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Mon Apr 6, 2020, 10:19 AM

A "Cryptic Epitope" to SARS-COV-1 Also Binds to SARS-COV-2: A Key to Vaccine Design.

The paper I'll discuss in this post is this one: A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV. (Meng Yuan1,*, Nicholas C. Wu1,*, Xueyong Zhu1, Chang-Chun D. Lee1, Ray T. Y. So2, Huibin Lv2, Chris K. P. Mok2,†, Ian A. Wilson1,3,†, Science, April 3 2020.)

I am logged in under my subscription, but I believe all Covid-19 related papers in the scientific literature are open sourced.

Some brief simplifications of what is in the paper: Most proteins are very large molecules, containing many hundreds of amino acids. The bulk of these do not conduct the "business" of the protein, although they may and often do play other roles such as signalling when a protein may be activated or deactivated.

The actual place where "business" is conducted is a short sequence of amino acids within the protein that is called the "epitope." They may be as small as a few amino acids long, but seldom comprise all that much of the protein's overall sequence. Drugs are often designed so as interfere with this functional "epitopic" region. Many blood pressure medicines, for example, interfere with the epitopic region of the ACE2 target of the SARS-Covid virus. (Clinical trials exploiting this area for potential Covid treatments is planned at the University of Minnesota for Covid patients not requiring critical care.)

It appears that antibodies in a patient who recovered from SARS-CoV-1, which also interacts with SARS-CoV-2, which is very good news indeed. It means that much of the work on earlier SARS viruses may be utilized in exploring both treatment and vaccine opportunities.

An excerpt from the text:

The ongoing outbreak of Coronavirus Disease 2019 (COVID-19) originally emerged in China during December 2019 (1) and had become a global pandemic by March 2020. COVID-19 is caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (2). Two other coronaviruses have caused world-wide outbreaks in the past two decades, namely SARS-CoV (2002–2003) and Middle East respiratory syndrome coronavirus (MERS-CoV) (2012–present). The surface spike glycoprotein (S), which is critical for virus entry through engaging the host receptor and mediating virus-host membrane fusion, is the major antigen of coronaviruses. The S proteins of SARS-CoV-2 and SARS-CoV, which are phylogenetically closely related, have an amino-acid sequence identity of around 77% (3). Such a high degree of sequence similarity raises the possibility that cross-reactive epitopes may exist.

CR3022, which was previously isolated from a convalescent SARS patient, is a neutralizing antibody that targets the receptor-binding domain (RBD) of SARS-CoV (4). The immunoglobulin heavy chain variable, diversity, and joining (IGHV, IGHD, and IGHJ) regions are encoded by germline genes IGHV5-51, IGHD3-10, and IGHJ6, while the light chain variable and joining regions are encoded by IGKV4-1 and IGKJ2 (4). Based on IgBlast analysis (5), the IGHV of CR3022 is 3.1% somatically mutated at the nucleotide sequence level, which results in eight amino-acid changes from the germline sequence, whereas IGKV of CR3022 is 1.3% somatically mutated resulting in three amino-acid changes from the germline sequence (fig. S1). A recent study has shown that CR3022 can also bind to the RBD of SARS-CoV-2 (6). This finding provides an opportunity to uncover a cross-reactive epitope.


A graphic from the text:



The caption:

Fig. 2 Conservation of epitope residues.
(A) Sequence alignment of SARS-CoV-2 RBD and SARS-CoV RBD. CR3022 epitope residues are colored cyan. ACE2-binding residues are colored magenta. Non-conserved epitope residues are marked by asterisks. (B to E) Interactions between the non-conserved epitope residues and CR3022 are shown. Amino-acid variants observed in SARS-CoV are in parenthesis. SARS-CoV-2 RBD is colored in cyan, CR3022 heavy chain in orange, and CR3022 light chain in yellow. Residues are numbered according to their positions on the SARS-CoV-2 S protein sequence. (B) While SARS-CoV-2 has an Ala at residue 372, SARS-CoV has a Thr, which introduces an N-glycosylation site at residue N370. (C) The potential location of N370 glycan in SARS-CoV RBD is indicated by the box. CR3022 is shown as an electrostatic potential surface presentation. (D) P384 interacts with T31, S96, and T100 of CR3022 heavy chain. Ala at this position in SARS-CoV would allow the backbone to adopt a different conformation when binding to CR3022. (E) T430 forms a hydrogen bond with S27f of CR3022 light chain. Met at this position in SARS-CoV would instead likely insert its side chain into the hydrophobic pocket formed by Y27d, I28, Y32, and W50 of CR3022 light chain.


The letters are codes to conveniently list each of the 20 amino acids coded by the DNA of eucaryotic cells. (Bacteria have 21 coded amino acids, including selenomethionine with the other 20.) For example, Y is tyrosine; N is asparagine; and W is tryptophan.

There is another paper that addresses more broadly the evolutionary differences between a wide array of Corona viruses, this one:

[link:Structure, Function, and Antigenicity of the SARSCoV-2 Spike Glycoprotein|Structure, Function, and Antigenicity of the SARSCoV-2 Spike Glycoprotein] (Walls et al., 2020, Cell 180, 1–12)

A graphic showing amino acid sequences that have evolutionary changes from one another as well as the conserved sequences is this one.



The caption:

Figure 1. ACE2 Is a Functional Receptor for SARS-CoV-2 S

(A) Entry of MLV pseudotyped with SARS-CoV-2 S, SARS-CoV S and SARS-CoV-2 Sfur/mut in VeroE6 cells. Data are represented as mean ± standard deviation of technical triplicates.

(B) Entry of MLV pseudotyped with SARS-CoV-2 S or SARS-CoV-2 Sfur/mut in BHK cells transiently transfected with hACE2. The experiments were carried out with two independent pseudovirus preparations and a representative experiment is shown. Data are represented as mean ± standard deviation of technical triplicates.

(C) Sequence alignment of SARS-CoV-2 S with multiple related SARS-CoV and SARSr-CoV S glycoproteins reveals the introduction of an S1/S2 furin cleavage site in this novel coronavirus. Identical and similar positions are respectively shown with white or red font. The four amino acid residue insertion at SARS-CoV-2 S positions 681-684 is indicated with periods. The entire sequence alignment is presented in Data S1.

(D) Western blot analysis of SARS-CoV S-MLV, SARS-CoV-2 S-MLV, and SARS-CoV-2 Sfur/mut-MLV pseudovirions. See also Data S1.


I did see some literature on the apparently conserved PRRA in this graphic sequence indicating that it was mutated in Covid-19, but I may have been mistaken, since I generated that sequence on my own from the RNA sequence and may have scanned that paper too quickly.

Some of this may be arcane to non-scientists, but it is significant. I will be pleased to answer any questions anyone may have to the best of my ability.

The world scientific community is on the case.

I wish you good health.

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Reply A "Cryptic Epitope" to SARS-COV-1 Also Binds to SARS-COV-2: A Key to Vaccine Design. (Original post)
NNadir Apr 2020 OP
efhmc Apr 2020 #1
littlemissmartypants Apr 2020 #2
cstanleytech Apr 2020 #3
NNadir Apr 2020 #4
cstanleytech Apr 2020 #5
NNadir Apr 2020 #6

Response to NNadir (Original post)

Mon Apr 6, 2020, 10:21 AM

1. Yikes. Will need some time and a higher degree than my BS to fathom this one.

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Response to NNadir (Original post)

Mon Apr 6, 2020, 10:33 AM

2. Thanks for sharing this, NNadir. I wish I could look at these

Through a microscope. I am fascinated by proteins and protein related diseases.

Be well and we'll see you on the other side.
❤ lmsp

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Response to NNadir (Original post)

Mon Apr 6, 2020, 11:10 AM

3. So to dumb it down for people like myself does this mean that some of the ace inhibitors people like

myself take might help make things more difficult for the virus to do its work?

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Response to cstanleytech (Reply #3)

Mon Apr 6, 2020, 11:30 AM

4. There was a commentary in JAMA Cardiology this morning considering this point.

Of course, the people at JAMA are not Trump types spewing unproven and conceivably dangerous theories. They're physicians.

Their immediate recommendation is that people who take ACE2 Inhibitors and ARBs (Angiotensin receptor binding drugs) inhibitors who are also infected with Covid-19 continue to do so.

They have proposed a clinical trial to test whether these drugs have clinical value in aiding recovery. At this point it's purely speculation. It is dangerous for people to take powerful drugs based on speculation. It would be nice if we had a President who understood that, but, in fact, it would be nice if we had a President at all.

The paper involving the medical hypothesis is here: Coronavirus Disease 2019 (COVID-19) Infection and Renin Angiotensin System Blockers

This paper caught my eye because I have recently understood by stumbling around the literature in connection with this disease, that I have mutant ACE2, since I tend to cough when taking ACE2 inhibitors and thus rely on ARBs to treat my hypertension.

This has made for some fun around the house where we are all isolated where I remark on my "superior" genetics.

There is no real evidence that people having my mutant ACE2 are immune to Covid-19; it's just a joke around here. It could be true, but I think it more highly speculative than the role of drugs acting on ACE2 being possible therapeutics for Covid-19.

But again, I ABSOLUTELY DO NOT RECOMMEND THAT ANYONE TRY THIS. I am NOT a doctor.

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Response to NNadir (Reply #4)

Mon Apr 6, 2020, 11:36 AM

5. Well I was simply asking as I currently take lisinopril. nt

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Response to cstanleytech (Reply #5)

Mon Apr 6, 2020, 11:44 AM

6. If the speculation proves to be true, that's a good thing.

Lisinopril is an ACE inhibitor. It is, in fact, the one I took that made me cough like hell. If you didn't cough, this means you're not a mutant like me.

It does seem however, that people with high blood pressure are high risk in Covid-19 pathology, so it's certainly not a general cure for the disease. It might prove possible to do a meta-analysis however of the survival and recovery rates of people taking drugs acting on the angiotensin system, and perhaps someone will do it.

I would continue to take my prescribed blood pressure drug to treat blood pressure but I would not assume any kind of immunity.

That's what I'm doing, but I'm still taking all precautions and in fact, acting as if I have the disease. If I do have it while experiencing mild symptoms, this means I am a risk to other people.

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