Impact of the SARS-CoV-2 nucleocapsid 203K/204R mutations on the inflammatory immune response in COVID-19 severity

• Published in: Genome Medicine Vol. 15; no. 1; pp. 54 - 16
• Main Authors: Shuaib, Muhammad, Adroub, Sabir, Mourier, Tobias, Mfarrej, Sara, Zhang, Huoming, Esau, Luke, Alsomali, Afrah, Alofi, Fadwa S, Ahmad, Adeel Nazir, Shamsan, Abbas, Khogeer, Asim, Hashem, Anwar M., Almontashiri, Naif A. M., Hala, Sharif, Pain, Arnab
• Format: Journal Article
• Language: English
• Published: England Springer Science and Business Media LLC 21.07.2023; BioMed Central Ltd; BioMed Central; BMC
• Subjects: Analysis; Biological response modifiers; Cell culture; Chemokines; COVID-19; COVID-19 - immunology; COVID-19 vaccines; Cytokine Storm; Cytokines; Data processing; Disease transmission; Drug development; Genes; Genetic aspects; Genetics; Genomes; Health aspects; HEK293 Cells; Host Immune Response; Humans; Immune response; Immunotherapy; Infection; Inflammation; Inflammation - immunology; Interferon; Interferon-stimulated Genes (Isgs); Leukocytes (neutrophilic); Lymphocytes; Medical research; Medicine; Medicine, Experimental; Mutation; N protein; Nucleocapsid (N) R203K/G204R (KR) mutations; Nucleocapsids; Pandemics; Patients; Proteins; Proteomics; QH426-470; R; SARS-CoV-2; SARS-CoV-2 - genetics; Severe acute respiratory syndrome coronavirus 2; Severity of Illness Index; Transcriptomes; Transcriptomics; Vaccine development; Variant Of Concern; Virus-like particle (VLP); United States > US; COVID-19; Virus-like particle (VLP); Interferon-stimulated genes (ISGs); SARS-CoV-2; Transcriptomics; Proteomics; Nucleocapsid (N) R203K/G204R (KR) mutations; Host immune response; Cytokine storm; Variant of concern
• ISSN: 1756-994X; 1756-994X
• DOI: 10.1186/s13073-023-01208-0

The excessive inflammatory responses provoked by SARS-CoV-2 infection are critical factors affecting the severity and mortality of COVID-19. Previous work found that two adjacent co-occurring mutations R203K and G204R (KR) on the nucleocapsid (N) protein correlate with increased disease severity in COVID-19 patients. However, links with the host immune response remain unclear. Here, we grouped nasopharyngeal swab samples of COVID-19 patients into two cohorts based on the presence and absence of SARS-CoV-2 nucleocapsid KR mutations. We performed nasopharyngeal transcriptome analysis of age, gender, and ethnicity-matched COVID-19 patients infected with either SARS-CoV-2 with KR mutations in the N protein (KR patients n = 39) or with the wild-type N protein (RG patients n = 39) and compared to healthy controls (n = 34). The impact of KR mutation on immune response was further characterized experimentally by transcriptomic and proteomic profiling of virus-like-particle (VLP) incubated cells. We observed markedly elevated expression of proinflammatory cytokines, chemokines, and interferon-stimulated (ISGs) genes in the KR patients compared to RG patients. Using nasopharyngeal transcriptome data, we found significantly higher levels of neutrophils and neutrophil-to-lymphocyte (NLR) ratio in KR patients than in the RG patients. Furthermore, transcriptomic and proteomic profiling of VLP incubated cells confirmed a similar hyper-inflammatory response mediated by the KR variant. Our data demonstrate an unforeseen connection between nucleocapsid KR mutations and augmented inflammatory immune response in severe COVID-19 patients. These findings provide insights into how mutations in SARS-CoV-2 modulate host immune output and pathogenesis and may contribute to more efficient therapeutics and vaccine development.