SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load

Tobias Mourier, Muhammad Shuaib, Sharif Hala, Sara Mfarrej, Fadwa Alofi, Raeece Naeem, Afrah Alsomali, David Jorgensen, Amit Kumar Subudhi, Fathia Ben Rached, Qingtian Guan, Rahul P. Salunke, Amanda Ooi, Luke Esau, Olga Douvropoulou, Raushan Nugmanova, Sadhasivam Perumal, Huoming Zhang, Issaac Rajan, Awad Al-OmariSamer Salih, Abbas Shamsan, Abbas Al Mutair, Jumana Taha, Abdulaziz Alahmadi, Nashwa Khotani, Abdelrahman Alhamss, Ahmed Mahmoud, Khaled Alquthami, Abdullah Dageeg, Asim Khogeer, Anwar M. Hashem, Paula Moraga, Eric Volz, Naif Almontashiri, Arnab Pain*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

16 Scopus citations


Monitoring SARS-CoV-2 spread and evolution through genome sequencing is essential in handling the COVID-19 pandemic. Here, we sequenced 892 SARS-CoV-2 genomes collected from patients in Saudi Arabia from March to August 2020. We show that two consecutive mutations (R203K/G204R) in the 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 increased interaction of GSK3A kinase simultaneously with hyper-phosphorylation of the adjacent serine site (S206) in the mutant N protein. Furthermore, the host cell transcriptome analysis suggests that the mutant N protein produces dysregulated interferon response genes. Here, we provide crucial information in linking the R203K/G204R mutations in the N protein to modulations of host-virus interactions and underline the potential of the nucleocapsid protein as a drug target during infection.

Original languageEnglish (US)
Article number601
JournalNature Communications
Issue number1
StatePublished - Dec 2022

Bibliographical note

Funding Information:
The authors are sincerely grateful to all hospital members for providing samples and collating metadata in such an unprecedented pandemic, along with the MOH and ethical committee, which rendered it permissible. We thank the KAUST Rapid Research Response Team (R3T) under the Vice President Research (VPR) office in KAUST for generous financial support. We also thank Erik Talley from KAUST Health Safety and Environment (HSE) and Hani Bukhari from KAUST Security for providing timely logistical support for samples transport during COVID-19 Curfew restrictions in the Kingdom. We extend our thanks and appreciation to GDRS director, PH. Athari Alotaibi (General Director for Research and Studies, MOH) for her vigorous facilitation of the research project, and Mohammad Fawzi (General Directorate of Health Affairs) for his help with the metadata collection. We also deeply thank Dr. Wael Hamzah Motair, Dr. Nader Hamzah Motair, Dr. Hatim Khogeer and the General Directorate of Health Affairs of Makkah Region (GDHAMR), MOH for all their help and assistance to our study. We thank Sebastian Gornik (University of Heidelberg) for critical comments on the preprint version of this manuscript. We gratefully acknowledge all of the authors from the originating laboratories responsible for obtaining the specimens and the submitting laboratories where genetic sequence data were generated and publicly shared via the GISAID Initiative, on which was partially used for additional support for some of the conclusions drawn in this study. This work was supported by the following grants: KAUST Rapid Research Response Team (R3T) by Vice President Research (VPR) office in KAUST. KAUST faculty baseline fund (BAS/1/1020-01-01) to AP. KACST Grants, Proposal number: 5-20-01-002-0008. MOH COVID-19 project grants number 341. MOH COVID-19 project grants number 754. The deputyship for Research and Innovation, Ministry of Education in Saudi Arabia, project number (436) to AMH. This project was conducted under the IRB approvals of the MOH (H-02-K-076-0420-285), KAUST (20IBEC14), and at the Dr. Suliman Al-Habib Medical group (HAP-01-R-082) in KSA.

Funding Information:
A.P. conceived the study and directed the work and acquired funding from KAUST and supplemental funding from King Abdulaziz City for Science and Technology (KACST). A.P., T.M., M.S., S.H. and S.M. designed the research. IRB and ethical approvals from MOH were acquired by A.K., A.H., N.A., A.M. and S.H. to cover the collection from several cities in the Kingdom. S.H. and A.K. acquired funding from the Saudi Ministry of Health (MOH) numbers 754 and 341, utilized in the study. S.H. organized and directed sample collection and metadata collections with aid from F.A., A.S., A.O., S.S., J.T., A.A., N.K., K.K., K.A. and A.D.; S.M. directed the wet lab work involving sample reception, metadata record-keeping, RNA extraction, quality control, and library preparation, with aid from A.S., F.B., R.S., M.S., A.O., L.E., O.D., S.H. and R.N.; Illumina sequencing runs were performed by S.M., L.E., S.P. and I.R.; Genome assemblies and submission to GISAID was done by R.N.; Phylogenetic and lineage analysis was done by R.N., Q.G., D.J. and E.V.; In-depth SNP data analysis was performed by T.M.; Statistical analysis done by P.E.M. and E.V.; Functional validation of this link was established by M.S.; Wet lab experiments and data analysis including affinity mass spectrometry, RNA interaction, host-cell transcriptome analysis was performed by M.S.; T.M. wrote the initial draft of the manuscript with input from M.S., S.M., S.H., R.N. and Q.G., followed by edits from A.P.; The final version was produced by T.M., M.S. and A.P. after input from all co-authors. F.A., R.N., D.J., A.S., A.S., F.B., Q.G., R.S. co-second authors contributed equally to this work. A.O., L.E., O.D., R.N. co-third authors contributed equally to this work. S.P., H.Z., I.R. co-fourth authors contributed equally to this work.

Publisher Copyright:
© 2022, The Author(s).

ASJC Scopus subject areas

  • General
  • Physics and Astronomy(all)
  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)


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