Saudi Arabian SARS-CoV-2 genomes implicate a mutant Nucleocapsid protein in modulating host interactions and increased viral load in COVID-19 patients

Mourier, T.; Shuaib, M.; Hala, S.; Mfarrej, S.; Alofi, F.; Naeem, R.; Alsomali, A.; Jorgensen, D.; Subudhi, A. K.; Ben Rached, F.; Guan, Q.; Salunke, R.; Ooi, A.; Esau, L.; Douvropoulou, O.; Nugmanova, R.; Perumal, S.; Zhang, H.; Rajan, I.; Al-Omari, A.; Salih, S.; Shamsan, A.; Al Mutair, A.; Taha, J.; Alahmadi, A.; Khotani, N.; Alhamss, A.; Mahmoud, A.; Alquthami, K.; Dageeg, A.; Khogeer, A.; Hashem, A. M.; Moraga, P.; Volz, E.; Almontashiri, N.; Pain, A.

Monitoring SARS-CoV-2 spread and evolution through genome sequencing is essential in handling the COVID-19 pandemic. The availability of patient hospital records is crucial for linking the genomic sequence information to virus function during the course of infections. Here, we sequenced 892 SARS-CoV-2 genomes collected from patients in Saudi Arabia from March to August 2020. From the assembled sequences, we estimate the SARS-CoV-2 effective population size and infection rate and outline the epidemiological dynamics of import and transmission events during this period in Saudi Arabia. We show that two consecutive mutations (R203K/G204R) in the SARS-CoV-2 nucleocapsid (N) protein are associated with higher viral loads in COVID-19 patients. Our comparative biochemical analysis reveals that the mutant N protein displays enhanced viral RNA binding and differential interaction with key host proteins. We found hyper-phosphorylation of the adjacent serine site (S206) in the mutant N protein by mass-spectrometry analysis. Furthermore, analysis of the host cell transcriptome suggests that the mutant N protein results in dysregulated interferon response genes. We provide crucial information in linking the R203K/G204R mutations in the N protein as a major modulator of host-virus interactions and increased viral load and underline the potential of the nucleocapsid protein as a drug target during infection.