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Mourier T, Shuaib M, Hala S, Mfarrej S, Alofi F, Naeem R, Alsomali A, Jorgensen D, Subudhi AK, Ben Rached F, Guan Q, Salunke RP, 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 AM, Moraga P, Volz E, Almontashiri N, Pain A. SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. Nat Commun 2022; 13:601. [PMID: 35105893 PMCID: PMC8807822 DOI: 10.1038/s41467-022-28287-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 01/12/2022] [Indexed: 02/06/2023] Open
Abstract
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.
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Affiliation(s)
- Tobias Mourier
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Muhammad Shuaib
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Sharif Hala
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia
| | - Sara Mfarrej
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Fadwa Alofi
- Infectious Diseases Department, King Fahad Hospital, Madinah, MOH, Saudi Arabia
| | - Raeece Naeem
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Afrah Alsomali
- Infectious Diseases Department, King Abdullah Medical Complex, Jeddah, MOH, Saudi Arabia
| | - David Jorgensen
- School of Public Health, Faculty of Medicine, Imperial College, Norfolk Place, St Mary's Campus, London, United Kingdom
| | - Amit Kumar Subudhi
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Fathia Ben Rached
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Qingtian Guan
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Rahul P Salunke
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Amanda Ooi
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Luke Esau
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Olga Douvropoulou
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Raushan Nugmanova
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Sadhasivam Perumal
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Huoming Zhang
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Issaac Rajan
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Awad Al-Omari
- Dr. Suliman Al-Habib Medical Group, Riyadh, Saudi Arabia
| | - Samer Salih
- Dr. Suliman Al-Habib Medical Group, Riyadh, Saudi Arabia
| | - Abbas Shamsan
- Dr. Suliman Al-Habib Medical Group, Riyadh, Saudi Arabia
| | | | - Jumana Taha
- Department of Neuroscience, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Abdulaziz Alahmadi
- Department of Preventive Medicine, Ministry of National Guard - Health Affairs, Riyadh, Saudi Arabia
| | - Nashwa Khotani
- Infectious Diseases Medical Department, Al Noor Specialist Hospital Makkah, Makkah, MOH, Saudi Arabia
| | - Abdelrahman Alhamss
- Gastroenterology Department, King Abdul Aziz Hospital Makkah, Makkah, MOH, Saudi Arabia
| | - Ahmed Mahmoud
- College of Applied Medical Sciences, Taibah University, Madinah, Saudi Arabia
| | - Khaled Alquthami
- Infectious Diseases Medical Department, Al Noor Specialist Hospital Makkah, Makkah, MOH, Saudi Arabia
| | - Abdullah Dageeg
- Department of Medicine, King Abdulaziz University Jeddah, Jeddah, Saudi Arabia
| | - Asim Khogeer
- Plan and Research Department, General Directorate of Health Affairs Makkah Region, Makkah, MOH, Saudi Arabia
| | - Anwar M Hashem
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Paula Moraga
- King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Science and Engineering Division (CEMSE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Eric Volz
- School of Public Health, Faculty of Medicine, Imperial College, Norfolk Place, St Mary's Campus, London, United Kingdom
| | - Naif Almontashiri
- College of Applied Medical Sciences, Taibah University, Madinah, Saudi Arabia
- Center for Genetics and Inherited Diseases, Taibah University, Almadinah Almunwarah, Saudi Arabia
| | - Arnab Pain
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia.
- Research Center for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20 W10 Kita-ku, Sapporo, 001-0020, Japan.
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