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Current RNA vaccines protect against worrying coronavirus variants

nature.com

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Re: Current RNA vaccines protect against worrying coronavirus variants

#301

Post by flobosg »

rantwasp wrote: post #268
flobosg wrote: post #69

Earlier quoted context omitted.

> while it’s technically the same protein Not technically, it’s actually the same protein/polypeptide sequence in both cases, 100% identical, including the proline mutations that stabilize the prefusion conformation. You can check that easily by translating and aligning in silico both coding RNA sequences. > the way it was optimized differs (not by much but it’s different) I’m assuming that you’re referring to the co…

here. do the diff yourself: https://github.com/NAalytics/Assemblies-of-putative-SARS-CoV... I’m not gonna go into how the virus was sequenced or what the process to generate the vaccine was, but in this case, I believe your claim of being 100% identical is wrong.

Please read carefully my previous post. Protein sequence != RNA sequence.

I already stated that both coding RNA sequences are different. It is their product, the protein sequence, that is 100% identical in both sequence and structure. The protein that, as you mentioned, is presented as an antigen to the immune system.

If you don’t believe me, and since you already found the FASTA mRNA sequence (or, more specifically, its cDNA equivalent) for both vaccines, you can translate[1] each spike protein RNA section and then align[2] both translated protein sequences.

This is what you get:

  #=======================================
  #
  # Aligned_sequences: 2
  # 1: Pfizer
  # 2: Moderna
  # Matrix: EBLOSUM62
  # Gap_penalty: 10.0
  # Extend_penalty: 0.5
  #
  # Length: 1273
  # Identity:    1273/1273 (100.0%)
  # Similarity:  1273/1273 (100.0%)
  # Gaps:           0/1273 ( 0.0%)
  # Score: 6727.0
  # 
  #
  #=======================================
  
  Pfizer             1 MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHS     50
                       ||||||||||||||||||||||||||||||||||||||||||||||||||
  Moderna            1 MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHS     50
  
  Pfizer            51 TQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNI    100
                       ||||||||||||||||||||||||||||||||||||||||||||||||||
  Moderna           51 TQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNI    100
  
  ...
  
  Pfizer          1201 QELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSC   1250
                       ||||||||||||||||||||||||||||||||||||||||||||||||||
  Moderna         1201 QELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSC   1250
  
  Pfizer          1251 GSCCKFDEDDSEPVLKGVKLHYT   1273
                       |||||||||||||||||||||||
  Moderna         1251 GSCCKFDEDDSEPVLKGVKLHYT   1273
[1]: https://web.expasy.org/translate/

[2]: https://www.ebi.ac.uk/Tools/psa/emboss_needle/

Re: Current RNA vaccines protect against worrying coronavirus variants

#302

Post by loceng »

lamontcg wrote: post #297
loceng wrote: post #253

Earlier quoted context omitted.

It sounds like you might be a good person to review and give your thoughts on this interview between Bret Weinstein, an evolutionary biologist, and Geert Vanden Bossche, a virologist, who discuss this in length and detail it for layperson? https://www.youtube.com/watch?v=BNyAovuUxro

Skimmed it, seems like its a lot of bullshit wrapped up in plausible sounding science. The H1N1 pandemic is an interesting historical model, and the more deadly later waves indicate that more virulent variants were produced in that pandemic as well. He seems to be arguing that vaccines are causing the variants and that natural herd immunity is better, which is bullshit. First of all the vaccines are 80-90% effective,…

The COVID-19 vaccine is less effective against the variants, and arguably unknown if immunity developed from dead-virus based vaccines would provide higher effectiveness against variants and reduce potential for escape.

You're arguing to ban critical thinkers having a conversation, perhaps instead you should be ban off social media for wanting to censor intellectuals/critical thinkers?

Especially since you're seemingly giving a well-thought out response but you immediately admit you skimmed it, and then wrongly claim they're pushing for herd immunity.

You also reference cross immunity, however those weren't using mRNA vaccines afaik, and so the mechanism and spread that the immunity will cover for variants won't be the same.

I was wrong, you're not as rational or thorough of a person I thought you might be based on your initial explanation that I responded to.

Re: Current RNA vaccines protect against worrying coronavirus variants

#303

Post by MockObject »

Pyramus wrote: post #299
MockObject wrote: post #288

Earlier quoted context omitted.

What would you like me to elaborate exactly?

Just interested how the vaccinations were done where you got it, small/big city, who administered it etc...

In New York City, at a large pharmacy chain, administered by a pharmacist. They're done like this, or at government run centers. The cost is handled by the government.

Re: Current RNA vaccines protect against worrying coronavirus variants

#304

Post by CorrectHorseBat »

miked85 wrote: post #202
CorrectHorseBat wrote: post #176

Earlier quoted context omitted.

Vaccines are not 100% effective, some people cannot take the vaccine (known allergic reactions, immunocompromised, ...) and continued spread of the virus can create new mutations.

It isn't 100%, no. But I am not sure what you are suggesting then. If you get the vaccine and are still scared and angry at people that may not have received it, there aren't many options for you aside from indefinite total lock-down.

Herd immunity. If enough people get vaccinated R0 gets under 1, and the spread stops by itself also protecting those who cannot get the vaccine or are unlucky that the vaccine does not work for them. They are protected by the herd.

Re: Current RNA vaccines protect against worrying coronavirus variants

#305

Post by garmaine »

koheripbal wrote: post #229
garmaine wrote: post #79

Earlier quoted context omitted.

So far ALL vaccines are effective against serious illness with all variants.

While this is very likely true, this has not been conclusively studied. Only certain variants have been studied against certain vaccines.

And for every single study of every single variant that has been studied, the vaccine in the study significantly reduces the incidence of severe cases of COVID-19 among the trial group. There is not a single study covering any variant for which this is not the case.

Yes we have obviously not tested every combination of vaccine and SARS-CoV-2 variant. But so far, the evidence that we have supports the working assumption that all vaccines drastically reduce, or in some cases eliminate entirely severe COVID-19 symptoms.

Re: Current RNA vaccines protect against worrying coronavirus variants

#306

Post by koheripbal »

garmaine wrote: post #305
koheripbal wrote: post #229

Earlier quoted context omitted.

While this is very likely true, this has not been conclusively studied. Only certain variants have been studied against certain vaccines.

And for every single study of every single variant that has been studied, the vaccine in the study significantly reduces the incidence of severe cases of COVID-19 among the trial group. There is not a single study covering any variant for which this is not the case. Yes we have obviously not tested every combination of vaccine and SARS-CoV-2 variant. But so far, the evidence that we have supports the working assumpti…

> we have obviously not tested every combination...

I mean, for transparency, we've only tested a very very small subset of the combinations, so it's not very indicative of anything.

Re: Current RNA vaccines protect against worrying coronavirus variants

#307

Post by bawolff »

neither_color wrote: post #214
bawolff wrote: post #96

Earlier quoted context omitted.

> Im social distancing, wearing a mask doing all the things necessary Those things are emergency measures, that are important, but not anywhere near as effective as vaccines are. They stop things from rapidly spiraling out of control so instead they just slowly spiral. Its a holding action, one with a pretty high cost, not a solution. > that has been rushed through trials They've had the same amount of safety testing…

I got the vaccine for solely practical reasons(it's becoming a requirement for international travel). Im not a hero, I didnt do it to save anybody. It has nothing to do with denying science and more to do with the fact that we can look at the same statistic and what you consider an existential threat and what I consider an existential threat are different. I still dont think accusing someone of selfishness is the pro…

> what you consider an existential threat and what I consider an existential threat are different

You're argument that not taking the vaccine is not being selfish is that the risk you are taking by forgoing the vaccine is only a threat to other people not a threat to yourself??

> Im not a hero

Obviously not. Nobody here is a hero. We're talking about an injection with extremely low risk of serious side effects, not storming the beaches of Normandy.

Re: Current RNA vaccines protect against worrying coronavirus variants

#308

Post by anoncake »

doktorhladnjak wrote: post #130
xeromal wrote: post #67

Earlier quoted context omitted.

We're past that now. It's known as Pfizer in the official language of too many cities and countries.

Can't we all just hate on the now official name for the vaccine of "Comirnaty"?

Marketing person asked to find a catchy name: "This is literally a Covid vaccine, I'll just grab a handful of scrabble pieces and it'll sell anyway"

Re: Current RNA vaccines protect against worrying coronavirus variants

#309

Post by mycall »

lamontcg wrote: post #297
loceng wrote: post #253

Earlier quoted context omitted.

It sounds like you might be a good person to review and give your thoughts on this interview between Bret Weinstein, an evolutionary biologist, and Geert Vanden Bossche, a virologist, who discuss this in length and detail it for layperson? https://www.youtube.com/watch?v=BNyAovuUxro

Skimmed it, seems like its a lot of bullshit wrapped up in plausible sounding science. The H1N1 pandemic is an interesting historical model, and the more deadly later waves indicate that more virulent variants were produced in that pandemic as well. He seems to be arguing that vaccines are causing the variants and that natural herd immunity is better, which is bullshit. First of all the vaccines are 80-90% effective,…

If mutations are random events, how does a virus know it is under more pressure because randomizing events occur less often?

Re: Current RNA vaccines protect against worrying coronavirus variants

#310

Post by takeda »

dharma1 wrote: post #131
flobosg wrote: post #69

Earlier quoted context omitted.

> while it’s technically the same protein Not technically, it’s actually the same protein/polypeptide sequence in both cases, 100% identical, including the proline mutations that stabilize the prefusion conformation. You can check that easily by translating and aligning in silico both coding RNA sequences. > the way it was optimized differs (not by much but it’s different) I’m assuming that you’re referring to the co…

Does this mean you can mix the two vaccines - ie. take two shots of moderna, and a later in the year a booster shot of (updated) Pfizer/BnT? So far I haven’t seen conclusive information about mixing the vaccines, but I think that will be the reality for booster shots late this year/early next year in the UK.

My understanding is that the reason it was required to have the same first and second dose was to make it easier tracing if there was a problem with a particular vaccine and to get the efficacy numbers manufacturers were promising.

From what I heard, in normal circumstances is even recommend to give a booster vaccine shot from a different manufacturer.

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