My uninformed speculation: vaccines may be so effective against Covid-19 (90-95% vs flu vaccine 70%) for the same reason why Covid-19 is so infectious – it binds strongly to biochemicals in the organism. If high affinity to the angiotensin-converting enzyme 2 on the surfaces of lung cells is positively correlated with strong binding to antibodies and immune cells, then the immune system, once triggered, removes the viral particles faster for those respiratory viruses that infect cells more easily. Strong binding and the consequent intense immune triggering may also be the reason for the life-threatening immune overreaction (cytokine storm) to the novel coronavirus.
This hypothesis could be tested on a cross-sectional dataset of viral diseases using some measure of the infectiousness of a disease, the effectiveness of a vaccine against it and the frequency of immune overreaction to it.
Infectiousness may be measured by ID50: what number of microbes makes half the organisms exposed to this number sick. This measure depends on the state of the organisms studied. For example, if people’s immune system is weaker in the winter on average, then ID50 measured in the winter is lower than in the summer.
Vaccine effectiveness is typically measured in percent – what fraction of vaccinated people are protected, in the sense that they do not catch the disease in circumstances in which unvaccinated people catch it. This measure of may depend on what the exposure to the disease is. For example, if a large enough dose of the microbe makes everyone sick, vaccinated or no, then exposure to this dose shows zero effect of the vaccine. Similarly, if a small enough dose fails to infect anyone, then the vaccine effect seems zero, but at least the lack of infections among the unvaccinated shows that no information about vaccine efficacy can be obtained from this exposure test.
Immune overreaction needs to be confidently ascribable to the disease studied for it to be a relevant measure for testing the theory about the connection between virulence and vaccine efficacy.