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The novel coronavirus, SARS-CoV-2, is thought to have emerged in China in 2019 and has since spread across the globe, causing a global pandemic. Understanding the structure and function of SARS-CoV-2 and its variants is essential in developing vaccines and therapies to tackle the COVID-19 disease.
Updated May 19, 2022
Early genomic analysis of SARS-CoV-2 revealed that it belongs to the betacoronavirus genus, lineage B, alongside SARS-CoV-21,2. Coronaviruses are enveloped, single-strand RNA viruses characterized by club-like spikes projecting from their surface and an unusually large RNA genome3. The SARS-CoV-2 genome encodes four major structural proteins: the spike (S) protein, nucleocapsid (N) protein, membrane (M) protein and the envelope (E) protein, each of which is essential to compose the viral particle 3.
Like all coronaviruses, SARS-CoV-2 utilizes the S glycoprotein to mediate entry into the host cell. This protein contains two subunits: the S1 subunit that contains the receptor-binding domain (RBD) and N-terminal domain (NTD), and a second S2 subunit that mediates the fusion of the viral and host cell membranes4.
SARS-CoV-2 S protein binds to the ACE2 receptor at the surface of host cells, initially through the S1 RBD. S1 is then shed from the viral surface, allowing S2 to fuse to the host cell membrane. This process is dependent upon activation of the S protein, by cleavage at two sites (S1/S2 and S2’) via the proteases Furin and TMPRSS2. Furin cleavage at the S1/S2 site may lead to conformational changes in the viral S protein that exposes the RBD and/or the S2 domain. TMPRSS2 cleavage of the SARS-CoV-2 S protein is believed to enable the fusion of the viral capsid with the host cell to permit viral entry5,6.
Exposure of the RBD in the S1 protein subunit creates an unstable subunit conformation. Consequently, during binding, S1 undergoes conformational rearrangement between two states, known as the up and down conformations. The down state transiently hides the RBD, while the up state exposes the RBD, but temporarily destabilizes the protein subunit7,8,9. Within the trimeric S protein, only one of the three RBD heads is present in the accessible conformation to bind the human Angiotensin 2 (hACE2) host cell receptor10.
Many of the mutations found in SARS-CoV-2 variants of concern (VoCs) are found in the S gene – most commonly within the S1/RBD regions. Many such mutations have been shown to improve affinity S1’s for ACE2 and promote RBD flexibility and cleavage efficiency to enhance infection11. Unlike previous variants, however, Omicron shows reduced cleavage efficiency as well as impaired cell entry in the presence of TMPRSS212. The reason for this is thought to be Omicron’s greater reliance on the endosomal pathway.
In addition to binding ACE2, increasing evidence suggests that SARS-CoV-2 can also bind other surface proteins to gain cell entry. Indeed, the increased transmissibility of SARS-CoV-2 compared with SARS-CoV could potentially be explained by an increased number of cellular receptors allowing the virus to penetrate host cells.
Both Neuropilin-1 and Neuropilin-2 have been shown to bind the cleaved form of the SARS-CoV-2 S protein to mediate host cell entry 13, 14. Neuropilin proteins are expressed in neurons, providing an entry system for the virus into the nervous system and this has been observed in the neuropathological analysis of human COVID-19 autopsies 14. Antibody blockade of the NP receptors, receptor mutagenesis and structural studies all support the role of NP as a cell receptor for SARS-CoV-2 S protein 13, 14. Binding to NP receptors on the cell surface, in addition to the known ACE2 receptor, was shown to potentiate SARS-CoV-2 infection and may explain the increased tissue tropism seen in SARS-CoV-2 infection, compared to SARS-CoV 13, 14.
An initial study suggested that the SARS-CoV-2 S protein was able to bind to CD147 on the cell surface and subsequently enter the cell 15. As part of this study, in vitro antiviral tests indicated that meplazumab, an anti-CD147 humanized antibody that blocks the interaction of the S protein with the CD147 cell surface receptor, significantly inhibited viral cell entry. Clinical trials into the potential of this antibody to treat COVID-19 are ongoing 16. As higher blood sugar levels are known to upregulate CD147 expression, this could help to explain why diabetes is a factor for poor prognosis in cases of COVID-19 17.
Frequent cellular targets of the SARS-CoV-2 virus within the human host are neuronal cells, the endothelial cells of blood vessels, and epithelial cells within the respiratory system and gastrointestinal tract 18. However, ACE2 is known to be expressed only at low levels within the brain 19. A structural modeling study indicated that SARS-CoV-2 can bind to sialic acid glycoproteins and gangliosides on the cell surface20, and sialic acid is known to be expressed at high levels on the surface of all of the cell types targeted by SARS-CoV-2 21, including neuronal cells. This is a common cell entry mechanism for other viruses, including influenza 22, MERS, SARS-CoV and HCoV-OC43 23, and could offer potential new therapeutic strategies using drugs to lower sialic acid levels in COVID-19 patients to help prevent SARS-CoV-2 cell entry 24.
In addition to these factors, a range of alternative entry receptors have been associated with SARS-CoV-2 cell entry, including C-type lectins, DC-SIGN, L-SIGN, AXL and TIM125.
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