SARS-CoV-2: Mapping its features that made it as a unique virus
Abstract
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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