Evolutionary trajectories of SARS-CoV-2 variants under immune selection

The emergence of SARS-CoV-2, the etiological agent of Covid-19, in late 2019, causing a to-date ongoing pandemic, is one of the foremost global health crises of the 21st century. The pandemic has claimed millions of lives and is a major source of morbidity and mortality, as well as a major burden on the global economy. In an unprecedented effort, multiple highly effective vaccines have been developed, tested and administered to hundreds of millions of people. The vaccinations have greatly contributed to the protection of highly vulnerable patient populations. In late 2020, we observed the evolution of multiple variants that have demonstrated worrying phenotypes, including the B1.1.7/Alpha and B.1.617.2/Delta variants. These variants have been proven to be more transmissible than the initial strain introduced into the population and show, among others, multiple mutations in the receptor-binding domain of the viral spike protein. The receptor-binding domain of the viral spike is also the target of potent, neutralizing antibodies elicited by vaccination or natural infection. This has sparked fear, that these variants may represent vaccine escape variants. Although some of the variants demonstrate escape from certain classes of neutralizing antibodies, the vaccines still offer broad, albeit reduced, protection from infection, hospitalization and death. Evolutionary theory predicts that adaptation to novel environments is often governed by few mutations with large effects. The observation of increased transmissibility of e.g., the B.1.1.7/Alpha and B.1.617.2/Delta variants is likely to be the result of adaptations to the human ACE-2 receptor. In the light of widespread administration of vaccine and natural infection-induced immunity, it is unclear how immune selection will shape the evolutionary trajectories of the SARS-CoV-2 variants. We hypothesize that SARS-CoV-2 variants may escape neutralizing polyclonal immune responses elicited by vaccination. Furthermore, we hypothesize that SARS-CoV-2 is not able to independently optimize transmissibility and immune evasion and that escape variants based on highly transmissible strains will demonstrate lower transmissibility. We aim to address the hypotheses with the following objectives: In Objective 1 we will select SARS-CoV-2 escape variants using serum from mice immunized with an inactivated, whole virion SARS-CoV-2 vaccine based on an early variant (SARS-CoV-2/human/USA/WA-CDC-WA1/2020), currently under development in the Taubenberger lab. We will select escape variants starting from SARS-CoV-2/human/USA/WA-CDC-WA1/2020, the B1.1.7/Alpha and B.1.617.2/Delta variants, which demonstrate clear differences in their transmissibility. We will select the escape variants by serially passaging the variants in increasing serum concentrations and identify mutations by whole genome sequencing.In Objective 2 and Objective 3 we will assess the plaque-purified escape variants for two different readouts of transmissibility. We will measure growth kinetics by competing the cognate wild-type ancestor with the escape mutants and we will measure infectivity of escape variants using a focus-forming assay. Variants predicted to be less transmissible should demonstrate lower growth rates and reduced capability to form foci.In Objective 4 we will assess the IC50 of the serum from vaccinated mice against the escape variants and we expect an inverse correlation between readouts of transmissibility and the IC50 value.Combined, these results will grant us insights into aspects of the evolutionary trajectories of SARS-CoV-2 variants of concern under immune selection. We will learn if SARS-CoV-2 variants can independently optimize affinity for the human ACE2 receptor and mediate immune escape, knowledge of paramount importance to judge the further development of the pandemic. Such results will ultimately hint towards the necessity of updating the SARS-CoV-2 vaccine and might inform further vaccine development.