Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2

Cell Host Microbe. 2021 Dec 8;29(12):1788-1801.e6. doi: 10.1016/j.chom.2021.11.005. Epub 2021 Nov 13.


Previous work found that the co-occurring mutations R203K/G204R on the SARS-CoV-2 nucleocapsid (N) protein are increasing in frequency among emerging variants of concern or interest. Through a combination of in silico analyses, this study demonstrates that R203K/G204R are adaptive, while large-scale phylogenetic analyses indicate that R203K/G204R associate with the emergence of the high-transmissibility SARS-CoV-2 lineage B.1.1.7. Competition experiments suggest that the 203K/204R variants possess a replication advantage over the preceding R203/G204 variants, possibly related to ribonucleocapsid (RNP) assembly. Moreover, the 203K/204R virus shows increased infectivity in human lung cells and hamsters. Accordingly, we observe a positive association between increased COVID-19 severity and sample frequency of 203K/204R. Our work suggests that the 203K/204R mutations contribute to the increased transmission and virulence of select SARS-CoV-2 variants. In addition to mutations in the spike protein, mutations in the nucleocapsid protein are important for viral spreading during the pandemic.

Keywords: COVID-19; R203K/G204R; SARS-CoV-2; fatality; fitness; infectivity; mutation; nucleocapsid; virulence.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Substitution*
  • Animals
  • COVID-19 / epidemiology
  • COVID-19 / pathology*
  • COVID-19 / virology
  • Cell Line
  • Coronavirus Nucleocapsid Proteins / chemistry
  • Coronavirus Nucleocapsid Proteins / genetics*
  • Coronavirus Nucleocapsid Proteins / metabolism
  • Cricetulus
  • Epithelial Cells / pathology
  • Epithelial Cells / virology
  • Gene Expression
  • Genetic Fitness
  • Genome, Viral*
  • Humans
  • Models, Molecular
  • Mutagenesis
  • Mutation*
  • Phosphoproteins / chemistry
  • Phosphoproteins / genetics
  • Phosphoproteins / metabolism
  • Phylogeny
  • Protein Conformation
  • SARS-CoV-2 / classification
  • SARS-CoV-2 / genetics*
  • SARS-CoV-2 / growth & development
  • SARS-CoV-2 / pathogenicity
  • Selection, Genetic
  • Severity of Illness Index
  • Virion / genetics
  • Virion / growth & development
  • Virion / pathogenicity
  • Virulence
  • Virus Replication


  • Coronavirus Nucleocapsid Proteins
  • Phosphoproteins
  • nucleocapsid phosphoprotein, SARS-CoV-2

Supplementary concepts

  • SARS-CoV-2 variants