The mutational landscape of SARS-CoV-2 provides new insight into viral evolution and fitness

Although vaccines and treatments have strengthened our ability to combat the COVID-19 pandemic, new variants of the SARS-CoV-2 continue to emerge in human populations. Because the evolution of SARS-CoV-2 is driven by mutation, a better understanding of its mutation rate and spectrum could improve our ability to forecast the trajectory of the pandemic. Here, we used circular RNA consensus sequencing (CirSeq) to determine the mutation rate of six SARS-CoV-2 variants and performed a short-term evolution experiment to determine the impact of these mutations on viral fitness. Our analyses indicate that the SARS-CoV-2 genome mutates at a rate of ~3 ´10 ^-6 /base per round of infection and that the spectrum is dominated by C®U transitions. Moreover, we discovered that the mutation rate is significantly reduced in regions that form base-pairing interactions and that mutations that affect these secondary structures are especially harmful to viral fitness. These observations provide new insight into the parameters that guide viral evolution and highlight fundamental weaknesses of the virus that may be exploited for therapeutic purposes.