SARS-CoV-2: Mapping its features that made it as a unique virus
Keywords:
epitopes; control strategies; immunopeptidome; vaccine; variant; SARS-CoV-2Abstract
SARS-CoV-2 has attracted the attention of nearly the whole world during the last four years. It is a Corona virus that is responsible for the deaths of millions. It is responsible for economic corruption in many countries. As a response, excessive vaccination programs were installed everywhere. But many variants are elevated, and the virus proves its ability to escape from the immune system because of different mutations. The progress in different scientific domains—instrumentation, bioinformatics, and the like—makes fast vaccine development easier. As a response, new strategies were introduced, including new vaccine production and administration strategies, genomic surveillance, immunopeptidome, gene sequencing, and the like, to enable the vaccine to cover all the targeted populations at the correct time and to install an early alarm system against any elevated new variants. This review contains more information about some important stations in the history of vaccine development and the strategies invented by scientists to control different viruses and other microbes. Some important issues that might influence the type of vaccine used for SARS-CoV-2 are addressed. They include their symptoms, the virus evasion of the innate immune system, the response of adaptive immunity, and the like. Although the world still needs to better understand the SARS-CoV-2 behavior to win the war against it, previous historical successful vaccine productions, important examples, and stations during the human struggle against the viruses are described and discussed.
References
1. Nielsen SS, Alvarez J, Bicout DJ, et al. SARS-CoV-2 in animals: susceptibility of animal species, risk for animal and public health, monitoring, prevention and control. EFSA Journal. 2023; 21(2).
2. Murphy C, Wong JY, Cowling BJ. Nonpharmaceutical interventions for managing SARS-CoV-2. Current Opinion in Pulmonary Medicine. 2023; 29(3): 184-190. doi: 10.1097/mcp.0000000000000949
3. Rossi M. Homer and Herodotus to Egyptian medicine. Vesalius; 2010.
4. Thomas R. Greek medicine and Babylonian wisdom: circulation of knowledge and channels of transmission in the archaic and classical periods. Stud Anc Med. 2004; 27: 175-185.
5. Kraut BH. Medicine and the arts. Histories: [excerpt] by Thucydides. Commentary. Academic Medicine. 2010; 85(6): 1008. doi: 10.1097/acm.0b013e3181dc67d4
6. Encyclopædia-Britannica. Pasteur, Louis: Encyclopædia Britannica Student and Home Edition. Encyclopædia Britannica; 2013.
7. de Wit E, van Doremalen N, Falzarano D, et al. SARS and MERS: recent insights into emerging coronaviruses. Nature Reviews Microbiology. 2016; 14(8): 523-534. doi: 10.1038/nrmicro.2016.81
8. Su S, Wong G, Shi W, et al. Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses. Trends in Microbiology. 2016; 24(6): 490-502. doi: 10.1016/j.tim.2016.03.003
9. Sadhukhan P, Ugurlu MT, Hoque MO. Effect of COVID-19 on Lungs: Focusing on Prospective Malignant Phenotypes. Cancers. 2020; 12(12): 3822. doi: 10.3390/cancers12123822
10. Li W, Moore MJ, Vasilieva N, et al. Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus. Nature. 2003; 426(6965): 450-454. doi: 10.1038/nature02145
11. Masters PS. The Molecular Biology of Coronaviruses. Advances in Virus Research. 2006; 66: 193-292. doi: 10.1016/S0065-3527(06)66005-3
12. Knoops K, Kikkert M, Worm SHE van den, et al. SARS-Coronavirus Replication Is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum. PLoS Biology. 2008; 6(9): e226. doi: 10.1371/journal.pbio.0060226
13. Low ZY, Zabidi NZ, Yip AJW, et al. SARS-CoV-2 Non-Structural Proteins and Their Roles in Host Immune Evasion. Viruses. 2022; 14(9): 1991. doi: 10.3390/v14091991
14. WHO. WHO Coronavirus (COVID-19) Dashboard. Available online: https://covid19.who.int/ (accessed on 2 October 2023).
15. Konno Y, Kimura I, Uriu K, et al. SARS-CoV-2 ORF3b Is a Potent Interferon Antagonist Whose Activity Is Increased by a Naturally Occurring Elongation Variant. Cell Reports. 2020; 32(12): 108185. doi: 10.1016/j.celrep.2020.108185
16. Li JY, Liao CH, Wang Q, et al. The ORF6, ORF8 and nucleocapsid proteins of SARS-CoV-2 inhibit type I interferon signaling pathway. Virus Research. 2020; 286: 198074. doi: 10.1016/j.virusres.2020.198074
17. Blanco-Melo D, Nilsson-Payant BE, Liu WC, et al. Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19. Cell. 2020; 181(5): 1036-1045.e9. doi: 10.1016/j.cell.2020.04.026
18. Burke JM, St Clair LA, Perera R, et al. SARS-CoV-2 infection triggers widespread host mRNA decay leading to an mRNA export block. RNA. 2021; 27(11): 1318-1329. doi: 10.1261/rna.078923.121
19. Diamond MS, Kanneganti TD. Innate immunity: the first line of defense against SARS-CoV-2. Nature Immunology. 2022; 23(2): 165-176. doi: 10.1038/s41590-021-01091-0
20. Weingarten-Gabbay S, Klaeger S, Sarkizova S, et al. SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs. Cold Spring Harbor Laboratory; 2020.
21. Ebinger JE, Fert-Bober J, Printsev I, et al. Antibody responses to the BNT162b2 mRNA vaccine in individuals previously infected with SARS-CoV-2. Nature Medicine. 2021; 27(6): 981-984. doi: 10.1038/s41591-021-01325-6
22. Sui L, Zhao Y, Wang W, et al. SARS-CoV-2 Membrane Protein Inhibits Type I Interferon Production Through Ubiquitin-Mediated Degradation of TBK1. Frontiers in Immunology. 2021; 12. doi: 10.3389/fimmu.2021.662989
23. Chen N, Zhou M, Dong X, et al. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: A descriptive study. The Lancet. 2020; 395(10223): 507-513.
24. Zhu N, Zhang D, Wang W, et al. A Novel Coronavirus from Patients with Pneumonia in China, 2019. New England Journal of Medicine. 2020; 382(8): 727-733. doi: 10.1056/nejmoa2001017
25. Zhou P, Yang XL, Wang XG, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020; 579(7798): 270-273. doi: 10.1038/s41586-020-2012-7
26. Wu Z, McGoogan JM. Characteristics of and Important Lessons from the Coronavirus Disease 2019 (COVID-19) Outbreak in China. JAMA. 2020; 323(13): 1239. doi: 10.1001/jama.2020.2648
27. Kantarcioglu B, Iqbal O, Lewis J, et al. An Update on the Status of Vaccine Development for SARS-CoV-2 Including Variants. Practical Considerations for COVID-19 Special Populations. Clinical and Applied Thrombosis/Hemostasis. 2022; 28: 107602962110566. doi: 10.1177/10760296211056648
28. Lee P, Kim CU, Seo SH, et al. Current Status of COVID-19 Vaccine Development: Focusing on Antigen Design and Clinical Trials on Later Stages. Immune Network. 2021; 21(1). doi: 10.4110/in.2021.21.e4
29. Sharma O, Sultan AA, Ding H, et al. A Review of the Progress and Challenges of Developing a Vaccine for COVID-19. Frontiers in Immunology. 2020; 11. doi: 10.3389/fimmu.2020.585354
30. Evans JP, Liu SL. Role of host factors in SARS-CoV-2 entry. Journal of Biological Chemistry. 2021; 297(1): 100847. doi: 10.1016/j.jbc.2021.100847
31. Milewska A, Zarebski M, Nowak P, et al. Human Coronavirus NL63 Utilizes Heparan Sulfate Proteoglycans for Attachment to Target Cells. Journal of Virology. 2014; 88(22): 13221-13230. doi: 10.1128/jvi.02078-14
32. Lang J, Yang N, Deng J, et al. Inhibition of SARS Pseudovirus Cell Entry by Lactoferrin Binding to Heparan Sulfate Proteoglycans. PLoS ONE. 2011; 6(8): e23710. doi: 10.1371/journal.pone.0023710
33. Vlasak R, Luytjes W, Spaan W, et al. Human and bovine coronaviruses recognize sialic acid-containing receptors similar to those of influenza C viruses. Proceedings of the National Academy of Sciences. 1988; 85(12): 4526-4529. doi: 10.1073/pnas.85.12.4526
34. Chan CM, Chu H, Wang Y, et al. Carcinoembryonic Antigen-Related Cell Adhesion Molecule 5 Is an Important Surface Attachment Factor That Facilitates Entry of Middle East Respiratory Syndrome Coronavirus. Journal of Virology. 2016; 90(20): 9114-9127. doi: 10.1128/jvi.01133-16
35. Yeager CL, Ashmun RA, Williams RK, et al. Human aminopeptidase N is a receptor for human coronavirus 229E. Nature. 1992; 357(6377): 420-422. doi: 10.1038/357420a0
36. Raj VS, Mou H, Smits SL, et al. Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC. Nature. 2013; 495(7440): 251-254. doi: 10.1038/nature12005
37. Collins AR. HLA Class I Antigen Serves as a Receptor for Human Coronavirus OC43. Immunological Investigations. 1993; 22(2): 95-103. doi: 10.3109/08820139309063393
38. Cantuti-Castelvetri L, Ojha R, Pedro LD, et al. Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity. Science. 2020; 370(6518): 856-860. doi: 10.1126/science.abd2985
39. Daly JL, Simonetti B, Klein K, et al. Neuropilin-1 is a host factor for SARS-CoV-2 infection. Science. 2020; 370(6518): 861-865. doi: 10.1126/science.abd3072
40. Hulswit RJG, Lang Y, Bakkers MJG, et al. Human coronaviruses OC43 and HKU1 bind to 9- O -acetylated sialic acids via a conserved receptor-binding site in spike protein domain A. Proceedings of the National Academy of Sciences. 2019; 116(7): 2681-2690. doi: 10.1073/pnas.1809667116
41. Bestle D, Heindl MR, Limburg H, et al. TMPRSS2 and furin are both essential for proteolytic activation of SARS-CoV-2 in human airway cells. Life Science Alliance. 2020; 3(9): e202000786. doi: 10.26508/lsa.202000786
42. Hoffmann M, Kleine-Weber H, Schroeder S, et al. SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell. 2020; 181(2): 271-280.e8. doi: 10.1016/j.cell.2020.02.052
43. Simmons G, Gosalia DN, Rennekamp AJ, et al. Inhibitors of cathepsin L prevent severe acute respiratory syndrome coronavirus entry. Proceedings of the National Academy of Sciences. 2005; 102(33): 11876-11881. doi: 10.1073/pnas.0505577102
44. Kawase M, Shirato K, van der Hoek L, et al. Simultaneous Treatment of Human Bronchial Epithelial Cells with Serine and Cysteine Protease Inhibitors Prevents Severe Acute Respiratory Syndrome Coronavirus Entry. Journal of Virology. 2012; 86(12): 6537-6545. doi: 10.1128/jvi.00094-12
45. Matsuyama S, Nagata N, Shirato K, et al. Efficient Activation of the Severe Acute Respiratory Syndrome Coronavirus Spike Protein by the Transmembrane Protease TMPRSS2. Journal of Virology. 2010; 84(24): 12658-12664. doi: 10.1128/JVI.01542-10
46. Glowacka I, Bertram S, Müller MA, et al. Evidence that TMPRSS2 Activates the Severe Acute Respiratory Syndrome Coronavirus Spike Protein for Membrane Fusion and Reduces Viral Control by the Humoral Immune Response. Journal of Virology. 2011; 85(9): 4122-4134. doi: 10.1128/jvi.02232-10
47. Shulla A, Heald-Sargent T, Subramanya G, et al. A Transmembrane Serine Protease Is Linked to the Severe Acute Respiratory Syndrome Coronavirus Receptor and Activates Virus Entry. Journal of Virology. 2011; 85(2): 873-882. doi: 10.1128/jvi.02062-10
48. Sungnak W, Huang N, et al. SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Nature Medicine. 2020; 26(5): 681-687. doi: 10.1038/s41591-020-0868-6
49. Milewska A, Falkowski K, Kalinska M, et al. Kallikrein 13: A new player in coronaviral infections. Available online: https://www.biorxiv.org/content/10.1101/2020.03.01.971499v1.full.pdf (accessed on 8 November 2023).
50. Zhou F, Yu T, Du R, et al. Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study. The Lancet. 2020; 395(10229): 1054-1062.
51. Essalmani R, Jain J, Susan-Resiga D, et al. Distinctive Roles of Furin and TMPRSS2 in SARS-CoV-2 Infectivity. Journal of Virology. 2022; 96(8). doi: 10.1128/jvi.00128-22
52. Ragotte RJ, Pulido D, Donnellan FR, et al. Human Basigin (CD147) Does Not Directly Interact with SARS-CoV-2 Spike Glycoprotein. mSphere. 2021; 6(4). doi: 10.1128/msphere.00647-21
53. Shilts J, Crozier TWM, Greenwood EJD, et al. No evidence for basigin/CD147 as a direct SARS-CoV-2 spike binding receptor. Scientific Reports. 2021; 11(1). doi: 10.1038/s41598-020-80464-1
54. Johnson BA, Xie X, Bailey AL, et al. Loss of furin cleavage site attenuates SARS-CoV-2 pathogenesis. Nature. 2021; 591(7849): 293-299. doi: 10.1038/s41586-021-03237-4
55. Liu C, von Brunn A, Zhu D. Cyclophilin A and CD147: novel therapeutic targets for the treatment of COVID-19. Medicine in Drug Discovery. 2020; 7: 100056. doi: 10.1016/j.medidd.2020.100056
56. Rahimi N. C-Type Lectin CD209L/L-SIGN and CD209/DC-SIGN: Cell Adhesion Molecules Turned to Pathogen Recognition Receptors. Biology. 2021; 10(1): 1. doi: 10.3390/biology10010001
57. Guo L, Liang Y, Li H, et al. Epigenetic glycosylation of SARS-CoV-2 impact viral infection through DC&L-SIGN receptors. iScience. 2021; 24(12): 103426. doi: 10.1016/j.isci.2021.103426
58. Amraei R, Yin W, Napoleon MA, et al. CD209L/L-SIGN and CD209/DC-SIGN act as receptors for SARS-CoV-2. Published online June 23, 2020. doi: 10.1101/2020.06.22.165803
59. Thépaut M, Luczkowiak J, Vivès C, et al. DC/L-SIGN recognition of spike glycoprotein promotes SARS-CoV-2 trans-infection and can be inhibited by a glycomimetic antagonist. PLOS Pathogens. 2021. doi: 10.1371/journal.ppat.1009576
60. Lempp FA, Soriaga LB, Montiel-Ruiz M, et al. Lectins enhance SARS-CoV-2 infection and influence neutralizing antibodies. Nature. 2021; 598(7880): 342-347. doi: 10.1038/s41586-021-03925-1
61. Sewald X, Ladinsky MS, Uchil PD, et al. Retroviruses use CD169-mediated trans-infection of permissive lymphocytes to establish infection. Science. 2015; 350(6260): 563-567. doi: 10.1126/science.aab2749
62. Kondo Y, Larabee JL, Gao L, et al. L-SIGN is a receptor on liver sinusoidal endothelial cells for SARS-CoV-2 virus. JCI Insight. 2021; 6(14). doi: 10.1172/jci.insight.148999
63. Ali YM, Ferrari M, Lynch NJ, et al. Lectin Pathway Mediates Complement Activation by SARS-CoV-2 Proteins. Frontiers in Immunology. 2021; 12. doi: 10.3389/fimmu.2021.714511
64. Anthony R. Faculty Opinions recommendation of SARS-CoV-2 exacerbates proinflammatory responses in myeloid cells through C-type lectin receptors and Tweety family member 2. Faculty Opinions—Post-Publication Peer Review of the Biomedical Literature; 2012.
65. Vora SM, Lieberman J, Wu H. Inflammasome activation at the crux of severe COVID-19. Nature Reviews Immunology. 2021; 21(11): 694-703. doi: 10.1038/s41577-021-00588-x
66. Soker S, Takashima S, Miao HQ, et al. Neuropilin-1 Is Expressed by Endothelial and Tumor Cells as an Isoform-Specific Receptor for Vascular Endothelial Growth Factor. Cell. 1998; 92(6): 735-745.
67. Kyrou I, Randeva HS, Spandidos DA, et al. Not only ACE2—the quest for additional host cell mediators of SARS-CoV-2 infection: Neuropilin-1 (NRP1) as a novel SARS-CoV-2 host cell entry mediator implicated in COVID-19. Signal Transduction and Targeted Therapy. 2021; 6(1). doi: 10.1038/s41392-020-00460-9
68. Gu Y, Cao J, Zhang X, et al. Receptome profiling identifies KREMEN1 and ASGR1 as alternative functional receptors of SARS-CoV-2. Cell Research. 2021; 32(1): 24-37. doi: 10.1038/s41422-021-00595-6
69. Hoffmann M, Pöhlmann S. Novel SARS-CoV-2 receptors: ASGR1 and KREMEN1. Cell Research. 2021; 32(1): 1-2. doi: 10.1038/s41422-021-00603-9
70. Staring J, van den Hengel LG, Raaben M, et al. KREMEN1 Is a Host Entry Receptor for a Major Group of Enteroviruses. Cell Host & Microbe. 2018; 23(5): 636-643.e5. doi: 10.1016/j.chom.2018.03.019
71. Zhao Y, Zhou D, Ni T, et al. Hand-foot-and-mouth disease virus receptor KREMEN1 binds the canyon of Coxsackie Virus A10. Nature Communications. 2020; 11(1). doi: 10.1038/s41467-019-13936-2
72. Lv J, Wang Z, Qu Y, et al. Distinct uptake, amplification, and release of SARS-CoV-2 by M1 and M2 alveolar macrophages. Cell Discovery. 2021; 7(1). doi: 10.1038/s41421-021-00258-1
73. Abassi Z, Knaney Y, Karram T, et al. The Lung Macrophage in SARS-CoV-2 Infection: A Friend or a Foe? Frontiers in Immunology. 2020; 11. doi: 10.3389/fimmu.2020.01312
74. Gracia-Hernandez M, Sotomayor EM, Villagra A. Targeting Macrophages as a Therapeutic Option in Coronavirus Disease 2019. Frontiers in Pharmacology. 2020; 11. doi: 10.3389/fphar.2020.577571
75. Parkos C, Brazil J. Faculty Opinions recommendation of Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia. Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature. Faculty Opinions Ltd; 2021.
76. Sefik E Qu R Junqueira C, et al. Inflammasome activation in infected macrophages drives COVID-19 pathology. Cold Spring Harbor Laboratory; 2021.
77. Bost P, Giladi A, Liu Y, et al. Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients. Cell. 2020; 181(7): 1475-1488.e12. doi: 10.1016/j.cell.2020.05.006
78. Chen ST, Park MD, Del Valle DM, et al. Shift of lung macrophage composition is associated with COVID-19 disease severity and recovery. Cold Spring Harbor Laboratory; 2022.
79. Sica A, Mantovani A. Macrophage plasticity and polarization: in vivo veritas. Journal of Clinical Investigation. 2012; 122(3): 787-795. doi: 10.1172/jci59643
80. Junqueira C, Crespo Â, Ranjbar S, et al. FcγR-mediated SARS-CoV-2 infection of monocytes activates inflammation. Nature. 2022; 606(7914): 576-584. doi: 10.1038/s41586-022-04702-4
81. Merad M, Martin JC. Pathological inflammation in patients with COVID-19: a key role for monocytes and macrophages. Nature Reviews Immunology. 2020; 20(6): 355-362. doi: 10.1038/s41577-020-0331-4
82. Bräutigam K, Reinhard S, Galván JA, et al. Systematic Investigation of SARS-CoV-2 Receptor Protein Distribution along Viral Entry Routes in Humans. Respiration. 2022; 101(6): 610-618. doi: 10.1159/000521317
83. Bräutigam K, Reinhard S, Wartenberg M, et al. Comprehensive analysis of SARS‐CoV‐2 receptor proteins in human respiratory tissues identifies alveolar macrophages as potential virus entry site. Histopathology. 2023; 82(6): 846-859. doi: 10.1111/his.14871
84. Zou X, Chen K, Zou J, et al. Single-cell RNA-seq data analysis on the receptor ACE2 expression reveals the potential risk of different human organs vulnerable to 2019-nCoV infection. Frontiers of Medicine. 2020; 14(2): 185-192. doi: 10.1007/s11684-020-0754-0
85. Synowiec A, Szczepański A, Barreto-Duran E, et al. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): a Systemic Infection. Clinical Microbiology Reviews. 2021; 34(2). doi: 10.1128/cmr.00133-20
86. Oran DP, Topol EJ. The Proportion of SARS-CoV-2 Infections That Are Asymptomatic. Annals of Internal Medicine. 2021; 174(5): 655-662.
87. Gao Z, Xu Y, Sun C, et al. A systematic review of asymptomatic infections with COVID-19. Journal of Microbiology, Immunology and Infection. 2021; 54(1): 12-16. doi: 10.1016/j.jmii.2020.05.001
88. Markov PV, Katzourakis A, Stilianakis NI. Antigenic evolution will lead to new SARS-CoV-2 variants with unpredictable severity. Nature Reviews Microbiology. 2022; 20(5): 251-252. doi: 10.1038/s41579-022-00722-z
89. Murray CJL, Piot P. The Potential Future of the COVID-19 Pandemic. JAMA. 2021; 325(13): 1249. doi: 10.1001/jama.2021.2828
90. Kayser V, Ramzan I. Vaccines and vaccination: history and emerging issues. Human Vaccines & Immunotherapeutics. 2021; 17(12): 5255-5268. doi: 10.1080/21645515.2021.1977057
91. Colson P, Fournier PE, Delerce J, et al. Culture and identification of a “Deltamicron” SARS-CoV-2 in a three cases cluster in southern France. Cold Spring Harbor Laboratory; 2022.
92. Lauring AS, Hodcroft EB. Genetic Variants of SARS-CoV-2—What Do They Mean? JAMA. 2021; 325(6): 529. doi: 10.1001/jama.2020.27124
93. Hossain A, Akter S, Rashid AA, et al. Unique mutations in SARS-CoV-2 Omicron subvariants’ non-spike proteins: Potential impacts on viral pathogenesis and host immune evasion. Microbial Pathogenesis. 2022; 170: 105699. doi: 10.1016/j.micpath.2022.105699
94. Wu L, Zhou L, Mo M, et al. SARS-CoV-2 Omicron RBD shows weaker binding affinity than the currently dominant Delta variant to human ACE2. Signal Transduction and Targeted Therapy. 2022; 7(1). doi: 10.1038/s41392-021-00863-2
95. Chen TH, Hsu MT, Lee MY, et al. Gastrointestinal Involvement in SARS-CoV-2 Infection. Viruses. 2022; 14(6): 1188. doi: 10.3390/v14061188
96. Plummer JT, Contreras D, Zhang W, et al. US Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Epsilon Variant: Highly Transmissible but With an Adjusted Muted Host T-Cell Response. Clin Infect Dis; 2022.
97. Callaway E. COVID vaccine boosters: the most important questions. Nature. 2021; 596(7871): 178-180. doi: 10.1038/d41586-021-02158-6
98. Klocke RA. Respiration human, Encyclopædia Britannica Student and Home Edition. Encyclopædia Britannica; 2013.
99. Li Q, Guan X, Wu P, et al. Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus–Infected Pneumonia. New England Journal of Medicine. 2020; 382(13): 1199-1207. doi: 10.1056/nejmoa2001316
100. Riou J, Althaus CL. Pattern of early human-to-human transmission of Wuhan 2019 novel coronavirus (2019-nCoV), December 2019 to January 2020. Eurosurveillance. 2020; 25(4). doi: 10.2807/1560-7917.es.2020.25.4.2000058
101. Wu CT, Lidsky PV, Xiao Y, et al. SARS-CoV-2 replication in airway epithelia requires motile cilia and microvillar reprogramming. Cell. 2023; 186(1): 112-130.e20. doi: 10.1016/j.cell.2022.11.030
102. Owen J, Punt J, Stranford S. KUBY Immunology, 7th ed. Freeman and Company; 2023.
103. Liu G, Lee JH, Parker ZM, et al. ISG15-dependent activation of the sensor MDA5 is antagonized by the SARS-CoV-2 papain-like protease to evade host innate immunity. Nature Microbiology. 2021; 6(4): 467-478. doi: 10.1038/s41564-021-00884-1
104. WHO. COVID-19 vaccine tracker and landscape. Available online: https://www.who.int/publications/m/item/draft-landscape-of-covid-19-candidatevaccines (accessed on 2 October 2023).
105. Liu C, Martins AJ, Lau WW, et al. Time-resolved systems immunology reveals a late juncture linked to fatal COVID-19. Cell. 2021; 184(7): 1836-1857.e22. doi: 10.1016/j.cell.2021.02.018
106. Wurfel MM, Gordon AC, Holden TD, et al. Toll-like Receptor 1 Polymorphisms Affect Innate Immune Responses and Outcomes in Sepsis. American Journal of Respiratory and Critical Care Medicine. 2008; 178(7): 710-720. doi: 10.1164/rccm.200803-462oc
107. Tisoncik JR, Korth MJ, Simmons CP, et al. Into the Eye of the Cytokine Storm. Microbiology and Molecular Biology Reviews. 2012; 76(1): 16-32. doi: 10.1128/mmbr.05015-11
108. Song P, Li W, Xie J, et al. Cytokine storm induced by SARS-CoV-2. Clinica Chimica Acta. 2020; 509: 280-287. doi: 10.1016/j.cca.2020.06.017
109. Ragab D, Salah Eldin H, Taeimah M, et al. The COVID-19 Cytokine Storm; What We Know So Far. Frontiers in Immunology. 2020; 11. doi: 10.3389/fimmu.2020.01446
110. Li F, Li J, Wang PH, et al. SARS-CoV-2 spike promotes inflammation and apoptosis through autophagy by ROS-suppressed PI3K/AKT/mTOR signaling. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease. 2021; 1867(12): 166260. doi: 10.1016/j.bbadis.2021.166260
111. Wang M, Chang W, Zhang L, et al. Pyroptotic cell death in SARS-CoV-2 infection: revealing its roles during the immunopathogenesis of COVID-19. International Journal of Biological Sciences. 2022; 18(15): 5827-5848. doi: 10.7150/ijbs.77561
112. Rabiu Abubakar A, Ahmad R, Rowaiye AB, et al. Targeting Specific Checkpoints in the Management of SARS-CoV-2 Induced Cytokine Storm. Life. 2022; 12(4): 478. doi: 10.3390/life12040478
113. Ghosh S, Das S, et al. A review on the eddect of COVID-19 in type 2 asthma and its management. Int Immunopharmacol. 2021; 91: 107309.
114. Massey BW, Jayathilake K, Meltzer HY. Respiratory Microbial Co-infection with SARS-CoV-2. Frontiers in Microbiology. 2020; 11. doi: 10.3389/fmicb.2020.02079
115. Bengoechea JA, Bamford CG. SARS‐CoV‐2, bacterial co‐infections, and AMR: the deadly trio in COVID‐19? EMBO Molecular Medicine. 2020; 12(7). doi: 10.15252/emmm.202012560
116. Boutin S, Hildebrand D, Boulant S, et al. Host factors facilitating SARS‐CoV‐2 virus infection and replication in the lungs. Cellular and Molecular Life Sciences. 2021; 78(16): 5953-5976. doi: 10.1007/s00018-021-03889-5
117. Ma L, Wang W, Le Grange JM, et al. Coinfection of SARS-CoV-2 and Other Respiratory Pathogens. Infection and Drug Resistance. 2020; 13: 3045-3053.
118. Mirzaei R, Goodarzi P, Asadi M, et al. Bacterial co‐infections with SARS‐CoV‐2. IUBMB Life. 2020; 72(10): 2097-2111. doi: 10.1002/iub.2356
119. Rhoades NS, Pinski AN, Monsibais AN, et al. Acute SARS-CoV-2 infection is associated with an increased abundance of bacterial pathogens, including Pseudomonas aeruginosa in the nose. Cell Reports. 2021; 36(9): 109637. doi: 10.1016/j.celrep.2021.109637
120. Qu J, Cai Z, Duan X, et al. Pseudomonas aeruginosa modulates alginate biosynthesis and type VI secretion system in two critically ill COVID-19 patients. Cell & Bioscience. 2022; 12(1). doi: 10.1186/s13578-022-00748-z
121. Fage C, Hénaut M, Carbonneau J, et al. Influenza A(H1N1)pdm09 Virus but Not Respiratory Syncytial Virus Interferes with SARS-CoV-2 Replication during Sequential Infections in Human Nasal Epithelial Cells. Viruses. 2022; 14(2): 395. doi: 10.3390/v14020395
122. Majchrzak M, Poręba M. The roles of cellular protease interactions in viral infections and programmed cell death: a lesson learned from the SARS-CoV-2 outbreak and COVID-19 pandemic. Pharmacological Reports. 2022; 74(6): 1149-1165.
123. Tojo K, Yamamoto N, Tamada N, et al. Early alveolar epithelial cell necrosis is a potential driver of COVID-19-induced acute respiratory distress syndrome. iScience. 2023; 26(1): 105748. doi: 10.1016/j.isci.2022.105748
124. Yang J, Wang W, Chen Z, et al. A vaccine targeting the RBD of the S protein of SARS-CoV-2 induces protective immunity. Nature. 2020; 586(7830): 572-577. doi: 10.1038/s41586-020-2599-8
125. Paolini A, Borella R, De Biasi S, et al. Cell Death in Coronavirus Infections: Uncovering Its Role during COVID-19. Cells. 2021; 10(7): 1585.
126. Ramlall V, Thangaraj PM, Meydan C, et al. Immune complement and coagulation dysfunction in adverse outcomes of SARS-CoV-2 infection. Nature Medicine. 2020; 26(10): 1609-1615. doi: 10.1038/s41591-020-1021-2
127. Lopez J, Mommert M, Mouton W, et al. Correction: Early nasal type I IFN immunity against SARS-CoV-2 is compromised in patients with autoantibodies against type I IFNs. Journal of Experimental Medicine. 2021; 218(10). doi: 10.1084/jem.2021121108132021c
128. Diamond MS, Lambris JD, Ting JP, et al. Considering innate immune responses in SARS-CoV-2 infection and COVID-19. Nature Reviews Immunology. 2022; 22(8): 465-470. doi: 10.1038/s41577-022-00744-x
129. Chauvineau-Grenier A, Bastard P, Servajean A, et al. Autoantibodies neutralizing type I interferons in 20% of COVID-19 deaths in a French hospital. Research Square Platform LLC.; 2021.
130. García JT, Bastard P, Planas-Serra L, et al. Neutralizing autoantibodies to type I IFNs in > 10% of patients with severe COVID-19 pneumonia hospitalized in Madrid, Spain. Research Square Platform LLC; 2021.
131. Wilk AJ, Rustagi A, Zhao NQ, et al. A single-cell atlas of the peripheral immune response in patients with severe COVID-19. Nature Medicine. 2020; 26(7): 1070-1076. doi: 10.1038/s41591-020-0944-y
132. Wilk AJ, Lee MJ, Wei B, et al. Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19. Journal of Experimental Medicine. 2021; 218(8). doi: 10.1084/jem.20210582
133. Wong LYR, Zheng J, Wilhelmsen K, et al. Eicosanoid signalling blockade protects middle-aged mice from severe COVID-19. Nature. 2022; 605(7908): 146-151. doi: 10.1038/s41586-022-04630-3
134. Biondo C, Midiri A, Gerace E, et al. SARS-CoV-2 Infection in Patients with Cystic Fibrosis: What We Know So Far. Life. 2022; 12(12): 2087. doi: 10.3390/life12122087
135. Selva KJ, Chung AW. Insights into how SARS-CoV2 infection induces cytokine storms. Trends in Immunology. 2022; 43(6): 417-419. doi: 10.1016/j.it.2022.04.007
136. Scully EP, Haverfield J, Ursin RL, et al. Considering how biological sex impacts immune responses and COVID-19 outcomes. Nature Reviews Immunology. 2020; 20(7): 442-447. doi: 10.1038/s41577-020-0348-8
137. Mallapaty S. The coronavirus is most deadly if you are older and male—new data reveal the risks. Nature. 2020; 585(7823): 16-17.
138. Akbar AN, Gilroy DW. Aging immunity may exacerbate COVID-19. Science. 2020; 369(6501): 256-257. doi: 10.1126/science.abb0762
139. Saifi S, Ravi V, Sharma S, et al. SARS-CoV-2 VOCs, Mutational diversity and clinical outcome: Are they modulating drug efficacy by altered binding strength? Genomics. 2022; 114(5): 110466. doi: 10.1016/j.ygeno.2022.110466
140. Thye AYK, Law JWF, Pusparajah P, et al. Emerging SARS-CoV-2 Variants of Concern (VOCs): An Impending Global Crisis. Biomedicines. 2021; 9(10): 1303. doi: 10.3390/biomedicines9101303
141. Tosta S, Moreno K, Schuab G, et al. Global SARS-CoV-2 genomic surveillance: What we have learned (so far). Infection, Genetics and Evolution. 2023; 108: 105405. doi: 10.1016/j.meegid.2023.105405
142. The-White-House. Fact Sheet: Biden Administration Announces $1.7 Billion Investment to Fight COVID-19 Variants. The White House; 2021.
143. Hoang T, da Silva AG, Jennison AV, et al. AusTrakka: Fast-tracking nationalized genomics surveillance in response to the COVID-19 pandemic. Nature Communications. 2022; 13(1). doi: 10.1038/s41467-022-28529-9
144. Tegally H, San JE, Cotten M, et al. The evolving SARS-CoV-2 epidemic in Africa: insights from rapidly expanding genomic surveillance. Science. 2022; 378: 6615.
145. Santiago GA, Flores B, González GL, et al. Genomic surveillance of SARS-CoV-2 in Puerto Rico enabled early detection and tracking of variants. Communications Medicine. 2022; 2(1). doi: 10.1038/s43856-022-00168-7
146. Grimaldi A, Panariello F, Annunziata P, et al. Improved SARS-CoV-2 sequencing surveillance allows the identification of new variants and signatures in infected patients. Genome Medicine. 2022; 14(1). doi: 10.1186/s13073-022-01098-8
147. Geidelberg L, Boyd O, Jorgensen D, et al. Genomic epidemiology of a densely sampled COVID-19 outbreak in China. Cold Spring Harbor Laboratory; 2020.
148. Stockdale JE, Liu P, Colijn C. The potential of genomics for infectious disease forecasting. Nature Microbiology. 2022; 7(11): 1736-1743. doi: 10.1038/s41564-022-01233-6
149. CDC. CDC’s Role in Tracking Variants. Available online: https://www.cdc.gov/coronavirus/2019-ncov/variants/cdc-role-surveillance.html (accessed on 2 October 2023).
150. Ellingford JM, George R, McDermott JH, et al. Genomic and healthcare dynamics of nosocomial SARS-CoV-2 transmission. eLife; 2021.
151. Houwaart T, Belhaj S, Tawalbeh E, et al. Integrated genomic surveillance enables tracing of person-to-person SARS-CoV-2 transmission chains during community transmission and reveals extensive onward transmission of travel-imported infections, Germany, June to July 2021. Eurosurveillance. 2022; 27(43). doi: 10.2807/1560-7917.es.2022.27.43.2101089
152. ECDC. European Centre for Disease Prevention and Control. Guidance for representative and targeted genomic SARS-CoV-2 monitoring–3 May 2021. ECDC; 2021.
153. Bhat S, Pandey A, Kanakan A, et al. Learning from Biological and Computational Machines: Importance of SARS-CoV-2 Genomic Surveillance, Mutations and Risk Stratification. Frontiers in Cellular and Infection Microbiology. 2021; 11. doi: 10.3389/fcimb.2021.783961
154. Robishaw JD, Alter SM, Solano JJ, et al. Genomic surveillance to combat COVID-19: challenges and opportunities. The Lancet Microbe. 2021; 2(9): e481-e484.
155. Carabelli AM, Peacock TP, Thorne LG, et al. SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nature Reviews Microbiology; 2023.
156. Ling-Hu T, Rios-Guzman E, Lorenzo-Redondo R, et al. Challenges and Opportunities for Global Genomic Surveillance Strategies in the COVID-19 Era. Viruses. 2022; 14(11): 2532. doi: 10.3390/v14112532
157. Jiang M, Zhang G, Liu H, et al. Epitope Profiling Reveals the Critical Antigenic Determinants in SARS-CoV-2 RBD-Based Antigen. Frontiers in Immunology. 2021; 12. doi: 10.3389/fimmu.2021.707977
158. Abd El-Baky N, Amara AAAF. Depending on Epitope Profile of COVID-19 mRNA Vaccine Recipients: Are They More Efficient Against the Arising Viral Variants? An Opinion Article. Frontiers in Medicine. 2022; 9. doi: 10.3389/fmed.2022.903876
159. Abd El-Baky N, Amara A, Redwan E. HLA-I and HLA-II Peptidomes of SARS-CoV-2: A Review. Vaccines. 2023; 11(3): 548. doi: 10.3390/vaccines11030548
160. Croft NP, Smith SA, Pickering J, et al. Most viral peptides displayed by class I MHC on infected cells are immunogenic. Proceedings of the National Academy of Sciences. 2019; 116(8): 3112-3117. doi: 10.1073/pnas.1815239116
161. Yerly D, Heckerman D, Allen TM, et al. Increased Cytotoxic T-Lymphocyte Epitope Variant Cross-Recognition and Functional Avidity Are Associated with Hepatitis C Virus Clearance. Journal of Virology. 2008; 82(6): 3147-3153. doi: 10.1128/jvi.02252-07
162. Hensen L, Illing PT, Rowntree LC, et al. T Cell Epitope Discovery in the Context of Distinct and Unique Indigenous HLA Profiles. Frontiers in Immunology. 2022; 13. doi: 10.3389/fimmu.2022.812393
163. Campbell KM, Steiner G, Wells DK, et al. Prioritization of SARS-CoV-2 epitopes using a pan-HLA and global population inference approach. Available online: https://www.biorxiv.org/content/10.1101/2020.03.30.016931v2.abstract (accessed on 8 October 2023).
164. Grifoni A, Sidney J, Zhang Y, et al. A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2. Cell Host & Microbe. 2020; 27(4): 671-680.e2. doi: 10.1016/j.chom.2020.03.002
165. Joshi A, Joshi BC, Mannan MA ul, et al. Epitope based vaccine prediction for SARS-COV-2 by deploying immuno-informatics approach. Informatics in Medicine Unlocked. 2020; 19: 100338. doi: 10.1016/j.imu.2020.100338
166. Kiyotani K, Toyoshima Y, Nemoto K, et al. Bioinformatic prediction of potential T cell epitopes for SARS-Cov-2. Journal of Human Genetics. 2020; 65(7): 569-575. doi: 10.1038/s10038-020-0771-5
167. Nelde A, Bilich T, Heitmann JS, et al. SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition. Nature Immunology. 2020; 22(1): 74-85. doi: 10.1038/s41590-020-00808-x
168. Lin L, Ting S, Yufei H, et al. Epitope-based peptide vaccines predicted against novel coronavirus disease caused by SARS-CoV-2. Virus Research. 2020; 288: 198082. doi: 10.1016/j.virusres.2020.198082
169. Poran A, Harjanto D, Malloy M, et al. Sequence-based prediction of SARS-CoV-2 vaccine targets using a mass spectrometry-based bioinformatics predictor identifies immunogenic T cell epitopes. Genome Medicine. 2020; 12(1). doi: 10.1186/s13073-020-00767-w
170. Zhang F, Gan R, Zhen Z, et al. Adaptive immune responses to SARS-CoV-2 infection in severe versus mild individuals. Signal Transduction and Targeted Therapy. 2020; 5(1). doi: 10.1038/s41392-020-00263-y
171. Sekine T, Perez-Potti A, Rivera-Ballesteros O, et al. Robust T Cell Immunity in Convalescent Individuals with Asymptomatic or Mild COVID-19. Cell. 2020; 183(1): 158-168.
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