Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis.

Abstract

While SARS-CoV-2 continues to adapt for human infection and transmission, genetic variation outside of the spike gene remains largely unexplored. This study investigates a highly variable region at residues 203-205 in the SARS-CoV-2 nucleocapsid protein. Recreating a mutation found in the alpha and omicron variants in an early pandemic (WA-1) background, we find that the R203K+G204R mutation is sufficient to enhance replication, fitness, and pathogenesis of SARS-CoV-2. The R203K+G204R mutant corresponds with increased viral RNA and protein both in vitro and in vivo. Importantly, the R203K+G204R mutation increases nucleocapsid phosphorylation and confers resistance to inhibition of the GSK-3 kinase, providing a molecular basis for increased virus replication. Notably, analogous alanine substitutions at positions 203+204 also increase SARS-CoV-2 replication and augment phosphorylation, suggesting that infection is enhanced through ablation of the ancestral 'RG' motif. Overall, these results demonstrate that variant mutations outside spike are key components in SARS-CoV-2's continued adaptation to human infection.

• Authors: Bryan A Johnson, Yiyang Zhou, Kumari G Lokugamage, Michelle N Vu, Nathen Bopp, Patricia A Crocquet-Valdes, Birte Kalveram, Craig Schindewolf, Yang Liu, Dionna Scharton, Jessica A Plante, Xuping Xie, Patricia Aguilar, Scott C Weaver, Pei-Yong Shi, David H Walker, Andrew L Routh, Kenneth S Plante, Vineet D Menachery
• Journal: PLoS pathogens (PLoS Pathog) Vol. 18 Issue 6 Pg. e1010627 (06 2022) ISSN: 1553-7374 [Electronic] United States
• PMID: 35728038 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't, Research Support, N.I.H., Extramural, Research Support, U.S. Gov't, P.H.S.)

Chemical References

• Spike Glycoprotein, Coronavirus
• spike protein, SARS-CoV-2
• Glycogen Synthase Kinase 3

Topics

• COVID-19 (genetics)
• Glycogen Synthase Kinase 3
• Humans
• Mutation
• Nucleocapsid
• SARS-CoV-2 (genetics)
• Spike Glycoprotein, Coronavirus (genetics)