There are multiple antigens to which our body could build antibodies. Let’s suspend disbelief related to the safety of mRNA vaccines for a moment so that we can ask this question. Even if we agreed with the mRNA approach then why builds a vaccine to target the toxic antigen instead of the neutral antigens? I’ve asked doctors this same question and they’re like 🤷♂️ ask the scientists.
Nucleocapsid (N) protein is present in the core of the virus and antibodies to it are found within IgG immune cells of cured hosts. So clearly natural immunity is targeting these antigens. https://www.nature.com/articles/s41598-021-83108-0
I have thought about this and the most charitable explanation I can come up with is maybe they targeted the S protein because it was the novel/dangerous part. Having the immune system pointed solely toward this protein induces mutation in this protein, or at least provides a hurdle where mutation here is favored.. Mutation is disorder and almost all mutation makes things less effective. Maybe it was an attempt to funnel the variants toward less effective spike protein?