Okay, let me see if I can help clarify some stories that people are undoubtedly seeing floating around about vaccine effectiveness and/or the new CV-19 strains. First of all, understand how a vaccine works. The vaccine is an attempt to push the immune system to recognize certain biochemical sequences as a troublesome invader and to therefore mass forces to eliminate the invader. A vaccine does this by presenting these sequences in the body and the body responding by creating antibodies and T cells, including memory versions of B cells (the antibody producers) and T cells. You sometimes have two dose vaccines in order to further prod the immune system to develop these cells. Assuming the vaccine works as intended, your immune system will have the capability to recognize and fight anything coming in with the targeted sequences.
This doesn’t happen overnight, the process of vaccine-aided adaptive immunity can take several weeks to develop. So there is nothing alarming about a person getting the first dose of a two-dose vaccine and a few days later testing positive, although even that first does should help limit the likelihood of serious disease.
What can go wrong? The assumption is that the presented sequences will prompt the body to make antibodies and T cells. If you have a defective immune system or a weakened one, that may not happen or may happen at a low level that doesn’t lead to a large adaptive immune response. Unfortunately old people typically don’t respond to vaccines as well as younger ones. So the vaccine is least likely to help the most vulnerable, but still should provide some protection for most of them.
Whoops, what if we got the sequences wrong or if they change? The way the adaptive immune system works is by recognizing certain chemical sequences. They don’t have to be exact matches, but pretty close. We are also assuming that we got critical sequences in the vaccine–ones that if blocked, will basically make the virus unable to enter cells or to replicate or cause other mischief. Or ones that will prompt T cells to kill the virus or any infected cells. This is a simplification, but sequence closeness is very important.
But, we know that viruses mutate constantly, maybe only one or two changes per replication cycle, maybe more. If there is enough of a change, you get a different strain or variant of the virus that may actually function differently–be more or less infectious, suppress the immune system more or less or other changes. If the changes are in sequences that were targeted by the vaccines, and they are significant enough, they may evade the vaccine-prompted adaptive immune response. You can end up with multiple strains of the same virus circulating at the same time, and with somewhat significantly different sequences. That is the case with influenza and why we get vaccinated every year and the vaccines don’t always work well.
I suspect this will be the long-run case with coronavirus as well–it isn’t going away, it is going to constantly mutate, we will need to continually update the vaccines and we will have to retake them regularly. As I have said from the start, we need to be realistic. We are going to have to learn to live with this virus and the toll it takes. Fortunately, it does not seem additive to influenza but substitutive, so I don’t think we are looking at some large additional morbidity and mortality toll. We should have been realistic at the start and we certainly need to get realistic now. But don’t freak out about either variants or vaccines. Totally to be expected. And the harder we suppress, the worse the problem can be. Leave it alone and deal with it as best we can, before we turn it into some kind of truly super-bug.