In this study, cooccurring mutations R203K/G204R in the nucleocapsid protein are demonstrated adaptive and associated with the emergence of a high-transmissibility SARS-CoV-2 lineage B.1.1.7. Through comparing a R203K/G204R mutant virus, created based on the USA-WA1/2020 SARS-CoV-2 strain, with the native virus in competition experiments, we found that the 203K/204R variants possess a replication advantage over the preceding R203/G204 variants, possibly related to ribonucleocapsid (RNP) assembly during virus replication. Moreover, the 203K/204R virus showed increased infectivity in a human lung cell line and induced increased damage to blood vessels in infected hamster lungs. Accordingly, we observed a positive association between increased COVID-19 severity and the incidence frequency of 203K/204R. Our work suggested a contribution of the 203K/204R mutations to the increased transmission and virulence of SARS-CoV-2. In addition to mutations in the spike protein, the mutations in the nucleocapsid protein are important for viral spreading during the pandemic.Funding Information: This work was supported by grants from the National Natural Science Foundation of China, SGC's Rapid Response Funding for COVID-19 (C-0002), the National Key Research and Development Program (2019YFC1604600), the National Natural Science Foundation of China (81970008 and 31200941), the Fundamental Research Funds for the Central Universities (2021CDJYGRH-009), the Youth Innovative Talents Training Project of Chongqing (CY210102) and the National Natural Science Foundation of HeBei province (19226631D).Declaration of Interests: The authors declare no competing interests.
Nucleocapsid Mutations R203K/G204R Increase the Infectivity, Fitness and Virulence of SARS-CoV-2