Right from omicron's first description, researchers were concerned about its variant of the SARS-CoV-2 virus. Looking over the list of mutations it carried, scientists could identify a number that would likely make the variant more infectious. Other mutations were even more worrying, as they would likely interfere with the immune system's ability to recognize the virus, allowing it to pose a risk to those who had been vaccinated or suffered from previous infections.
Buried in the subtext of these worries was a clear implication: scientists could simply look at the sequence of amino acids in the spike protein of a coronavirus and get a sense of how well the immune system would respond to it.
That knowledge is based on years of studying how the immune system operates, combined with a lot of specific information regarding its interactions with SARS-CoV-2. What follows is a description of these interactions, along with their implications for viral evolution and present and future variants.
To understand the immune system's function, it's easiest to break its responses into categories. To begin with, there's the innate immune response, which tends to recognize general features of pathogens rather than specific properties of individual bacteria or viruses. The innate response doesn't get fine-tuned by vaccination or prior exposure to a virus, so it's not really relevant to the discussion of variants.