Association of SARS-CoV-2 Nucleocapsid Protein Mutations with Patient Demographic and Clinical Characteristics during the Delta and Omicron Waves
SARS-CoV-2 genomic mutations outside the spike protein that may increase transmissibility and disease severity have not been well characterized. This study identified mutations in the nucleocapsid protein and their possible association with patient characteristics. We analyzed 695 samples from patie...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-05-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/11/5/1288 |
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| author | Feda A. Alsuwairi Asma N. Alsaleh Madain S. Alsanea Ahmed A. Al-Qahtani Dalia Obeid Reem S. Almaghrabi Basma M. Alahideb Maha A. AlAbdulkareem Maysoon S. Mutabagani Sahar I. Althawadi Sara A. Altamimi Abeer N. Alshukairi Fatimah S. Alhamlan |
| author_facet | Feda A. Alsuwairi Asma N. Alsaleh Madain S. Alsanea Ahmed A. Al-Qahtani Dalia Obeid Reem S. Almaghrabi Basma M. Alahideb Maha A. AlAbdulkareem Maysoon S. Mutabagani Sahar I. Althawadi Sara A. Altamimi Abeer N. Alshukairi Fatimah S. Alhamlan |
| author_sort | Feda A. Alsuwairi |
| collection | DOAJ |
| description | SARS-CoV-2 genomic mutations outside the spike protein that may increase transmissibility and disease severity have not been well characterized. This study identified mutations in the nucleocapsid protein and their possible association with patient characteristics. We analyzed 695 samples from patients with confirmed COVID-19 in Saudi Arabia between 1 April 2021, and 30 April 2022. Nucleocapsid protein mutations were identified through whole genome sequencing. 𝜒<sup>2</sup> tests and <i>t</i> tests assessed associations between mutations and patient characteristics. Logistic regression estimated the risk of intensive care unit (ICU) admission or death. Of the 60 mutations identified, R203K was the most common, followed by G204R, P13L, E31del, R32del, and S33del. These mutations were associated with reduced risk of ICU admission. P13L, E31del, R32del, and S33del were also associated with reduced risk of death. By contrast, D63G, R203M, and D377Y were associated with increased risk of ICU admission. Most mutations were detected in the SR-rich region, which was associated with low risk of death. The C-tail and central linker regions were associated with increased risk of ICU admission, whereas the N-arm region was associated with reduced ICU admission risk. Consequently, mutations in the N protein must be observed, as they may exacerbate viral infection and disease severity. Additional research is needed to validate the mutations’ associations with clinical outcomes. |
| first_indexed | 2024-03-11T03:28:03Z |
| format | Article |
| id | doaj.art-19c6671a9a264c8f927eb062e42824c8 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-11T03:28:03Z |
| publishDate | 2023-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-19c6671a9a264c8f927eb062e42824c82023-11-18T02:34:32ZengMDPI AGMicroorganisms2076-26072023-05-01115128810.3390/microorganisms11051288Association of SARS-CoV-2 Nucleocapsid Protein Mutations with Patient Demographic and Clinical Characteristics during the Delta and Omicron WavesFeda A. Alsuwairi0Asma N. Alsaleh1Madain S. Alsanea2Ahmed A. Al-Qahtani3Dalia Obeid4Reem S. Almaghrabi5Basma M. Alahideb6Maha A. AlAbdulkareem7Maysoon S. Mutabagani8Sahar I. Althawadi9Sara A. Altamimi10Abeer N. Alshukairi11Fatimah S. Alhamlan12Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi ArabiaBotany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi ArabiaDepartment of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi ArabiaDepartment of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi ArabiaDepartment of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi ArabiaOrgan Transplant Center of Excellence, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi ArabiaDepartment of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi ArabiaDepartment of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi ArabiaDepartment of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi ArabiaDepartment of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi ArabiaDepartment of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi ArabiaCollege of Medicine, Alfaisal University, Riyadh 11533, Saudi ArabiaDepartment of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi ArabiaSARS-CoV-2 genomic mutations outside the spike protein that may increase transmissibility and disease severity have not been well characterized. This study identified mutations in the nucleocapsid protein and their possible association with patient characteristics. We analyzed 695 samples from patients with confirmed COVID-19 in Saudi Arabia between 1 April 2021, and 30 April 2022. Nucleocapsid protein mutations were identified through whole genome sequencing. 𝜒<sup>2</sup> tests and <i>t</i> tests assessed associations between mutations and patient characteristics. Logistic regression estimated the risk of intensive care unit (ICU) admission or death. Of the 60 mutations identified, R203K was the most common, followed by G204R, P13L, E31del, R32del, and S33del. These mutations were associated with reduced risk of ICU admission. P13L, E31del, R32del, and S33del were also associated with reduced risk of death. By contrast, D63G, R203M, and D377Y were associated with increased risk of ICU admission. Most mutations were detected in the SR-rich region, which was associated with low risk of death. The C-tail and central linker regions were associated with increased risk of ICU admission, whereas the N-arm region was associated with reduced ICU admission risk. Consequently, mutations in the N protein must be observed, as they may exacerbate viral infection and disease severity. Additional research is needed to validate the mutations’ associations with clinical outcomes.https://www.mdpi.com/2076-2607/11/5/1288SARS-CoV-2COVID-19DeltaOmicronnucleocapsid (N) proteinmutation |
| spellingShingle | Feda A. Alsuwairi Asma N. Alsaleh Madain S. Alsanea Ahmed A. Al-Qahtani Dalia Obeid Reem S. Almaghrabi Basma M. Alahideb Maha A. AlAbdulkareem Maysoon S. Mutabagani Sahar I. Althawadi Sara A. Altamimi Abeer N. Alshukairi Fatimah S. Alhamlan Association of SARS-CoV-2 Nucleocapsid Protein Mutations with Patient Demographic and Clinical Characteristics during the Delta and Omicron Waves Microorganisms SARS-CoV-2 COVID-19 Delta Omicron nucleocapsid (N) protein mutation |
| title | Association of SARS-CoV-2 Nucleocapsid Protein Mutations with Patient Demographic and Clinical Characteristics during the Delta and Omicron Waves |
| title_full | Association of SARS-CoV-2 Nucleocapsid Protein Mutations with Patient Demographic and Clinical Characteristics during the Delta and Omicron Waves |
| title_fullStr | Association of SARS-CoV-2 Nucleocapsid Protein Mutations with Patient Demographic and Clinical Characteristics during the Delta and Omicron Waves |
| title_full_unstemmed | Association of SARS-CoV-2 Nucleocapsid Protein Mutations with Patient Demographic and Clinical Characteristics during the Delta and Omicron Waves |
| title_short | Association of SARS-CoV-2 Nucleocapsid Protein Mutations with Patient Demographic and Clinical Characteristics during the Delta and Omicron Waves |
| title_sort | association of sars cov 2 nucleocapsid protein mutations with patient demographic and clinical characteristics during the delta and omicron waves |
| topic | SARS-CoV-2 COVID-19 Delta Omicron nucleocapsid (N) protein mutation |
| url | https://www.mdpi.com/2076-2607/11/5/1288 |
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