List of potential pleiotropy mutations in SARS-CoV-2 Evolution

By analyzing a large set of SARS-CoV-2 sequences (~ 2 million) collected from early 2020 to mid-2021, we found that high frequency mutations within hosts are sometimes detrimental during between-host transmission. This highlights potential inverse selection pressures within- versus between-hosts. We also identified a group of nonsynonymous changes with their frequencies are significantly higher than neutral expectation, yet they have never experienced clonal expansion (10-3 - 10-2). These mutations are likely maintained by pleiotropy, a condition where mutations increase some components of fitness at a cost to others.