitofusin (MFN) 2, silence mitochondrial ATGs, and reduce virus titers, indicating that CSFV promotes virus replication by activating mitochondrial autophagy (Gou et al., 2017). Infectious time seems to be an important factor affecting CSFV-autophagy interaction. At the early stage of infection, CSFV infection inhibits autophagy by reducing the phosphorylation of the Akt/mTORC1/S6 pathway. At the late stage of infection, the CSFV activates mTORC1 to inhibit autophagy, which is conducive to the dynamic balance of cell survival and virus replication (Luo et al., 2018). Several nonstructural proteins encoded by CSFV can regulate autophagy. For example, by binding to LC3, the NS5A protein increases the expression of ATGs and activates complete autophagy, thus promoting virus replication. Notably, the phosphorylation of NS5A at 81 and 92 aa within its N-terminal region is essential for activating autophagy (Zhang et al., 2021a). Further, NS3 directly binds to lactate dehydrogenase B (LDHB), a key glycolysis metabolic enzyme that catalyzes the transformation of pyruvate and lactic acid in the anaerobic glycolysis pathway and inhibits LDHB, activating mitochondrial autophagy (Fan et al., 2021).

JEV is a mosquito-borne virus belonging to the family Flaviridae and genus flavivirus (Sharma et al., 2021), and it is the main cause of viral encephalitis (Sharma et al., 2021). The genome is a positive single-stranded RNA that encodes three structural proteins [nucleocapsid (C), membrane protein (M), and envelope protein (E)] and seven nonstructural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) (Yun and Lee, 2018). Three different JEV-autophagy interplay models have been reported so far. In the first model, JEV infection activates autophagy to promote virus replication. Li et al. (2012) discovered that JEV virions can activate autophagy to promote virus replication. Autophagy is associated with the early infection steps of JEV infection. NS1 is colocalized with nonlipidated LC3 to influence the replication of JEV. Further analysis indicated that the viral replication is associated with ER-associated degradation (ERAD) pathway (Sharma et al., 2014). JEV C, M, and NS3 proteins can also activate autophagy. Among them, NS3 targets immunity-related GTPase M (IRGM) to activate autophagy and promote virus replication (Wang et al., 2015b). In the second model, JEV infection inhibits autophagy and promotes virus replication. JEV infection upregulates NEDD4, such as E3 ubiquitin protein ligase (Nedd4), in SK-N-SH neuroblastoma cells, thereby inhibiting autophagy and promoting virus replication (Xu et al., 2017). In the third model, JEV infection activates autophagy to inhibit virus replication. JEV infection in Neuro2a cells activates autophagy through ERS induced by XBP1 and ATF6. The depletion of XBP1 and ATF6 inhibits autophagy and increases JEV-infected cell death (Sharma et al., 2017; Sharma et al., 2018).

Porcine reproductive and respiratory syndrome virus (PRRSV) is a pathogen that causes severe respiratory distress and high mortality in piglets and reproductive failure in sows (Rossow, 1998). PRRSV belongs to the genus Arterivirus of the Arteriviridae family of order Nidovirales, and its genome is a single positive-stranded RNA (Cavanagh, 1997; Ziebuhr et al., 2000). An increasing number of studies have demonstrated that PRRSV infection can activate autophagy (Liu et al., 2012). PRRSV infection increases the transformation of LC3-I to LC3-II and double-membrane vesicles; 3-MA and ATG7-/beclin-1 knockdown inhibit virus replication; and rapamycin treatment induces autophagy to increase virus replication (Chen et al., 2012; Liu et al., 2012). (Wang et al., 2015a) subsequently confirmed in vivo that HP-PRRSV activates autophagy in thymocytes and bystander cells. PPRSV infection activates ERS through the PERK and IRE1 pathways to induce autophagy, and ERS and autophagy promote virus replication (Chen et al., 2020). Several viral proteins have been shown to be involved in autophagy activation. Upon PRRSV infection of Marc145 cells, Rab11a plays a role in autophagosome maturation and fuses with autophagosomes to form amphisomes for virus release (Wang et al., 2017a). In addition, NSP2 colocalizes with LC3 and activates incomplete autophagy to enhance viral replication by inhibiting the fusion of lysosomes and autophagosomes (Sun et al., 2012a). Except for NSP2, NSP3 can also activate the formation of autophagosomes (Zhang et al., 2019b). Furthermore, it has been verified that PRRSV activates mitophagy, lipophagy, and aggrephagy (Li et al., 2016; Wang et al., 2019a; Cao et al., 2020). The infection of PRRSV in Marc145 cells activates mitophagy to promote virus replication (Li et al., 2016), and PRRSV downregulates N-myc downstream regulated 1 (NDRG) to promote lipophagy, thus resulting in the production of large amounts of free fatty acids to provide materials for virus replication (Wang et al., 2019a). In addition, PRRSV infection can induce aggrephagy through the binding of NSP2 tail domain to cellular protein 14-3-3 ϵ (Cao et al., 2020). Notably, the PRRSV-induced autophagy of thymic epithelial cells can regulate the development of T cells (Wang et al., 2020).

Porcine coronaviruses are positive single-strand RNA viruses with an envelope (Gorbalenya et al., 2006; Guo et al., 2016). At present, coronaviruses are divided into four genera according to phylogenetic clustering: alphacoronavirus, betacoronavirus, gammacoronavirus, and deltacoronavirus (Carstens and Ball, 2009; Woo et al., 2010; Guo et al., 2016). Transmissible gastroenteritis virus (TGEV) and porcine epidemic diarrhea virus (PEDV) belong to alphacoronavirus, porcine hemagglutinating encephalomyelitis virus (PHEV) belongs to betacoronavirus, and porcine deltacoronavirus (PDCOV) belongs to deltacoronavirus (de Groot et al., 2011). TGEV causes watery diarrhea, dehydration, and vomiting in two-week-old piglets (Underdahl et al., 1975). PEDV is the pathogen of epidemic diarrhea in pigs, which can cause severe diarrhea and vomiting in sucking piglets with high mortality (Li et al., 2012; Crawford et al., 2016). PHEV infection usually causes encephalomyelitis and vomiting in piglets (Ding et al., 2017), and PDCOV infection causes severe dehydration and vomiting in piglets (Jung et al., 2015; Jung et al., 2016). Many studies have reported an interaction between porcine coronaviruses and autophagy. (1) TGEV and autophagy: At present, there is controversy about the interaction between TGEV and autophagy. Guo et al. (2016) reported that TGEV infection in ST and PK15 cells increases the bilayer and monolayer vesicle structures, and increases esterified LC3. TGEV replication is negatively regulated by autophagy (Guo et al., 2016). However, another research team reported that TGEV infection in porcine epithelial cells (IPEC-J2) induces mitophagy to maintain cell survival and potentially promote virus replication (Zhu et al., 2016). This finding suggests that autophagy induced by TGEV infection in different cells varies and may have multiple mechanisms. (2) PEDV and autophagy: The research findings on the relationship between PEDV and autophagy are also controversial. Vero and IPEC-J2 cells infected with PEDV show autophagy activation, which promotes virus replication (Guo et al., 2017; Lin et al., 2020). PEDV infection can activate ERS, depending on the PERK and IER1 pathways, by increasing ROS production to activate autophagy (Sun et al., 2021). Controversially, Ko et al. (2017) reported that PEDV infection in porcine intestinal epithelial cells (IECs) activates autophagy, which in turn inhibits viral replication. Similarly. PEDV infection in Vero and LLC-PK1 cells upregulates the expression of bone marrow stromal cell antigen 2 (BST2), which recruits the E3 ubiquitin ligase membrane-associated ring-CH-type finger 8 (MARCH8) to catalyze the ubiquitination of PEDV N protein. The ubiquitinated N protein was recognized by NDP52, delivered to autophagy-lysosomes, and selectively degraded, resulting in the inhibition of virus replication (Kong et al., 2020). Several PEDV viral proteins play roles in autophagy activation. Nsp6 activates autophagy mainly through the PI3K/Akt/mTOR pathway, while ORF3 upregulates the GRP78 protein and activates the PERK-eIF2α signal pathway to induce ERS, thus activating autophagy (Zou et al., 2019; Lin et al., 2020). (3) PHEV and autophagy: PHEV infection activates autophagy independent of the classic AMPK-mTORC1-ULK1 pathway (Li et al., 2021c). Additionally, PHEV induces incomplete autophagy, which is necessary for replication (Ding et al., 2017). Mechanismly, PHEV inhibits mTORC1 activation to activate atypical autophagy by downregulating the expression of transcription factor EB (TFEB) (Wang et al., 2021b). (4) PDCOV and autophagy: PDCOV infection activates complete autophagy through the p38 signal pathway to promote virus replication (Qin et al., 2019; Duan et al., 2021). It is worth noting that inactivated PDCOV can also activate autophagy, but it is not as strong as infectious PDCOV (Duan et al., 2021).

Egg drop syndrome virus (EDSV) belongs to the genus Atadenovirus of the family Adenoviridae, and its genome is double-stranded linear DNA (Fu et al., 2013; Larson et al., 2015). The quality of poultry eggs decreases due to EDSV, and the clinical symptoms are soft-shell eggs, thin-shell eggs, and shell-free eggs (Huang et al., 2015). To date, only one report has verified the interaction between EDSV and autophagy. Wang et al. (2018) reported that EDSV infection in duck embryo fibroblasts (DEFs) cells activates complete autophagy through the class I PI3K/Akt/mTOR pathway and exploits autophagy to enhance its replication.

Duck enteritis virus (DEV) is the pathogen of duck viral enteritis, causing damage to the blood vessels, intestinal mucosa, and lymphoid organs in ducks (Wang et al., 2013). DEV is a member of the family Herpesviridae, the subfamily Alphaherpesvirinae, and the genus Mardicirus. The genome is double-stranded linear DNA (Wu et al., 2019). Growing evidence has shown that DEV can induce autophagy. Yin et al., (2017c) reported that DEV infection activates complete autophagy, which is beneficial for virus replication in duck embryo fibroblast (DEF) cells. Subsequently, it was found that DEV infection could activate autophagy through a variety of mechanisms. First, DEV activates autophagy by activating ERS, mediated by the activation of the PERK and IRE1 pathways (Yin et al., 2017a). Second, DEV induces autophagy through the activation of the AMPK-TSC2-mTOR signaling pathway mediated by energy metabolism damage (Yin et al., 2017b). Third, DEV infection induces autophagy by increasing the concentration of Ca²⁺ in the cytoplasm and activating the CaMKKβ-AMPK signaling pathway (Yin et al., 2018). Fourth, DEV infection downregulates miR-30a-5p, leading to the upregulation of beclin-1 and increasing beclin-1-mediated autophagy (Wu et al., 2019).

Influenza A viruses (IAVs) are members of the Orthomyxoviridae family and contain a segmented single-strand RNA (Zeng et al., 2021). IAVs are important zoonotic pathogens (Zeng et al., 2021). They can be divided into different subtypes according to the glycoprotein hemagglutinin (HA) and neuraminidase (NA) (Hsu, 2018). At present, there are 18 HA subtypes and 11 NA subtypes (Zhang et al., 2019a). The interaction between autophagy and IAVs has been widely studied. Here, we briefly summarize the interactions between H1N1, H9N2, H5N1, and autophagy. (1) H1N1 and autophagy: H1N1 infection in A549 and MEF cells induced incomplete autophagy, which contributes to IAV replication in a time-dependent manner (Feizi et al., 2017; Yeganeh et al., 2018; Zhang et al., 2020a) Mechanismly, H1N1 activates autophagy by activating the PI3 K pathway (Zhang et al., 2019a). H1N1 also downregulates heterodimeric transcription factor hypoxia-inducible factor 1 (HIF-1α) to reduce glycolysis, and subsequently increases autophagy mediated by the AMPKα-ULK1 signaling pathway (Zhao et al., 2020). At the early stage of infection, H1N1 degrades the antioxidant enzyme superoxide dismutase type 1 (SOD1) by autophagy, leading to the production of ROS (Jung et al., 2018). H1N1 NS1 indirectly induces autophagy by upregulating the synthesis of HA and M2 (Zhirnov and Klenk, 2013). Controversially, Yu et al. (2019) found that H1N1 inhibits autophagy by promoting the formation of circular RNA GATAD2A in A549 cells, thereby promoting virus replication. (2) H5N1 and autophagy: At present, it is reported that H5N1 has a variety of mechanisms to activate autophagy and promote virus replication. H5N1 can activate autophagy through the AKT-mTOR or TSC2 pathway (Ma et al., 2011; Sun et al., 2012b). In addition, H5N1 induces functional autophagy by activating JNK and inhibiting the PI3 K pathway (Zhang et al., 2019a). Another study demonstrated that PB2, NP, and M2 encoded by H5N1 cooperatively functioned in autophagy activation. Initially, the interaction between PB2 protein and heat shock protein 90 kDa α [cytosolic], class A member 1 (HSP90AA1) promotes the synthesis of viral RNA. The binding of NP and LC3 is beneficial to the export of vRNP. Subsequently, the interaction between M2 and LC3 leads to the release of infectious viral particles, thus accelerating the production of the virus offspring (Wang et al., 2019b). (2) H9N2 and autophagy: H9N2 induces autophagy by regulating oxidative stress via the Akt/TSC2/mTOR pathway, activates autophagy by activating both the PI3K and JNK pathways, and promotes virus replication (Zhang et al., 2021c). In short, autophagy is activated in host cells infected with IAV, with some differences in the upstream pathway according to different subtypes (Zhang et al., 2019a).

NDV is a member of the genus Avulavirus of the family Paramyxoviridae. Its genome is a single negative-stranded RNA (Alexander, 2000). Birds are the natural hosts of NDV, making it highly contagious in birds. At present, there are many studies on the interaction between NDV and autophagy. Meng et al. (2012a) found that NDV infection in U251 cells activates complete autophagy to promote virus replication (Meng et al., 2012a). It has been verified that NDV infection activates autophagy to maintain cell survival and NDV replication in chicken cells and tissues (Sun et al., 2014; Kang et al., 2017). In addition, the low virulent strain of NDV and its recombinant strain can activate autophagy (Meng et al., 2014; Bu et al., 2015; Bu et al., 2016). The NDV low virulent strain LaSota activates mitophagy to promote virus replication by inhibiting apoptosis (Meng et al., 2014). Moreover, the recombinant avirulent NDV LaSota strain expressing the rabies virus glycoprotein (rL-RVG) activates ERS through three branches of AFT6, PERK, and IRE1, thus activating autophagy in gastric carcinoma cells (Bu et al., 2015; Bu et al., 2016). Notably, NDV-encoded nucleocapsid protein (NP) or phosphoprotein (P) can effectively activate autophagy, and Hemagglutinin-neuraminidase (HN) and fusion (F)proteins cooperatively activate autophagy (Cheng et al., 2016; Ren et al., 2019). HN and F proteins activate autophagy by activating the AMPK/mTORC/ULK1 pathway (Cheng et al., 2016; Ren et al., 2019). Remarkably, NDV infection leads to the reprogramming of cellular energy metabolism via the degradation of sirtuin 3 (SIRT3) by mitophagy (Gong et al., 2021).

Infectious bronchitis virus (IBV) is a kind of avian coronavirus that is the pathogen of avian bronchitis and causes great losses to the poultry industry (Cottam et al., 2014). IBV belongs to the subfamily Coronavirinae, family Coronaviridae, and order Nidovirales, and the genome is positive for single-strand RNA (Cottam et al., 2011; Fung and Liu, 2019). Increasing evidence shows that IBV interacts with autophagy. Cottam et al. (2011) found that IBV-encoded nonstructural protein 6 (nsp6) promoted the formation of autophagosomes and fusion with lysosomes through the activation of class III PI3K. In addition, nsp6 inhibits the expansion of autophagosomes (Cottam et al., 2014). Moreover, ATG5, IRE1, and ERK1/2 are necessary for autophagy induced by IBV infection (Fung and Liu, 2019).

Infectious bursal disease virus (IBDV) is the pathogen causing bursa of Fabricius injury in birds, especially in 3–6-week-old chickens with high mortality (Burkhardt and Muller, 1987; Sharma et al., 2000). IBDV belongs to the genus Avibirnavirus in the family Birnaviridae (Muller et al., 1979). The genome is segment double-stranded RNA (dsRNA) (Muller et al., 1979; Li and Zheng, 2020). Evidence suggests that IBDV can subvert autophagy to promote virus replication. At the early stage of IBDV infection, LC3-II flux and dephosphorylation of AKT-mTORC increases (Hu et al., 2015). VP2 binds to HSP90AA1 to trigger autophagy through the AKT-mTORC pathway, and knockdown of HSP90AA1 inhibits autophagy (Hu et al., 2015). Additionally, at the early stages of IBDV infection, VP3, another viral protein, binds to beclin-1 and 3-phosphoinositide dependent protein kinase 1 (PDRK1), destroying the PIK3C3-beclin-1 and PIK3C3-PDPK1 complexes, and inhibiting the formation and maturation of autophagosomes (Zhang et al., 2020b). At the late stage of infection, IBDV increases the flux of LC3-II and promotes the fusion of autophagosomes and lysosomes, but p62 is not degraded (Wang et al., 2017c). Transmission electron microscopy showed that the intact IBDV virions were arranged around p62, indicating that virus-induced incomplete autophagy provides an acid environment for virus maturation and release (Wang et al., 2017c).

Avian reovirus (ARV) and Muscovy duck reovirus (MDRV) belong to the genus Orthoreovirus of the family Reoviridae, and their genomes are segmented into dsRNA (Hieronymus et al., 1983). ARV is the pathogen of viral arthritis, chronic respiratory disease, egg drop, dwarf syndrome, and malabsorption syndrome in chickens, while MDRV is the pathogen of liver white spot disease in ducklings (Benavente and Martinez-Costas, 2007; Wu et al., 2017). Both ARV and MDRV activate autophagy and exploit autophagy to promote self-replication. ARV infection in chicken cells induces complete autophagy through the PI3K/Akt/mTOR pathway to assist virus replication (Meng et al., 2012b; Duan et al., 2015). The NLS region of the nonstructural protein p17 encoded by ARV induces autophagy by activating phosphatase and tensin deleted on chromosome 10 (PTEN), AMPK, and dsRNA-dependent protein kinase (PKR)/eIF2 pathways (Chi et al., 2013; Li et al., 2015). Moreover, p17 mediates the inhibition of Akt, leading to the activation of autophagy (Huang et al., 2017). In comparison, MDRV infection activates incomplete autophagy (Li et al., 2021b). MDRV promotes the fusion of autophagosomes and lysosomes, but inhibits the degradation of autolysosomes. The envelope protein σA and nonstructural protein σNS encoded by MDRV play important roles in this process (Wu et al., 2017; Li et al., 2021b).

ALV-J belongs to the genus of Alpharetrovirus of the Retroviridae family, and its genome is RNA (Rajabzadeh et al., 2010). ALV-J is a pathogen that causes tumor-related diseases in poultry (Lu et al., 2013). At present, few studies have examined the interaction between ALV-J and autophagy. Lu et al. (2013) reported for the first time that ALV-J infection in DF-1 cells decreases the expression of LC3-II and autophagosome-related proteins, and autophagy activated by rapamycin treatment inhibits virus replication, suggesting that ALV-J infection enhances virus replication by inhibiting autophagy. Another study demonstrated that ALV-J inhibits autophagy through the GADD45β/MEKK4/p38MAPK signaling pathway (Liao et al., 2020).

The Duck hepatitis A virus (DHAV) is a member of the genus Avihepadnavirus of the family Picornaviridae, and the viral genome is a positive single-stranded RNA (Liu et al., 2021). DHAV has a high mortality rate in young ducklings (Ming et al., 2019). DHAV infection in duck embryonic hepatocytes (DEHs) cells increases incomplete autophagy and promotes virus replication (Ming et al., 2019). The viroporin-like 2B protein encoded by DHAV-1 has been proven to induce incomplete autophagy (Liu et al., 2021).