Pre-Existing Immunity in Emerging Pandemics

In 2020 when the Covid-19 pandemic was spreading over the world people were becoming infected with a coronavirus they had never seen before. In most people this lead to a fairly innocent infection, in some this lead to severe disease, and others remained entirely asymptomatic after becoming infected. Experimental evidence suggests that those remaining asymptomatic had pre-existing immunity to the new SARS-CoV-2 thanks to earlier infections with seasonal coronaviruses. We develop an approach to predict who is more likely to be protected by pre-existing immunity to a completely new pandemic virus by setting the clock back to January 2020, when the protein sequence of the Wuhan virus was uncovered. Using recently developed algorithms for measuring similarity and antigenicity, we predict which protein fragments in the Wuhan virus were sufficiently similar to protein fragments from other common viruses. Since common viruses elicit widespread immunity in the population, such overlapping fragments (epitopes) are expected to provide some level of pre-existing immunity to a novel virus like SARS-CoV-2. This resulted in list of about 13 SARS-CoV-2 epitopes that at least some individuals in the populations should have encountered before. We validated our approach by demonstrating that we correctly predicted previous published examples of preexisting immunity to SARS-CoV2-2.