2,562
Views
1
CrossRef citations to date
0
Altmetric
Coronaviruses

Mutations in SARS-CoV-2 variant nsp6 enhance type-I interferon antagonism

, , , , , , & show all
Article: 2209208 | Received 21 Feb 2023, Accepted 26 Apr 2023, Published online: 14 May 2023

References

  • Zhou P, Yang XL, Wang XG, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020;579:270–273.
  • Rambaut A, Holmes EC, O’Toole Á, et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2020;5:1403–1407.
  • Faria NR, Mellan TA, Whittaker C, et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in manaus, Brazil. Science (80-). 2021;821:815–821.
  • Parums DV. Editorial: World Health Organization (WHO) Variants of Concern Lineages Under Monitoring (VOC-LUM) in response to the global spread of lineages and sublineages of Omicron, or B.1.1.529, SARS-CoV-2. Med. Sci. Monit. 2022;28:e937676.
  • Walls AC, Park YJ, Tortorici MA, et al. Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell. 2020;181:281–292.e6.
  • Wang Q, Zhang Y, Wu L, et al. Structural and functional basis of SARS-CoV-2 entry by using human ACE2. Cell. 2020;181:894–904.e9.
  • Patel R, Kaki M, Potluri VS, et al. A comprehensive review of SARS-CoV-2 vaccines: Pfizer, Moderna & Johnson & Johnson. Hum Vaccines Immunother. 2022;18;2002083. doi:10.1080/21645515.2021.2002083.
  • Abdolmaleki G, Taheri MA, Paridehpour S, et al. A comparison between SARS-CoV-1 and SARS-CoV2: an update on current COVID-19 vaccines. DARU. J Pharm Sci. 2022;30:379–406.
  • Plante JA, Liu Y, Liu J, et al. Spike mutation D614G alters SARS-CoV-2 fitness. Nature. 2021;592:116–121.
  • Rashid F, Dzakah EE, Wang H, et al. The ORF8 protein of SARS-CoV-2 induced endoplasmic reticulum stress and mediated immune evasion by antagonizing production of interferon beta. Virus Res. 2021;296:198350.
  • Colson P, Gautret P, Delerce J, et al. The emergence spread and vanishing of a French SARS-CoV-2 variant.pdf. J Med Virol. 2023;95:e28102.
  • Ricciardi S, Guarino AM, Giaquinto L, et al. The role of NSP6 in the biogenesis of the SARS-CoV-2 replication organelle. Nature. 2022;606:761–768.
  • Lin Jw, Tang C, Wei Hc, et al. Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response. Cell Host Microbe. 2021;29:489–502.e8.
  • Laha S, Chakraborty J, Das S, et al. Characterizations of SARS-CoV-2 mutational profile, spike protein stability and viral transmission. Infect Genet Evol. 2020;85:104445.
  • Nagy Á, Pongor S, Győrffy B. Different mutations in SARS-CoV-2 associate with severe and mild outcome. Int J Antimicrob Agents. 2021;57:106272.
  • Wang R, Chen J, Gao K, et al. Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Commun Biol. 2021;4:1–14.
  • Ramesh S, Govindarajulu M, Parise RS, et al. Emerging SARS-CoV-2 variants: a review of its mutations, Its implications and vaccine efficacy. Vaccines. 2021;9:1195.
  • Bills CJ, Xia X, Shi P-Y. The multiple roles of nsp6 in the molecular pathogenesis of SARS-CoV-2. Antiviral Res, 2023;105590.
  • Cui J, Li F, Shi ZL. Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol. 2019;17:181–192.
  • Kim D, Lee JY, Yang JS, et al. The architecture of SARS-CoV-2 transcriptome. Cell. 2020;181:914–921.e10.
  • Xia H, Cao Z, Xie X, et al. Evasion of type I interferon by SARS-CoV-2. Cell Rep. 2020;33:108234.
  • Miorin L, Kehrer T, Sanchez-Aparicio MT, et al. SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling. Proc Natl Acad Sci USA. 2020;117:28344–28354.
  • Yuen CK, Lam JY, Wong WM, et al. SARS-CoV-2 nsp13, nsp14, nsp15 and orf6 function as potent interferon antagonists. Emerg Microbes Infect. 2020;9:1418–1428.
  • Lei X, Dong X, Ma R, et al. Activation and evasion of type I interferon responses by SARS-CoV-2. Nat Commun. 2020;11:1–12.
  • Shemesh M, Aktepe TE, Deerain JM, et al. SARS-CoV-2 suppresses IFNβ production mediated by NSP1, 5, 6, 15, ORF6 and ORF7b but does not suppress the effects of added interferon. 2021;17:e1009800. doi:10.1371/journal.ppat.1009800.
  • Guo K, Barrett BS, Morrison JH, et al. Interferon resistance of emerging SARS-CoV-2 variants. Proc Natl Acad Sci U S A. 2022;119:e2203760119.
  • Liu Y, Liu J, Johnson BA, et al. Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. Cell Rep. 2022;39:110829.
  • Xie X, Lokugamage KG, Zhang X, et al. Engineering SARS-CoV-2 using a reverse genetic system. Nat Protoc. 2021;16:1761–1784.
  • Xie X, Muruato A, Lokugamage KG, et al. An infectious cDNA clone of SARS-CoV-2. Cell Host Microbe. 2020;27:841–848. e3.
  • Xia H, Yeung J, Kalveram B, et al. Cross-neutralization and viral fitness of SARS-CoV-2 Omicron sublineages. Emerg Microbes Infect. 2023;12:e2161422. doi:10.1080/22221751.2022.2161422.
  • Xia H, Luo H, Shan C, et al. An evolutionary NS1 mutation enhances Zika virus evasion of host interferon induction. Nat Commun. 2018;9, 414. doi:10.1038/s41467-017-02816-2.
  • Gangavarapu K, Latif AA, Mullen JL, et al. Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations. Nat Methods. 2023;20:512–522.
  • Omasits U, Ahrens CH, Müller S, et al. Protter: interactive protein feature visualization and integration with experimental proteomic data. Bioinformatics. 2014;30:884–886.
  • Klein S, Cortese M, Winter SL, et al. SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography. Nat Commun. 2020;11:1–10.
  • Angelini MM, Akhlaghpour M, Neuman BW, et al. Severe acute respiratory syndrome coronavirus nonstructural proteins 3, 4, and 6 induce double-membrane vesicles. MBio. 2013;4:e00524-13. doi:10.1128/mBio.00524-13.
  • Hagemeijer MC, Monastyrska I, Griffith J, et al. Membrane rearrangements mediated by coronavirus nonstructural proteins 3 and 4. Virology. 2014;458–459:125–135.
  • Scutigliani EM, Kikkert M. Cytokine & growth factor reviews interaction of the innate immune system with positive-strand RNA virus replication organelles. Cytokine Growth Factor Rev. 2017;37:17–27.
  • Knoops K, Kikkert M, Van Den Worm SHE, et al. SARS-coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum. PLoS Biol. 2008;6:1957–1974.
  • Cortese M, Lee J, Cerikan B, et al. Integrative imaging reveals SARS-CoV-2-induced reshaping of subcellular morphologies. Cell Host Microbe. 2020;28:853–866.
  • Liu J, Liu Y, Shan C, et al. Role of mutational reversions and fitness restoration in Zika virus spread to the Americas. Nat Commun. 2021;12:595.
  • Liu Y, Liu J, Plante KS, et al. The N501Y spike substitution enhances SARS-CoV-2 infection and transmission. Nature. 2022;602:249–299.
  • Plante JA, Mitchell BM, Plante KS, et al. The variant gambit: COVID-19’s next move. Cell Host Microbe. 2021;29:508–515.
  • Shan C, Xia H, Haller SL, et al. A Zika virus envelope mutation preceding the 2015 epidemic enhances virulence and fitness for transmission. Proc Natl Acad Sci USA. 2020;117:20190–20197. doi:10.1073/pnas.2005722117.
  • Gordon DE, Jang GM, Bouhaddou M, et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020;583:459–468.
  • Echavarría-Consuegra L, Cook GM, Busnadiego I, et al. Manipulation of the unfolded protein response: a pharmacological strategy against coronavirus infection. 2021;17:e1009644. doi:10.1371/journal.ppat.1009644.
  • Brodin P. Immune determinants of COVID-19 disease presentation and severity. Nat Med. 2021;27:28–33.
  • Sun X, Liu Y, Huang Z, et al. SARS-CoV-2 non-structural protein 6 triggers NLRP3-dependent pyroptosis by targeting ATP6AP1. Cell Death Differ. 2022;29:1240–1254.
  • Sun X, Yu J, Wong SH, et al. SARS-CoV-2 targets the lysosome to mediate airway inflammatory cell death. Autophagy. 2022;18:2246–2248.
  • Nishitsuji H, Iwahori S, Ohmori M, et al. Ubiquitination of SARS-CoV-2 NSP6 and ORF7a facilitates NF-κB activation. MBio. 2022;13:1–18.
  • Chen D, Chin CV, Kenney D, et al. Spike and nsp6 are key determinants of SARS-CoV-2 Omicron BA.1 attenuation. Nature. 2023;615:143–150. doi:10.1038/s41586-023-05697-2.