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Research Articles

Structural and functional effects of the L84S mutant in the SARS-COV-2 ORF8 dimer based on microsecond molecular dynamics study

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Pages 5770-5787 | Received 10 Jan 2023, Accepted 17 Jun 2023, Published online: 04 Jul 2023

References

  • Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
  • Ali Hosseini Rad, S. M., & McLellan, A. D. (2020). Implications of SARS-COV-2 mutations for genomic RNA structure and host microRNA targeting. International Journal of Molecular Sciences, 21(13), 4807. https://doi.org/10.3390/ijms21134807
  • Batool, M., Shah, M., Patra, M. C., Yesudhas, D., & Choi, S. (2017). Structural insights into the Middle East respiratory syndrome coronavirus 4a protein and its dsRNA binding mechanism. Scientific Reports, 7(1), 1–14. https://doi.org/10.1038/s41598-017-11736-6
  • Benkert, P., Tosatto, S. C. E., & Schomburg, D. (2008). QMEAN: A comprehensive scoring function for model quality assessment. Proteins, 71(1), 261–277. https://doi.org/10.1002/prot.21715
  • Benson, D. A., Cavanaugh, M., Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2012). GenBank. Nucleic Acids Research, 41(D1), D36–D42. https://doi.org/10.1093/nar/gks1195
  • Best, R. B., Hummer, G., & Eaton, W. A. (2013). Native contacts determine protein folding mechanisms in atomistic simulations. Proceedings of the National Academy of Sciences of the United States of America, 110(44), 17874–17879. https://doi.org/10.1073/pnas.1311599110
  • Bienert, S., Waterhouse, A., De Beer, T. A. P., Tauriello, G., Studer, G., Bordoli, L., & Schwede, T. (2017). The SWISS-MODEL Repository-new features and functionality. Nucleic Acids Research, 45(D1), D313–D319. https://doi.org/10.1093/nar/gkw1132
  • Brito, A. F., & Pinney, J. W. (2017). Protein–protein interactions in virus–host systems, 8(August), 1–11. https://doi.org/10.3389/fmicb.2017.01557
  • Bromberg, Y., Yachdav, G., & Rost, B. (2008). SNAP predicts effect of mutations on protein function. Bioinformatics (Oxford, England), 24(20), 2397–2398. https://doi.org/10.1093/bioinformatics/btn435
  • Case, D. A., Cheatham, T. E., 3rd, Darden, T., Gohlke, H., Luo, R., Merz, K. M. J., Onufriev, A., Simmerling, C., Wang, B., & Woods, R. J. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry, 26(16), 1668–1688. https://doi.org/10.1002/jcc.20290
  • Ceraolo, C., & Giorgi, F. M. (2020). Genomic variance of the 2019-nCoV coronavirus. Journal of Medical Virology, 92(5), 522–528. https://doi.org/10.1002/jmv.25700
  • Chan, J. F. W., Kok, K. H., Zhu, Z., Chu, H., To, K. K. W., Yuan, S., & Yuen, K. Y. (2020). Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerging Microbes & Infections, 9(1), 221–236. https://doi.org/10.1080/22221751.2020.1719902
  • Chan, J. F.-W., Yuan, S., Kok, K.-H., To, K. K.-W., Chu, H., Yang, J., Xing, F., Liu, J., Yip, C. C.-Y., Poon, R. W.-S., Tsoi, H.-W., Lo, S. K.-F., Chan, K.-H., Poon, V. K.-M., Chan, W.-M., Ip, J. D., Cai, J.-P., Cheng, V. C.-C., Chen, H., Hui, C. K.-M., & Yuen, K.-Y. (2020). A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: A study of a family cluster. Lancet (London, England), 395(10223), 514–523. https://doi.org/10.1016/S0140-6736(20)30154-9
  • Chaudhari, A. M., Singh, I., Joshi, M., Patel, A., & Joshi, C. (2023). Defective ORF8 dimerization in SARS-CoV-2 delta variant leads to a better adaptive immune response due to abrogation of ORF8–MHC1 interaction. Molecular Diversity, 27(1), 45–57. https://doi.org/10.1007/s11030-022-10405-9
  • Cheng, Y., & Peng, X. (2021). In silico study on the effects of disulfide bonds in ORF8 of SARS-CoV-2, 1–20.
  • Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S., & Richardson, D. C. (2010). MolProbity: All-atom structure validation for macromolecular crystallography. Acta Crystallographica. Section D, Biological Crystallography, 66(Pt 1), 12–21. https://doi.org/10.1107/S0907444909042073
  • Chowdhury, S. M., Talukder, S. A., Khan, A. M., Afrin, N., Ali, M. A., Islam, R., Parves, R., Al Mamun, A., Sufian, M. A., Hossain, M. N., Hossain, M. A., & Halim, M. A. (2020). Antiviral peptides as promising therapeutics against SARS-CoV-2. The Journal of Physical Chemistry: B, 124(44), 9785–9792. https://doi.org/10.1021/acs.jpcb.0c05621
  • Cosar, B., Karagulleoglu, Z. Y., Unal, S., Ince, A. T., Uncuoglu, D. B., Tuncer, G., Kilinc, B. R., Ozkan, Y. E., Ozkoc, H. C., Demir, I. N., Eker, A., Karagoz, F., Simsek, S. Y., Yasar, B., Pala, M., Demir, A., Atak, I. N., Mendi, A. H., Bengi, V. U., & Demir-Dora, D. (2022). SARS-CoV-2 mutations and their viral variants. Cytokine & Growth Factor Reviews, 63(2), 10–22. https://doi.org/10.1016/J.CYTOGFR.2021.06.001
  • Dai, L., & Gao, G. F. (2021). Viral targets for vaccines against COVID-19. Nature Reviews: Immunology, 21(2), 73–82. https://doi.org/10.1038/s41577-020-00480-0
  • Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
  • Durham, E., Dorr, B., Woetzel, N., Staritzbichler, R., & Meiler, J. (2009). Solvent accessible surface area approximations for rapid and accurate protein structure prediction. Journal of Molecular Modeling, 15(9), 1093–1108. https://doi.org/10.1007/s00894-009-0454-9
  • Efaz, F. M., Islam, S., Talukder, S. A., Akter, S., Tashrif, M. Z., Ali, M. A., Sufian, M. A., Parves, M. R., Islam, M. J., & Halim, M. A. (2021). Repurposing fusion inhibitor peptide against SARS-CoV-2. Journal of Computational Chemistry, 42(32), 2283–2293. https://doi.org/10.1002/jcc.26758
  • Eisenberg, D., Lüthy, R., & Bowie, J. U. (1997). VERIFY3D: Assessment of protein models with three-dimensional profiles. In Methods in enzymology (Vol. 277, pp. 396–404). Academic Press. https://doi.org/10.1016/S0076-6879(97)77022-8
  • Fasnacht, M., Butenhof, K., Goupil-Lamy, A., Hernandez-Guzman, F., Huang, H., Yan, L. (2014). Automated antibody structure prediction using Accelrys tools: Results and best practices. Proteins, 82(8), 1583–1598. https://doi.org/10.1002/PROT.24604
  • Flower, T. G., Buffalo, C. Z., Hooy, R. M., Allaire, M., Ren, X., & Hurley, J. H. (2021). Structure of SARS-COV-2 ORF8, a rapidly evolving immune evasion protein. Proceedings of the National Academy of Sciences, 118(2), 14-25. https://doi.org/10.1073/pnas.2021785118
  • Goddard, T. D., Huang, C. C., Meng, E. C., Pettersen, E. F., Couch, G. S., Morris, J. H., & Ferrin, T. E. (2018). UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Protein Science: A Publication of the Protein Society, 27(1), 14–25. https://doi.org/10.1002/PRO.3235
  • Gordon, D. E., Jang, G. M., Bouhaddou, M., Xu, J., Obernier, K., White, K. M., O’Meara, M. J., Rezelj, V. V., Guo, J. Z., Swaney, D. L., Tummino, T. A., Hüttenhain, R., Kaake, R. M., Richards, A. L., Tutuncuoglu, B., Foussard, H., Batra, J., Haas, K., Modak, M., & Krogan, N. J. (2020). A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature, 583(7816), 459–468. https://doi.org/10.1038/s41586-020-2286-9
  • Grant, B. J., Rodrigues, A. P. C., ElSawy, K. M., McCammon, J. A., & Caves, L. S. D. (2006). Bio3d: An R package for the comparative analysis of protein structures. Bioinformatics (Oxford, England), 22(21), 2695–2696. https://doi.org/10.1093/BIOINFORMATICS/BTL461
  • Gray, V. E., Hause, R. J., & Fowler, D. M. (2017). Analysis of large-scale mutagenesis data to assess the impact of single amino acid substitutions. Genetics, 207(1), 53–61. https://doi.org/10.1534/GENETICS.117.300064/-/DC1/TABLES1.XLS
  • Grifoni, A., Sidney, J., Zhang, Y., Scheuermann, R. H., Peters, B., & Sette, A. (2020). A sequence homology and bioinformatic approach can predict candidate targets for immune responses to SARS-CoV-2. Cell Host & Microbe, 27(4), 671–680.e2. https://doi.org/10.1016/j.chom.2020.03.002
  • Gu, C., Mao, X., Chen, D., Yu, B., & Yang, Q. (2019). Isoleucine plays an important role for maintaining immune function. Current Protein & Peptide Science, 20(7), 644–651. https://doi.org/10.2174/1389203720666190305163135
  • Haddad, Y., Adam, V., & Heger, Z. (2020). Ten quick tips for homology modeling of high-resolution protein 3D structures. PLOS Computational Biology, 16(4), e1007449. https://doi.org/10.1371/journal.pcbi.1007449
  • Harvey, W. T., Carabelli, A. M., Jackson, B., Gupta, R. K., Thomson, E. C., Harrison, E. M., Ludden, C., Reeve, R., Rambaut, A., Peacock, S. J., & Robertson, D. L., COVID-19 Genomics UK (COG-UK) Consortium. (2021). SARS-CoV-2 variants, spike mutations and immune escape. Nature Reviews: Microbiology, 19(7), 409–424. https://doi.org/10.1038/s41579-021-00573-0
  • Hassan, S. S., Aljabali, A. A. A., Panda, P. K., Ghosh, S., Attrish, D., Choudhury, P. P., Seyran, M., Pizzol, D., Adadi, P., Abd El-Aziz, T. M., Soares, A., Kandimalla, R., Lundstrom, K., Lal, A., Azad, G. K., Uversky, V. N., Sherchan, S. P., Baetas-da-Cruz, W., Uhal, B. D., & Tambuwala, M. M. (2021). A unique view of SARS-COV-2 through the lens of ORF8 protein. Computers in Biology & Medicine, 133(April), 104380. https://doi.org/10.1016/j.compbiomed.2021.104380
  • Hassan, S. S., Kodakandla, V., Redwan, E. M., Lundstrom, K., Choudhury, P. P., Mohamed, T., El-Aziz, A., Takayama, K., Kandimalla, R., Lal, A., Serrano-Aroca, A., Azad, G. K., Aljabali, A. A. A., Palu, G., Chauhan, G., Adadi, P., Tambuwala, M., Brufsky, A. M., Baetas-Da-Cruz, W., & Uversky, V. N. (2021). An issue of concern: Unique truncated ORF8 protein variants of SARS-CoV-2. BioRxiv, May, 20210525445557. https://doi.org/10.1101/2021.05.25.445557
  • Hirano, Y., Okimoto, N., Fujita, S., & Taiji, M. (2021). Molecular dynamics study of conformational changes of Tankyrase 2 binding subsites upon ligand binding. 6(27), 17609-17620. https://doi.org/10.1021/acsomega.1c02159
  • Hollingsworth, S. A., & Dror, R. O. (2018). Molecular dynamics simulation for all. Neuron, 99(6), 1129–1143. https://doi.org/10.1016/j.neuron.2018.08.011
  • Islam, M. J., Khan, A. M., Parves, M. R., Hossain, M. N., & Halim, M. A. (2019). Prediction of deleterious non-synonymous SNPs of human STK11 gene by combining algorithms, molecular docking, and molecular dynamics simulation. Scientific Reports, 9(1), 16426. https://doi.org/10.1038/s41598-019-52308-0
  • Islam, M. J., Nawal Islam, N., Siddik Alom, M., Kabir, M., & Halim, M. A. (2022). A review on structural, non-structural, and accessory proteins of SARS-CoV-2: Highlighting drug target sites. Immunobiology, 228(1), 152302. https://doi.org/10.1016/J.IMBIO.2022.152302
  • Iyer, M., Li, Z., Jaroszewski, L., Sedova, M., & Godzik, A. (2020). Difference contact maps: From what to why in the analysis of the conformational flexibility of proteins. Plos One, 15(3), e0226702. https://doi.org/10.1371/journal.pone.0226702
  • Kabsch, W., & Sander, C. (1983). Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22(12), 2577–2637. https://doi.org/10.1002/bip.360221211
  • Kagami, L. P., das Neves, G. M., Timmers, L. F. S. M., Caceres, R. A., & Eifler-Lima, V. L. (2020). Geo-measures: A PyMOL plugin for protein structure ensembles analysis. Computational Biology & Chemistry, 87, 107322. https://doi.org/10.1016/j.compbiolchem.2020.107322
  • Kalhan, S. C., & Hanson, R. W. (2012). Resurgence of serine: An often neglected but indispensable amino acid. The Journal of Biological Chemistry, 287(24), 19786–19791. https://doi.org/10.1074/jbc.R112.357194
  • Kapla, J., Rodríguez-Espigares, I., Ballante, F., Selent, J., & Carlsson, J. (2021). Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models ? PLoS Comput Biol, 17(5), e1008936. https://doi.org/10.1371/journal.pcbi.1008936
  • Karshikoff, A., Nilsson, L., & Ladenstein, R. (2015). Rigidity versus flexibility: The dilemma of understanding protein thermal stability. The FEBS Journal, 282(20), 3899–3917. https://doi.org/10.1111/febs.13343
  • Kellogg, E. H., Lange, O. F., & Baker, D. (2012). Evaluation and optimization of discrete state models of protein folding. The Journal of Physical Chemistry. B, 116(37), 11405–11413. https://doi.org/10.1021/jp3044303
  • Kim, T. K. (2015). T test as a parametric statistic. Korean Journal of Anesthesiology, 68(6), 540–546. https://doi.org/10.4097/KJAE.2015.68.6.540
  • Koyama, T., Platt, D. E., & Parida, L. (2020). Variant analysis of COVID-19 genomes. Bulletin of the World Health Organization, 98(7), 495–504. https://doi.org/10.2471/BLT.20.253591
  • Krieger, E., Darden, T., Nabuurs, S. B., Finkelstein, A., & Vriend, G. (2004). Making optimal use of empirical energy functions: Force-field parameterization in crystal space. Proteins, 57(4), 678–683. https://doi.org/10.1002/prot.20251
  • Krieger, F., Fierz, B., Bieri, O., Drewello, M., & Kiefhaber, T. (2003). Dynamics of unfolded polypeptide chains as model for the earliest steps in protein folding. Journal of Molecular Biology, 332(1), 265–274. https://doi.org/10.1016/S0022-2836(03)00892-1
  • Lal, S. K. (2010). Molecular biology of the SARS-Coronavirus. In S. K. Lal (Ed.), Molecular biology of the SARS-coronavirus. Springer. https://doi.org/10.1007/978-3-642-03683-5
  • Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26(2), 283–291. https://doi.org/10.1107/S0021889892009944
  • Lefèvre, F., Rémy, M. H., & Masson, J. M. (1997). Alanine-stretch scanning mutagenesis: A simple and efficient method to probe protein structure and function. Nucleic Acids Research, 25(2), 447–448. https://doi.org/10.1093/nar/25.2.447
  • Li, Q., Guan, X., Wu, P., Wang, X., Zhou, L., Tong, Y., Ren, R., Leung, K. S. M., Lau, E. H. Y., Wong, J. Y., Xing, X., Xiang, N., Wu, Y., Li, C., Chen, Q., Li, D., Liu, T., Zhao, J., Liu, M., & Feng, Z. (2020). Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia. The New England Journal of Medicine, 382(13), 1199–1207. https://doi.org/10.1056/nejmoa2001316
  • Mahtarin, R., Islam, S., Islam, M. J., Ullah, M. O., Ali, M. A., & Halim, M. A. (2022). Structure and dynamics of membrane protein in SARS-CoV-2. Journal of Biomolecular Structure & Dynamics, 40(10), 4725–4738. https://doi.org/10.1080/07391102.2020.1861983
  • Maršavelski, A., Lesjak, S., Močibob, M., Weygand-Đurašević, I., & Tomić, S. (2014). A single amino acid substitution affects the substrate specificity of the seryl-tRNA synthetase homologue. Molecular Biosystems, 10(12), 3207–3216. https://doi.org/10.1039/c4mb00416g
  • Mercadante, D., Gräter, F., & Daday, C. (2018). CONAN: A tool to decode dynamical information from molecular interaction maps. Biophysical Journal, 114(6), 1267–1273. https://doi.org/10.1016/j.bpj.2018.01.033
  • Mohammad, S., Bouchama, A., Alharbi, B. M., Rashid, M., Khatlani, T. S., Gaber, N. S., & Malik, S. S. (2020). SARS‐CoV‐2 ORF8 and SARS‐COV ORF8ab: Genomic divergence and functional convergence. Pathogens, 9(9), 677. https://doi.org/10.3390/pathogens9090677
  • Omotoso, O. E., Babalola, A. D., & Matareek, A. (2021). Mutational hotspots and conserved domains of SARS-CoV-2 genome in African population. Beni-Suef University Journal of Basic & Applied Sciences, 10(1), 11. https://doi.org/10.1186/s43088-021-00102-1
  • Orellana, L. (2019). Large-scale conformational changes and protein function: breaking the in silico barrier. Frontiers in Molecular Biosciences, 6(November), 117. https://doi.org/10.3389/fmolb.2019.00117
  • Papaleo, E., Mereghetti, P., Fantucci, P., Grandori, R., & De Gioia, L. (2009). Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: The myoglobin case. Journal of Molecular Graphics & Modelling, 27(8), 889–899. https://doi.org/10.1016/j.jmgm.2009.01.006
  • Pavlin, M., Qasem, Z., Sameach, H., Gevorkyan-Airapetov, L., Ritacco, I., Ruthstein, S., & Magistrato, A. (2019). Unraveling the impact of cysteine-to-serine mutations on the structural and functional properties of Cu(I)-binding proteins. International Journal of Molecular Sciences, 20(14), 3462. https://doi.org/10.3390/ijms20143462
  • Pereira, F. (2020). Evolutionary dynamics of the SARS-CoV-2 ORF8 accessory gene. Infection, Genetics & Evolution: Journal of Molecular Epidemiology & Evolutionary Genetics in Infectious Diseases, 85, 104525. https://doi.org/10.1016/J.MEEGID.2020.104525
  • Principle Component Analysis of Multivariate Time Series. (2019). Principle component analysis of multivariate time series (pp. 139–161). John Wiley & Sons, Ltd. https://doi.org/10.1002/9781119502951.ch4
  • Ramos, R. M., & Moreira, I. S. (2013). Computational alanine scanning mutagenesis—An improved methodological approach for protein–DNA complexes. Journal of Chemical Theory & Computation, 9(9), 4243–4256. https://doi.org/10.1021/ct400387r
  • Rashid, F., Suleman, M., Shah, A., Dzakah, E. E., Wang, H., Chen, S., & Tang, S. (2021). Mutations in SARS-CoV-2 ORF8 altered the bonding network with interferon regulatory factor 3 to evade host immune system. Frontiers in Microbiology, 12(July), 703145. https://doi.org/10.3389/fmicb.2021.703145
  • Römer, R. A., Römer, N. S., & Wallis, A. K. (2021). Flexibility and mobility of SARS-CoV-2- related protein structures. Scientific Reports, 11(1), 13. https://doi.org/10.1038/s41598-021-82849-2
  • Saksena, N., Bonam, S. R., & Miranda-Saksena, M. (2021). Epigenetic lens to visualize the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in COVID-19 pandemic. Frontiers in Genetics, 12(March), 581726. https://doi.org/10.3389/fgene.2021.581726
  • Shu, Y., & McCauley, J. (2017). GISAID: Global initiative on sharing all influenza data: From vision to reality. Eurosurveillance, 22(13), 2–4. https://doi.org/10.2807/1560-7917.ES.2017.22.13.30494
  • Singh, J., Samal, J., Kumar, V., Sharma, J., Agrawal, U., Ehtesham, N. Z., Sundar, D., Rahman, S. A., Hira, S., & Hasnain, S. E. (2021). Structure–function analyses of new SARS-CoV-2 variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, diagnostic, therapeutic and public health implications. Viruses, 13(3), 439. https://doi.org/10.3390/v13030439
  • Ss, H., Aaa, A., Pk, P., S, G., D, A., Pp, C., M, S., D, P., P, A., Tm, A. E.-A., A, S., R, K., K, L., A, L., Gk, A., Vn, U., Sp, S., W., B.-C., Bd, U., & Mm, T. (2021). A unique view of SARS-CoV-2 through the lens of ORF8 protein. Computers in Biology & Medicine, 133. https://doi.org/10.1016/J.COMPBIOMED.2021.104380
  • Tang, J. W., Toovey, O. T. R., Harvey, K. N., & Hui, D. D. S. (2021). Introduction of the South African SARS-CoV-2 variant 501Y.V2 into the UK. The Journal of Infection, 82(4), e8–e10. https://doi.org/10.1016/j.jinf.2021.01.007
  • Tang, X., Wu, C., Li, X., Song, Y., Yao, X., Wu, X., Duan, Y., Zhang, H., Wang, Y., Qian, Z., Cui, J., & Lu, J. (2020). On the origin and continuing evolution of SARS-CoV-2. National Science Review, 7(6), 1012–1023. https://doi.org/10.1093/nsr/nwaa036
  • Tan, Y., Schneider, T., Leong, M., Aravind, L., & Zhang, D. (2020). Novel immunoglobulin domain proteins provide insights into. mBio, 11(3), 1–12. https://doi.org/10.1128/mBio.00760-20
  • Thakur, S., Sasi, S., Pillai, S. G., Nag, A., Shukla, D., Singhal, R., Phalke, S., & Velu, G. S. K. (2022). SARS-CoV-2 mutations and their impact on diagnostics, therapeutics and vaccines. Frontiers in Medicine, 9, 815389. https://doi.org/10.3389/FMED.2022.815389/BIBTEX
  • Valcarcel, A., Bensussen, A., Álvarez-Buylla, E. R., & Díaz, J. (2021). Structural analysis of SARS-CoV-2 ORF8 protein: Pathogenic and therapeutic implications. Frontiers in Genetics, 12(September), 693227. https://doi.org/10.3389/fgene.2021.693227
  • Vankadari, N. (2020). Overwhelming mutations or SNPs of SARS-CoV-2: A point of caution. Gene, 752(January), 144792. https://doi.org/10.1016/j.gene.2020.144792
  • V'kovski, P., Kratzel, A., Steiner, S., Stalder, H., & Thiel, V. (2021). Coronavirus biology and replication: Implications for SARS-CoV-2. Nature Reviews: Microbiology, 19(3), 155–170. https://doi.org/10.1038/s41579-020-00468-6
  • Wang, R., Chen, J., Gao, K., Hozumi, Y., Yin, C., & Wei, G. W. (2021). Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Communications Biology, 4(1), 1–14. https://doi.org/10.1038/s42003-021-01754-6
  • Wang, X., Lam, J. Y., Chen, L., Au, S. W. N., To, K. K. W., Yuen, K. Y., & Kok, K. H. (2021). Mining of linear B cell epitopes of SARS-CoV-2 ORF8 protein from COVID-19 patients. Emerging Microbes & Infections, 10(1), 1016–1023. https://doi.org/10.1080/22221751.2021.1931465
  • Wu, A., Peng, Y., Huang, B., Ding, X., Wang, X., Niu, P., Meng, J., Zhu, Z., Zhang, Z., Wang, J., Sheng, J., Quan, L., Xia, Z., Tan, W., Cheng, G., & Jiang, T. (2020). Genome composition and divergence of the novel coronavirus (2019-nCoV) originating in China. Cell Host & Microbe, 27(3), 325–328. https://doi.org/10.1016/j.chom.2020.02.001
  • Wu, F., Zhao, S., Yu, B., Chen, Y. M., Wang, W., Song, Z. G., Hu, Y., Tao, Z. W., Tian, J. H., Pei, Y. Y., Yuan, M. L., Zhang, Y. L., Dai, F. H., Liu, Y., Wang, Q. M., Zheng, J. J., Xu, L., Holmes, E. C., & Zhang, Y. Z. (2020). A new coronavirus associated with human respiratory disease in China. Nature, 579(7798), 265–269. https://doi.org/10.1038/s41586-020-2008-3
  • Wu, X., Xia, T., Shin, W.-J., Yu, K.-M., Jung, W., Herrmann, A., Foo, S.-S., Chen, W., Zhang, P., Lee, J.-S., Poo, H., Comhair, S. A. A., Jehi, L., Choi, Y. K., Ensser, A., & Jung, J. U. (2022). Viral mimicry of interleukin-17A by SARS-CoV-2 ORF8. MBio. mBio, 13(2). https://doi.org/10.1128/mbio.00402-22
  • Young, B. E., Fong, S.-W., Chan, Y.-H., Mak, T.-M., Ang, L. W., Anderson, D. E., Lee, C. Y.-P., Amrun, S. N., Lee, B., Goh, Y. S., Su, Y. C. F., Wei, W. E., Kalimuddin, S., Chai, L. Y. A., Pada, S., Tan, S. Y., Sun, L., Parthasarathy, P., Chen, Y. Y. C., & Ng, L. F. P. (2020). Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study. Lancet (London, England), 396(10251), 603–611. https://doi.org/10.1016/S0140-6736(20)31757-8
  • Zhang, Y., Zhang, J., Chen, Y., Luo, B., Yuan, Y., Huang, F., Yang, T., Yu, F., Liu, J., Liu, B., Song, Z., Chen, J., Pan, T., Zhang, X., Li, Y., Li, R., Huang, W., Xiao, F., & Zhang, H. (2020). The ORF8 protein of SARS-CoV-2 mediates immune evasion through potently downregulating MHC-I. BioRxiv. https://doi.org/10.1101/2020.05.24.111823

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