In contrast to what has been found with bacteria, xenophagy does not appear to be the main means by which autophagy controls viral infections. To date, few reports have observed complete viral particles within autophagosomes. One such study showed that HSV-1 lacking ICP34.5 (a virulent factor able to bind to BECLIN-1 in order to inhibit autophagy) induces PKR-dependent autophagy, and is found inside autophagosomes for ultimate degradation (Talloczy et al., 2006). However, this virus replicates in permissive cells as efficiently as wild-type HSV-1 in autophagy-competent or -deficient cells suggesting virus xenophagy is not an important antiviral arm of cellular immunity (Alexander et al., 2007; Orvedahl et al., 2007). Nevertheless, this process is potentially a way used by cells to control viral infections immediately following virus entry. Indeed, to enter a cell, viruses can use different pathways, including clathrin-dependent endocytosis and phagocytosis. Interestingly, autophagy-associated proteins can be recruited to nascent phagosomes to accelerate phagosome maturation and the degradation of its content. Moreover, the clathrin-associated plasma membrane can contribute to the formation of autophagosomes (Sanjuan et al., 2007; Ravikumar et al., 2010). Thus, both pathways might contribute to the xenophagy of cell-entering viral particles. Furthermore, following endocytosis, damage on bacteria-containing vesicles is recognized through vesicle-exposed endogenous danger signals, such as ubiquitination, cytosolic glycans or diacylglycerol, eliciting autophagy recruitment for bacterial degradation (Dupont et al., 2009; Shahnazari et al., 2010; Thurston et al., 2012). Although virus-containing endosomes exposing subtle damage/modifications or viral proteins for selective autophagy targeting have not yet been reported, this represents an interesting perspective. However, beyond the capacity of virus xenophagy to limit virus infectivity, autophagy might be more evolved to eliminate individual viral components, such as those essential for the virus life cycle, a process referred to as virophagy (Orvedahl et al., 2011). For example, SQSTM1 binds to the Sindbis virus capsid and targets this viral protein to autophagy for degradation, thereby protecting cells from capsid accumulation-induced cell death. However, in contrast to most targets of SQSTM1 for selective autophagy, this interaction appears to be independent of ubiquitination. Thus, cellular autophagy adaptors might recognize viral components for selective autophagy that are virus-specific, or conserved among virus families. Indeed, a recent mammalian genetic screen highlighted 141 genes involved in the selective targeting of the Sindbis virus capsid to autophagy (Orvedahl et al., 2011). These genes belong to different cellular biological functions, suggesting that multiple molecular pathways may contribute to virophagy. Interestingly, one of these genes, SMURF1, may also contribute to the targeting of HSV-1ΔICP34.5 to autophagosomes, suggesting that viral components shared by different virus families might be detected through similar molecular processes for virus selective autophagy. Moreover, through a protein–protein interactome analysis, more than 35% of 44 proteins of the autophagy network, including SLRs, were reported to interact with RNA virus proteins belonging to five different RNA virus families (Gregoire et al., 2011). Interestingly, whereas some autophagy-associated proteins are targeted only by one RNA virus, others are commonly targeted by several RNA virus families. Whether any of these interactions contribute to virophagy remains to be determined, but together these high-throughput approaches open up interesting new perspectives to identify molecular pathways combating viral infection via selective autophagy.