FIGURE LEGENDS
Figure 1. SARS-CoV-2 structure and genome. A)SARS-CoV-2 is a positive-sense RNA enveloped virus with the spike (S), membrane (M), envelope (E) proteins embedded in the lipid envelope, while the nucleocapsid (N) protein is associated with the RNA.B) The 5’ end of the genome is comprised of ORFa/ab encoding 2 large polyproteins including the replicase protein crucial for self-generation of the non-structural proteins (nsp) while ORFs 2-10 encode the viral structural proteins (S, M, E and N) and accessory proteins. C) The homotrimers spike proteins of 8-12 nm length are heavily decorated with N-glycans moieties that can be recognised by antibodies, C-type lectins and mannose binding proteins that aid viral attachment to permissible cells, activate the complement system and may be recognised by macrophages and antibodies (D).
Figure 2. SARS-CoV-2 subversion of interferon pathways.SARS-CoV-2 infects permissible cells via the angiotensin converting enzyme two (ACE2). Following infection (A) the virion or viral RNA is sensed by either the cGas/STING pathway where stimulator of interferon genes (STING) engages TBK1, or via retinoid inducible gene I (RIG-I) and melanoma differentiation-associated gene 5 (MDA5). These pathways lead to activation of IRF3 and/or NFkB inducing type I/III IFN that is recognised by IFN receptors (B) and subsequent induction of the interferon stimulated genes (ISGs) and proteins many of which have potent antiviral activities. Based on the knowledge of other coronaviruses especially SARS-CoV, and emerging data from SARS-CoV-2 many of the non-structural, structural and accessory protein subvert and inhibit numerous steps in these pathways thereby inhibiting IFN production allowing increased viral replication.
Figure 3. SARS-CoV-2 activates innate immune pathways.SARS-CoV-2 infects permissible cells via the angiotensin converting enzyme two (ACE2) and is taken by in the endosome where the virus is recognised by Toll-like receptor 7/9 triggering MyD88 pathway, or TLR 3 via the TRIF pathway (A). PAMPS and DAMPS are also recognised by TLR4 (B) or RAGE (C) triggering HMGB1induced damage and (D) NLRP3 inflammasome activation. During viral replication ORF3a and E proteins form viroporins that augment ROS production and inflammasome activation.
Figure 4. SARS-CoV-2 is a vascular and coagulation disease.A) Binding of SARS-CoV-2 to ACE2 blocks ACE2-induced formation of antioxidant angiotensin, facilitating oxygen free-radical formation. Infection in some people also triggers pyroptosis, complement activation(B) and hyperinflammation with influx of macrophages, NK cells and neutrophils (C). This self-augmenting cycle triggers further cell damage and DAMPS and PAMPs release as well as ROS production. D) Activation of neutrophils induces neutrophil extracellular traps (NET) aided by the N protein and generated in response to ROS-induced endothelial cell damage. Disruption of the vascular barrier and endothelial cell exposure to proinflammatory cytokine and ROS increases expression of P-selectin, von Willebrand factor (vWF) and fibrinogen, that attract platelets triggering expression of tissue factor. Together this sequence activates the complement system, one of many pathways that crucially activates the coagulation cascade leading to thrombi formation.
Suppl Figure 1. Replication Cycle of SARS-CoV-2 . Based on knowledge emerging from the SARS-CoV-2 infection and other coronaviruses, the cycle comprises of viral binding to the host cell via ACE-2 (1) and virion uptake into the endosome. (2) The positive stranded RNA allows direct translation of the genome (which is capped by nsp – see text for details) generating the replicase polyprotein and subsequent viral proteins some of which are necessary to form the double membrane vesicles (DMV) (3). The replicase polyprotein enzyme synthesises the negative strands to transcribe the small subgenomic positive RNAs (4). These are used to produce the other viral proteins (N, S,M and E and accessory proteins) and the positive RNA strands for the new virions. The nucleocapsid protein binds to the RNA. The S, M and E proteins are incorporated in the lipid envelope in the ER. The new virons assemble in the ER-Golgi intermediate compartment (ERGIC) and exocytosed in the Golgi complex (6). Finally, mature SARS-CoV-2 virions are released from the host cell (7).