SARS-CoV-2 is an enveloped virus, meaning that it has a lipid envelope around its capsid, where the genetic material is stored.

There are four major structural proteins in SARS-CoV-2, the spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins. The S, E, and M proteins can be found on the envelope. However, E (75aa) and M (222aa) are much smaller than S protein (1273aa), making them much harder to target.

As the time of writing (July 2021), all currently authorized COVID-19 RNA vaccines (Pfizer-BioNTech and Moderna) target the S protein so do all the currently authorized adenovirus vector vaccines (Oxford–AstraZeneca, Sputnik V, Janssen, Convidecia, Sputnik Light), and all the currently authorized subunit vaccines (EpiVacCorona, ZF2001, Abdala, Soberana 02). The exception are the inactivated virus vaccines (Sinopharm, CoronaVac, Covaxin) as they use the whole virus.

The region of a protein an antibody targets is the epitope. The antibodies human body produces come from different lineage of B cells and target different epitopes. The delta variant has five mutations in the S protein. If an epitope is in some regions not containing those five mutations, then its corresponding antibody can still binds to the mutant S protein. This is why the current vaccine can still provide some level of protection against the mutant strains.

It should be kept in mind that as long as there are active transmissions, any virus will mutate and escape the vaccine. Every vaccines is optimized for the virus at the time of its design. It is not optimized for mutants afterward. This is why flu shots are required every year since the influenza virus strain changes. This is also why a booster shot may be necessary for COVID-19.

The things need to be modified depends on the types of vaccine. For RNA and adenovirus vector vaccines, the RNA and DNA sequences needs to be modified to reflect the new spike protein on the mutant strains. This is essentially the same process for subunit vaccines. The viral protein in a subunit vaccine is made in cell cultures and the viral protein in a RNA/adenovirus vector vaccine is made by the human body. For the inactivated virus vaccine, a new cell culture infected by the mutant virus is needed.

Since the number of new cases are on the raise again, it is worth repeating that as long as there are active transmissions, any virus will mutate and escape the vaccine. The pandemic does not go away not matter how hard we pretend it to be.

Vaccines work by arming the immune system to be able to detect and respond to a virus. The covid vaccines work by exposing the body to a small part of the Sars-Cov-2 virus, specifically the "spike" protein; the spike protein of any mutants looks the same to the body, the protection created by the vaccine should remain functional. However, as a virus goes through its infection cycle it will accumulate mutations, some of which may alter the spike protein and allow it to "escape" or evade the immune response. This typically means the vaccine has to be altered to protect against the new mutation. In the past, when vaccines were typically actual parts of viral proteins or deactivated viral protocols, this could be more challenging, as the new mutant particle or protein would need to be isolated, and purified for these vaccines. The marvel of the mRNA vaccines that Pfizer and Moderna developed is that instead of using a part of the virus itself, the vaccine is the mRNA that codes for a part of the virus, that the body then translates into protein and presents to the immune system to build immunity. Now, instead of having to make a vaccine with a new viral particle, these vaccines can be used to target mutant viruses simply by changing the coding of the mRNA so that the viral protein the body produces is the new mutant version. So any mutants that manage to escape the immune response of the original vaccine can be counteracted by vaccine boosters that update the body's immune response to the Sars-Cov-2 virus.

The answer to both your questions depends on the vaccine. The Pfizer, Moderna, Astrazeneca and Johnson and Johnson vaccines are amazing because they can be modified almost instantaneously....this is because these vaccines contain the instructions to make the spike protein, and that can be changed very, very easily in all of these. There are some details that could make it more difficult than that, but in theory it could take Moderna one day to start changing the variant spike protein in their vaccine. This is a real game changer for immunology!

Other vaccines, like SinoVac or Novavax are different. These are whole dead viruses that need to be grown and then killed. These are called inactivated vaccines. So those companies could isolate the delta variant and make a vaccine, but that would take a lot longer.

So that gets to your last question...since the Pfizer, Moderna Astrazeneca and Johnson and Johnson only make the spike protein, that is the only thing your body responds too. But when you are exposed to an inactivated vaccine, you are exposed to, and react to, the whole virus.

In the case of the mRNA vaccines (Pfizer and Moderna), modifying them to be effective against virus variants is relatively straightforward. Instead of delivering the mRNA "blueprint" for the spike protein of the original virus, you deliver one that has the blueprint for the protein of the variant. One can also deliver more than one mRNA, or try to come up with a blueprint for a protein that has features that stay conserved (that is, the same) between as many variants as possible, to have a chance of the vaccine working even against future mutations.

This and the required testing will take some time, and then there is final testing for approval. So the process is fast relative to developing a new vaccine but still can not happen within just a few weeks.

The reason the spike protein is the preferred protein to deliver the blueprint for is that it is the protein that is the most "visible"/accessible on the outside of the virus. In other words, it's the part of the virus that the immune system will have the easiest time "seeing" and attacking.

The COVID-19 vaccines work by introducing the genetic material (which is called mRNA) that codes for the spike protein found in COVID-19 viruses to your immune system. The immune system learns to recognize this mRNA by reading the mRNA and producing a limited number of the encoded spike proteins. It then records the shape of the protein, deploying antibodies to memorize the shape and destroy the protein. Any later infection can then be easily fought off because of the antibodies are already present.

The current publicly available COVID-19 vaccines are focused around the spike protein because its combination of mRNA and protein elicits a quick immune response, something scientists found out thanks to research that started in 2002 on similar viruses (SARS and MERS). Based on this research, they also learned how to purify mRNA to remove contaminants, how to modify the genetic code to stabilize the protein in a state that is still recognizable as foreign but not harmful, and how to reduce inflammatory response to the mRNA to improve safety.

We have put almost all our eggs into this spike basket, it is the main ingredient in all our pandemic shots. However, spikes easily mutate, so companies and scientists are looking to find more vaccine ingredients and identifiers. They are reformulating their vaccines to be effective against spike mutations (e.g. the Delta mutation) by adding redundancies to the system. For example, if the spike is unrecognizable, the nucleocapsid protein found inside virus cells may still be good insurance since it mutates more slowly than the spike.

For more information:
1. https://jamanetwork.com/journals/jama/fullarticle/2770485
2. https://www.umassmed.edu/news/news-archives/2020/12/inside-the-new-mrna-vaccines-for-covid-19/
3. https://www.news-medical.net/health/What-are-Spike-Proteins.aspx#:~:text=One%20of%20the%20key%20biological,cells%20and%20cause%20infection
4. https://www.theatlantic.com/science/archive/2021/05/spike-protein-vaccines-covid/618954/

Yes, vaccines can and are modified to be effective against new virus variants. This is how flu shots are updated each year: the vaccines have been modified to deal with new influenza viruses. In the future, these flu shots will likely contain vaccines against COVID as well, since it does not look like we will be able to destroy the COVID virus, with the number of people who choose not to be vaccinated.

I don't know the biology of coronaviruses or their vaccines well enough to be able to tell you exactly how all of the different vaccines work. I do know that the different vaccines are more or less effective against different viral variants, which does tell us that the vaccines are themselves at least somewhat different as well.

Yes - the amazing thing is that we started getting Covid-19 vaccines so quickly. Usually it takes years to develop a vaccine. There's still no AIDS vaccine after about 35 yrs. The internet says it often takes 10-15 yrs to develop a vaccine.

Here's a post from the World Health Organization that is also encouraging:
Delta Variant and Vaccines.

Here's an article about differences between the different vaccines. The spike protein seems to be involved in all of them, which is reasonable, but in different ways:
Covid vaccine comparison