SARS-CoV-2: What makes it different?

By Vaenya Singhal

A novel coronavirus (SARS-CoV-2) infectious disease, COVID-19, broke out in Wuhan (China) in December 2019 and has gained rapid momentum since. The outbreak was declared as a global pandemic by the WHO in March 2020, and as of 15th September, the total number of COVID cases reported are skyrocketing at 29.2 million. Several types of coronaviruses (CoVs), first discovered in domestic poultry in the 1930s, have caused respiratory, liver, neurological and gastrointestinal diseases in animals. However, only seven are known to infect humans, three of which can cause severe, and sometimes fatal, respiratory infections. These have led to major outbreaks of deadly pneumonia in the 21st century. SARS-CoV, identified in 2003, led to the outbreak of SARS, while MERS-CoV, identified in 2012 was the cause of Middle East respiratory syndrome (MERS). These CoVs are zoonotic pathogens which begin in infected animals and are transmitted to other animals and then to humans (Tesini, 2020). While SARS infected around 8,400 individuals with 900 deaths and a mortality rate of 9%, MERS hit about 2,500 people and killed about 850 of them, rendering a shocking fatality rate of 34%. In comparison to these, COVID-19 has a lower fatality rate but significantly higher rates of person-to-person transmission and there are several reasons which are potential contributors to this (Thomas, 2020).

Sequencing of SARS-CoV-2 determined that it is a novel coronavirus that shares 88% sequence identity with two bat derived SARS-like coronaviruses, suggesting bats are its origin. Research also shows that this CoV shares a 79.5% sequence identity with SARS-CoV. Coronaviruses are mainly composed of four structural proteins: namely Spike, membrane, envelope and nucleocapsid. Spike, a highly glycosylated trimeric protein of CoVs determines its diversity and host trophism, regulates binding to host cells surface receptors and facilitates virus-cell membrane fusion (WU & YANG, 2020). The S proteins, vital for virus entry, assemble into trimers on the surface of virions to form the distinct ‘corona’ or crown-like appearance. It comprises of a short intracellular tail, a transmembrane anchor and a large ectodomain. The ectodomains of all CoV S proteins are organized into two domains: an N-terminal S1 domain, responsible for receptor binding and C-terminal S2 domain, responsible for membrane fusion. The protein rests in a metastable prefusion conformation which undergoes substantial structural rearrangement to allow fusion of the viral membrane with the host cell membrane. This occurs on binding of the S1 subunit to the host cell receptor which destabilizes the prefusion trimer, resulting in shedding of the S1 subunit and transition of S2 subunit to a stable post-fusion conformation. The receptor binding domain (RBD) of S1 undergoes hinge-like conformational movements to engage with the host cell receptor, by transiently hiding or exposing the determinants of receptor binding (Wrapp & Wang, 2020). The sequences analysis of the SARS-CoV-2 S protein has shown only 75% identity with the SARS-CoV S protein, whereas the analysis of the receptor binding motif in the S protein showed that most of the amino acid residues crucial for receptor binding were conserved between the two CoVs, suggesting that the two strains utilize the same host receptor for cell entry. There is biophysical and structural evidence that show that the entry surface receptor utilized by these CoVs is Angiotensin-Converting Enzyme 2 (ACE-2). 

The differences between SARS-CoV-2 and other viruses results in a much extensive spread of the COVID-19 due to several reasons. A study made use of Cryo-electron micrography to determine the structure of SARS-CoV-2 Spike protein. Its comparison with S protein of SARS-CoV, combined with biophysical detection, revealed that SARS-CoV-2 binds ten times more strongly to cellular ACE2 receptors. Furthermore, the crystal structure of SARS-CoV-2 RBD-ACE2 complex showed a distinct conformational change in the key loop of complex binding interface. Binding free energy calculations also indicate a stronger binding for SARS-CoV-2 RBD in comparison to SARS RBD. This partially explains how SARS-CoV-2 is more infectious (WU & YANG, 2020). The S protein of SARS-CoV-2 has found to harbour RRAR, a unique furin-like cleavage site (FCS) at the boundary between S1/S2 subunits, which gets processed during biogenesis and sets the virus apart from SARS-CoV and SARS-related CoVs. It is responsible for SARS-CoV-2’s high infectivity and transmissibility (Xia & Lan, 2020). The motif allows spikes to be cut into S1 and S2 by furin-like proteases before maturity, without separation, providing S1 with the flexibility to change conformation to fit the host receptor. The unique FCS provides a gain-of-function, allowing easy entry into host cell for infection, thus effectively spreading throughout the human population. Similarly, previous studies show that insertion of FCS containing multiple basic amino acids in the cleavage site of the hemagglutinin is in congruence with high virulence of influenza viruses (Xia & Lan, 2020). Analysis of expression of furin shows that it is distributed in several organs with slight difference in expression levels. Combined with the infection mechanism of SARS-CoV-2, the widespread distribution of furin increases the SARS-CoV-2 infection of other organs. The efficiency of fusion is also increased as the spike protein of SARS-CoV-2 can be cleaved at multiple stages. 

These findings suggest that furin-like proteases may be potential drug targets for anti-SARS-CoV-2 treatment. Combined administration of targeting different SARS-CoV-2 proteases with furin inhibitors may also serve as an effective therapeutic strategy (WU & YANG, 2020). Overall, while SARS and MERS have higher fatality rates in comparison to COVID-19, SARS-CoV-2 is way more infectious leading to a significantly greater number of deaths than from SARS and MERS, due to reasons that have been discussed above. This makes limiting the spread of the virus and development of effective therapeutic remedies, the urgent need of the hour.

References:

ACE-2: The Receptor for SARS-CoV-2. Available from: https://www.rndsystems.com/resources/articles/ace-2-sars-receptor-identified .

Tesini, B. (2020) Coronaviruses and Acute Respiratory Syndromes (COVID-19, MERS, and SARS). Available from: https://www.msdmanuals.com/professional/infectious-diseases/respiratory-viruses/coronaviruses-and-acute-respiratory-syndromes-covid-19-mers-and-sars .

Thomas, L. (2020) How (easily) does the novel coronavirus spread? Available from: https://www.news-medical.net/news/20200401/How-(easily)-does-the-novel-coronavirus-spread.aspx .

Wrapp, D. & Wang, N. (2020) Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Aaas. 367 (6483), 1260-1263. Available from: https://science.sciencemag.org/content/367/6483/1260.

WU, C. & YANG, Y. (2020) Furin, a potential therapeutic target for COVID-19. ChinaXiv. Available from: http://chinaxiv.org/abs/202002.00062.Xia, S. & Lan, Q. (2020) The role of furin cleavage site in SARS-CoV-2 spike protein-mediated membrane fusion in the presence or absence of trypsin. Nature. Available from: https://www.nature.com/articles/s41392-020-0184-0.