3  Possible mechanisms underlying viral infection
SARS-CoV-2 was initially identified and isolated from a cluster of patients with similar symptoms (fever, cough, and dyspnea) and radiologic findings of ground-glass opacity on chest CT [6]. Next-generation sequencing and real-time reverse transcription polymerase chain reaction (RT-PCR) targeting to a consensus RNA-dependent RNA polymerase (RdRp) region of panβ-CoV demonstrated the pathogen to be a novel beta coronavirus [7]. Electron microscopy revealed the solar appearance of virion particles, whose morphology was consistent with that of the Coronaviridae family [7].
SARS-CoV-2 most likely originated from bats due to its substantially high homology (96% nucleotide sequence identity) with SARS-like bat coronaviruses (BatCoV RaTG13) [11], [12]. A possible mechanism of the emergence of SARS-CoV-2 is that the accumulative mutations in its genome enabled the virus to cross the animal–human barrier. However, animal-to-human transmission is unlikely to have been the main driver for the COVID-19 pandemic.
SARS-CoV-2 employs mechanisms similar to those of SARS-CoV for receptor recognition and cell entry. The spike (S) protein on the virion surface facilitates the entry of the virus into the target cells by attachment to its cognate receptor, angiotensin-converting enzyme 2 (ACE2), on the cell surface. Transmembrane serine proteases of the target cells, such as FURIN or transmembrane protease serine 2 (TMPRSS2), induce cleavage of the S protein before membrane fusion for cellular entry [13]. Therefore, cells that co-express ACE2 and serine protease could be the primary targets of SARS-CoV-2. Single-cell RNA-sequencing studies have also confirmed the expression of ACE2 and TMPRSS2 in a vast array of cells, including lung alveolar epithelial type II cells, nasal goblet cells, cholangiocytes, colonocytes, esophageal keratinocytes, gastrointestinal epithelial cells, pancreatic β-cells, and renal proximal tubules and podocytes [14]. These observations have provided probable explanations for multiple-organ infection and injury via direct viral tissue damage. Moreover, clinical observations have demonstrated extrapulmonary manifestations, ranging from hematologic, cardiovascular, renal, gastrointestinal and hepatobiliary, endocrinologic, neurologic, and ophthalmologic to dermatologic systems [14].
SARS-CoV-2 attacks the host through direct tissue damage, endothelial cell damage and thrombosis, dysregulation of the immune response, and disorders of the renin-angiotensin-aldosterone system [15]. COVID-19 infection is accompanied by an aggressive inflammatory response with the release of massive pro-inflammatory cytokines in an event known as the “cytokine storm” [16], [17]. Plasma collected from COVID-19 patients with pneumonia has shown markedly increased concentrations of pro-inflammatory cytokines (interleukin-1β (IL-1β), interleukin-1 receptor antagonist (IL-1RA), IL-7, IL-8, IL-9, IL-10, fibroblast growth factor, granulocyte colony stimulating factor (G-CSF), granulocyte-macrophage colony-stimulating factor (GM-CSF), interferon-γ (IFN-γ), interferon-inducible protein-10 (IP-10), monocyte chemotactic protein-1 (MCP-1), macrophage inflammatory protein-1 alpha (MIP-1α), macrophage inflammatory protein-1 beta (MIP-1β), platelet-derived growth factor (PDGF), tumor necrosis factor-α (TNF-α), and vascular endothelial growth factor (VEGF)) [18]. Critical illness in patients has also been associated with an elevated level of IL-2, IL-7, IL-10, G-CSF, IP10, MCP-1, MIP-1α, and TNF-α plasma concentrations as compared with mild cases. These events drive the recruitment of immune cells such as macrophages, neutrophils, and T cells into the sites of infection, causing destabilization of endothelial cell to cell and the vascular barrier and diffusing alveolar damage, and ultimately leading to multi-organ failure and subsequent death.
ACE2 is the key determinant of viral transmissibility. Recent studies have demonstrated that the receptor binding domain of the S protein from SARS-CoV-2 displays a 10- to 20-fold higher binding capacity with ACE2 compared with that of SARS-CoV [19], [20], which may partially explain the increased transmissibility of SARS-CoV-2 [21]. SARS-CoV-2 shows a gradient of reduced infectivity from the proximal to distal respiratory tract, which coincides with the finding of progressively decreased expression of ACE2 from the oropharynx to the alveoli [22]. SARS-CoV-2 infection might be initiated from the nasal passages, followed by the aspiration of virions seeding along the respiratory tract to the lungs, rather than causing direct lung infection. A more possible process might involve high loads of virus shedding from the initially infected respiratory tract, along with the secretion of mucus accumulating at the oropharynx cavity, and finally arriving at the tracheobronchial tree via aspiration [23].
Molecular dynamics simulations suggest that SARS-CoV-2 has a distinct binding interface to ACE2, with higher affinities and a different network of residue-residue contacts than other coronaviruses [2]. SARS-CoV-2 has a larger contact area than SARS-CoV with more conserved residues for ACE2 attachment. Unlike coronaviruses with low pathogenicity, SARS-CoV-2 exhibits enhancement of the nuclear localization signals in the nucleocapsid protein and distinct inserts in the spike glycoprotein, which appear to be associated with the high case-fatality rate [24].
SARS-CoV-2 could evolve into diverse lineages with different magnitudes of virulence and transmissibility via mutations [25]. Several studies have documented a SARS-CoV-2 variant, aspartic acid (D) with substitution of glycine (G) at codon 614 in the S protein [25], [26], [27], [28], which is located on a B-cell epitope with a highly immunodominant region on the receptor binding domain. An in vitro study suggested that a D614G pseudotype variant was nine times more infectious than the D614 strains [29]. Strains carrying this mutation have become dominant since December 2019, and have been frequently observed in European countries (e.g., the Netherlands, Switzerland, and France) but not as frequently in China. Strikingly, the variant S-D614G distinguishes the SARS-CoV-2 strains that may have caused fatal infections in European populations [27]. A study on the alignment of 10 022 SARS-CoV-2 genomes from infected persons in 68 countries identified 6294 samples carrying the D614G mutation; almost all of these genomes also had another co-mutation in the proteins responsible for replication (ORF1ab P4715L; RdRp P323L) that might affect the speed of replication [28]. D614G was predicted to fine-tune the spike conformation and result in a loss of immunogenicity for B-cell recognition, a dominated process to stimulate adaptive immunity against SARS-CoV-2 infection.