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-Omari; Samer 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

doi:10.1038/s41467-022-28287-8

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 journal › Article › peer-review

16 Scopus citations

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.

Original language	English (US)
Article number	601
Journal	Nature Communications
Volume	13
Issue number	1
DOIs	https://doi.org/10.1038/s41467-022-28287-8
State	Published - 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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10.1038/s41467-022-28287-8

Cite this

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. P., Ooi, A., Esau, L., Douvropoulou, O., Nugmanova, R., Perumal, S., Zhang, H., Rajan, I., ... Pain, A. (2022). SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. Nature Communications, 13(1), [601]. https://doi.org/10.1038/s41467-022-28287-8

@article{b7c4e3276c1c4df5b603692af0f93b04,

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

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.",

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

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: {\textcopyright} 2022, The Author(s).",

year = "2022",

month = dec,

doi = "10.1038/s41467-022-28287-8",

language = "English (US)",

volume = "13",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Publishing Group",

number = "1",

}

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 2022, 'SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load', Nature Communications, vol. 13, no. 1, 601. https://doi.org/10.1038/s41467-022-28287-8

TY - JOUR

T1 - SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load

AU - Mourier, Tobias

AU - Shuaib, Muhammad

AU - Hala, Sharif

AU - Mfarrej, Sara

AU - Alofi, Fadwa

AU - Naeem, Raeece

AU - Alsomali, Afrah

AU - Jorgensen, David

AU - Subudhi, Amit Kumar

AU - Ben Rached, Fathia

AU - Guan, Qingtian

AU - Salunke, Rahul P.

AU - Ooi, Amanda

AU - Esau, Luke

AU - Douvropoulou, Olga

AU - Nugmanova, Raushan

AU - Perumal, Sadhasivam

AU - Zhang, Huoming

AU - Rajan, Issaac

AU - Al-Omari, Awad

AU - Salih, Samer

AU - Shamsan, Abbas

AU - Al Mutair, Abbas

AU - Taha, Jumana

AU - Alahmadi, Abdulaziz

AU - Khotani, Nashwa

AU - Alhamss, Abdelrahman

AU - Mahmoud, Ahmed

AU - Alquthami, Khaled

AU - Dageeg, Abdullah

AU - Khogeer, Asim

AU - Hashem, Anwar M.

AU - Moraga, Paula

AU - Volz, Eric

AU - Almontashiri, Naif

AU - Pain, Arnab

N1 - 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).

PY - 2022/12

Y1 - 2022/12

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85124061905&partnerID=8YFLogxK

U2 - 10.1038/s41467-022-28287-8

DO - 10.1038/s41467-022-28287-8

M3 - Article

C2 - 35105893

AN - SCOPUS:85124061905

SN - 2041-1723

VL - 13

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 601

ER -

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

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