FWIW, eptope prediction tools google search:
https://www.google.com/search?client=…
Human leukocyte antigen susceptibility map for SARS-CoV-2
https://www.medrxiv.org/content/10.11…
Association of HLA class I with severe acute respiratory syndrome coronavirus infection
https://www.researchgate.net/profile/…
Sorry, I’m new in Eterna’s community, and actually on Eterna in general, and I know this post could make the citizens science’s basic idea behind Eterna’s project weaker, but it’s not my intent. I’ve seen this news I think could be helpful for researcher to fight COVID-19 via RNA based vaccines and therapies. The company D-Wave, together with other partners, give free access to their mixed (quantistic and traditional) computational resources to anyone which is researching on a solution for COVID-19, and also give free support by computational experts that know how to get the best from the quantum hybrid technology. I hope I haven’t made big mistakes in reporting the news, anyway I put the links below.
Hoping this could help you solving this problem,
Link to the news: https://www.google.com/url?sa=t&sourc…
Link to D-Wave site, look at the top of the page:
https://www.google.com/url?sa=t&sourc…
hACE2-
“Six hot spot residues including Phe486, Leu455, Ser494, Gln493, Tyr505 and Asn501 in the RBD of SARS-CoV-2 were displayed in stick model.”
preprint:
Computational analysis suggests putative intermediate animal hosts of the SARS-CoV-2
https://www.biorxiv.org/content/10.11…
Recapitulates major features of COVID-19 in humans and suggests aerosol transmission–
Infection and Rapid Transmission of SARS-CoV-2in Ferrets
https://www.cell.com/pb-assets/journa…
Recapitulates major features of COVID-19 in humans and suggests aerosol transmission–
Infection and Rapid Transmission of SARS-CoV-2in Ferrets
https://www.cell.com/pb-assets/journa…
Personal work you may not feel is relevant, I however do. The SARS-CoV-2 Wuhan-Hu-1 submission’s complementary genome and proteome.
Molecular Mechanism for Antibody-Dependent Enhancement of Coronavirus Entry
https://www.msi.umn.edu/~lifang/flpap…
Here is a full genome for the complement of SARS-CoV-2 Wuhan-Hu-1.
We find it useful and alarming to see what the complement genome does.
https://www.dropbox.com/s/a19bsktjt86…
Interesting read and list:
Therapeutic options for the 2019 novel coronavirus (2019-nCoV)
https://media.nature.com/original/mag…
Designing of a next generation multi epitope based vaccine (MEV) 1 against SARS-COV-2: Immunoinformatics and in silico approaches
https://www.biorxiv.org/content/10.1101/2020.02.28.970343v1.full.pdf
Plant-derived vaccine protects animals
https://www.researchgate.net/profile/Ase_Uttenthal/publication/14148994_Plant_derived_vaccine_protec…
Potentially bad news for Spike-based vaccines.
Any reports on MEV type vaccines?
There is a paper published yesterday or today by The Lancet, EBioMedicine, that the U. of Pittsburgh School of Medicine has a potential vaccine. It seems to say that they are combining “pieces of viral protein” from the spike protein. Maybe they they are involving multiple epitopes?
While the virus doesn’t mutate frequently, researchers are now identifying a few different strains. A paper published yesterday in China (Yao MedRxiv) sequenced a couple strains with as many as 30-nt mutated as discussed in this article: https://www.scmp.com/news/china/science/article/3080771/coronavirus-mutations-affect-deadliness-strains-chinese-study
A separate paper out of Singapore (Su BioRxiv) published March 11th identified a 382-nt deletion in the first strain that hit Singapore that they believe explains why Singapore had such a mild first wave. (Rhiju, I added both papers to the dropbox under viral_mRNA_structure.)
Using a plasmid to inject E-protein down regulates ER stress of SARS, RSV and drug induced stress and apoptosis.
(I’ve seen all the signatures mentioned in my personal work on SARS-CoV-2)
“These data indicated that SARS-CoV E protein alone reduced different types of stress, such as cytosolic (genes hsp90 AA1, UBB,hspH1), ER (gene SERPINH1) and mitochondrial stress (genehsp10 E1), produced by infection with at least two different respiratory viruses (SARS-CoV and RSV).”
Severe Acute Respiratory Syndrome Coronavirus Envelope Protein Regulates Cell Stress Response and Apoptosis
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3197621/pdf/ppat.1002315.pdf
Since E-protein of SARS-CoV and SARS-CoV-2 is 100% conserved
this may be a good tactic combined with the plasmid injection in the paper above.
Severe Acute Respiratory Syndrome Coronaviruses with Mutations in the E Protein Are Attenuated and Promising Vaccine Candidates
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4403406/pdf/zjv3870.pdf
Molecular Basis of Coronavirus Virulence and Vaccine Development
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7112271/pdf/main.pdf