Coronavirus disease 2019 (COVID-19) was first identified in Wuhan, China in December 2019, and then rapidly spread to all parts of the world. The World Health Organization (WHO), on 11 March, denoted COVID-19 as a pandemic, which was caused by novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [1,2,3,4,5,6,7].

Human coronaviruses (CoVs) were first reported in 1962. On the basis of the International Committee on Taxonomy of Viruses (ICTV), CoVs belong to Riboviria realm, Nidovirales order, Coronaviridae family, Orthocoronavirinae subfamily. CoVs are enveloped positive single-stranded RNA viruses classified into four genera, based on their protein sequence: alpha CoVs, beta CoVs, gamma CoVs, and delta CoVs. The intermediate hosts for alpha- and beta-coronaviruses are bats and rodents, whereas birds fulfill this role for gamma- and delta-coronaviruses [8,9,10].

Beta-coronaviruses are categorized into A, B, C, and D lineages, which cause most human coronavirus infections. Up to now, six beta-coronaviruses have been identified: HCoV-OC43, HCoV-HKU1, HCoV-229E, MERS-CoV, SARS-CoV, and SARS-CoV-2 [9, 10].

Over the past two decades, three epidemic or pandemic outbreaks of CoV infection have occurred (SARS-CoV in 2002, MERS-CoV in 2012, and SARS-CoV-2 from 2019 onward). All these viruses were capable of infecting human airways, especially the lower respiratory tract, and causing acute respiratory distress syndrome (ARDS) and multiorgan failure (MOF), with high mortality rates [1, 11, 12].

Common clinical symptoms in patients with COVID-19 include nonproductive cough, fever, myalgia, fatigue, diarrhea, hypoxemia, and dyspnea, often leading to ARDS and/or multiple organ dysfunction syndrome (MODS). Whereas some patient have none or only mild symptoms, others may be prone to more serious COVID-19 infections, and then require hospitalization and intensive care [13, 14]. Pneumonia and respiratory failure is the most prevalent pathological cause of death in COVID-19, and in patients who require mechanical ventilation, mortality can be very high [15, 16].

SARS-CoV-2 entry into human cells is mediated mainly by the viral spike (S) protein. Airway epithelial cells, ciliated cells, goblet cells, and, more recently, olfactory neurons are the most studied routes for viral entry. When the virus infects these epithelial cells, the pathogenic process commences, and in favorable conditions the virus begins to multiply rapidly, then spread to infect other target cells and organs. Angiotensin-converting enzyme 2 (ACE2) is the most common receptor for SARS-CoV-2 S protein, but recently other receptors have been identified that can interact with S protein [17,18,19].

During COVID-19 infections, the air–blood barrier can be disturbed by apoptosis or necrosis of epithelial cells and endothelial cells, as well as damage to the basement membrane. This airway damage can lead to respiratory failure and death. On the other hand, it has been suggested that COVID-19 is largely an endothelial disease. It is known that there are different receptors and other mediators expressed in endothelial cells, which can help SARS-CoV-2 to gain entry [20,21,22,23,24]. When the SARS-CoV-2 virus infects endothelial cells, it affects their secreted mediators, tight cell junctions, and overall survival [25].

It has been reported that coagulopathy is commonly observed in patients with severe COVID-19, and that endothelial cells as well as platelets play a key role in this process. Similar to endothelial cells, platelets express receptors and secretory granules, which can be affected by the pathogen [26,27,28,29].

SARS-CoV-2 can affect target cells either directly by binding to surface receptors, or indirectly by cytokines secreted from other cells. Cytokines are signaling molecules secreted by a wide range of cell types. They are critically involved in many biological processes. Cytokines have either proinflammatory or anti-inflammatory effects. These molecules can produce a “cytokine storm” or overproduction of proinflammatory cytokines leading to further damage, especially involving feedback loops. The cytokine storm has been widely reviewed [30,31,32].

The SARS-CoV-2 pathogenesis process involves a variety of cells, which can interact with each other and with cytokines, leading to the destruction of the air–blood barrier and causing coagulopathy. This can eventually lead to pulmonary edema, ARDS and/or MODS, and finally death. Our goal in this article is to provide a comprehensive overview of the cells and processes involved in COVID-19-related respiratory failure. Firstly, we discuss the pulmonary epithelium and SARS-CoV-2 entry mechanism, followed by the influence of COVID-19 on endothelial cells and platelets, and finally we suggest how all these factors interact together, to understand the pathophysiology of pulmonary complications induced by SARS-CoV-2 infection.

The airway epithelium is vital for its varied functions, such as warming and humidifying the inhaled air, clearing and defending the airways from inspired pathogens, and forming the epithelial half of the air–blood barrier. The most important point of SARS-COVID-2 entry is the respiratory tract, and epithelial cells are the most important targets of this virus. Therefore, it is necessary to review the various cell types in the respiratory epithelium (Fig. 1).

Pulmonary epithelium and cell penetration pathways of SARS-CoV-2. A One of the important ports of virus entry is respiratory epithelial cells. Upper airways are lined with pseudostratified epithelium. In distal airways, height of the epithelium decreases and eventually becomes squamous in the alveoli. It consists mainly of ciliated cells as well as goblet cells, Clara/club cells, basal cells, and neuroendocrine cells. Ciliated cells have hair-like projections, which help move up mucus that rests on them. Goblet cells produce and secrete mucin. Club cells secret specific proteins and surfactant protein (SP)-A, SP-B, and SP-D. Alveolar type 1 and 2 cells are involved in gas exchange and the generation of SPs, respectively. Stem cells in this epithelium include basal cells, “variant” club cells, neuroendocrine cells, and cell population in bronchoalveolar duct junctions. B SARS‐CoV‐2 entry into the host cells occurs via direct membrane fusion (1) and endocytosis (2). In both pathways, spike (S) protein must bind to host cell receptors such as ACE2, NRP1, CLR, MGL, L-SIGN, DC-SIGN, TLRs, and GRP78. In endocytosis-mediated entry, following binding to cell receptor, virus entry into the host cell occurs and the S protein is activated in endosomes by furin cleavage. Fusion occurs by cathepsin-L action, and virus genetic material is released into cytosol, entering the virus through direct fusion mediated by proteases such as TMPRSS2 and/or furin. S protein interacts with a host cell receptor and becomes activated. Eventually, the membranes are merged and the virus releases its genetic material (RNA) via the formed pore into the cytosol. SARS-CoV-2 RNA is replicated and transcribed by host organelles such as ribosomes, Golgi apparatus, rough endoplasmic reticulum (rER), etc. Finally, the virus spreads to other cells and tissues. SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; NRP1, neuropilin-1; ACE2, angiotensin-converting enzyme 2; MGL, macrophage galactose-type lectin; CLR, C-lectin type receptors; L-SIGN, homolog dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin related; DC-SIGN, dendritic cell-specific intracellular adhesion molecule-3-grabbing non-integrin; TLRs, Toll-like receptors; GRP78, non-immune receptor glucose-regulated protein 78; TMPRSS2, transmembrane protease, serine 2

A pseudostratified epithelium covers the upper airways, consisting of basal cells, ciliated cells as the main cell type, goblet cells, Clara or club cells, and a limited number of neuroendocrine cells [33, 34]. Columnar ciliated cells have 200–300 individual cilia and are the main cell type in this epithelium. Their hair-like projections move backwards and forwards at a rapid frequency (8–20 Hz) and help move mucus upwards through the tract. Goblet cells are also columnar, like ciliated cells. They produce and secrete mucin, a glycoprotein, into the airway for trapping inhaled particles and pathogens, also for and moisturizing the epithelium [33, 35]. Clara or club cells are cube-shaped cells that secret proteins (e.g., CCSP) and surfactant proteins (SP)-A, SP-B, and SP-D. These proteins are involved in the composition of lung fluid [33, 36].

In distal airways and bronchioles, the Clara cells become more abundant and the lung epithelium gradually becomes more columnar in nature. The height of the epithelium decreases and eventually becomes squamous within the alveoli. Alveolar type 1 and 2 (AT1, AT2) cells are two important cell types in the alveolar epithelium. They are involved in gas exchange and surfactant production, respectively [37, 38].

The most important cause of respiratory failure and alveolar edema in COVID-19 is destruction of the integrity of the pulmonary epithelium. Airway stem cells have a crucial role in maintaining and repairing the epithelial integrity. The self-renewing stem cells are able to generate several different types of daughter cells [39, 40]. Owing to the difficulties of direct studies in human lung, there is insufficient knowledge about the human lung epithelial stem cell niche. Knowledge on the repair and maintenance of lung function has been largely based on animal studies. In animals, airway stem cells are found in three niches within the tract: upper airway submucosal glands, small airway branching points, and the bronchoalveolar duct junction (BADJ). The cells in these niches are capable of generating various cell types [40].

These include: basal cells, “variant” Clara cells, neuroendocrine cells, and the cell population in the BADJ. BADJ stem cells can differentiate into AT1, Clara, and AT2 cells [41,42,43]. It has been found that AT2 cells can replace lost AT1 cells in the alveolar epithelium (Fig. 1) [44]. Further studies should be performed on the function of these cells in humans, and whether they can help to treat respiratory failure in patients with COVID-19 and control its subsequent complications.

The coronavirus virion is made up of nucleocapsid (N), membrane (M), envelope (E), and spike (S) proteins, which are structural proteins. The S protein mediates viral attachment, membrane fusion, and entry, thus determining tissue and cell tropism as well as host range in the Coronaviridae family [45]. Therefore, coronavirus infection of target cells depends on interactions of S proteins with cellular receptors [46]; for example, MHV uses murine biliary glycoproteins in the immunoglobulin superfamily; HCoV-229E and TGEV use human and porcine aminopeptidase N (APN), respectively; FIPV and FeCoV use feline APN, which can also be utilized by HCoV-229E and TGEV; and BCoV and HCoV-OC43 use N-acetyl-9-O-acetyl neuraminic acid moieties. Expression of the cloned receptor glycoproteins in cells of a foreign species can render them susceptible to infection with coronavirus virions [45]. Thus, coronavirus–receptor interactions are an important determinant of the species specificity of coronavirus infection.

SARS‐CoV‐2 enters the host cells via endocytosis of a receptor–virus complex, or by direct membrane fusion (Fig. 1). In both pathways, the SARS-CoV-2 S protein, a trimeric class I transmembrane glycoprotein, must bind to cell receptors like ACE2 in the host. Respiratory epithelial and endothelial cells, monocytes, and alveolar macrophages show broad expression of ACE2 [47, 48].

In addition to ACE2, several molecules have been suggested to serve as alternative receptors for SARS-CoV and SARS-CoV-2. These include C-type lectins, DC-SIGN and L-SIGN. Lectins are involved in the recognition of a broad range of pathogens and mediate intercellular adhesion. Although lectins and phosphatidylserine receptors enhance viral entry, they are nonspecific and do not support efficient infection by SARS-CoV or SARS-CoV-2 in the absence of ACE2, and thus “attachment factors” would better describe these molecules. Similarly, CD147, a transmembrane glycoprotein expressed ubiquitously in epithelial and immune cells, was proposed to be an alternative receptor for SARS-CoV and SARS-CoV-2 infection [49]. Although a modest increase in viral entry was observed with higher levels of CD147, and although its upregulation was observed in obesity and diabetes [49], which are potential risk factors for severe COVID-19, the role of CD147 in SARS-CoV-2 infection has been disputed on the basis of the inability of CD147 to bind the S protein [50]. Two groups identified neuropilin 1 (NRP1) as a host factor for SARS-CoV-2 [51, 52]. Although NRP1 is expressed in olfactory and respiratory epithelial cells, its expression is low in ciliated cells, the primary target cells for SARS-CoV-2 in the airway, while it is high in goblet cells, which are not susceptible to SARS-CoV-2. Nonetheless, NRP1 was shown to enhance TMPRSS2-mediated entry (see the next section) of wild-type SARS-CoV-2 but not that of mutant virus that lacks the multibasic furin-cleavage site [49]. NRP1 was also shown to bind S1 through the multibasic furin-cleavage site and to promote S1 shedding and expose the S2′ site to TMPRSS2 [53]. Recently, the structure of ACE2 in complex with a neutral amino acid transporter, B0AT1, was analyzed by cryogenic electron microscopy in the presence and absence of the SARS-CoV-2 S protein [54]. ACE2 was previously shown to be essential for B0AT1 expression in the small intestine [55]. While B0AT1 is expressed in the gastrointestinal tract and kidney, it is not present in the lung. However, a B0AT1 homolog in the lung might contribute to SARS-CoV-2 infection. Additional studies are warranted to confirm the role of NRP1 and B0AT1 in SARS-CoV-2 infection [49].

Toll-like receptors (TLRs) recognize pathogen-associated molecular patterns and induce the production of type I interferons. Of these, TLR3, TLR7, TLR8, and TLR9 mount antiviral immune responses: TLR3 recognizes double-stranded RNA viruses, TLR9 recognizes unmethylated CpG in viral DNA, and, relevant to coronaviruses, TLR7 and TLR8 bind G/U-rich single-stranded viral RNA [49]. Many interferon-stimulated gene products were identified as important for SARS-CoV-2 replication, but only a few of them are involved in the entry steps: interferon-induced transmembrane proteins (IFITMs) [56, 57] and lymphocyte antigen 6 family member E (LY6E) [58, 59]. Recently, IFITM2 was shown to restrict SARS-CoV-2 entry [56]. IFITM proteins prevent viruses from traversing the endosomal membrane to access cellular cytoplasm by an unclear mechanism. Such a restriction can be bypassed if SARS-CoV were directed to enter cells exclusively at the plasma membrane [60].

LY6E is a glycophosphatidylinositol-anchored cell surface protein and was shown to inhibit or promote replication of some viruses [49]. Recently, LY6E was shown to impair infection by SARS-CoV, SAR-CoV-2, and MERS-CoV by inhibiting the S-protein-mediated membrane fusion, and mice lacking LY6E expression in immune cells were highly susceptible to mouse hepatitis virus, also a coronavirus [59]. Unlike IFITM-mediated restriction, LY6E-mediated inhibition was not overcome by TMPRSS2 expression (58). Further study is warranted to clarify the distinct roles of LY6E in regulating infection with SARS-CoV-2 and other viruses.

In endocytosis-mediated entry, after binding to a cell receptor, the virus penetrates into the host cells, and the S protein is activated in endosomes by furin cleavage. The endosomes undergo fusion with lysosomes by the action of cathepsin L proteolysis to form the endolysosome stage. Finally, after the fusion of membranes is completed, the viral RNA enters the host cell cytosol. Proteases are responsible for allowing viral entry through direct fusion, including transmembrane protease serine 2 (TMPRSS2) or furin. After the S protein interacts with the host cell receptor, S protein activation occurs. Eventually, the membranes are merged and the virus transfer its RNA through the formed pore into the cytosol [61, 62].

The RNA of SARS-CoV-2 is translated into structural proteins and nonstructural proteins (NSPs). These proteins are necessary for virus survival, multiplication, and virulence. In addition to the S protein other structural proteins, such as envelope glycoprotein (E), membrane glycoprotein (M), and nucleocapsid (N) proteins, are synthesized as accessory proteins [63].

The replication and transcription of the RNA sequence of SARS-CoV-2 occurs by a large multisubunit viral replicase–transcriptase complex. The structural proteins and genomic material are packaged into a new virus, which is secreted by exocytosis to spread to additional cells. The NSPs have many important functions in virus pathogenesis, such as stimulating the replication enzyme (RNA polymerase), proofreading of the SARS-CoV-2 genome, suppression of interferon (IFN) signaling, blocking the translation of host RNA, and stimulating cytokine expression. SARS‐CoV‐2 triggers an immune response through proinflammatory cytokine production associated with a weak protective IFN response to viral infection [64,65,66].

As shown in Fig. 2, endothelial cells ACE2 [20], transmembrane serine protease 2 (TMPRSS2) [21], sialic acid receptors (a surface adhesion molecule) [22], extracellular matrix metalloproteinase inducer (CD147, or basigin), TLR2, TLR4, TLR5, and TLR9 [23], and NRP1 [24] are all reportedly implicated in SARS-CoV-2 entry. Moreover, it is reported that cathepsin B and L are also essential entry factors in COVID-19. L-SIGN is reportedly expressed in type II human alveolar cells, and pulmonary endothelial cells also mediate SARS-CoV-2 entry [67].

Suggested pattern for cell interactions in COVID-19, leading to pulmonary edema. In ECs, ACE2, CD147, NRP1, TLRs, L-SIGN, TMPRSS2, and sialic acid receptors may mediate SARS-CoV-2 penetration. PAF is released by a variety of cell types. ECs express PAFR. PAF/PAFR complex in ECs induces the production of cytokines such as CXCL1, TNF-α, IFN-γ, and IL-6. ECs may have TNFRs that cause surface expression of ICAM-1, E-selectin, and VCAM-1. In adherens junctions, important cytosolic partner(s) for VE-cadherin are α- and β-catenin and for nectins is afadin. TNF inhibits the expression of VE-cadherin, blocks its contact with β-catenin, affects actin cytoskeleton remodeling, and activates the NF-κB pathway, resulting in elevated expression of inflammatory genes. Some tight-junction-associated proteins include occludin, claudins, jAMs, ZO1, ZO2, ZO3, and PALS1 (A). SARS-CoV-2 E protein interacts with PALS. TNF disrupts claudin-5. TNF-α destroys JAM-A, claudin-4, and claudin-5. EC death occurs by apoptosis and/or necrosis. In the extrinsic pathway, TRAILR and Fas stimulation cause caspase-8 activation. Caspase-8 stimulates the caspase cascade that ultimately leads to apoptosis. FasL is released by neutrophils and lymphocytes. NK cells and cytotoxic T cells secrete perforin and granzymes that, through direct exposure to target cells, secrete perforin and granzymes, resulting in induction of apoptosis and/or necrosis. The molecular mechanism of necrosis is not clear, though it probably occurs via the release of lysosomal enzymes and generation of ROS, and in necrosis significant ATP depletion is seen. Fas and TNF stimulate both apoptosis and necrosis. ECs release t-PA, mediating the conversion of plasminogen to plasmin, and MMPs, lysing ECM. t-PA enhances neutrophil degranulation and MMP-9 secretion. Cell infiltration is facilitated by MMPs that result in leukopenia. Infected cells secrete numerous cytokines and DAMPs. DAMPs induce NETosis. NETs include DNA, histones, and enzymes such as serine protease. They are a scaffold for platelets, red blood cells (RBCs), and plasma proteins. Histones can activate pro-FSAP. FSAP, a serine protease, is a mediator of plasminogen-to-plasmin conversion. NETs activate FXII to convert prothrombin to thrombin. Thrombin converts fibrinogen to fibrin. Fibrin contributes to blood clot formation. Thrombin, NET serine proteases, and histones activate platelets. vWF is secreted by ECs and enhances platelet adhesion and aggregation. Basophils are secreted by IL-4, IL-6, and IL-13 production. They affect mature human B cells. IL-4 is correlated with the concentration of IgG antibodies, but IL-6 is inversely associated with them. Eosinophils produce NO and EETs to limit viral replication. NO inhibits platelet activation. On the other hand, EETs and MBP mediate platelet activation. Activated eosinophils secrete IL-2, IL-8, IL-12, and INF λ. EDN induces the TLR2–MyD88 signal pathway in DCs, resulting in IL-12, IL-27, and IL-18 secretion that increases NK cell activity and induces secretion of IFN-γ. IFN-γ is also secreted by NK cells. DCs also produces IL-6, significantly. ECP and EDN activate apoptotic pathways. ECP also stimulates necrosis process. In addition, increased levels of MBP and ECP stimulate the degranulation of perivascular MCs. MCs release IL-6, IL-1β, and TNF. NK cell activity can decrease by IL-6 and IL-1β. ROS can also be an inhibitor for NK cells. Eosinophils produce ROS. NK cells activate apoptosis and necrosis by secretion of FasL, TRAIL, perforin, and granzymes. B-cell and T-cell interactions lead to plasma cell generation (colonal expansion, antibody secretion) and production of either proinflammatory cytokines such as IL-12, IL-6 and IL-15 or anti-inflammatory cytokines such as IL-10, IL-35, and TGF-β by B cells. IL-12 and IL-6 provide positive feedback in B- and T-cell interactions. IL-15 enhances CD8+ T-cell activity. GM-CSF are produced by macrophages, B cells, T cells, NK cells, and ECs. GM-CSF stimulate the differentiation of monocytes. M1 produce proinflammatory cytokine such as IL-1β, IL-6, TNF-α, and IL-12 and INFs. M2 releases types I and III collagen, MMPs, and anti-inflammatory cytokines such as IL-10 or TGF-β. M2 can be transited into fibroblasts by TGF-β mediation, leading to pulmonary fibrosis. M1 stimulates Th cells. IFN-γ, TNF-β, and IL-2 are secreted by Th cells that activate macrophages. M1 activates NK cells by IL-1β, IFN-β, and IL-15. Alveolar macrophages release IL-1, IL-6, TNFs, and IL-8. Type 2 pneumocytes also play a major role in the formation of cytokine storms. Destruction of the air–blood barrier leads to infiltration of cells associated with alveolar epithelial cells secreting many cytokines, such as IL-1B, IL-2, IL-6, IL-7, IL-8, IL-10, IL-17, TNF, etc., out of control, resulting in further and further injury. Finally, lung edema and pulmonary failure occurs (B). COVID-19, coronavirus disease 2019; ACE2, angiotensin-converting enzyme 2; ECs, endothelial cells; CD147, cluster of differentiation 147; TLRs, Toll-like receptors; NRP1, neuropilin-1; L-SIGN, homolog dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin related; serine 2; TMPRSS2, transmembrane protease, SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; PAFR, platelet-activating factor receptor; PAF, platelet-activating factor; TNF, tumor necrosis factor; IL, interleukin; IFN, interferon; TNFRs, tumor necrosis factor receptor; ICAM-1, intercellular adhesion molecule-1; VCAM-1, vascular cell adhesion molecule-1; VE-cadherin, vascular endothelial cadherin; ZO, zonula occludens; JAMs, junctional adhesion molecules; E protein, envelope protein; PALS1, protein associated with LIN7 1, MAGUK family member; TRAIL, TNF-related apoptosis-inducing ligand; t-PA, tissue plasminogen activator; NK cells, natural killer cells; NF-κB, nuclear factor kappa-light-chain-enhancer of activated B cells; MMPs, matrix metalloproteinases; ECM, extracellular matrix; FSAP, factor VII activating protease; DAMPs, damage-associated molecular pattern; NETs, neutrophil extracellular traps; NO, nitric oxide; vWF, von Willebrand factor; EETs, eosinophil extracellular traps; EDN, eosinophil-derived neurotoxin; MBP, major basic protein; MyD88, myeloid differentiation factor 88; ECP, eosinophil cationic protein; DCs, dendritic cells; MCs, mast cells; GM-CSF, granulocyte–macrophage colony-stimulating factor; TGF-β, transforming growth factor beta; M1, type 1 macrophages; M2, type 2 macrophages; Th cells, T-helper cells

When the SARS-CoV-2 enters endothelial cells, it adversely affects these cells. Moreover, endothelial cells can be affected by molecules produced by other cells fighting against the virus. These molecules can bind to their receptors expressed on the endothelial cell surface. Platelet-activating factor (PAF) is one molecule released by a variety of cell types and tissues, but the main source of PAF is leukocytes. PAF mediates the inflammation process. Platelet-activating factor receptor (PAFR) is thought to be formed on the cytoplasmic or nuclear membrane of various cells, in particular endothelial cells, platelets, and leukocytes. The PAF/PAFR complex in endothelial cells may induce increased vascular permeability, hypotension, and expression of cytokines such as CXCL1, interleukin 6 (IL6), tumor necrosis factor-alpha (TNF-α), and IFN-γ [68,