Coronaviruses are a large family of viruses that cause illness in both animals and humans. They are divided into four genera: α, β, γ and δ. Among these, humans are primarily susceptible to coronaviruses from the α and β genera. The β genera, in particular, include three highly pathogenic species: severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the Corona Virus Disease 2019 (COVID-19) pandemic, as well as severe acute respiratory syndrome coronavirus (SARS-CoV) and middle east respiratory syndrome coronavirus (MERS-CoV) (Fig. 1). On the other hand, there are four low-pathogenic species commonly associated with mild respiratory symptoms, namely human coronavirus (HCoV) 229E, NL63, OC43, and HKU1 (Fig. 1), which are classified under the α and β genera. Bat SARS-like coronaviruses belong to β genera also show potential for human emergence [1, 2] (Fig. 1). Infection with these low-pathogenic coronaviruses typically results in symptoms resembling the common cold [3].

Phylogenetic tree of highly pathogenic coronavirus (red), low-pathogenic coronavirus (blue) and the other SARS-related coronavirus. Reference sequences of representative coronaviruses include phylogenetic analysis was performed with the CLC program by the neighbor-joining method on the basis of the Kimura two-parameter model

COVID-19, caused by SARS-CoV-2, emerged in late 2019 and has become a global pandemic. By the end of 2023, there have been over 770 million reported cases and over 6.9 million deaths worldwide [4]. Previous large-scale coronavirus outbreaks include SARS in 2002 (caused by SARS-CoV) and MERS in 2012 (caused by MERS-CoV). The cumulative number of infections for SARS and MERS was a approximately 8,000 [5] and 2,600 [6], respectively, with cumulative death toll of 774 [5] and 936 [6].

The virus particles of SARS-CoV, MERS-CoV, and SARS-CoV-2 include genomic RNA and four structural proteins, spike (S), envelope (E), membrane (M) and nucleocapsid (N). Non-structural proteins are not necessarily incorporated into the virus particles, except ORF3a, ORF7a, ORF7b, ORF9b of SARS-CoV [7, 8] and ORF3a, ORF7a of SARS-CoV-2 [9] (Fig. 2A). SARS-CoV, MERS-CoV, and SARS-CoV-2 are positive-sense, single-stranded RNA viruses with genomes of about 30,000 bases in length. Their genomes include 5' end cap-like structure, structural proteins S, E, M and N, non-structural proteins, and 3'-end poly A tails [10,11,12,13,14,15] (Fig. 2B). Comparing different human-susceptible coronavirus genomes, it’s evident that highly pathogenic coronaviruses encode more non-structural proteins than low-pathogenic coronaviruses (Fig. 2B). Many studies have demonstrated that different non-structural proteins can help highly pathogenic coronaviruses evade host immune responses more effectively and promote viral replication in different ways. Regulation of apoptosis is one of the important way [16,17,18,19,20,21,22,23,24,25]. In this review, we summarize the current knowledge of the apoptosis induced by highly pathogenic coronaviruses and their molecular mechanisms, as well as the potential applications of apoptosis inhibitors as antiviral drugs.

General structural pattern diagram and genome of coronavirus. A, Coronavirus particles include E, M, N, S, genomic RNA and secondary components such as ORF3a, ORF7a, ORF7b, ORF9b of SARS-CoV and ORF3a, ORF7a of SARS-CoV-2. B, Schematic diagram of the genomic organization and encoded proteins of SARS-related coronavirus. The highly pathogenic coronaviruses (red) encode more non-structural proteins

Apoptosis, a programmed cell death process, was originally proposed by J.F. Kerr in 1972 [26]. The classical apoptosis is primarily categorized into three pathways based on the origin of the apoptotic signal: the endogenous endoplasmic reticulum (ER) stress pathway, the endogenous DNA damage pathway and the exogenous death receptor pathway.

Endogenous apoptosis mainly includes ER stress pathway and DNA damage pathway. When DNA damage (such as DNA double-strand break) occurs, DNA damage response (DDR) kinases ataxia-telangiectasia mutated (ATM), ATM- and Rad3-Related (ATR), DNA-dependent protein kinase (DNA-PK) are activated [27], and then a large amount of H2AX is rapidly phosphorylated at Ser-139 to produce phosphorylated histone H2AX (γH2AX) and bind to the damage sites [28], further activating p53 to phosphorylation, and promoting apoptosis by regulating the transcription of apoptosis-related genes (Fig. 3A). When unfolded protein response (UPR) and other factors induce ER stress, the protein kinase RNA–like endoplasmic reticulum kinase (PERK), inositol requiring enzyme 1α (IRE1α), and activating transcription factor 6 (ATF6) pathways are activated, resulting in enhanced C/EBP homologous protein (CHOP) expression and endogenous apoptosis (Fig. 3B). In response to signals such as DNA damage and ER stress, pro-apoptotic BH3-only proteins (BAD, BID, BIM, PUMA, NOXA, etc.) competitively bind to anti-apoptotic proteins (BCL-2, BCL-xL, MCL-1), releasing pro-apoptotic proteins (BAX, BAK, BOK) from anti-apoptotic proteins [29]. Free pro-apoptotic proteins form oligomers, leading to their activation and translocation to the outer mitochondrial membrane, forming channels. These channels cause mitochondrial outer membrane permeabilization (MOMP), resulting in the release of cytochrome C from the intermembrane space of mitochondria into the cytoplasm. Cytochrome C works with procaspase-9 and apoptotic protease activating factor 1 (APAF1) to form apoptosomes, which activates caspase-9. Then, activated caspase-9 cleaves procaspase-3, generating caspase-3. Caspase-3 further cleaves the DNA repair enzyme poly ADP-ribose polymerase (PARP), leading to DNA repair dysregulation and eventually triggering endogenous apoptosis [30,31,32,33,34] (Fig. 3).

Overview of apoptosis activation by proteins encoded by highly pathogenic coronaviruses. A, Exogenous death receptor apoptotic pathway and intrinsic DNA damage-induced apoptosis pathway. B, Intrinsic ER stress-induced apoptosis pathway. The majority of proteins encoded by highly pathogenic coronaviruses enhance the activity of pro-apoptotic proteins (indicated by red arrows) and suppress the function of anti-apoptotic proteins (indicated by blue arrows). Certain structural proteins (depicted in blue) exhibit the capability to inhibit apoptosis

The exogenous pathway relies on the activation of death receptors on the cell surface. When extracellular death ligands (such as FasL, TNF and TRAIL) bind to death receptors (Fas, TNFR1, TRAILR1, TRAILR2), a death-inducing signaling complex (DISC) containing the intracellular death domain of the death receptor, Fas-associating death domain protein (FADD)/ TNFR1-associated death domain protein (TRADD) and caspase-8 was formed. Caspase-8 is activated through oligomerization and subsequently, cleaves procaspase-3 to generate caspase-3, eventually exogenous apoptosis. Activated caspase-8, on the other hand, cleaves BH3-interacting domain death agonist (BID) into truncated BID (tBID), promotes the translocation of tBID from the cytosol to the mitochondria, which contribute to MOMP, ultimately leading to apoptosis [30,31,32, 34] (Fig. 3A).

In conclusion, apoptosis is regulated by complex signal transduction pathways involving both endogenous and exogenous pathways. Understanding the mechanisms and interactions involved in apoptosis signal transduction is crucial for unraveling the intricate processes underlying cell death and survival and developing novel therapeutic strategies targeting apoptosis-related diseases.

Traditionally, apoptosis has been regarded as a means for host cells to rescue themselves and facilitate viral clearance [35, 36]. However, compelling evidence is emerging to suggest that apoptosis can act as a double-edged sword, capable of benefiting both DNA and RNA viruses in promoting their self-replication [37, 38].

Remarkably, it has been observed that caspase-deficient cells exhibit a heightened antiviral ability compared to normal cells [39]. Mitochondrial stress is one of the ways that SARS-CoV-2 activates the cyclic GMP-AMP synthase-stimulator of interferon gene (cGAS-STING) signaling pathway, which causes mitochondrial dysfunction and releases mitochondrial DNA (mtDNA) from the mitochondria into the cytoplasm [40], resulting in upregulating of type I interferon (IFN-I) expression. In order to antagonize the antiviral effect of interferon, the virus employs a strategy by enhancing the apoptosis signal, activating caspase-3 and caspase-7, both of which play crucial roles downstream in the apoptotic pathway [41]. These activated caspases not only cleave and inactivate IFN-I [42], but also promote mtDNA degradation, and inhibit the activation of cGAS-STING signaling pathway [41, 43]. Consequently, the virus evades the surveillance and clearance by the host immune system, establishing a favorable environment for its survival.

In the long-term struggle between viruses and hosts, some viruses have developed strategies to manipulate cellular processes. For highly pathogenic coronaviruses such as MERS-CoV, SARS-CoV, and SARS-CoV-2 mentioned above, inducing apoptosis is an important way to promote viral replication, aggravate tissue and organ damage, and motivate the development of diseases [37, 38].

Studies have demonstrated that apoptosis is associated with lung injury, multi-organ failure in COVID-19 patients [44,45,46]. Notably, SARS-CoV-2 predominantly induces apoptosis in respiratory epithelial cells rather than necrosis. This preference is evidenced by the abundance of apoptotic cells and scarcity of necrotic cells following invasion of human respiratory epithelial cells [47]. This characteristic may reflect the virus’s “cleverness” in adopting immune “silencing” apoptosis as a survival strategy given that apoptosis is more suitable for the virus’s survival than necrosis, which can trigger excessive production of inflammatory factors. Following SARS-CoV-2 infection, the virus persists longer in the nasal mucosa compared to the lungs, with lower production of inflammatory factors [48]. This is due to nasal mucosal epithelial cells primarily undergoing apoptosis after viral infection, whereas in the lungs, the apoptosis rate is lower and the pyroptosis rate is higher [48], while apoptosis of immune silence is more conducive to viral replication. Notably, the virus is predominantly present in superficial epithelial cells in the early stages of infection, and gradually invades submucosal cells as the disease progresses [48]. Therefore, apoptosis may favor the spread of the virus from nasal mucosal epithelial cells to submucosal cells, that is, apoptosis can promote the spread of SARS-CoV-2.

Moreover, evidence suggests that SARS-CoV-2 triggers apoptosis in lung epithelial cells, destroys the alveolar capillary barrier, thereby promoting the development of pulmonary edema and acute respiratory distress syndrome (ARDS), and aggravating lung injury in patients with COVID-19, resulting in high mortality [35, 49,50,51,52]. Patients with severe COVID-19 were more likely to develop apoptosis than those with mild symptoms, highlighting the direct relationship between apoptosis levels and severity and mortality of COVID-19 patients [53]. During SARS-CoV-2 infection, the apoptosis ratio of B lymphocytes, T lymphocytes [54, 55] and monocytes [53] is also elevated. This coupled with impaired phagocytosis and anti-inflammatory function of macrophages and monocytes after phagocytosing apoptosis cells [56], particularly in severe clinical cases, suggests that enhanced apoptosis of immune cells may contribute to the severe clinical symptoms of COVID-19 patients. Additionally, SARS-CoV-2-induced apoptosis in β pancreatic cells contributes to abnormal glucose metabolism, which aggravates diabetes [57]. In summary, apoptosis aggravates multiple organ failure and microcirculation disorders through various mechanisms, leading to higher patient mortality rates and poor clinical outcomes.

MERS-CoV activates both endogenous and exogenous apoptotic pathways, leading to extensive apoptosis of bronchial epithelial cells, renal cells, macrophages, dendritic cells and other cells, resulting in high morbidity and mortality among MERS patients [58,59,60]. Due to elevated dipeptidyl peptidase-4 (DPP4) receptor expression on T lymphocytes, they become more vulnerable to MERS-CoV infection, triggering apoptosis. MERS-CoV targets lymphoid organs like the spleen and tonsils, infecting T lymphocytes at various developmental stages, leading to extensive apoptosis and subsequent lymphocyte depletion. This immune system paralysis exacerbates viral infection, culminating in a severe prognosis for patients [59]. Yeung ML et al. discovered that MERS-CoV induces apoptosis in kidney cells by upregulating the expression of smad family member 7 (Smad7) and fibroblast growth factor 2 (FGF2), thus facilitating viral release and dissemination of infection in kidneys and other tissues. Consequently, the incidence of renal failure in MERS patients surpasses that of other human coronavirus infections [58]. Notably, MERS-CoV uses caspase-6, a component of the apoptosis cascade, to cleave the N protein, producing small fragments that act as interferon antagonists and suppress the host immune response, thus promoting replication [38]. The inhibition of caspase-6 can attenuate MERS-CoV replication in human lung tissue and human intestinal organoids, and also improve the pathological changes of the lung in vivo caused by the virus [38].

Furthermore, SARS-CoV infection triggers significant apoptosis in lung epithelial cells [61, 62], lymphocytes [63, 64], liver [65], thyroid [66] and kidney [67] cells. Microarray analysis of host genes showed that the expression of 13 pro-apoptotic genes was up-regulated after SARS-CoV infection, while only 3 pro-apoptotic genes were up-regulated after infection with the low-pathogenic coronavirus HCoV-229E. Thus, highly pathogenic coronaviruses enhance pathogenicity by inducing apoptosis. It is with regret that cross-sectional comparisons of the apoptosis-inducing capacity of highly pathogenic coronaviruses are still lacking in the field. Further study of this may help us understand the important role of apoptosis in the pathogenesis of highly pathogenic coronaviruses.

The induction of apoptosis to promote viral replication is not exclusive to coronaviruses but is a common survival strategy employed by many viruses, including cowpox viruses (CPXV) [68], porcine epidemic diarrhea virus (PEDV) [69, 70], herpes simplex virus (HSV) [71, 72], Epstein-Barr virus (EBV) [73], human immunodeficiency virus (HIV) [74,75,76,77,78,79,80,81,82,83], Zika virus (ZIKV) [84], Hepatitis C virus (HCV) [85,86,87,88,89,90,91,92], and others. Therefore, the virus exploits apoptosis to enhance its replication, leading to a substantial increase in the number of infected cells undergoing apoptosis, aggravating the patient’s condition. Apoptosis serves as a crucial tactic for viruses to suppress host immune responses and facilitate infection. Understanding the intricate interplay between apoptosis and viral infectious diseases is vital for deciphering the complexities underlying viral pathogenesis. Further exploration of these mechanisms holds pro