A Detailed Overview of SARS-CoV-2 Omicron: Its Sub-Variants, Mutations and Pathophysiology, Clinical Characteristics, Immunological Landscape, Immune Escape, and Therapies
Abstract
:1. Introduction
2. Sub-Variants of Omicron Variant
3. Different Mutations and Pathophysiology Condition
4. Omicron Variant-Associated Disease Intensity
5. Clinical Characteristics and Symptom Prevalence
6. Infection, Reinfection, and Transmissibility
7. Omicron Entry and Associated Immunological Features inside the Host Cells
8. Interaction of Host ACE2 and Capability of Binding with RBD
9. Phylogenomics and Distribution of Omicron and Its Sub-Variants
10. Immune Escape of Emerging Omicron Variant and Its Sub-Variant
11. Antiviral Drugs and Antibody-Based Therapeutics against the Omicron and Its Sub-Variants
11.1. Efficacy of Antiviral Drugs
11.2. Efficiency Therapeutic Antibodies
12. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
- Zhu, N.; Zhang, D.; Wang, W.; Li, X.; Yang, B.; Song, J.; Zhao, X.; Huang, B.; Shi, W.; Lu, R. A novel coronavirus from patients with pneumonia in China, 2019. N. Engl. J. Med. 2020, 382, 727–733. [Google Scholar] [CrossRef] [PubMed]
- Huang, C.; Wang, Y.; Li, X.; Ren, L.; Zhao, J.; Hu, Y.; Zhang, L.; Fan, G.; Xu, J.; Gu, X. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet 2020, 395, 497–506. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- He, X.; Hong, W.; Pan, X.; Lu, G.; Wei, X. SARS-CoV-2 Omicron variant: Characteristics and prevention. MedComm 2021, 2, 838–845. [Google Scholar] [CrossRef] [PubMed]
- Azgari, C.; Kilinc, Z.; Turhan, B.; Circi, D.; Adebali, O. The mutation profile of SARS-CoV-2 is primarily shaped by the host antiviral defense. Viruses 2021, 13, 394. [Google Scholar] [CrossRef] [PubMed]
- Simmonds, P. Rampant C→ U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses: Causes and consequences for their short-and long-term evolutionary trajectories. Msphere 2020, 5, e00408–e00420. [Google Scholar] [CrossRef]
- Jung, C.; Kmiec, D.; Koepke, L.; Zech, F.; Jacob, T.; Sparrer, K.M.J.; Kirchhoff, F. Omicron: What Makes the Latest SARS-CoV-2 Variant of Concern So Concerning? J. Virol. 2022, 96, e0207721. [Google Scholar] [CrossRef]
- Cherian, S.; Potdar, V.; Jadhav, S.; Yadav, P.; Gupta, N.; Das, M.; Rakshit, P.; Singh, S.; Abraham, P.; Panda, S. SARS-CoV-2 spike mutations, L452R, T478K, E484Q and P681R, in the second wave of COVID-19 in Maharashtra, India. Microorganisms 2021, 9, 1542. [Google Scholar] [CrossRef]
- Davies, N.G.; Abbott, S.; Barnard, R.C.; Jarvis, C.I.; Kucharski, A.J.; Munday, J.D.; Pearson, C.A.; Russell, T.W.; Tully, D.C.; Washburne, A.D. Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science 2021, 372, eabg3055. [Google Scholar] [CrossRef]
- Tegally, H.; Moir, M.; Everatt, J.; Giovanetti, M.; Scheepers, C.; Wilkinson, E.; Subramoney, K.; Moyo, S.; Amoako, D.G.; Althaus, C.L. Continued emergence and evolution of Omicron in South Africa: New BA.4 and BA.5 lineages. medRxiv 2022. [Google Scholar] [CrossRef]
- Volz, E.; Mishra, S.; Chand, M.; Barrett, J.C.; Johnson, R.; Geidelberg, L.; Hinsley, W.R.; Laydon, D.J.; Dabrera, G.; O’Toole, Á. Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature 2021, 593, 266–269. [Google Scholar] [CrossRef]
- Callaway, E. What Omicron’s BA.4 and BA.5 variants mean for the pandemic. Nature 2022, 606, 848–849. [Google Scholar] [CrossRef]
- Brüssow, H. COVID-19: Omicron—The latest, the least virulent, but probably not the last variant of concern of SARS-CoV-2. Microb. Biotechnol. 2022, 15, 1927–1939. [Google Scholar] [CrossRef]
- Dhama, K.; Nainu, F.; Frediansyah, A.; Yatoo, M.I.; Mohapatra, R.K.; Chakraborty, S.; Zhou, H.; Islam, M.R.; Mamada, S.S.; Kusuma, H.I.; et al. Global emerging Omicron variant of SARS-CoV-2: Impacts, challenges and strategies. J. Infect. Public Health 2022, 16, 4–14. [Google Scholar] [CrossRef]
- Callaway, E. Heavily mutated Omicron variant puts scientists on alert. Nature 2021, 600, 21. [Google Scholar] [CrossRef]
- Liu, Y.; Rocklöv, J. The effective reproductive number of the Omicron variant of SARS-CoV-2 is several times relative to Delta. J. Travel Med. 2022, 29, taac037. [Google Scholar] [CrossRef]
- Fan, Y.; Li, X.; Zhang, L.; Wan, S.; Zhang, L.; Zhou, F. SARS-CoV-2 Omicron variant: Recent progress and future perspectives. Signal Transduct. Target. Ther. 2022, 7, 141. [Google Scholar] [CrossRef]
- Callaway, E.; Ledford, H. How bad is Omicron? What scientists know so far. Nature 2021, 600, 197–199. [Google Scholar] [CrossRef]
- Taylor, C.A.; Whitaker, M.; Anglin, O.; Milucky, J.; Patel, K.; Pham, H.; Chai, S.J.; Alden, N.B.; Yousey-Hindes, K.; Anderson, E.J.; et al. COVID-NET Surveillance Team. COVID-19-Associated Hospitalizations Among Adults During SARS-CoV-2 Delta and Omicron Variant Predominance, by Race/Ethnicity and Vaccination Status—COVID-NET, 14 States, July 2021-January 2022. MMWR Morb. Mortal. Wkly. Rep. 2022, 71, 466–473. [Google Scholar] [CrossRef]
- Mohapatra, R.K.; Kandi, V.; Sarangi, A.K.; Verma, S.; Tuli, H.S.; Chakraborty, S.; Chakraborty, C.; Dhama, K. The recently emerged BA. 4 and BA. 5 lineages of Omicron and their global health concerns amid the ongoing wave of COVID-19 pandemic–Correspondence. Int. J. Surg. 2022, 103, 106698. [Google Scholar] [CrossRef]
- Chakraborty, C.; Bhattacharya, M.; Sharma, A.R.; Dhama, K.; Lee, S.S. The rapid emergence of multiple sublineages of Omicron (B.1.1.529) variant: Dynamic profiling via molecular phylogenetics and mutational landscape studies. J. Infect. Public Health 2022, 15, 1234–1258. [Google Scholar] [CrossRef]
- Callaway, E. Are COVID surges becoming more predictable? New Omicron variants offer a hint. Nature 2022, 605, 204–206. [Google Scholar] [CrossRef] [PubMed]
- Cele, S.; Jackson, L.; Khoury, D.S.; Khan, K.; Moyo-Gwete, T.; Tegally, H.; San, J.E.; Cromer, D.; Scheepers, C.; Amoako, D.; et al. SARS-CoV-2 Omicron has extensive but incomplete escape of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection. medRxiv 2021. [Google Scholar] [CrossRef]
- Cao, Y.; Wang, J.; Jian, F.; Xiao, T.; Song, W.; Yisimayi, A.; Huang, W.; Li, Q.; Wang, P.; An, R. Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Nature 2022, 602, 657–663. [Google Scholar] [CrossRef] [PubMed]
- Hoffmann, M.; Kruger, N.; Schulz, S.; Cossmann, A.; Rocha, C.; Kempf, A.; Nehlmeier, I.; Graichen, L.; Moldenhauer, A.S.; Winkler, M.S.; et al. The Omicron variant is highly resistant against antibody-mediated neutralization: Implications for control of the COVID-19 pandemic. Cell 2022, 185, 447–456.e11. [Google Scholar] [CrossRef] [PubMed]
- Wilhelm, A.; Widera, M.; Grikscheit, K.; Toptan, T.; Schenk, B.; Pallas, C.; Metzler, M.; Kohmer, N.; Hoehl, S.; Marschalek, R. Limited neutralisation of the SARS-CoV-2 Omicron subvariants BA. 1 and BA. 2 by convalescent and vaccine serum and monoclonal antibodies. EBioMedicine 2022, 82, 104158. [Google Scholar] [CrossRef]
- Peter, A.S.; Grüner, E.; Socher, E.; Fraedrich, K.; Richel, E.; Mueller-Schmucker, S.; Cordsmeier, A.; Ensser, A.; Sticht, H.; Überla, K. Characterization of SARS-CoV-2 Escape Mutants to a Pair of Neutralizing Antibodies Targeting the RBD and the NTD. Int. J. Mol. Sci. 2022, 23, 8177. [Google Scholar] [CrossRef]
- Chakraborty, C.; Bhattacharya, M.; Sharma, A.R.; Dhama, K.; Agoramoorthy, G. A comprehensive analysis of the mutational landscape of the newly emerging Omicron (B.1.1.529) variant and comparison of mutations with VOCs and VOIs. GeroScience 2022, 44, 2393–2425. [Google Scholar] [CrossRef]
- Mohapatra, R.K.; Tiwari, R.; Sarangi, A.K.; Islam, M.R.; Chakraborty, C.; Dhama, K. Omicron (B.1.1.529) variant of SARS-CoV-2: Concerns, challenges, and recent updates. J. Med. Virol. 2022, 94, 2336–2342. [Google Scholar] [CrossRef]
- Bhattacharya, M.; Sharma, A.R.; Dhama, K.; Agoramoorthy, G.; Chakraborty, C. Omicron variant (B.1.1.529) of SARS-CoV-2: Understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. GeroScience 2022, 44, 619–637. [Google Scholar] [CrossRef]
- Carrazco-Montalvo, A.; Herrera-Yela, A.; Alarcon-Vallejo, D.; Gutierrez-Pallo, D.; Armendariz-Castillo, I.; Andrade-Molina, D.; Munoz-Mawyin, K.; Fernandez-Cadena, J.C.; Morey-Leon, G.; Usfq Covid, C.; et al. Omicron Sub-Lineages (BA.1.1.529 + BA.*) Current Status in Ecuador. Viruses 2022, 14, 1177. [Google Scholar] [CrossRef]
- Kumar, S.; Karuppanan, K.; Subramaniam, G. Omicron (BA.1) and sub-variants (BA.1.1, BA.2, and BA.3) of SARS-CoV-2 spike infectivity and pathogenicity: A comparative sequence and structural-based computational assessment. J. Med. Virol. 2022, 94, 4780–4791. [Google Scholar] [CrossRef]
- Desingu, P.A.; Nagarajan, K.; Dhama, K. Emergence of Omicron third lineage BA.3 and its importance. J. Med. Virol. 2022, 94, 1808–1810. [Google Scholar] [CrossRef]
- Mohapatra, R.K.; Kandi, V.; Verma, S.; Dhama, K. Challenges of the Omicron (B.1.1.529) Variant and Its Lineages: A Global Perspective. Chembiochem 2022, 23, e202200059. [Google Scholar] [CrossRef]
- Khandia, R.; Singhal, S.; Alqahtani, T.; Kamal, M.A.; El-Shall, N.A.; Nainu, F.; Desingu, P.A.; Dhama, K. Emergence of SARS-CoV-2 Omicron (B.1.1.529) variant, salient features, high global health concerns and strategies to counter it amid ongoing COVID-19 pandemic. Environ. Res. 2022, 209, 112816. [Google Scholar] [CrossRef]
- Tegally, H.; Moir, M.; Everatt, J.; Giovanetti, M.; Scheepers, C.; Wilkinson, E.; Subramoney, K.; Makatini, Z.; Moyo, S.; Amoako, D.G.; et al. Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa. Nat. Med. 2022. [Google Scholar] [CrossRef]
- Rahman, S.; Hossain, M.J.; Nahar, Z.; Shahriar, M.; Bhuiyan, M.A.; Islam, M.R. Emerging SARS-CoV-2 Variants and Subvariants: Challenges and Opportunities in the Context of COVID-19 Pandemic. Environ. Health Insights 2022, 16, 11786302221129396. [Google Scholar] [CrossRef]
- Cao, Y.; Yisimayi, A.; Jian, F.; Song, W.; Xiao, T.; Wang, L.; Du, S.; Wang, J.; Li, Q.; Chen, X.; et al. BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection. Nature 2022, 608, 593–602. [Google Scholar] [CrossRef]
- Basky, G.; Vogel, L. XE, XD & XF: What to know about the Omicron hybrid variants. CMAJ 2022, 194, E654–E655. [Google Scholar] [CrossRef]
- Chakraborty, C.; Bhattacharya, M.; Sharma, A.R.; Dhama, K. Recombinant SARS-CoV-2 variants XD, XE, and XF: The emergence of recombinant variants requires an urgent call for research—Correspondence. Int. J. Surg. 2022, 102, 106670. [Google Scholar] [CrossRef]
- Mohapatra, R.K.; Kandi, V.; Tuli, H.S.; Chakraborty, C.; Dhama, K. The recombinant variants of SARS-CoV-2: Concerns continues amid COVID-19 pandemic. J. Med. Virol. 2022, 94, 3506–3508. [Google Scholar] [CrossRef]
- Rahimi, F.; Talebi Bezmin Abadi, A. Hybrid SARS-CoV-2 variants. Int. J. Surg. 2022, 102, 106656. [Google Scholar] [CrossRef] [PubMed]
- Roemer, C.; Hisner, R.; Frohberg, N.; Sakaguchi, H.; Gueli, F.; Peacock, T.P. SARS-CoV-2 Evolution, Post-Omicron. virological.org. 911. Available online: https://virological.org/t/sars-cov-2-evolution-post-omicron/911 (accessed on 6 August 2022).
- Ingraham, N.E.; Ingbar, D.H. The omicron variant of SARS-CoV-2: Understanding the known and living with unknowns. Clin. Transl. Med. 2021, 11, e685. [Google Scholar] [CrossRef] [PubMed]
- Kupferschmidt, K. Where did ‘weird’ Omicron come from? Science 2021, 374, 1179. [Google Scholar] [CrossRef] [PubMed]
- Karim, S.S.A.; Karim, Q.A. Omicron SARS-CoV-2 variant: A new chapter in the COVID-19 pandemic. Lancet 2021, 398, 2126–2128. [Google Scholar] [CrossRef] [PubMed]
- Cui, Z.; Liu, P.; Wang, N.; Wang, L.; Fan, K.; Zhu, Q.; Wang, K.; Chen, R.; Feng, R.; Jia, Z.; et al. Structural and functional characterizations of infectivity and immune evasion of SARS-CoV-2 Omicron. Cell 2022, 185, 860–871.e13. [Google Scholar] [CrossRef] [PubMed]
- Cameroni, E.; Bowen, J.E.; Rosen, L.E.; Saliba, C.; Zepeda, S.K.; Culap, K.; Pinto, D.; VanBlargan, L.A.; De Marco, A.; di Iulio, J. Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift. Nature 2022, 602, 664–670. [Google Scholar] [CrossRef]
- Mannar, D.; Saville, J.W.; Zhu, X.; Srivastava, S.S.; Berezuk, A.M.; Tuttle, K.S.; Marquez, A.C.; Sekirov, I.; Subramaniam, S. SARS-CoV-2 Omicron variant: Antibody evasion and cryo-EM structure of spike protein–ACE2 complex. Science 2022, 375, 760–764. [Google Scholar] [CrossRef]
- Zhang, X.; Wu, S.; Wu, B.; Yang, Q.; Chen, A.; Li, Y.; Zhang, Y.; Pan, T.; Zhang, H.; He, X. SARS-CoV-2 Omicron strain exhibits potent capabilities for immune evasion and viral entrance. Signal Transduct. Target. Ther. 2021, 6, 430. [Google Scholar] [CrossRef]
- Wu, L.; Zhou, L.; Mo, M.; Liu, T.; Wu, C.; Gong, C.; Lu, K.; Gong, L.; Zhu, W.; Xu, Z. SARS-CoV-2 Omicron RBD shows weaker binding affinity than the currently dominant Delta variant to human ACE2. Signal Transduct. Target. Ther. 2022, 7, 8. [Google Scholar] [CrossRef]
- Han, P.; Li, L.; Liu, S.; Wang, Q.; Zhang, D.; Xu, Z.; Han, P.; Li, X.; Peng, Q.; Su, C. Receptor binding and complex structures of human ACE2 to spike RBD from omicron and delta SARS-CoV-2. Cell 2022, 185, 630–640.e10. [Google Scholar] [CrossRef]
- Bhattacharya, M.; Chatterjee, S.; Lee, S.S.; Chakraborty, C. Therapeutic applications of nanobodies against SARS-CoV-2 and other viral infections: Current update. Int. J. Biol. Macromol. 2022, 229, 70–80. [Google Scholar] [CrossRef]
- Yin, W.; Xu, Y.; Xu, P.; Cao, X.; Wu, C.; Gu, C.; He, X.; Wang, X.; Huang, S.; Yuan, Q.; et al. Structures of the Omicron spike trimer with ACE2 and an anti-Omicron antibody. Science 2022, 375, 1048–1053. [Google Scholar] [CrossRef]
- Ledford, H. How severe are Omicron infections. Nature 2021, 600, 577–578. [Google Scholar] [CrossRef]
- Yang, T.-J.; Yu, P.-Y.; Chang, Y.-C.; Liang, K.-H.; Tso, H.-C.; Ho, M.-R.; Chen, W.-Y.; Lin, H.-T.; Wu, H.-C.; Hsu, S.-T.D. Effect of SARS-CoV-2 B. 1.1. 7 mutations on spike protein structure and function. Nat. Struct. Mol. Biol. 2021, 28, 731–739. [Google Scholar] [CrossRef]
- Leung, K.; Shum, M.H.; Leung, G.M.; Lam, T.T.; Wu, J.T. Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. Eurosurveillance 2021, 26, 2002106. [Google Scholar] [CrossRef]
- Zuckerman, N.S.; Fleishon, S.; Bucris, E.; Bar-Ilan, D.; Linial, M.; Bar-Or, I.; Indenbaum, V.; Weil, M.; Lustig, Y.; Mendelson, E. A unique SARS-CoV-2 spike protein P681H variant detected in Israel. Vaccines 2021, 9, 616. [Google Scholar] [CrossRef]
- Tuekprakhon, A.; Nutalai, R.; Dijokaite-Guraliuc, A.; Zhou, D.; Ginn, H.M.; Selvaraj, M.; Liu, C.; Mentzer, A.J.; Supasa, P.; Duyvesteyn, H.M. Antibody escape of SARS-CoV-2 Omicron BA. 4 and BA. 5 from vaccine and BA. 1 serum. Cell 2022, 185, 2422–2433.e13. [Google Scholar] [CrossRef]
- Garrett, N.; Tapley, A.; Andriesen, J.; Seocharan, I.; Fisher, L.H.; Bunts, L.; Espy, N.; Wallis, C.L.; Randhawa, A.K.; Ketter, N. High rate of asymptomatic carriage associated with variant strain omicron. medRxiv 2022. [Google Scholar] [CrossRef]
- Wolter, N.; Jassat, W.; Walaza, S.; Welch, R.; Moultrie, H.; Groome, M.; Amoako, D.G.; Everatt, J.; Bhiman, J.N.; Scheepers, C. Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: A data linkage study. Lancet 2022, 399, 437–446. [Google Scholar] [CrossRef]
- Izcovich, A.; Ragusa, M.A.; Tortosa, F.; Lavena Marzio, M.A.; Agnoletti, C.; Bengolea, A.; Ceirano, A.; Espinosa, F.; Saavedra, E.; Sanguine, V. Prognostic factors for severity and mortality in patients infected with COVID-19: A systematic review. PLoS ONE 2020, 15, e0241955. [Google Scholar] [CrossRef]
- Christensen, P.A.; Olsen, R.J.; Long, S.W.; Snehal, R.; Davis, J.J.; Saavedra, M.O.; Reppond, K.; Shyer, M.N.; Cambric, J.; Gadd, R. Signals of significantly increased vaccine breakthrough, decreased hospitalization rates, and less severe disease in patients with Coronavirus disease 2019 caused by the Omicron variant of severe acute respiratory syndrome Coronavirus 2 in Houston, Texas. Am. J. Pathol. 2022, 192, 642–652. [Google Scholar] [CrossRef] [PubMed]
- Islam, F.; Dhawan, M.; Nafady, M.H.; Emran, T.B.; Mitra, S.; Choudhary, O.P.; Akter, A. Understanding the omicron variant (B.1.1.529) of SARS-CoV-2: Mutational impacts, concerns, and the possible solutions. Ann. Med. Surg. 2022, 78, 103737. [Google Scholar] [CrossRef]
- Chakraborty, C.; Sharma, A.R.; Bhattacharya, M.; Agoramoorthy, G.; Lee, S.S. A Paradigm Shift in the Combination Changes of SARS-CoV-2 Variants and Increased Spread of Delta Variant (B.1.617.2) across the World. Aging Dis. 2022, 13, 927–942. [Google Scholar] [CrossRef]
- Bhattacharya, M.; Chatterjee, S.; Sharma, A.R.; Lee, S.S.; Chakraborty, C. Delta variant (B.1.617.2) of SARS-CoV-2: Current understanding of infection, transmission, immune escape, and mutational landscape. Folia Microbiol. 2022, 1–12. [Google Scholar] [CrossRef] [PubMed]
- Duong, B.V.; Larpruenrudee, P.; Fang, T.; Hossain, S.I.; Saha, S.C.; Gu, Y.; Islam, M.S. Is the SARS CoV-2 Omicron Variant Deadlier and More Transmissible Than Delta Variant? Int. J. Environ. Res. Public Health 2022, 19, 4586. [Google Scholar] [CrossRef] [PubMed]
- Zhou, H.; Mohlenberg, M.; Thakor, J.C.; Tuli, H.S.; Wang, P.; Assaraf, Y.G.; Dhama, K.; Jiang, S. Sensitivity to Vaccines, Therapeutic Antibodies, and Viral Entry Inhibitors and Advances To Counter the SARS-CoV-2 Omicron Variant. Clin. Microbiol. Rev. 2022, 35, e0001422. [Google Scholar] [CrossRef]
- Kupferschmidt, K.; Vogel, G. How bad is Omicron? Some clues are emerging. Science 2021, 374, 1304–1305. [Google Scholar] [CrossRef]
- Chen, N.; Zhou, M.; Dong, X.; Qu, J.; Gong, F.; Han, Y.; Qiu, Y.; Wang, J.; Liu, Y.; Wei, Y. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: A descriptive study. Lancet 2020, 395, 507–513. [Google Scholar] [CrossRef] [Green Version]
- Guan, W.-J.; Ni, Z.-Y.; Hu, Y.; Liang, W.-H.; Ou, C.-Q.; He, J.-X.; Liu, L.; Shan, H.; Lei, C.; Hui, D.S. China medical treatment expert group for Covid-19. Clin. Charact. Coronavirus Dis. 2019, 382, 1708–1720. [Google Scholar]
- Alemi, F.; Vang, J.; Wojtusiak, J.; Guralnik, E.; Peterson, R.; Roess, A.; Jain, P. Differential diagnosis of COVID-19 and influenza. PLOS Glob. Public Health 2022, 2, e0000221. [Google Scholar] [CrossRef]
- Menni, C.; Valdes, A.M.; Polidori, L.; Antonelli, M.; Penamakuri, S.; Nogal, A.; Louca, P.; May, A.; Figueiredo, J.C.; Hu, C. Symptom prevalence, duration, and risk of hospital admission in individuals infected with SARS-CoV-2 during periods of omicron and delta variant dominance: A prospective observational study from the ZOE COVID Study. Lancet 2022, 399, 1618–1624. [Google Scholar] [CrossRef]
- Iuliano, A.D. Trends in disease severity and health care utilization during the early Omicron variant period compared with previous SARS-CoV-2 high transmission periods—United States, December 2020–January 2022. MMWR. Morb. Mortal. Wkly. Rep. 2022, 71, 146–152. [Google Scholar] [CrossRef]
- Lewnard, J.A.; Hong, V.X.; Patel, M.M.; Kahn, R.; Lipsitch, M.; Tartof, S.Y. Clinical outcomes associated with SARS-CoV-2 Omicron (B.1.1.529) variant and BA.1/BA.1.1 or BA.2 subvariant infection in southern California. Nat. Med. 2022, 28, 1933–1943. [Google Scholar] [CrossRef]
- Ludvigsson, J.F. Convulsions in children with COVID-19 during the Omicron wave. Acta Paediatr. 2022, 111, 1023–1026. [Google Scholar] [CrossRef]
- Suzuki, R.; Yamasoba, D.; Kimura, I.; Wang, L.; Kishimoto, M.; Ito, J.; Morioka, Y.; Nao, N.; Nasser, H.; Uriu, K. Attenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variant. Nature 2022, 603, 700–705. [Google Scholar] [CrossRef]
- Shuai, H.; Chan, J.F.-W.; Hu, B.; Chai, Y.; Yuen, T.T.-T.; Yin, F.; Huang, X.; Yoon, C.; Hu, J.-C.; Liu, H. Attenuated replication and pathogenicity of SARS-CoV-2 B.1.1.529 Omicron. Nature 2022, 603, 693–699. [Google Scholar] [CrossRef]
- Bouzid, D.; Visseaux, B.; Kassasseya, C.; Daoud, A.; Fémy, F.; Hermand, C.; Truchot, J.; Beaune, S.; Javaud, N.; Peyrony, O.; et al. Comparison of Patients Infected With Delta Versus Omicron COVID-19 Variants Presenting to Paris Emergency Departments: A Retrospective Cohort Study. Ann. Intern. Med. 2022, 175, 831–837. [Google Scholar] [CrossRef]
- Kneidinger, N.; Hecker, M.; Bessa, V.; Hettich, I.; Wald, A.; Wege, S.; Nolde, A.B.; Oldigs, M.; Syunyaeva, Z.; Wilkens, H.; et al. Outcome of lung transplant recipients infected with SARS-CoV-2/Omicron/B.1.1.529: A Nationwide German study. Infection 2022, 9, 1–9. [Google Scholar] [CrossRef]
- Feikin, D.R.; Abu-Raddad, L.J.; Andrews, N.; Davies, M.A.; Higdon, M.M.; Orenstein, W.A.; Patel, M.K. Assessing vaccine effectiveness against severe COVID-19 disease caused by omicron variant. Report from a meeting of the World Health Organization. Vaccine 2022, 40, 3516–3527. [Google Scholar] [CrossRef]
- Chen, X.; Yan, X.; Sun, K.; Zheng, N.; Sun, R.; Zhou, J.; Deng, X.; Zhuang, T.; Cai, J.; Zhang, J. Estimation of disease burden and clinical severity of COVID-19 caused by Omicron BA.2 in Shanghai, February-June 2022. Emerg. Microbes Infect. 2022, 11, 2800–2807. [Google Scholar] [CrossRef]
- Halfmann, P.J.; Iida, S.; Iwatsuki-Horimoto, K.; Maemura, T.; Kiso, M.; Scheaffer, S.M.; Darling, T.L.; Joshi, A.; Loeber, S.; Singh, G. SARS-CoV-2 Omicron virus causes attenuated disease in mice and hamsters. Nature 2022, 603, 687–692. [Google Scholar] [CrossRef] [PubMed]
- Akkız, H. The Biological Functions and Clinical Significance of SARS-CoV-2 Variants of Corcern. Front. Med. 2022, 20, 849217. [Google Scholar] [CrossRef] [PubMed]
- Thye, A.Y.; Law, J.W.; Pusparajah, P.; Letchumanan, V.; Chan, K.G.; Lee, L.H. Emerging SARS-CoV-2 Variants of Concern (VOCs): An Impending Global Crisis. Biomedicines 2021, 9, 1303. [Google Scholar] [CrossRef]
- Chakraborty, C.; Sharma, A.R.; Bhattacharya, M.; Mallik, B.; Nandi, S.S.; Lee, S.S. Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. Infect. Genet. Evol. 2022, 101, 105282. [Google Scholar] [CrossRef] [PubMed]
- Bian, L.; Gao, Q.; Gao, F.; Wang, Q.; He, Q.; Wu, X.; Mao, Q.; Xu, M.; Liang, Z. Impact of the Delta variant on vaccine efficacy and response strategies. Expert Rev. Vaccines 2021, 10, 1201–1209. [Google Scholar] [CrossRef]
- Zhang, J.; Chen, N.; Zhao, D.; Zhang, J.; Hu, Z.; Tao, Z. Clinical Characteristics of COVID-19 Patients Infected by the Omicron Variant of SARS-CoV-2. Front. Med. 2022, 9, 912367. [Google Scholar] [CrossRef]
- Andrews, N.; Stowe, J.; Kirsebom, F.; Toffa, S.; Rickeard, T.; Gallagher, E.; Gower, C.; Kall, M.; Groves, N.; O’Connell, A.-M. Covid-19 vaccine effectiveness against the Omicron (B.1.1.529) variant. N. Engl. J. Med. 2022, 386, 1532–1546. [Google Scholar] [CrossRef]
- Kupferschmidt, K. Scientists see a ‘really, really tough winter’ with Omicron. Science 2021, 374, 1421–1422. [Google Scholar] [CrossRef]
- Dong, Y.; Dai, T.; Liu, J.; Zhang, L.; Zhou, F. Coronavirus in Continuous Flux: From SARS-CoV to SARS-CoV-2. Adv. Sci. 2020, 7, 2001474. [Google Scholar] [CrossRef]
- Dimeglio, C.; Migueres, M.; Mansuy, J.M.; Saivin, S.; Miedouge, M.; Chapuy-Regaud, S.; Izopet, J. Antibody titers and breakthrough infections with Omicron SARS-CoV-2. J. Infect. 2022, 84, e13–e15. [Google Scholar] [CrossRef]
- Nguyen, N.N.; Houhamdi, L.; Hoang, V.T.; Delerce, J.; Delorme, L.; Colson, P.; Brouqui, P.; Fournier, P.E.; Raoult, D.; Gautret, P. SARS-CoV-2 reinfection and COVID-19 severity. Emerg. Microbes Infect. 2022, 11, 894–901. [Google Scholar] [CrossRef]
- Sheehan, M.M.; Reddy, A.J.; Rothberg, M.B. Reinfection Rates Among Patients Who Previously Tested Positive for Coronavirus Disease 2019: A Retrospective Cohort Study. Clin. Infect. Dis. 2021, 73, 1882–1886. [Google Scholar] [CrossRef]
- Pulliam, J.R.C.; van Schalkwyk, C.; Govender, N.; von Gottberg, A.; Cohen, C.; Groome, M.J.; Dushoff, J.; Mlisana, K.; Moultrie, H. Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa. Science 2022, 376, eabn4947. [Google Scholar] [CrossRef]
- Araf, Y.; Akter, F.; Tang, Y.D.; Fatemi, R.; Parvez, M.S.A.; Zheng, C.; Hossain, M.G. Omicron variant of SARS-CoV-2: Genomics, transmissibility, and responses to current COVID-19 vaccines. J. Med. Virol. 2022, 94, 1825–1832. [Google Scholar] [CrossRef]
- Long, B.; Carius, B.M.; Chavez, S.; Liang, S.Y.; Brady, W.J.; Koyfman, A.; Gottlieb, M. Clinical update on COVID-19 for the emergency clinician: Presentation and evaluation. Am. J. Emerg. Med. 2022, 54, 46–57. [Google Scholar] [CrossRef]
- UK Health Security Agency. SARS-CoV-2 Variants of Concern and Variants under Investigation in England; Technical Briefing 28; UK Health Security Agency: London, UK, 2021.
- Mahase, E. Omicron sub-lineage BA.2 may have “substantial growth advantage,” UKHSA reports. BMJ 2022, 376, o263. [Google Scholar] [CrossRef]
- Brandal, L.T.; MacDonald, E.; Veneti, L.; Ravlo, T.; Lange, H.; Naseer, U.; Feruglio, S.; Bragstad, K.; Hungnes, O.; Odeskaug, L.E.; et al. Outbreak caused by the SARS-CoV-2 Omicron variant in Norway, November to December 2021. Eurosurveillance 2021, 26, 2101147. [Google Scholar] [CrossRef]
- Chaguza, C.; Coppi, A.; Earnest, R.; Ferguson, D.; Kerantzas, N.; Warner, F.; Young, H.P.; Breban, M.I.; Billig, K.; Koch, R.T.; et al. Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated persons. Med 2022, 3, 325–334.e4. [Google Scholar] [CrossRef]
- Meng, B.; Abdullahi, A.; Ferreira, I.; Goonawardane, N.; Saito, A.; Kimura, I.; Yamasoba, D.; Gerber, P.P.; Fatihi, S.; Rathore, S.; et al. Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity. Nature 2022, 603, 706–714. [Google Scholar] [CrossRef]
- Hui, K.P.Y.; Ho, J.C.W.; Cheung, M.C.; Ng, K.C.; Ching, R.H.H.; Lai, K.L.; Kam, T.T.; Gu, H.; Sit, K.Y.; Hsin, M.K.Y.; et al. SARS-CoV-2 Omicron variant replication in human bronchus and lung ex vivo. Nature 2022, 603, 715–720. [Google Scholar] [CrossRef]
- Riediker, M.; Briceno-Ayala, L.; Ichihara, G.; Albani, D.; Poffet, D.; Tsai, D.H.; Iff, S.; Monn, C. Higher viral load and infectivity increase risk of aerosol transmission for Delta and Omicron variants of SARS-CoV-2. Swiss Med. Wkly. 2022, 152, w30133. [Google Scholar] [CrossRef] [PubMed]
- Migueres, M.; Dimeglio, C.; Tremeaux, P.; Abravanel, F.; Raymond, S.; Lhomme, S.; Mansuy, J.M.; Izopet, J. Influence of immune escape and nasopharyngeal virus load on the spread of SARS-CoV-2 Omicron variant. J. Infect. 2022, 84, e7–e9. [Google Scholar] [CrossRef] [PubMed]
- Wrapp, D.; Wang, N.; Corbett, K.S.; Goldsmith, J.A.; Hsieh, C.L.; Abiona, O.; Graham, B.S.; McLellan, J.S. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science 2020, 367, 1260–1263. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Pia, L.; Rowland-Jones, S. Omicron entry route. Nat. Reviews. Immunol. 2022, 22, 144. [Google Scholar] [CrossRef]
- Peacock, T.P.; Goldhill, D.H.; Zhou, J.; Baillon, L.; Frise, R.; Swann, O.C.; Kugathasan, R.; Penn, R.; Brown, J.C.; Sanchez-David, R.Y.; et al. The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets. Nat. Microbiol. 2021, 6, 899–909. [Google Scholar] [CrossRef]
- Du, X.; Tang, H.; Gao, L.; Wu, Z.; Meng, F.; Yan, R.; Qiao, S.; An, J.; Wang, C.; Qin, F.X. Omicron adopts a different strategy from Delta and other variants to adapt to host. Signal Transduct. Target. Ther. 2022, 7, 45. [Google Scholar] [CrossRef]
- Syed, A.M.; Ciling, A.; Khalid, M.M.; Sreekumar, B.; Chen, P.Y.; Kumar, G.R.; Silva, I.; Milbes, B.; Kojima, N.; Hess, V.; et al. Omicron mutations enhance infectivity and reduce antibody neutralization of SARS-CoV-2 virus-like particles. medRxiv 2022. [Google Scholar] [CrossRef]
- Willett, B.J.; Grove, J.; MacLean, O.A.; Wilkie, C.; De Lorenzo, G.; Furnon, W.; Cantoni, D.; Scott, S.; Logan, N.; Ashraf, S.; et al. SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nat. Microbiol. 2022, 7, 1161–1179. [Google Scholar] [CrossRef]
- Kared, H.; Wolf, A.S.; Alirezaylavasani, A.; Ravussin, A.; Solum, G.; Tran, T.T.; Lund-Johansen, F.; Vaage, J.T.; Nissen-Meyer, L.S.; Nygaard, U.C.; et al. Immune responses in Omicron SARS-CoV-2 breakthrough infection in vaccinated adults. Nat. Commun. 2022, 13, 4165. [Google Scholar] [CrossRef]
- Goutam Mukherjee, A.; Ramesh Wanjari, U.; Murali, R.; Chaudhary, U.; Renu, K.; Madhyastha, H.; Iyer, M.; Vellingiri, B.; Valsala Gopalakrishnan, A. Omicron variant infection and the associated immunological scenario. Immunobiology 2022, 227, 152222. [Google Scholar] [CrossRef]
- Kumar, S.; Thambiraja, T.S.; Karuppanan, K.; Subramaniam, G. Omicron and Delta variant of SARS-CoV-2: A comparative computational study of spike protein. J. Med. Virol. 2022, 94, 1641–1649. [Google Scholar] [CrossRef]
- Da Costa, C.H.S.; de Freitas, C.A.B.; Alves, C.N.; Lameira, J. Assessment of mutations on RBD in the Spike protein of SARS-CoV-2 Alpha, Delta and Omicron variants. Sci. Rep. 2022, 12, 8540. [Google Scholar] [CrossRef]
- Callebaut, K.; Stoefs, A.; Stylemans, D.; Soetens, O.; Crombe, F.; Vancutsem, E.; Imamura, H.; Wybo, I.; De Geyter, D.; Pierard, D.; et al. Healthcare-Associated SARS-CoV-2 Reinfection after 3 Months with a Phylogenetically Distinct Omicron Variant: A Case Report. Viruses 2022, 14, 1852. [Google Scholar] [CrossRef]
- Kandeel, M.; El-Deeb, W. Omicron variant receptor-binding domain phylogenetics and molecular dynamics. Comput. Biol. Med. 2022, 146, 105633. [Google Scholar] [CrossRef]
- Chakraborty, C.; Sharma, A.R.; Bhattacharya, M.; Lee, S.S. A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. Front. Immunol. 2022, 13, 801522. [Google Scholar] [CrossRef]
- Chakraborty, C.; Bhattacharya, M.; Sharma, A.R. Emerging mutations in the SARS-CoV-2 variants and their role in antibody escape to small molecule-based therapeutic resistance. Curr. Opin. Pharmacol. 2022, 62, 64–73. [Google Scholar] [CrossRef]
- Chakraborty, C.; Bhattacharya, M.; Sharma, A.R.; Mohapatra, R.K.; Chakraborty, S.; Pal, S.; Dhama, K. Immediate need for next-generation and mutation-proof vaccine to protect against current emerging Omicron sublineages and future SARS-CoV-2 variants: An urgent call for researchers and vaccine companies—Correspondence. Int. J. Surg. 2022, 106, 106903. [Google Scholar] [CrossRef]
- Chakraborty, C.; Bhattacharya, M.; Sharma, A.R.; Mallik, B. Omicron (B.1.1.529)—A new heavily mutated variant: Mapped location and probable properties of its mutations with an emphasis on S-glycoprotein. Int. J. Biol. Macromol. 2022, 219, 980–997. [Google Scholar] [CrossRef]
- Chalkias, S.; Harper, C.; Vrbicky, K.; Walsh, S.R.; Essink, B.; Brosz, A.; McGhee, N.; Tomassini, J.E.; Chen, X.; Chang, Y.; et al. A Bivalent Omicron-Containing Booster Vaccine against Covid-19. N. Engl. J. Med. 2022, 387, 1279–1291. [Google Scholar] [CrossRef]
- Chakraborty, C.; Bhattacharya, M.; Dhama, K. Cases of BA.2.75 and recent BA.2.75.2 subvariant of Omicron are increasing in India: Is it alarming at the global level? Ann. Med. Surg. 2022, 84, 104963. [Google Scholar] [CrossRef]
- Cerutti, G.; Guo, Y.; Zhou, T.; Gorman, J.; Lee, M.; Rapp, M.; Reddem, E.R.; Yu, J.; Bahna, F.; Bimela, J.; et al. Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite. Cell Host Microbe 2021, 29, 819–833.e7. [Google Scholar] [CrossRef] [PubMed]
- Dejnirattisai, W.; Zhou, D.; Ginn, H.M.; Duyvesteyn, H.M.E.; Supasa, P.; Case, J.B.; Zhao, Y.; Walter, T.S.; Mentzer, A.J.; Liu, C.; et al. The antigenic anatomy of SARS-CoV-2 receptor binding domain. Cell 2021, 184, 2183–2200.e22. [Google Scholar] [CrossRef] [PubMed]
- McCallum, M.; De Marco, A.; Lempp, F.A.; Tortorici, M.A.; Pinto, D.; Walls, A.C.; Beltramello, M.; Chen, A.; Liu, Z.; Zatta, F.; et al. N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2. Cell 2021, 184, 2332–2347.e16. [Google Scholar] [CrossRef] [PubMed]
- Zhang, L.; Cao, L.; Gao, X.S.; Zheng, B.Y.; Deng, Y.Q.; Li, J.X.; Feng, R.; Bian, Q.; Guo, X.L.; Wang, N.; et al. A proof of concept for neutralizing antibody-guided vaccine design against SARS-CoV-2. Natl. Sci. Rev. 2021, 8, nwab053. [Google Scholar] [CrossRef] [PubMed]
- Sun, C.; Kang, Y.F.; Liu, Y.T.; Kong, X.W.; Xu, H.Q.; Xiong, D.; Xie, C.; Liu, Y.H.; Peng, S.; Feng, G.K.; et al. Parallel profiling of antigenicity alteration and immune escape of SARS-CoV-2 Omicron and other variants. Signal Transduct. Target. Ther. 2022, 7, 42. [Google Scholar] [CrossRef]
- Cerutti, G.; Guo, Y.; Liu, L.; Zhang, Z.; Luo, Y.; Huang, Y.; Wang, H.H.; Ho, D.D.; Sheng, Z.; Shapiro, L. Cryo-EM structure of the SARS-CoV-2 Omicron spike. Cell Rep. 2022, 38, 110428. [Google Scholar] [CrossRef]
- Takashita, E.; Kinoshita, N.; Yamayoshi, S.; Sakai-Tagawa, Y.; Fujisaki, S.; Ito, M.; Iwatsuki-Horimoto, K.; Chiba, S.; Halfmann, P.; Nagai, H.; et al. Efficacy of Antibodies and Antiviral Drugs against Covid-19 Omicron Variant. N. Engl. J. Med. 2022, 386, 995–998. [Google Scholar] [CrossRef]
- Arbel, R.; Wolff Sagy, Y.; Hoshen, M.; Battat, E.; Lavie, G.; Sergienko, R.; Friger, M.; Waxman, J.G.; Dagan, N.; Balicer, R.; et al. Nirmatrelvir Use and Severe Covid-19 Outcomes during the Omicron Surge. N. Engl. J. Med. 2022, 387, 790–798. [Google Scholar] [CrossRef]
- Bojkova, D.; Widera, M.; Ciesek, S.; Wass, M.N.; Michaelis, M.; Cinatl, J., Jr. Reduced interferon antagonism but similar drug sensitivity in Omicron variant compared to Delta variant of SARS-CoV-2 isolates. Cell Res. 2022, 32, 319–321. [Google Scholar] [CrossRef]
- Vangeel, L.; Chiu, W.; De Jonghe, S.; Maes, P.; Slechten, B.; Raymenants, J.; Andre, E.; Leyssen, P.; Neyts, J.; Jochmans, D. Remdesivir, Molnupiravir and Nirmatrelvir remain active against SARS-CoV-2 Omicron and other variants of concern. Antivir. Res. 2022, 198, 105252. [Google Scholar] [CrossRef]
- Wong, G.L.; Yip, T.C.; Lai, M.S.; Wong, V.W.; Hui, D.S.; Lui, G.C. Incidence of Viral Rebound After Treatment With Nirmatrelvir-Ritonavir and Molnupiravir. JAMA Netw. Open 2022, 12, e2245086. [Google Scholar] [CrossRef]
- Wong, C.K.H.; Au, I.C.H.; Lau, K.T.K.; Lau, E.H.Y.; Cowling, B.J.; Leung, G.M. Real-world effectiveness of early molnupiravir or nirmatrelvir-ritonavir in hospitalised patients with COVID-19 without supplemental oxygen requirement on admission during Hong Kong’s omicron BA.2 wave: A retrospective cohort study. Lancet Infect. Dieases 2022, 12, 1681–1693. [Google Scholar] [CrossRef]
- Saravolatz, L.D.; Depcinski, S.; Sharma, M. Molnupiravir and Nirmatrelvir-Ritonavir: Oral COVID Antiviral Drugs. Clin. Infect. Dis. 2022, ciac180. [Google Scholar] [CrossRef]
- Bhattacharya, M.; Chatterjee, S.; Mallik, B.; Sharma, A.R.; Chakraborty, C. Therapeutic Role of Neutralizing Antibody for the Treatment against SARS-CoV-2 and Its Emerging Variants: A Clinical and Pre-Clinical Perspective. Vaccines 2022, 10, 1612. [Google Scholar] [CrossRef]
- Tada, T.; Zhou, H.; Dcosta, B.M.; Samanovic, M.I.; Chivukula, V.; Herati, R.S.; Hubbard, S.R.; Mulligan, M.J.; Landau, N.R. Increased resistance of SARS-CoV-2 Omicron variant to neutralization by vaccine-elicited and therapeutic antibodies. EBioMedicine 2022, 78, 103944. [Google Scholar] [CrossRef]
- Shah, M.; Woo, H.G. Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies. Front. Immunol. 2021, 12, 830527. [Google Scholar] [CrossRef]
- Zhou, B.; Zhou, R.; Tang, B.; Chan, J.F.; Luo, M.; Peng, Q.; Yuan, S.; Liu, H.; Mok, B.W.; Chen, B.; et al. A broadly neutralizing antibody protects Syrian hamsters against SARS-CoV-2 Omicron challenge. Nat. Commun. 2022, 13, 3589. [Google Scholar] [CrossRef]
- Fang, Z.; Monteiro, V.S.; Hahn, A.M.; Grubaugh, N.D.; Lucas, C.; Chen, S. Bivalent mRNA vaccine booster induces robust antibody immunity against Omicron lineages BA.2, BA.2.12.1, BA.2.75 and BA.5. Cell Discov. 2022, 8, 108. [Google Scholar] [CrossRef]
- Bhattacharya, M.; Sharma, A.R.; Dhama, K.; Agoramoorthy, G.; Chakraborty, C. Hybrid immunity against COVID-19 in different countries with a special emphasis on the Indian scenario during the Omicron period. Int. Immunopharmacol. 2022, 108, 108766. [Google Scholar] [CrossRef]
- Pilz, S.; Ioannidis, J.P.A. Does natural and hybrid immunity obviate the need for frequent vaccine boosters against SARS-CoV-2 in the endemic phase? Eur. J. Clin. Investig. 2022, e13906. [Google Scholar] [CrossRef]
- Nguyen, T.M.; Zhang, Y.; Pandolfi, P.P. Virus against virus: A potential treatment for 2019-nCov (SARS-CoV-2) and other RNA viruses. Cell Res. 2020, 30, 189–190. [Google Scholar] [CrossRef] [PubMed]
Sl. No | Omicron Sub-Variant Name | Mutations in S Protein | |
---|---|---|---|
RBD Region | Other Than RBD Region | ||
1. | BA.1 | G339D, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H | A67V, HV69-, T95I, G142D, VYY143-, NL211I, 215EPE, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F |
2. | BA.2 | G339D, S373P, S375F, T376A, D405N, R408S, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H | T19I, LPP24-26-/A27S, G142D, V213G, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K |
3. | BA.3 | G339D, S373P, S375F, D405N, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H | A67V, HV69-, T95I, G142D, VYY143-, NL211I, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K |
4. | BA.4 | G339D, S371F, S373P, S375F, T376A, D405A, R408S, K417N, N440K, L452R, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H | T19I, L24_P26del, A27S, H69_V70del, G142D, V213G, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K |
5. | BA.5 | G339, S371F, S373P, S375F, T376A, D405A, R408S, K417N, N440K, L452Q, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H | T19I, L24_P26del, A27S, G142D, V213G, D614G, H655Y, N679K, P681H, S704L, N764K, D796Y, Q954H, N969K |
SL. NO. | Vaccine | Country of Origin | Company Name | Clinical Trial Number | Phase | Recruitment Status | Number of Participants | Remark |
---|---|---|---|---|---|---|---|---|
1. | ABO1009-DP vaccine | China | Suzhou Abogen Biosciences Co., Ltd. | NCT05433194 | Phase I | Not Yet recruiting | 48 | A clinical trial which aimed to monitor the safety and efficacy profile of this vaccine against Omicron in fully vaccinated subjects below 18 years |
2. | Inactivated Omicron COVID-19 vaccine (Vero Cell) Inactivated | China | China National Biotec Group Company Limited | NCT05365724 | Phase II | Recruiting | 280 | A non-randomized trial which aims to monitor the safety and efficacy profiles of the vaccine in non-vaccinated subjects below 18 years old |
3. | mRNA-1273.214 Vaccine | Israel | Sheba Medical Center | NCT05383560 | Phase II | Not Yet recruiting | 150 | A placebo controlled study aimed to evaluate the immunogenicity of Omicron-matched booster doses in adult subjects |
4. | SCTV01E | China | Sinocelltech Ltd. | NCT05308576 | Phase III | Not Yet recruiting | 12,000 | A randomized study which monitored the safety profile of SCTV01E in subjects aging 12 years or older |
5. | BIBP Omicron Inactivated COVID-19 vaccine | Hong Kong | China National Biotec Group Company Limited | NCT05382871 | Phase III | Recruiting | 1800 | A randomized study which monitors the safety and efficacy of this vaccine in subjects who previously received two or three doses of any vaccine |
6. | mRNA-1273.214 (bivalent Omicron-containing vaccine) | United States | ModernaTX, Inc. | NCT04927065 | Phase III | Active | 5158 | Immunogenicity and safety evaluation of bivalent mRNA vaccine boosters for SARS-CoV-2 variants |
7. | Pfizer-BioNTech bivalent (Omicron-specific) vaccine | Australia | Murdoch Childrens Research Institute | NCT05543356 | Phase III | Withdrawn | 1143 | Evaluation of bivalent Omicron-specific COVID-19 vaccine booster dose (Pfizer-BioNTech) in healthy adults |
8. | Pfizer-BioNTech COVID-19 bivalent vaccine | United States | National Institute of Allergy and Infectious Diseases (NIAID) | NCT04977479 | Phase II | Active | 17 | Safety analysis of the COVID-19 mRNA vaccine (2nd dose) to individuals who had a systemic allergic reaction to a prior dose |
9. | Bivalent booster of mRNA based COVID-19 vaccine | United States | National Institute of Allergy and Infectious Diseases (NIAID) | NCT05518487 | Phase II | Not Yet recruiting | 80 | Safety and immunogenicity study of single dose of bivalent (mRNA-based) vaccine to individuals (kidney transplant recipient) with a persistently low SARS CoV-2 antibody titer |
10. | Bivalent mRNA COVID-19 vaccine | United States | National Institute of Allergy and Infectious Diseases (NIAID) | NCT05077254 | Phase II | Recruiting | 400 | Evaluation of Ab response to an extra dose of bivalent (mRNA-based) COVID-19 vaccination in subject of immunosuppression reduction in organ (kidney and liver) transplant recipients |
Sl. No. | Therapeutic Antibodies | Neutralization Efficacy in Different Omicron Sub-Variants | ||||
---|---|---|---|---|---|---|
BA.1 | BA.2 | BA.3 | BA.4 | BA.5 | ||
1. | Tixagevimab | Low | Low | Low | Low | Low |
2. | Bamlanivimab | Low | Low | Low | Low | Low |
3. | Imdevimab | Low | Moderate | Low | Moderate | Moderate |
4. | Regdanvimab | Low | Low | - | - | - |
5. | Sotrovimab | Moderate | Moderate | Moderate | Moderate | Moderate |
6. | Casirivimab | Low | Low | Low | Low | Low |
7. | Cilgavimab | Low | High | High | High | High |
8. | Etesevimab | Low | Low | Low | Low | Low |
9. | Bebtelovimab | High | High | High | High | High |
10. | Bamlanivimab + Etesevimab | Low | Low | Low | Low | Low |
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Chatterjee, S.; Bhattacharya, M.; Nag, S.; Dhama, K.; Chakraborty, C. A Detailed Overview of SARS-CoV-2 Omicron: Its Sub-Variants, Mutations and Pathophysiology, Clinical Characteristics, Immunological Landscape, Immune Escape, and Therapies. Viruses 2023, 15, 167. https://doi.org/10.3390/v15010167
Chatterjee S, Bhattacharya M, Nag S, Dhama K, Chakraborty C. A Detailed Overview of SARS-CoV-2 Omicron: Its Sub-Variants, Mutations and Pathophysiology, Clinical Characteristics, Immunological Landscape, Immune Escape, and Therapies. Viruses. 2023; 15(1):167. https://doi.org/10.3390/v15010167
Chicago/Turabian StyleChatterjee, Srijan, Manojit Bhattacharya, Sagnik Nag, Kuldeep Dhama, and Chiranjib Chakraborty. 2023. "A Detailed Overview of SARS-CoV-2 Omicron: Its Sub-Variants, Mutations and Pathophysiology, Clinical Characteristics, Immunological Landscape, Immune Escape, and Therapies" Viruses 15, no. 1: 167. https://doi.org/10.3390/v15010167