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Zabidi NZ, Liew HL, Farouk IA, Puniyamurti A, Yip AJW, Wijesinghe VN, Low ZY, Tang JW, Chow VTK, Lal SK. Evolution of SARS-CoV-2 Variants: Implications on Immune Escape, Vaccination, Therapeutic and Diagnostic Strategies. Viruses 2023; 15:v15040944. [PMID: 37112923 PMCID: PMC10145020 DOI: 10.3390/v15040944] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 is associated with a lower fatality rate than its SARS and MERS counterparts. However, the rapid evolution of SARS-CoV-2 has given rise to multiple variants with varying pathogenicity and transmissibility, such as the Delta and Omicron variants. Individuals with advanced age or underlying comorbidities, including hypertension, diabetes and cardiovascular diseases, are at a higher risk of increased disease severity. Hence, this has resulted in an urgent need for the development of better therapeutic and preventive approaches. This review describes the origin and evolution of human coronaviruses, particularly SARS-CoV-2 and its variants as well as sub-variants. Risk factors that contribute to disease severity and the implications of co-infections are also considered. In addition, various antiviral strategies against COVID-19, including novel and repurposed antiviral drugs targeting viral and host proteins, as well as immunotherapeutic strategies, are discussed. We critically evaluate strategies of current and emerging vaccines against SARS-CoV-2 and their efficacy, including immune evasion by new variants and sub-variants. The impact of SARS-CoV-2 evolution on COVID-19 diagnostic testing is also examined. Collectively, global research and public health authorities, along with all sectors of society, need to better prepare against upcoming variants and future coronavirus outbreaks.
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Affiliation(s)
- Nur Zawanah Zabidi
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Hern Liang Liew
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Isra Ahmad Farouk
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Ashwini Puniyamurti
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Ashley Jia Wen Yip
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | | | - Zheng Yao Low
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Julian W Tang
- Department of Respiratory Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - Vincent T K Chow
- Infectious Diseases Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Sunil K Lal
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
- Tropical Medicine & Biology Platform, Monash University, Subang Jaya 47500, Selangor, Malaysia
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52
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Sadeghi K, Zadheidar S, Zebardast A, Nejati A, Faraji M, Ghavami N, Kalantari S, Salimi V, Yavarian J, Abedi A, Jandaghi NZS, Mokhtari‐Azad T. Genomic surveillance of SARS-CoV-2 strains circulating in Iran during six waves of the pandemic. Influenza Other Respir Viruses 2023; 17:e13135. [PMID: 37078070 PMCID: PMC10106497 DOI: 10.1111/irv.13135] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/25/2023] [Accepted: 04/03/2023] [Indexed: 04/21/2023] Open
Abstract
Background SARS-CoV-2 genomic surveillance is necessary for the detection, monitoring, and evaluation of virus variants, which can have increased transmissibility, disease severity, or other adverse effects. We sequenced 330 SARS-CoV-2 genomes during the sixth wave of the COVID pandemic in Iran and compared them with five previous waves, for identifying SARS-CoV-2 variants, the genomic behavior of the virus, and understanding its characteristics. Methods After viral RNA extraction from clinical samples collected during the COVID-19 pandemic, next generation sequencing was performed using the Nextseq and Nanopore platforms. The sequencing data were analyzed and compared with reference sequences. Results In Iran during the first wave, V and L clades were detected. The second wave was recognized by G, GH, and GR clades. Circulating clades during the third wave were GH and GR. In the fourth wave, GRY (alpha variant), GK (delta variant), and one GH clade (beta variant) were detected. All viruses in the fifth wave were in GK clade (delta variant). In the sixth wave, Omicron variant (GRA clade) was circulating. Conclusions Genome sequencing, a key strategy in genomic surveillance systems, helps to detect and monitor the prevalence of SARS-CoV-2 variants, monitor the viral evolution of SARS-CoV-2, identify new variants for disease prevention, control, and treatment, and also provide information for and conduct public health measures in this area. With this system, Iran could be ready for surveillance of other respiratory virus diseases besides influenza and SARS-CoV-2.
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Affiliation(s)
- Kaveh Sadeghi
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Sevrin Zadheidar
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Arghavan Zebardast
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Ahmad Nejati
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Marziyeh Faraji
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Nastaran Ghavami
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Shirin Kalantari
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Vahid Salimi
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Jila Yavarian
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
- Research Center for Antibiotic Stewardship & Antimicrobial ResistanceTehran University of Medical SciencesTehranIran
| | - Adel Abedi
- Mathematics DepartmentShahid Beheshti UniversityTehranIran
| | | | - Talat Mokhtari‐Azad
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
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53
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Khan MS, Kim E, Hingrat QL, Kleinman A, Ferrari A, Sammartino JC, Percivalle E, Xu C, Huang S, Kenniston TW, Cassaniti I, Baldanti F, Pandrea I, Gambotto A, Apetrei C. Tetravalent SARS-CoV-2 S1 Subunit Protein Vaccination Elicits Robust Humoral and Cellular Immune Responses in SIV-Infected Rhesus Macaque Controllers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.532808. [PMID: 36993692 PMCID: PMC10055053 DOI: 10.1101/2023.03.15.532808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The COVID-19 pandemic has highlighted the need for safe and effective vaccines to be rapidly developed and distributed worldwide, especially considering the emergence of new SARS-CoV-2 variants. Protein subunit vaccines have emerged as a promising approach due to their proven safety record and ability to elicit robust immune responses. In this study, we evaluated the immunogenicity and efficacy of an adjuvanted tetravalent S1 subunit protein COVID-19 vaccine candidate composed of the Wuhan, B.1.1.7 variant, B.1.351 variant, and P.1 variant spike proteins in a nonhuman primate model with controlled SIVsab infection. The vaccine candidate induced both humoral and cellular immune responses, with T- and B cell responses mainly peaking post-boost immunization. The vaccine also elicited neutralizing and cross-reactive antibodies, ACE2 blocking antibodies, and T-cell responses, including spike specific CD4+ T cells. Importantly, the vaccine candidate was able to generate Omicron variant spike binding and ACE2 blocking antibodies without specifically vaccinating with Omicron, suggesting potential broad protection against emerging variants. The tetravalent composition of the vaccine candidate has significant implications for COVID-19 vaccine development and implementation, providing broad antibody responses against numerous SARS-CoV-2 variants.
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Affiliation(s)
- Muhammad S. Khan
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, PA 15213, USA
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - Eun Kim
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, PA 15213, USA
| | - Quentin Le Hingrat
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Adam Kleinman
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Alessandro Ferrari
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS Policlinico San Matteo, Via Taramelli 5, 27100 Pavia, Italy
| | - Jose C Sammartino
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS Policlinico San Matteo, Via Taramelli 5, 27100 Pavia, Italy
| | - Elena Percivalle
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS Policlinico San Matteo, Via Taramelli 5, 27100 Pavia, Italy
| | - Cuiling Xu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Shaohua Huang
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, PA 15213, USA
| | - Thomas W. Kenniston
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, PA 15213, USA
| | - Irene Cassaniti
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS Policlinico San Matteo, Via Taramelli 5, 27100 Pavia, Italy
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS Policlinico San Matteo, Via Taramelli 5, 27100 Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, 27100 Pavia, Italy
| | - Ivona Pandrea
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Andrea Gambotto
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, PA 15213, USA
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Cristian Apetrei
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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54
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Gerardi V, Rohaim MA, Naggar RFE, Atasoy MO, Munir M. Deep Structural Analysis of Myriads of Omicron Sub-Variants Revealed Hotspot for Vaccine Escape Immunity. Vaccines (Basel) 2023; 11:vaccines11030668. [PMID: 36992252 DOI: 10.3390/vaccines11030668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/18/2023] Open
Abstract
The emergence of the Omicron variant has reinforced the importance of continued SARS-CoV-2 evolution and its possible impact on vaccine effectiveness. Specifically, mutations in the receptor-binding domain (RBD) are critical to comprehend the flexibility and dynamicity of the viral interaction with the human agniotensin-converting enzyme 2 (hACE2) receptor. To this end, we have applied a string of deep structural and genetic analysis tools to map the substitution patterns in the S protein of major Omicron sub-variants (n = 51) with a primary focus on the RBD mutations. This head-to-head comparison of Omicron sub-variants revealed multiple simultaneous mutations that are attributed to antibody escape, and increased affinity and binding to hACE2. Our deep mapping of the substitution matrix indicated a high level of diversity at the N-terminal and RBD domains compared with other regions of the S protein, highlighting the importance of these two domains in a matched vaccination approach. Structural mapping identified highly variable mutations in the up confirmation of the S protein and at sites that critically define the function of the S protein in the virus pathobiology. These substitutional trends offer support in tracking mutations along the evolutionary trajectories of SAR-CoV-2. Collectively, the findings highlight critical areas of mutations across the major Omicron sub-variants and propose several hotspots in the S proteins of SARS-CoV-2 sub-variants to train the future design and development of COVID-19 vaccines.
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Affiliation(s)
- Valeria Gerardi
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, UK
| | - Mohammed A Rohaim
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, UK
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
| | - Rania F El Naggar
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, UK
- Department of Virology, Faculty of Veterinary Medicine, University of Sadat City, Sadat 32897, Egypt
| | - Mustafa O Atasoy
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, UK
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, UK
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A high-resolution melt curve toolkit to identify lineage-defining SARS-CoV-2 mutations. Sci Rep 2023; 13:3887. [PMID: 36890186 PMCID: PMC9994400 DOI: 10.1038/s41598-023-30754-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 02/28/2023] [Indexed: 03/10/2023] Open
Abstract
The emergence of severe acute respiratory syndrome 2 (SARS-CoV-2) variants of concern (VOCs), with mutations linked to increased transmissibility, vaccine escape and virulence, has necessitated the widespread genomic surveillance of SARS-CoV-2. This has placed a strain on global sequencing capacity, especially in areas lacking the resources for large scale sequencing activities. Here we have developed three separate multiplex high-resolution melting assays to enable the identification of Alpha, Beta, Delta and Omicron VOCs. The assays were evaluated against whole genome sequencing on upper-respiratory swab samples collected during the Alpha, Delta and Omicron [BA.1] waves of the UK pandemic. The sensitivities of the eight individual primer sets were all 100%, and specificity ranged from 94.6 to 100%. The multiplex HRM assays have potential as a tool for high throughput surveillance of SARS-CoV-2 VOCs, particularly in areas with limited genomics facilities.
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56
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Ford ES, Simmons W, Karmarkar EN, Yoke LH, Braimah AB, Orozco JJ, Ghiuzeli CM, Barnhill S, Sack CL, Benditt JO, Roychoudhury P, Greninger AL, Shapiro AE, Hammond JL, Rusnak JM, Dolsten M, Boeckh M, Liu C, Cheng GS, Corey L. Successful Treatment of Prolonged, Severe Coronavirus Disease 2019 Lower Respiratory Tract Disease in a B cell Acute Lymphoblastic Leukemia Patient With an Extended Course of Remdesivir and Nirmatrelvir/Ritonavir. Clin Infect Dis 2023; 76:926-929. [PMID: 36326680 PMCID: PMC10226728 DOI: 10.1093/cid/ciac868] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
A patient with B-cell acute lymphoblastic leukemia (ALL) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had persistent, progressive pneumonia with viremia after 5 months of infection despite monoclonal antibodies, intravenous (IV) remdesivir and prolonged oral steroids. Twenty days of nirmatrelvir/ritonavir and 10 days of IV remdesivir led to full recovery.
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Affiliation(s)
- Emily S Ford
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
| | - William Simmons
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Ellora N Karmarkar
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Leah H Yoke
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
| | - Ayodale B Braimah
- Division of General Internal Medicine, Department of Medicine, University of Washington,Seattle, Washington, USA
| | - Johnnie J Orozco
- Clinical Research Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Division of Medical Oncology, Department of Medicine, University of Washington,Seattle, Washington, USA
| | - Cristina M Ghiuzeli
- Clinical Research Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Division of Hematology, Department of Medicine, University of Washington,Seattle, Washington, USA
| | - Serena Barnhill
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington,Seattle, Washington, USA
| | - Coralynn L Sack
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington,Seattle, Washington, USA
| | - Joshua O Benditt
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington,Seattle, Washington, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Department of Laboratory Medicine, University of Washington,Seattle, Washington, USA
| | - Alexander L Greninger
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Department of Laboratory Medicine, University of Washington,Seattle, Washington, USA
| | - Adrienne E Shapiro
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Department of Global Health, University of Washington,Seattle, Washington, USA
| | | | | | | | - Michael Boeckh
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
| | - Catherine Liu
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
| | - Guang-Shing Cheng
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington,Seattle, Washington, USA
| | - Lawrence Corey
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Department of Laboratory Medicine, University of Washington,Seattle, Washington, USA
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57
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Milligan EC, Olstad K, Williams CA, Mallory M, Cano P, Cross KA, Munt JE, Garrido C, Lindesmith L, Watanabe J, Usachenko JL, Hopkins L, Immareddy R, Shaan Lakshmanappa Y, Elizaldi SR, Roh JW, Sammak RL, Pollard RE, Yee JL, Herbek S, Scobey T, Miehlke D, Fouda G, Ferrari G, Gao H, Shen X, Kozlowski PA, Montefiori D, Hudgens MG, Edwards DK, Carfi A, Corbett KS, Graham BS, Fox CB, Tomai M, Iyer SS, Baric R, Reader R, Dittmer DP, Van Rompay KKA, Permar SR, De Paris K. Infant rhesus macaques immunized against SARS-CoV-2 are protected against heterologous virus challenge 1 year later. Sci Transl Med 2023; 15:eadd6383. [PMID: 36454813 PMCID: PMC9765459 DOI: 10.1126/scitranslmed.add6383] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The U.S. Food and Drug Administration only gave emergency use authorization of the BNT162b2 and mRNA-1273 SARS-CoV-2 vaccines for infants 6 months and older in June 2022. Yet questions regarding the durability of vaccine efficacy, especially against emerging variants, in this age group remain. We demonstrated previously that a two-dose regimen of stabilized prefusion Washington SARS-CoV-2 S-2P spike (S) protein encoded by mRNA encapsulated in lipid nanoparticles (mRNA-LNP) or purified S-2P mixed with 3M-052, a synthetic Toll-like receptor (TLR) 7/8 agonist, in a squalene emulsion (Protein+3M-052-SE) was safe and immunogenic in infant rhesus macaques. Here, we demonstrate that broadly neutralizing and spike-binding antibodies against variants of concern (VOCs), as well as T cell responses, persisted for 12 months. At 1 year, corresponding to human toddler age, we challenged vaccinated rhesus macaques and age-matched nonvaccinated controls intranasally and intratracheally with a high dose of heterologous SARS-CoV-2 B.1.617.2 (Delta). Seven of eight control rhesus macaques exhibited severe interstitial pneumonia and high virus replication in the upper and lower respiratory tract. In contrast, vaccinated rhesus macaques had faster viral clearance with mild to no pneumonia. Neutralizing and binding antibody responses to the B.1.617.2 variant at the day of challenge correlated with lung pathology and reduced virus replication. Overall, the Protein+3M-052-SE vaccine provided superior protection to the mRNA-LNP vaccine, emphasizing opportunities for optimization of current vaccine platforms. The observed efficacy of both vaccines 1 year after vaccination supports the implementation of an early-life SARS-CoV-2 vaccine.
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Affiliation(s)
- Emma C Milligan
- Department of Microbiology and Immunology, Children's Research Institute, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Katherine Olstad
- California National Primate Research Center, University of California at Davis, Davis, CA 95616, USA
| | - Caitlin A Williams
- Department of Pediatrics, Weill Cornell Medical College, New York, NY 10065, USA
| | - Michael Mallory
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Patricio Cano
- Lineberger Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kaitlyn A Cross
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jennifer E Munt
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Carolina Garrido
- Center for Immunology and Infectious Diseases, University of California at Davis, Davis, CA 95616, USA
| | - Lisa Lindesmith
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jennifer Watanabe
- California National Primate Research Center, University of California at Davis, Davis, CA 95616, USA
| | - Jodie L Usachenko
- California National Primate Research Center, University of California at Davis, Davis, CA 95616, USA
| | - Lincoln Hopkins
- California National Primate Research Center, University of California at Davis, Davis, CA 95616, USA
| | - Ramya Immareddy
- California National Primate Research Center, University of California at Davis, Davis, CA 95616, USA
| | | | - Sonny R Elizaldi
- Center for Immunology and Infectious Diseases, University of California at Davis, Davis, CA 95616, USA.,Graduate Group in Immunology, University of California at Davis, Davis, CA 95616, USA
| | - Jamin W Roh
- Center for Immunology and Infectious Diseases, University of California at Davis, Davis, CA 95616, USA.,Graduate Group in Immunology, University of California at Davis, Davis, CA 95616, USA
| | - Rebecca L Sammak
- California National Primate Research Center, University of California at Davis, Davis, CA 95616, USA
| | - Rachel E Pollard
- School of Veterinary Medicine, University of California at Davis, Davis, CA 95616, USA
| | - JoAnn L Yee
- California National Primate Research Center, University of California at Davis, Davis, CA 95616, USA
| | - Savannah Herbek
- Department of Pediatrics, Weill Cornell Medical College, New York, NY 10065, USA
| | - Trevor Scobey
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dieter Miehlke
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Genevieve Fouda
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Guido Ferrari
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Hongmei Gao
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaoying Shen
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Pamela A Kozlowski
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - David Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Michael G Hudgens
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | | - Kizzmekia S Corbett
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20852, USA
| | - Christopher B Fox
- Access to Advanced Health Institute, Seattle, WA 98102, USA.,Department of Global Health, University of Washington, Seattle, WA 98105, USA
| | - Mark Tomai
- 3M Corporate Research Materials Laboratory, Saint Paul, MN 55144, USA
| | - Smita S Iyer
- California National Primate Research Center, University of California at Davis, Davis, CA 95616, USA.,Center for Immunology and Infectious Diseases, University of California at Davis, Davis, CA 95616, USA
| | - Ralph Baric
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rachel Reader
- California National Primate Research Center, University of California at Davis, Davis, CA 95616, USA
| | - Dirk P Dittmer
- Department of Microbiology and Immunology, Children's Research Institute, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Pediatrics, Weill Cornell Medical College, New York, NY 10065, USA
| | - Koen K A Van Rompay
- California National Primate Research Center, University of California at Davis, Davis, CA 95616, USA.,Department of Pathology, Microbiology and Immunology, University of California at Davis, Davis, CA 95616, USA
| | - Sallie R Permar
- Department of Pediatrics, Weill Cornell Medical College, New York, NY 10065, USA
| | - Kristina De Paris
- Department of Microbiology and Immunology, Children's Research Institute, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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58
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Das NC, Chakraborty P, Bayry J, Mukherjee S. Comparative Binding Ability of Human Monoclonal Antibodies against Omicron Variants of SARS-CoV-2: An In Silico Investigation. Antibodies (Basel) 2023; 12:antib12010017. [PMID: 36975364 PMCID: PMC10045060 DOI: 10.3390/antib12010017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 02/26/2023] Open
Abstract
Mutation(s) in the spike protein is the major characteristic trait of newly emerged SARS-CoV-2 variants such as Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Delta-plus. Omicron (B.1.1.529) is the latest addition and it has been characterized by high transmissibility and the ability to escape host immunity. Recently developed vaccines and repurposed drugs exert limited action on Omicron strains and hence new therapeutics are immediately needed. Herein, we have explored the efficiency of twelve therapeutic monoclonal antibodies (mAbs) targeting the RBD region of the spike glycoprotein against all the Omicron variants bearing a mutation in spike protein through molecular docking and molecular dynamics simulation. Our in silico evidence reveals that adintivimab, beludivimab, and regadanivimab are the most potent mAbs to form strong biophysical interactions and neutralize most of the Omicron variants. Considering the efficacy of mAbs, we incorporated CDRH3 of beludavimab within the framework of adintrevimab, which displayed a more intense binding affinity towards all of the Omicron variants viz. BA.1, BA.2, BA.2.12.1, BA.4, and BA.5. Furthermore, the cDNA of chimeric mAb was cloned in silico within pET30ax for recombinant production. In conclusion, the present study represents the candidature of human mAbs (beludavimab and adintrevimab) and the therapeutic potential of designed chimeric mAb for treating Omicron-infected patients.
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Affiliation(s)
- Nabarun Chandra Das
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol 713 340, India
| | - Pritha Chakraborty
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol 713 340, India
| | - Jagadeesh Bayry
- Department of Biological Sciences & Engineering, Indian Institute of Technology Palakkad, Palakkad 678 623, India
- Correspondence: (J.B.); or (S.M.)
| | - Suprabhat Mukherjee
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol 713 340, India
- Correspondence: (J.B.); or (S.M.)
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Molnupiravir: A Versatile Prodrug against SARS-CoV-2 Variants. Metabolites 2023; 13:metabo13020309. [PMID: 36837928 PMCID: PMC9962121 DOI: 10.3390/metabo13020309] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
The nucleoside analog β-D-N4-hydroxycytidine is the active metabolite of the prodrug molnupiravir and is accepted as an efficient drug against COVID-19. Molnupiravir targets the RNA-dependent RNA polymerase (RdRp) enzyme, which is responsible for replicating the viral genome during the replication process of certain types of viruses. It works by disrupting the normal function of the RdRp enzyme, causing it to make mistakes during the replication of the viral genome. These mistakes can prevent the viral RNA from being transcribed, converted into a complementary DNA template, translated, or converted into a functional protein. By disrupting these crucial steps in the viral replication process, molnupiravir can effectively inhibit the replication of the virus and reduce its ability to cause disease. This review article sheds light on the impact of molnupiravir and its metabolite on SARS-CoV-2 variants of concern, such as delta, omicron, and hybrid/recombinant variants. The detailed mechanism and molecular interactions using molecular docking and dynamics have also been covered. The safety and tolerability of molnupiravir in patients with comorbidities have also been emphasized.
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60
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Lee M, Major M, Hong H. Distinct Conformations of SARS-CoV-2 Omicron Spike Protein and Its Interaction with ACE2 and Antibody. Int J Mol Sci 2023; 24:3774. [PMID: 36835186 PMCID: PMC9967551 DOI: 10.3390/ijms24043774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Since November 2021, Omicron has been the dominant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant that causes the coronavirus disease 2019 (COVID-19) and has continuously impacted human health. Omicron sublineages are still increasing and cause increased transmission and infection rates. The additional 15 mutations on the receptor binding domain (RBD) of Omicron spike proteins change the protein conformation, enabling the Omicron variant to evade neutralizing antibodies. For this reason, many efforts have been made to design new antigenic variants to induce effective antibodies in SARS-CoV-2 vaccine development. However, understanding the different states of Omicron spike proteins with and without external molecules has not yet been addressed. In this review, we analyze the structures of the spike protein in the presence and absence of angiotensin-converting enzyme 2 (ACE2) and antibodies. Compared to previously determined structures for the wildtype spike protein and other variants such as alpha, beta, delta, and gamma, the Omicron spike protein adopts a partially open form. The open-form spike protein with one RBD up is dominant, followed by the open-form spike protein with two RBD up, and the closed-form spike protein with the RBD down. It is suggested that the competition between antibodies and ACE2 induces interactions between adjacent RBDs of the spike protein, which lead to a partially open form of the Omicron spike protein. The comprehensive structural information of Omicron spike proteins could be helpful for the efficient design of vaccines against the Omicron variant.
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Affiliation(s)
- Myeongsang Lee
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Marian Major
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Huixiao Hong
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
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61
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Jäger M, Dichtl S, Bellmann-Weiler R, Reindl M, Lass-Flörl C, Wilflingseder D, Posch W. Serum Neutralization Against SARS-CoV-2 Variants Is Heterogenic and Depends on Vaccination Regimen. J Infect Dis 2023; 227:528-532. [PMID: 36315869 PMCID: PMC9927074 DOI: 10.1093/infdis/jiac432] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/24/2022] [Accepted: 10/28/2022] [Indexed: 11/05/2022] Open
Abstract
Omicron variants are still the dominant SARS-CoV-2 viruses worldwide, therefore determination of the level of protection from infection and severe disease is essential. Here, we investigated humoral and cellular immunity of individuals immunized by ChAdOx1, BNT162b2, and mRNA-1273 and our results show that IgG and neutralization titers wane over time. However, strongest neutralization against Omicron BA.1 and T-cell responses were detected in ChAdOx1 vaccinees 6 months after the second dose, while no long-lasting neutralization was shown against BA.2 in any cohort. Crucially, our investigation revealed that immunity against variants of concern is heterogenic and dependent on the immunization status.
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Affiliation(s)
- Michael Jäger
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Stefanie Dichtl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Rosa Bellmann-Weiler
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Markus Reindl
- Clinical Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Doris Wilflingseder
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Wilfried Posch
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
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Singh J, Anantharaj A, Panwar A, Rani C, Bhardwaj M, Kumar P, Chattopadhyay P, Devi P, Maurya R, Mishra P, Pandey AK, Pandey R, Medigeshi GR. BA.1, BA.2 and BA.2.75 variants show comparable replication kinetics, reduced impact on epithelial barrier and elicit cross-neutralizing antibodies. PLoS Pathog 2023; 19:e1011196. [PMID: 36827451 PMCID: PMC9994724 DOI: 10.1371/journal.ppat.1011196] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 03/08/2023] [Accepted: 02/09/2023] [Indexed: 02/26/2023] Open
Abstract
The Omicron variant of SARS-CoV-2 is capable of infecting unvaccinated, vaccinated and previously-infected individuals due to its ability to evade neutralization by antibodies. With multiple sub-lineages of Omicron emerging in the last 12 months, there is inadequate information on the quantitative antibody response generated upon natural infection with Omicron variant and whether these antibodies offer cross-protection against other sub-lineages of Omicron variant. In this study, we characterized the growth kinetics of Kappa, Delta and Omicron variants of SARS-CoV-2 in Calu-3 cells. Relatively higher amounts infectious virus titers, cytopathic effect and disruption of epithelial barrier functions was observed with Delta variant whereas infection with Omicron sub-lineages led to a more robust induction of interferon pathway, lower level of virus replication and mild effect on epithelial barrier. The replication kinetics of BA.1, BA.2 and BA.2.75 sub-lineages of the Omicron variant were comparable in cell culture and natural infection in a subset of individuals led to a significant increase in binding and neutralizing antibodies to the Delta variant and all the three sub-lineages of Omicron but the level of neutralizing antibodies were lowest against the BA.2.75 variant. Finally, we show that Cu2+, Zn2+ and Fe2+ salts inhibited in vitro RdRp activity but only Cu2+ and Fe2+ inhibited both the Delta and Omicron variants in cell culture. Thus, our results suggest that high levels of interferons induced upon infection with Omicron variant may counter virus replication and spread. Waning neutralizing antibody titers rendered subjects susceptible to infection by Omicron variants and natural Omicron infection elicits neutralizing antibodies that can cross-react with other sub-lineages of Omicron and other variants of concern.
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Affiliation(s)
- Janmejay Singh
- Bioassay Laboratory and Clinical and Cellular Virology Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Anbalagan Anantharaj
- Bioassay Laboratory and Clinical and Cellular Virology Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Aleksha Panwar
- Bioassay Laboratory and Clinical and Cellular Virology Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Chitra Rani
- Bioassay Laboratory and Clinical and Cellular Virology Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Monika Bhardwaj
- Bioassay Laboratory and Clinical and Cellular Virology Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Parveen Kumar
- Bioassay Laboratory and Clinical and Cellular Virology Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Partha Chattopadhyay
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Priti Devi
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ranjeet Maurya
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Pallavi Mishra
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Anil Kumar Pandey
- Employees State Insurance Corporation Medical College and Hospital, Faridabad, Haryana, India
| | - Rajesh Pandey
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Guruprasad R. Medigeshi
- Bioassay Laboratory and Clinical and Cellular Virology Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana, India
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Mao S, Li S, Zhang Y, Long L, Peng J, Cao Y, Mao JZ, Qi X, Xin Q, San G, Ding J, Jiang J, Bai X, Wang Q, Xu P, Xia H, Lu L, Xie L, Kong D, Zhu S, Xu W. A highly efficient needle-free-injection delivery system for mRNA-LNP vaccination against SARS-CoV-2. NANO TODAY 2023; 48:101730. [PMID: 36570700 PMCID: PMC9767897 DOI: 10.1016/j.nantod.2022.101730] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/05/2022] [Accepted: 12/13/2022] [Indexed: 05/14/2023]
Abstract
Despite the various vaccines that have been developed to combat the coronavirus disease 2019 (COVID-19) pandemic, the persistent and unpredictable mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) require innovative and unremitting solutions to cope with the resultant immune evasion and establish a sustainable immune barrier. Here we introduce a vaccine-delivery system with a combination of a needle-free injection (NFI) device and a SARS-CoV-2-Spike-specific mRNA-Lipid Nanoparticle (LNP) vaccine. The benefits are duller pain and a significant increase of immunogenicity compared to the canonical needle injection (NI). From physicochemical and bioactivity analyses, the structure of the mRNA-LNP maintains stability upon NFI, contradictory to the belief that LNPs are inclined towards destruction under the high-pressure conditions of NFI. Moreover, mRNA-LNP vaccine delivered by NFI induces significantly more binding and neutralizing antibodies against SARS-CoV-2 variants than the same vaccine delivered by NI. Heterogeneous vaccination of BA.5-LNP vaccine with NFI enhanced the generation of neutralizing antibodies against Omicron BA.5 variants in rabbits previously vaccinated with non-BA.5-specific mRNA-LNP or other COVID-19 vaccines. NFI parameters can be adjusted to deliver mRNA-LNP subcutaneously or intramuscularly. Taken together, our results suggest that NFI-based mRNA-LNP vaccination is an effective substitute for the traditional NI-based mRNA-LNP vaccination.
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Affiliation(s)
- Shanhong Mao
- School of Biomedical Engineering, Capital Medical University, Beijing 100069, China
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Shiyou Li
- Tricision Biotherapeutic Inc, Beijing 100176, Zhuhai 519040, China
| | - Yuxin Zhang
- Beijing QS Medical Technology Co.,Ltd., Beijing 100176, China
| | - Luoxin Long
- School of Biomedical Engineering, Capital Medical University, Beijing 100069, China
| | - Junfeng Peng
- Tricision Biotherapeutic Inc, Beijing 100176, Zhuhai 519040, China
| | - Yuanyan Cao
- School of Biomedical Engineering, Capital Medical University, Beijing 100069, China
| | - Jessica Z Mao
- School of Veterinary Medicine & Biomedical Sciences, Texas A&M, College Station, TX 77843, USA
| | - Xin Qi
- Beijing QS Medical Technology Co.,Ltd., Beijing 100176, China
| | - Qi Xin
- Tricision Biotherapeutic Inc, Beijing 100176, Zhuhai 519040, China
| | - Guoliang San
- Beijing QS Medical Technology Co.,Ltd., Beijing 100176, China
| | - Jing Ding
- Beijing QS Medical Technology Co.,Ltd., Beijing 100176, China
| | - Jun Jiang
- Tricision Biotherapeutic Inc, Beijing 100176, Zhuhai 519040, China
| | - Xuejiao Bai
- Tricision Biotherapeutic Inc, Beijing 100176, Zhuhai 519040, China
| | - Qianting Wang
- Tricision Biotherapeutic Inc, Beijing 100176, Zhuhai 519040, China
| | - Pengfei Xu
- Tricision Biotherapeutic Inc, Beijing 100176, Zhuhai 519040, China
| | - Huan Xia
- Tricision Biotherapeutic Inc, Beijing 100176, Zhuhai 519040, China
| | - Lijun Lu
- Tricision Biotherapeutic Inc, Beijing 100176, Zhuhai 519040, China
| | - Liangzhi Xie
- Beijing Engineering Research Center of Protein and Antibody, Sinocelltech Ltd., Beijing 100176, China
| | - Desheng Kong
- Beijing Engineering Research Center of Protein and Antibody, Sinocelltech Ltd., Beijing 100176, China
| | - Shuangli Zhu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Wenbo Xu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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Khan MS, Kim E, Huang S, Kenniston TW, Gambotto A. Trivalent SARS-CoV-2 S1 Subunit Protein Vaccination Induces Broad Humoral Responses in BALB/c Mice. Vaccines (Basel) 2023; 11:314. [PMID: 36851191 PMCID: PMC9967783 DOI: 10.3390/vaccines11020314] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/18/2023] [Accepted: 01/28/2023] [Indexed: 02/04/2023] Open
Abstract
This paper presents a novel approach for improving the efficacy of COVID-19 vaccines against emergent SARS-CoV-2 variants. We have evaluated the immunogenicity of unadjuvanted wild-type (WU S1-RS09cg) and variant-specific (Delta S1-RS09cg and OM S1-RS09cg) S1 subunit protein vaccines delivered either as a monovalent or a trivalent antigen in BALB/c mice. Our results show that a trivalent approach induced a broader humoral response with more coverage against antigenically distinct variants, especially when compared to monovalent Omicron-specific S1. This trivalent approach was also found to have increased or equivalent ACE2 binding inhibition, and increased S1 IgG endpoint titer at early timepoints, against SARS-CoV-2 spike variants when compared monovalent Wuhan, Delta, or Omicron S1. Our results demonstrate the utility of protein subunit vaccines against COVID-19 and provide insights into the impact of variant-specific COVID-19 vaccine approaches on the immune response in the current SARS-CoV-2 variant landscape. Particularly, our study provides insight into effects of further increasing valency of currently approved SARS-CoV-2 vaccines, a promising approach for improving protection to curtail emerging viral variants.
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Affiliation(s)
- Muhammad S. Khan
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Eun Kim
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Shaohua Huang
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Thomas W. Kenniston
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Andrea Gambotto
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
- Department of Medicine, Division of Infectious Disease, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
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Rapid System to Detect Variants of SARS-CoV-2 in Nasopharyngeal Swabs. Viruses 2023; 15:v15020353. [PMID: 36851567 PMCID: PMC9966895 DOI: 10.3390/v15020353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/28/2023] Open
Abstract
Currently, the reference method for identifying the presence of variants of SARS-CoV-2 is whole genome sequencing. Although it is less expensive than in the past, it is still time-consuming, and interpreting the results is difficult, requiring staff with specific skills who are not always available in diagnostic laboratories. The test presented in this study aimed to detect, using traditional real-time PCR, the presence of the main variants described for the spike protein of the SARS-CoV-2 genome. The primers and probes were designed to detect the main deletions that characterize the different variants. The amplification targets were deletions in the S gene: 25-27, 69-70, 241-243, and 157-158. In the ORF1a gene, the deletion 3675-3677 was chosen. Some of these mutations can be considered specific variants, while others can be identified by the simultaneous presence of one or more deletions. We avoided using point mutations in order to improve the speed of the test. Our test can help clinical and medical microbiologists quickly recognize the presence of variants in biological samples (particularly nasopharyngeal swabs). The test can also be used to identify variants of the virus that could potentially be more diffusive as well as not responsive to the vaccine.
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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. [PMID: 36680207 PMCID: PMC9866114 DOI: 10.3390/v15010167] [Citation(s) in RCA: 92] [Impact Index Per Article: 92.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
The COVID-19 pandemic has created significant concern for everyone. Recent data from many worldwide reports suggest that most infections are caused by the Omicron variant and its sub-lineages, dominating all the previously emerged variants. The numerous mutations in Omicron's viral genome and its sub-lineages attribute it a larger amount of viral fitness, owing to the alteration of the transmission and pathophysiology of the virus. With a rapid change to the viral structure, Omicron and its sub-variants, namely BA.1, BA.2, BA.3, BA.4, and BA.5, dominate the community with an ability to escape the neutralization efficiency induced by prior vaccination or infections. Similarly, several recombinant sub-variants of Omicron, namely XBB, XBD, and XBF, etc., have emerged, which a better understanding. This review mainly entails the changes to Omicron and its sub-lineages due to it having a higher number of mutations. The binding affinity, cellular entry, disease severity, infection rates, and most importantly, the immune evading potential of them are discussed in this review. A comparative analysis of the Delta variant and the other dominating variants that evolved before Omicron gives the readers an in-depth understanding of the landscape of Omicron's transmission and infection. Furthermore, this review discusses the range of neutralization abilities possessed by several approved antiviral therapeutic molecules and neutralizing antibodies which are functional against Omicron and its sub-variants. The rapid evolution of the sub-variants is causing infections, but the broader aspect of their transmission and neutralization has not been explored. Thus, the scientific community should adopt an elucidative approach to obtain a clear idea about the recently emerged sub-variants, including the recombinant variants, so that effective neutralization with vaccines and drugs can be achieved. This, in turn, will lead to a drop in the number of cases and, finally, an end to the pandemic.
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Affiliation(s)
- Srijan Chatterjee
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata 700126, West Bengal, India
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore 756020, Odisha, India
| | - Sagnik Nag
- Department of Biotechnology, School of Biosciences & Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata 700126, West Bengal, India
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Chakraborti S, Gill J, Goswami R, Kumar S, Chandele A, Sharma A. Structural Profiles of SARS-CoV-2 Variants in India. Curr Microbiol 2023; 80:1. [PMID: 36414797 PMCID: PMC9684916 DOI: 10.1007/s00284-022-03094-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 10/17/2022] [Indexed: 11/24/2022]
Abstract
India was severely affected by several waves of SARS-CoV-2 infection that occurred during April-June 2021 (second wave) and December 2021-January 2022 (third wave) and thereafter, resulting in >10 million new infections and a significant number of deaths. Global Initiative on Sharing Avian Influenza Data database was used to collect the sequence information of ~10,000 SARS-CoV-2 patients from India and our sequence analysis identified three variants B.1.1.7 (alpha, α), B1.617.2 (delta, Δ), B.1.1.529 (Omicron, Oo) and one Omicron sub-variant BA.2.75 as the primary drivers for SARS-CoV-2 waves in India. Structural visualization and analysis of important mutations of alpha, delta, Omicron and its sub-variants of SARS-CoV-2 Receptor-Binding Domain (RBD) was performed and our analysis clearly shows that mutations occur throughout the RBD, including the RBD surface responsible for human angiotensin-converting enzyme 2 (hACE-2) receptor-binding. A comparison between alpha, delta and omicron variants/sub-variants reveals many omicron mutations in the hACE-2 binding site and several other mutations within 5 Å of this binding region. Further, computational analysis highlights the importance of electrostatic interactions in stabilizing RBD-hACE-2-binding, especially in the omicron variant. Our analysis explores the likely role of key alpha, delta and omicron mutations on binding with hACE-2. Taken together, our study provides novel structural insights into the implications of RBD mutations in alpha, delta and omicron and its sub-variants that were responsible for India's SARS-CoV-2 surge.
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Affiliation(s)
- Soumyananda Chakraborti
- National Institute of Malaria Research, New Delhi, 110077, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India.
| | - Jasmita Gill
- National Institute of Malaria Research, New Delhi, 110077, India.
| | - Ritu Goswami
- National Institute of Malaria Research, New Delhi, 110077, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India
| | - Sanjeev Kumar
- ICGEB-Emory Vaccine Center, Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Anmol Chandele
- ICGEB-Emory Vaccine Center, Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Amit Sharma
- National Institute of Malaria Research, New Delhi, 110077, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, 201002, India
- Structural Parasitology, Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
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68
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Zhou Y, Zhi H, Teng Y. The outbreak of SARS-CoV-2 Omicron lineages, immune escape, and vaccine effectivity. J Med Virol 2023; 95:e28138. [PMID: 36097349 PMCID: PMC9538491 DOI: 10.1002/jmv.28138] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 08/03/2022] [Accepted: 09/07/2022] [Indexed: 01/11/2023]
Abstract
As of November 2021, several SARS-CoV-2 variants appeared and became dominant epidemic strains in many countries, including five variants of concern (VOCs) Alpha, Beta, Gamma, Delta, and Omicron defined by the World Health Organization during the COVID-19 pandemic. As of August 2022, Omicron is classified into five main lineages, BA.1, BA.2, BA.3, BA.4, BA.5 and some sublineages (BA.1.1, BA.2.12.1, BA.2.11, BA.2.75, BA.4.6) (https://www.gisaid.org/). Compared to the previous VOCs (Alpha, Beta, Gamma, and Delta), all the Omicron lineages have the most highly mutations in the spike protein, and with 50 mutations accumulated throughout the genome. Early data indicated that Omicron BA.2 sublineage had higher infectivity and more immune escape than the early wild-type (WT) strain, the previous VOCs, and BA.1. Recently, global surveillance data suggest a higher transmissibility of BA.4/BA.5 than BA.1, BA.1.1 and BA.2, and BA.4/BA.5 is becoming dominant strain in many countries globally.
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Affiliation(s)
- Yongbing Zhou
- Department of Clinical Laboratory, Hangzhou Third People's Hospital, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huilin Zhi
- Department of Dermatology, Hangzhou Third People's Hospital, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yong Teng
- Department of Clinical Laboratory, Hangzhou Third People's Hospital, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Neohesperidin and spike RBD interaction in omicron and its sub-variants: In silico, structural and simulation studies. Comput Biol Med 2023; 152:106392. [PMID: 36502697 PMCID: PMC9721375 DOI: 10.1016/j.compbiomed.2022.106392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 10/29/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged first around December 2019 in the city of Wuhan, China. Since then, several variants of the virus have emerged with different biological properties. This pandemic has so far led to widespread infection cycles with millions of fatalities and infections globally. In the recent cycle, a new variant omicron and its three sub-variants BA.1, BA.2 and BA.3 have emerged which seems to evade host immune defences and have brisk infection rate. Particularly, BA.2 variant has shown high transmission rate over BA.1 strain in different countries including India. In the present study, we have evaluated a set of eighty drugs/compounds using in silico docking calculations in omicron and its variants. These molecules were reported previously against SARS-CoV-2. Our docking and simulation analyses suggest differences in affinity of these compounds in omicron and BA.2 compared to SARS-CoV-2. These studies show that neohesperidin, a natural flavonoid found in Citrus aurantium makes a stable interaction with spike receptor domain of omicron and BA.2 compared to other variants. Free energy binding analyses further validates that neohesperidin forms a stable complex with spike RBD in omicron and BA.2 with a binding energy of -237.9 ± 18.7 kJ/mol and -164.1 ± 17.5 kJ/mol respectively. Key residual differences in the RBD interface of these variants form the basis for differential interaction affinities with neohesperidin as drug binding site overlaps with RBD-human ACE2 interface. These data might be useful for the design and development of novel scaffolds and pharmacophores to develop specific therapeutic strategies against these novel variants.
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70
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Guest PC, Hawkins SFC, Rahmoune H. Rapid Detection of SARS-CoV-2 Variants of Concern by Genomic Surveillance Techniques. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1412:491-509. [PMID: 37378785 DOI: 10.1007/978-3-031-28012-2_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
This chapter describes the application of genomic, transcriptomic, proteomic, and metabolomic methods in the study of SARS-CoV-2 variants of concern. We also describe the important role of machine learning tools to identify the most significant biomarker signatures and discuss the latest point-of-care devices that can be used to translate these findings to the physician's office or to bedside care. The main emphasis is placed on increasing our diagnostic capacity and predictability of disease outcomes to guide the most appropriate treatment strategies.
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Affiliation(s)
- Paul C Guest
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Department of Psychiatry, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
- Laboratory of Translational Psychiatry, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | | | - Hassan Rahmoune
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
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71
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Ahmadi K, Shahbazi B, Zakeri AJ, Gouklani H. Characterization of SARS-CoV-2 omicron variants from Iran and evaluation of the effect of mutations on the spike, nucleocapsid, ORF8, and ORF9b proteins function. J Biomol Struct Dyn 2022; 41:11415-11430. [PMID: 36576175 DOI: 10.1080/07391102.2022.2162131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/18/2022] [Indexed: 12/29/2022]
Abstract
The SARS-CoV-2 'Omicron' strain, with 15 mutations in the receptor binding domain (RBD), was detected in South Africa and rapidly spread worldwide. SARS-CoV-2 ORF9b protein by binding to the TOM70 receptor and ORF8 protein by binding to MHC-I, IF3 receptors inhibit the host's immune response. In this study, genomics variations were evaluated for 96 samples isolated from Iran from March to July 2022 using the Nextclade web server and informatics tools. We identified the mutations occurring in the SARS-CoV-2 proteins. We also evaluated the effect of mutations on spike protein interaction with the ACE2 receptor, ORF9b protein interaction with the TOM70 receptor, and structural stability of ORF8 and nucleocapsid proteins using docking and molecular dynamics. Results indicated that during March and April 2022, the BA.2 strain was dominant in the south of Iran, while during June 2022, the BA.5 strain was dominant. BF.5 strain had the most divergence among SARS-CoV-2 strains reported from south of Iran. The binding affinity of BA.5 and BF.5 strains spike protein to ACE2 receptor is similar, and compared to BA.2 strain, was stronger. The BF.5 ORF9b K40R mutation causes a better binding affinity of the protein to the TOM70 receptor. Also, mutations that occurred in the ORF8 protein led to instability in the dimer formation of this protein and improved immune response for mutations that occurred in BA.2 strain, while this mutation did not occur in BF.5 strain. The mutations that were detected in nucleocapsid protein CTD and NTD domains caused the stability of these domains.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Khadijeh Ahmadi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Behzad Shahbazi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Abdul-Jabbar Zakeri
- Social Determinants in Health Promotion Research Center, Research Institute for Health, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Hamed Gouklani
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
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Replacement dynamics and the pathogenesis of the Alpha, Delta and Omicron variants of SARS-CoV-2. Epidemiol Infect 2022; 151:e32. [PMID: 36535802 PMCID: PMC9990386 DOI: 10.1017/s0950268822001935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
New SARS-CoV-2 variants causing COVID-19 are a major risk to public health worldwide due to the potential for phenotypic change and increases in pathogenicity, transmissibility and/or vaccine escape. Recognising signatures of new variants in terms of replacing growth and severity are key to informing the public health response. To assess this, we aimed to investigate key time periods in the course of infection, hospitalisation and death, by variant. We linked datasets on contact tracing (Contact Tracing Advisory Service), testing (the Second-Generation Surveillance System) and hospitalisation (the Admitted Patient Care dataset) for the entire length of contact tracing in the England - from March 2020 to March 2022. We modelled, for England, time delay distributions using a Bayesian doubly interval censored modelling approach for the SARS-CoV-2 variants Alpha, Delta, Delta Plus (AY.4.2), Omicron BA.1 and Omicron BA.2. This was conducted for the incubation period, the time from infection to hospitalisation and hospitalisation to death. We further modelled the growth of novel variant replacement using a generalised additive model with a negative binomial error structure and the relationship between incubation period length and the risk of a fatality using a Bernoulli generalised linear model with a logit link. The mean incubation periods for each variant were: Alpha 4.19 (95% credible interval (CrI) 4.13-4.26) days; Delta 3.87 (95% CrI 3.82-3.93) days; Delta Plus 3.92 (95% CrI 3.87-3.98) days; Omicron BA.1 3.67 (95% CrI 3.61-3.72) days and Omicron BA.2 3.48 (95% CrI 3.43-3.53) days. The mean time from infection to hospitalisation was for Alpha 11.31 (95% CrI 11.20-11.41) days, Delta 10.36 (95% CrI 10.26-10.45) days and Omicron BA.1 11.54 (95% CrI 11.38-11.70) days. The mean time from hospitalisation to death was, for Alpha 14.31 (95% CrI 14.00-14.62) days; Delta 12.81 (95% CrI 12.62-13.00) days and Omicron BA.2 16.02 (95% CrI 15.46-16.60) days. The 95th percentile of the incubation periods were: Alpha 11.19 (95% CrI 10.92-11.48) days; Delta 9.97 (95% CrI 9.73-10.21) days; Delta Plus 9.99 (95% CrI 9.78-10.24) days; Omicron BA.1 9.45 (95% CrI 9.23-9.67) days and Omicron BA.2 8.83 (95% CrI 8.62-9.05) days. Shorter incubation periods were associated with greater fatality risk when adjusted for age, sex, variant, vaccination status, vaccination manufacturer and time since last dose with an odds ratio of 0.83 (95% confidence interval 0.82-0.83) (P value < 0.05). Variants of SARS-CoV-2 that have replaced previously dominant variants have had shorter incubation periods. Conversely co-existing variants have had very similar and non-distinct incubation period distributions. Shorter incubation periods reflect generation time advantage, with a reduction in the time to the peak infectious period, and may be a significant factor in novel variant replacing growth. Shorter times for admission to hospital and death were associated with variant severity - the most severe variant, Delta, led to significantly earlier hospitalisation, and death. These measures are likely important for future risk assessment of new variants, and their potential impact on population health.
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73
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SARS-CoV-2 Spike Protein Induces Hemagglutination: Implications for COVID-19 Morbidities and Therapeutics and for Vaccine Adverse Effects. Int J Mol Sci 2022; 23:ijms232415480. [PMID: 36555121 PMCID: PMC9779393 DOI: 10.3390/ijms232415480] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022] Open
Abstract
Experimental findings for SARS-CoV-2 related to the glycan biochemistry of coronaviruses indicate that attachments from spike protein to glycoconjugates on the surfaces of red blood cells (RBCs), other blood cells and endothelial cells are key to the infectivity and morbidity of COVID-19. To provide further insight into these glycan attachments and their potential clinical relevance, the classic hemagglutination (HA) assay was applied using spike protein from the Wuhan, Alpha, Delta and Omicron B.1.1.529 lineages of SARS-CoV-2 mixed with human RBCs. The electrostatic potential of the central region of spike protein from these four lineages was studied through molecular modeling simulations. Inhibition of spike protein-induced HA was tested using the macrocyclic lactone ivermectin (IVM), which is indicated to bind strongly to SARS-CoV-2 spike protein glycan sites. The results of these experiments were, first, that spike protein from these four lineages of SARS-CoV-2 induced HA. Omicron induced HA at a significantly lower threshold concentration of spike protein than the three prior lineages and was much more electropositive on its central spike protein region. IVM blocked HA when added to RBCs prior to spike protein and reversed HA when added afterward. These results validate and extend prior findings on the role of glycan bindings of viral spike protein in COVID-19. They furthermore suggest therapeutic options using competitive glycan-binding agents such as IVM and may help elucidate rare serious adverse effects (AEs) associated with COVID-19 mRNA vaccines, which use spike protein as the generated antigen.
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74
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Farahat RA, Abdelaal A, Umar TP, El-Sakka AA, Benmelouka AY, Albakri K, Ali I, Al-Ahdal T, Abdelazeem B, Sah R, Rodriguez-Morales AJ. The emergence of SARS-CoV-2 Omicron subvariants: current situation and future trends. LE INFEZIONI IN MEDICINA 2022; 30:480-494. [PMID: 36482957 PMCID: PMC9714996 DOI: 10.53854/liim-3004-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/03/2022] [Indexed: 12/12/2022]
Abstract
The SARS-CoV-2 Omicron variant (B.1.1.529) has been the most recent variant of concern (VOC) established by the World Health Organization (WHO). Because of its greater infectivity and immune evasion, this variant quickly became the dominant type of circulating SARS-CoV-2 worldwide. Our literature review thoroughly explains the current state of Omicron emergence, particularly by comparing different omicron subvariants, including BA.2, BA.1, and BA.3. Such elaboration would be based on structural variations, mutations, clinical manifestation, transmissibility, pathogenicity, and vaccination effectiveness. The most notable difference between the three subvariants is the insufficiency of deletion (Δ69-70) in the spike protein, which results in a lower detection rate of the spike (S) gene target known as (S) gene target failure (SGTF). Furthermore, BA.2 had a stronger affinity to the human Angiotensin-converting Enzyme (hACE2) receptor than other Omicron sub-lineages. Regarding the number of mutations, BA.1.1 has the most (40), followed by BA.1, BA.3, and BA.3 with 39, 34, and 31 mutations, respectively. In addition, BA.2 and BA.3 have greater transmissibility than other sub-lineages (BA.1 and BA.1.1). These characteristics are primarily responsible for Omicron's vast geographical spread and high contagiousness rates, particularly BA.2 sub-lineages.
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Affiliation(s)
| | - Abdelaziz Abdelaal
- Harvard Medical School, Boston, MA,
USA,Boston University, MA,
USA,General Practitioner, Tanta University Hospitals,
Egypt
| | | | | | | | - Khaled Albakri
- Faculty of Medicine, The Hashemite University, Zarqa,
Jordan
| | - Iftikhar Ali
- Department of Pharmacy, Paraplegic Center, Peshawar,
Pakistan
| | - Tareq Al-Ahdal
- Institute of Global Health (HIGH), Heidelberg University, Heidelberg,
Germany
| | - Basel Abdelazeem
- Department of Internal Medicine, McLaren Health Care, Flint, Michigan,
USA,Department of Internal Medicine, Michigan State University, East Lansing, Michigan,
USA
| | - Ranjit Sah
- Department of Microbiology, Tribhuvan University Teaching Hospital, Institute of Medicine, Kathmandu,
Nepal,Dr. D.Y Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pune, Maharashtra,
India
| | - Alfonso J. Rodriguez-Morales
- Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de Las Américas, Pereira, Risaralda,
Colombia,Faculty of Medicine, Institución Universitaria Vision de Las Americas, Pereira, Risaralda,
Colombia,Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut P.O. Box 36,
Lebanon,Master of Clinical Epidemiology and Biostatistics, Universidad Científica del Sur, Lima,
Perú
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75
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Kobusiak-Prokopowicz M, Fułek K, Fułek M, Kaaz K, Mysiak A, Kurpas D, Beszłej JA, Brzecka A, Leszek J. Cardiovascular, Pulmonary, and Neuropsychiatric Short- and Long-Term Complications of COVID-19. Cells 2022; 11:cells11233882. [PMID: 36497138 PMCID: PMC9735460 DOI: 10.3390/cells11233882] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/05/2022] Open
Abstract
Beginning with the various strategies of the SARS-CoV-2 virus to invade our bodies and manifest infection, and ending with the recent long COVID, we are witnessing the evolving course of the disease in addition to the pandemic. Given the partially controlled course of the COVID-19 pandemic, the greatest challenge currently lies in managing the short- and long-term complications of COVID-19. We have assembled current knowledge of the broad spectrum of cardiovascular, pulmonary, and neuropsychiatric sequelae following SARS-CoV-2 infection to understand how these clinical manifestations collectively lead to a severe form of the disease. The ultimate goal would be to better understand these complications and find ways to prevent clinical deterioration.
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Affiliation(s)
| | - Katarzyna Fułek
- Lower Silesian Oncology, Pulmonology and Hematology Center, 53-413 Wroclaw, Poland
| | - Michał Fułek
- Department and Clinic of Internal Medicine, Occupational Diseases, Hypertension and Clinical Oncology, Wroclaw Medical University, 50-556 Wroclaw, Poland
- Correspondence: (M.F.); (J.L.)
| | - Konrad Kaaz
- Department of Cardiology, Institute of Heart Diseases, Wroclaw Medical University, 50-556 Wroclaw, Poland
| | - Andrzej Mysiak
- Department of Cardiology, Institute of Heart Diseases, Wroclaw Medical University, 50-556 Wroclaw, Poland
| | - Donata Kurpas
- Department and Clinic of Family Medicine, Wroclaw Medical University, 51-141 Wroclaw, Poland
| | | | - Anna Brzecka
- Department of Pulmonology and Lung Oncology, Wroclaw Medical University, 53-439 Wroclaw, Poland
| | - Jerzy Leszek
- Department and Clinic of Psychiatry, Wroclaw Medical University, 50-367 Wroclaw, Poland
- Correspondence: (M.F.); (J.L.)
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76
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Protection of vaccination versus hybrid immunity against infection with COVID-19 Omicron variants among Health-Care Workers. Vaccine 2022; 40:7195-7200. [PMID: 36150972 PMCID: PMC9482842 DOI: 10.1016/j.vaccine.2022.09.042] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND AIM The Omicron COVID-19 variants BA.1* and BA.2* evade immune system leading to increased transmissibility and breakthrough infections. We aim to test the hypothesis that immunity achieved post COVID-19 infection combined with vaccination (hybrid immunity), is more effective against Omicron infection than vaccination alone in a health-care setting. METHODS Data on regular pre-emptive PCR testing from all Health-Care Workers (HCWs) at Laiko University Hospital from 29th December 2020, date on which the national COVID-19 immunization program began in Greece, until 24th May 2022, were retrospectively collected and recorded. The infection rate was calculated after December 21st, 2021, when Omicron was the predominant circulating variant in Greece, as the total number of infections (positive PCR COVID-19 test regardless of symptoms) divided by the total person-months at risk. RESULTS Of 1,305 vaccinated HCWs who were included in the analysis [median age of 47 (IQR: 36, 56) years, 66.7 % women], 13 % and 87 % had received 2 or 3 vaccine doses (full and booster vaccination), respectively. A COVID-19 infection had occurred in 135 of 1,305 of participants prior to Omicron predominance. Of those 135 HCWs with hybrid immunity only 13 (9.6 %) were re-infected. Of the 154 and 1,016 HCWs with full and booster vaccination-induced immunity, respectively, 71 (46.1 %, infection rate 13.4/100 person-months) and 448 (44.1 %, infection rate 12.2/100 person-months) were infected during the follow up period. No association between gender or age and COVID-19 infection was found and none of the participants had a severe infection or died. CONCLUSIONS Hybrid immunity confers higher protection by almost 5-fold compared to full or booster vaccination for COVID-19 infection with the Omicron variant among HCWs who are at high risk of exposure. This may inform public health policies on how to achieve optimal immunity in terms of the timing and mode of vaccination.
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77
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Roohani J, Keikha M. Global challenge with the SARS-CoV-2 omicron BA.2 (B.1.1.529.2) subvariant: Should we be concerned? World J Virol 2022; 11:496-501. [PMID: 36483099 PMCID: PMC9724199 DOI: 10.5501/wjv.v11.i6.496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/23/2022] [Accepted: 10/04/2022] [Indexed: 11/24/2022] Open
Abstract
BA.2 is a novel omicron offshoot of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has gone viral. There is limited knowledge regarding this variant of concern. Current evidence suggests that this variant is more contagious but less severe than previous SARS-CoV-2 variants. However, there is concern regarding the virus mutations that could influence pathogenicity, transmissibility, and immune evasion.
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Affiliation(s)
- Jalil Roohani
- Department of Biotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad 13131-99137, Iran
| | - Masoud Keikha
- Department of Medical Microbiology, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
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78
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Is a booster dose of COVID-19 vaccines effective on newly dominant omicron subvariants among university students? Comparison between BA.1 and BA.2 dominancy. Am J Infect Control 2022:S0196-6553(22)00813-6. [PMID: 36435404 PMCID: PMC9683852 DOI: 10.1016/j.ajic.2022.11.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 11/17/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Although the COVID-19 Omicron BA.1 subvariant was initially predominant, the BA.2 subvariant has now replaced it. Effectiveness of a booster dose vaccination for BA.2 remains unclear among university students. METHODS We enrolled 562 Japanese university students who became a close contact and underwent polymerase chain reaction testing. We compared infection rates and cumulative incidence rates of severe fever among the students according to the COVID-19 vaccine doses received between BA.1-dominant (January 1-March 31, 2022) and BA.2-dominant (April 1-July 31, 2022) periods. RESULTS Infection rates for BA.1 were 32% with 3 doses, 49% with 2 doses, and 68% in the unvaccinated (P = .008). The odds ratio (OR) for infection following 3 doses during BA.1 was 0.46 (95% confidence interval [CI] = 0.25-0.82, P = .009). Infection rates for BA.2 were 45% with 3 doses, 62% with 2 doses, and 64% in the unvaccinated (P = .02). The OR for infection following 3 doses during BA.2 was 0.50 (95% CI = 0.31-0.82, P = .006). Effectiveness of vaccine for BA.2 tended to decrease for both 3 (45% vs 32%, P = .06) and 2 doses (62% vs 49%, P = .07) compared with those for BA.1. CONCLUSIONS Booster dose effectiveness tended to decrease but remained significant against BA.2 subvariant predominancy among Japanese university students.
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79
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Aralis Z, Comer S, Ansorg H, Palmer C, Smith J, Feinstein SC, Fitzgibbons LN, Arias C. Efficient Tracing of the SARS-CoV-2 Omicron Variants in Santa Barbara County Using a Rapid Quantitative Reverse Transcription PCR Assay. Diagnostics (Basel) 2022; 12:2805. [PMID: 36428863 PMCID: PMC9689663 DOI: 10.3390/diagnostics12112805] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 11/18/2022] Open
Abstract
The emergence of the SARS-CoV-2 Omicron variant in 2021 is associated with a global surge of cases in late 2021 and early 2022. Identifying the introduction of novel SARS-CoV-2 variants to a population is imperative to inform decisions by clinicians and public health officials. Here, we describe a quantitative reverse transcription PCR-based assay (RT-qPCR) targeting unique mutations in the Omicron BA.1/BA1.1 and BA.2 viral genomes. This assay accurately and precisely detect the presence of these Omicron variants in patient samples in less than four hours. Using this assay, we tested 270 clinical samples and detected the introduction of Omicron BA.1/BA1.1 and BA.2 in the Santa Barbara County (SBC) population in December 2021 and February 2022, respectively. Identifying Omicron variants using this RT-qPCR assay showed complete concordance with whole viral genome sequencing; both assays indicated that Omicron was the dominant variant in SB County. Our data substantiate that RT-qPCR-based virus detection assays offer a fast and inexpensive alternative to NGS for virus variant-specific detection approach, which allows streamlining the detection of Omicron variants in patient samples.
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Affiliation(s)
- Zach Aralis
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
- Department of Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Stewart Comer
- Santa Barbara County Public Health Department, Santa Barbara, CA 93106, USA
- Department of Pathology, Santa Barbara Cottage Hospital, Santa Barbara, CA 93106, USA
- Pacific Diagnostic Laboratories, Santa Barbara, CA 93106, USA
| | - Henning Ansorg
- Santa Barbara County Public Health Department, Santa Barbara, CA 93106, USA
| | - Carl Palmer
- LegacyWorks Group, Santa Barbara, CA 93106, USA
| | - Jennifer Smith
- California NanoSystems Institute, University of California, Santa Barbara, CA 93106, USA
| | - Stuart C. Feinstein
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
| | - Lynn N. Fitzgibbons
- Department of Medical Education, Division of Infectious Diseases, Santa Barbara Cottage Hospital, Santa Barbara, CA 93106, USA
| | - Carolina Arias
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
- Department of Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
- Center for Stem Cell Biology and Engineering, University of California, Santa Barbara, CA 93106, USA
- Infectious Disease Initiative, Chan Zuckerberg BioHub, San Francisco, CA 93106, USA
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Sharma P, Kumar M, Tripathi MK, Gupta D, Vishwakarma P, Das U, Kaur P. Genomic and structural mechanistic insight to reveal the differential infectivity of omicron and other variants of concern. Comput Biol Med 2022; 150:106129. [PMID: 36195045 PMCID: PMC9493144 DOI: 10.1016/j.compbiomed.2022.106129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/04/2022] [Accepted: 09/18/2022] [Indexed: 11/17/2022]
Abstract
BACKGROUND The genome of SARS-CoV-2, is mutating rapidly and continuously challenging the management and preventive measures adopted and recommended by healthcare agencies. The spike protein is the main antigenic site that binds to the host receptor hACE-2 and is recognised by antibodies. Hence, the mutations in this site were analysed to assess their role in differential infectivity of lineages having these mutations, rendering the characterisation of these lineages as variants of concern (VOC) and variants of interest (VOI). METHODS In this work, we examined the genome sequence of SARS-CoV-2 VOCs and their phylogenetic relationships with the other PANGOLIN lineages. The mutational landscape of WHO characterized variants was determined and mutational diversity was compared amongst the different severity groups. We then computationally studied the structural impact of the mutations in receptor binding domain of the VOCs. The binding affinity was quantitatively determined by molecular dynamics simulations and free energy calculations. RESULTS The mutational frequency, as well as phylogenetic distance, was maximum in the case of omicron followed by the delta variant. The maximum binding affinity was for delta variant followed by the Omicron variant. The increased binding affinity of delta strain followed by omicron as compared to other variants and wild type advocates high transmissibility and quick spread of these two variants and high severity of delta variant. CONCLUSION This study delivers a foundation for discovering the improved binding knacks and structural features of SARS-CoV-2 variants to plan novel therapeutics and vaccine candidates against the virus.
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Affiliation(s)
- Priyanka Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
| | - Mukesh Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
| | - Manish Kumar Tripathi
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
| | - Deepali Gupta
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
| | - Poorvi Vishwakarma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
| | - Uddipan Das
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
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81
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Shin DH, Smith DM, Choi JY. SARS-CoV-2 Omicron Variant of Concern: Everything You Wanted to Know about Omicron but Were Afraid to Ask. Yonsei Med J 2022; 63:977-983. [PMID: 36303305 PMCID: PMC9629902 DOI: 10.3349/ymj.2022.0383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/05/2022] [Indexed: 01/25/2023] Open
Abstract
As soon as the first case of the omicron variant of severe acute respiratory syndrome coronavirus 2 was reported in November 2021, it quickly spread worldwide with the emergence of several subvariants. Compared to previous variants, omicron was heavily mutated, especially for those in the Spike (S) protein and its receptor-binding domain. These mutations allowed the viruses to evade immune responses (i.e., previous infections and vaccine-elicited) and increase in transmissibility. Although vaccine effectiveness is decreased for omicron, boosters remain effective for protecting against severe diseases. Also, bivalent vaccines have been developed to increase vaccine effectiveness. Interestingly, although omicron is highly infectious, it has less morbidity and mortality compared to previously identified variants, such as delta. Additionally, the mutations that allow the virus to evade immune responses also allow it to evade many of the monoclonal antibodies developed at the beginning of the pandemic for treatment. Here, we reviewed the omicron variant's epidemiology, genetics, transmissibility, disease severity, and responsiveness to vaccine and treatments.
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Affiliation(s)
- Dong Hoon Shin
- Department of Medicine, University of California San Diego, La Jolla, USA
| | - Davey M Smith
- Department of Medicine, University of California San Diego, La Jolla, USA
- Veterans Affairs San Diego Healthcare System, San Diego, USA
| | - Jun Yong Choi
- Division of Infectious Diseases, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
- AIDS Research Institute, Yonsei University College of Medicine, Seoul, Korea.
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Chakraborty C, Bhattacharya M, Sharma AR, Dhama K, Lee SS. 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. [PMID: 36270226 DOI: 10.1016/j.jiph.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/27/2022] [Accepted: 10/05/2022] [Indexed: 11/28/2022] Open
Abstract
PURPOSE The recent Omicron (B.1.1.529) variant poses a significant threat to global health. This variant has spread worldwide, and several sublineages have rapidly emerged. Study tried to analyze the microevolution of this variant. METHODS We studied the molecular phylogenetics, divergence, geographical distributions, frequencies, risk mutations for antibody affinity, and mutational landscape for Omicron sublineages using in silico analysis and statistical models. The risk mutation of spike for nAb affinity was analyzed and illustrated by statistical plots. Finally, the mutational properties of the spike mutations and their stability were predicted and demonstrated. RESULTS First, we studied the microevolutionary Omicron sublineages using molecular phylogenetics. Simultaneously, we revealed divergence events of the Omicron sublineages and observed the lowest minimum divergence of 51 in clade 21K and the highest maximum divergence of 90 in clade 21L. We have demonstrated cluster analyses, geographical distributions, frequencies of Omicron and its sublineages. Finally, we evaluated the mutational landscape of the Omicron sublineages. In this mutational study, we performed a genome-wide analysis of general mutations, mutations in the non-spike genome, and spike mutations of Omicron sublineages. The risk mutation of S-glycoprotein for nAb affinity has been analyzed for Omicron sublineages. Here, we found that some sublineages have all four significant highly destabilizing mutations. Such sublineages are BA.1 (G446S, E484A, T95I, and D614G), BA.2 (H655Y, Q493R, G493S, and D614G), BA.4 (N501Y, Y505H, N969K, and D614G), and BA.2.75 (Q454H, T547K, N764K, D614G and G446S). Finally, from the mutation stability prediction through ΔΔG, we observed that BA.1 and BA.4 had two destabilizing and two stabilizing mutations. Similarly, BA.2, BA.5, and BA.2.12.1 have one destabilizing and three stabilizing mutations. However, all four mutations in BA.2.75 are stabilizing mutations. CONCLUSIONS Our molecular phylogenetic studies provided a deeper understanding of the microevolution of sublineages and the creation of Omicron. Similarly, this study might help scientists develop pan-coronavirus vaccines that consider their mutational properties.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal 700126, India.
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore 756020, Odisha, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging &Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-Do 24252, Republic of Korea
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Sang-Soo Lee
- Institute for Skeletal Aging &Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-Do 24252, Republic of Korea.
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83
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Zhao J, Zhu J, Huang C, Zhu X, Zhu Z, Wu Q, Yuan R. Uncovering the information immunology journals transmitted for COVID-19: A bibliometric and visualization analysis. Front Immunol 2022; 13:1035151. [PMID: 36405695 PMCID: PMC9670819 DOI: 10.3389/fimmu.2022.1035151] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/17/2022] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Since the global epidemic of the coronavirus disease 2019 (COVID-19), a large number of immunological studies related to COVID-19 have been published in various immunology journals. However, the results from these studies were discrete, and no study summarized the important immunological information about COVID-19 released by these immunology journals. This study aimed to comprehensively summarize the knowledge structure and research hotspots of COVID-19 published in major immunology journals through bibliometrics. METHODS Publications on COVID-19 in major immunology journals were obtained from the Web of Science Core Collection. CiteSpace, VOSviewer, and R-bibliometrix were comprehensively used for bibliometric and visual analysis. RESULTS 1,331 and 5,000 publications of 10 journals with high impact factors and 10 journals with the most papers were included, respectively. The USA, China, England, and Italy made the most significant contributions to these papers. University College London, National Institute of Allergy and Infectious Diseases, Harvard Medical School, University California San Diego, and University of Pennsylvania played a central role in international cooperation in the immunology research field of COVID-19. Yuen Kwok Yung was the most important author in terms of the number of publications and citations, and the H-index. CLINICAL INFECTIOUS DISEASES and FRONTIERS IN IMMUNOLOGY were the most essential immunology journals. These immunology journals mostly focused on the following topics: "Delta/Omicron variants", "cytokine storm", "neutralization/neutralizing antibody", "T cell", "BNT162b2", "mRNA vaccine", "vaccine effectiveness/safety", and "long COVID". CONCLUSION This study systematically uncovered a holistic picture of the current research on COVID-19 published in major immunology journals from the perspective of bibliometrics, which will provide a reference for future research in this field.
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Affiliation(s)
- Jiefeng Zhao
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Jinfeng Zhu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Chao Huang
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xiaojian Zhu
- Center for Digestive Disease, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Zhengming Zhu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Qinrong Wu
- Department of General Surgery, Yingtan City People’s Hospital, Yingtan, Jiangxi, China
| | - Rongfa Yuan
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
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Tauzin A, Gong SY, Chatterjee D, Ding S, Painter MM, Goel RR, Beaudoin-Bussières G, Marchitto L, Boutin M, Laumaea A, Okeny J, Gendron-Lepage G, Bourassa C, Medjahed H, Goyette G, Williams JC, Bo Y, Gokool L, Morrisseau C, Arlotto P, Bazin R, Fafard J, Tremblay C, Kaufmann DE, De Serres G, Richard J, Côté M, Duerr R, Martel-Laferrière V, Greenplate AR, Wherry EJ, Finzi A. A boost with SARS-CoV-2 BNT162b2 mRNA vaccine elicits strong humoral responses independently of the interval between the first two doses. Cell Rep 2022; 41:111554. [PMID: 36244343 PMCID: PMC9533674 DOI: 10.1016/j.celrep.2022.111554] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 07/27/2022] [Accepted: 10/03/2022] [Indexed: 11/23/2022] Open
Abstract
Due to the recrudescence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections worldwide, mainly caused by the Omicron variant of concern (VOC) and its sub-lineages, several jurisdictions are administering an mRNA vaccine boost. Here, we analyze humoral responses induced after the second and third doses of an mRNA vaccine in naive and previously infected donors who received their second dose with an extended 16-week interval. We observe that the extended interval elicits robust humoral responses against VOCs, but this response is significantly diminished 4 months after the second dose. Administering a boost to these individuals brings back the humoral responses to the same levels obtained after the extended second dose. Interestingly, we observe that administering a boost to individuals that initially received a short 3- to 4-week regimen elicits humoral responses similar to those observed in the long interval regimen. Nevertheless, humoral responses elicited by the boost in naive individuals do not reach those present in previously infected vaccinated individuals.
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Affiliation(s)
- Alexandra Tauzin
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Shang Yu Gong
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | | | - Shilei Ding
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
| | - Mark M Painter
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Rishi R Goel
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Guillaume Beaudoin-Bussières
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Lorie Marchitto
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Marianne Boutin
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Annemarie Laumaea
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - James Okeny
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | | | | | | | | | - Justine C Williams
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Yuxia Bo
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Laurie Gokool
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
| | | | | | - Renée Bazin
- Héma-Québec, Affaires Médicales et Innovation, Quebec, QC G1V 5C3, Canada
| | - Judith Fafard
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada
| | - Cécile Tremblay
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Daniel E Kaufmann
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Médecine, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Gaston De Serres
- Institut National de Santé Publique du Québec, Quebec, QC H2P 1E2, Canada
| | - Jonathan Richard
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Marceline Côté
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Ralf Duerr
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - Valérie Martel-Laferrière
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Allison R Greenplate
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - E John Wherry
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada.
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Rahman S, Hossain MJ, Nahar Z, Shahriar M, Bhuiyan MA, Islam MR. Emerging SARS-CoV-2 Variants and Subvariants: Challenges and Opportunities in the Context of COVID-19 Pandemic. ENVIRONMENTAL HEALTH INSIGHTS 2022; 16:11786302221129396. [PMID: 36299441 PMCID: PMC9585367 DOI: 10.1177/11786302221129396] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/09/2022] [Indexed: 05/30/2023]
Abstract
The COVID-19 pandemic has become the most devastating pandemic of the 21st century since its appearance in December 2019. Like other RNA viruses, continuous mutation is common for coronavirus to create several variants and subvariants. The main reason behind this mutation and evolvement of SARS-CoV-2 was its structural spike (S) glycoprotein. Coronavirus has become a threat to global public health due to its high mutation capability and antibody neutralizing capacity. According to the World Health Organization (WHO), there are 5 major variants of concern (VOC) are Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529). Recently, different Omicron subvariants have gained worldwide dominance, such as BA.1, BA.2, BA.3, BA.4, and BA.5. However, there is a discernible drop in this symptomatic sickness globally due to the success of numerous monoclonal antibodies and vaccinations. Here we also discussed the currently dominant Omicron subvariants and the effectiveness of antiviral agents and vaccines. Based on the available data and our knowledge, we can suggest that the global healthcare organizations can decide on the declaration of the end of the pandemic phase of COVID-19 soon; however, the covid-19 will continue.
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Affiliation(s)
- Smaranika Rahman
- Department of Pharmacy, University of
Asia Pacific, Farmgate, Dhaka, Bangladesh
| | - Md. Jamal Hossain
- Department of Pharmacy, State
University of Bangladesh, Dhanmondi, Dhaka, Bangladesh
| | - Zabun Nahar
- Department of Pharmacy, University of
Asia Pacific, Farmgate, Dhaka, Bangladesh
| | - Mohammad Shahriar
- Department of Pharmacy, University of
Asia Pacific, Farmgate, Dhaka, Bangladesh
| | | | - Md. Rabiul Islam
- Department of Pharmacy, University of
Asia Pacific, Farmgate, Dhaka, Bangladesh
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Targeting Natural Plant Metabolites for Hunting SARS-CoV-2 Omicron BA.1 Variant Inhibitors: Extraction, Molecular Docking, Molecular Dynamics, and Physicochemical Properties Study. Curr Issues Mol Biol 2022; 44:5028-5047. [PMID: 36286057 PMCID: PMC9600405 DOI: 10.3390/cimb44100342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/12/2022] [Accepted: 10/18/2022] [Indexed: 12/02/2022] Open
Abstract
(1) Background: SARS-CoV-2 Omicron BA.1 is the most common variation found in most countries and is responsible for 99% of cases in the United States. To overcome this challenge, there is an urgent need to discover effective inhibitors to prevent the emerging BA.1 variant. Natural products, particularly flavonoids, have had widespread success in reducing COVID-19 prevalence. (2) Methods: In the ongoing study, fifteen compounds were annotated from Echium angustifolium and peach (Prunus persica), which were computationally analyzed using various in silico techniques. Molecular docking calculations were performed for the identified phytochemicals to investigate their efficacy. Molecular dynamics (MD) simulations over 200 ns followed by molecular mechanics Poisson–Boltzmann surface area calculations (MM/PBSA) were performed to estimate the binding energy. Bioactivity was also calculated for the best components in terms of drug likeness and drug score. (3) Results: The data obtained from the molecular docking study demonstrated that five compounds exhibited remarkable potency, with docking scores greater than −9.0 kcal/mol. Among them, compounds 1, 2 and 4 showed higher stability within the active site of Omicron BA.1, with ΔGbinding values of −49.02, −48.07, and −67.47 KJ/mol, respectively. These findings imply that the discovered phytoconstituents are promising in the search for anti-Omicron BA.1 drugs and should be investigated in future in vitro and in vivo research.
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Tulimilli SV, Dallavalasa S, Basavaraju CG, Kumar Rao V, Chikkahonnaiah P, Madhunapantula SV, Veeranna RP. Variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Vaccine Effectiveness. Vaccines (Basel) 2022; 10:vaccines10101751. [PMID: 36298616 PMCID: PMC9607623 DOI: 10.3390/vaccines10101751] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 10/07/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
The incidence and death toll due to SARS-CoV-2 infection varied time-to-time; and depended on several factors, including severity (viral load), immune status, age, gender, vaccination status, and presence of comorbidities. The RNA genome of SARS-CoV-2 has mutated and produced several variants, which were classified by the SARS-CoV-2 Interagency Group (SIG) into four major categories. The first category; “Variant Being Monitored (VBM)”, consists of Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), Epsilon (B.1.427, B.1.429), Eta (B.1.525), Iota (B.1.526), Kappa (B.1.617.1), Mu (B.1.621), and Zeta (P.2); the second category; “Variants of Concern” consists of Omicron (B.1.1.529). The third and fourth categories include “Variants of Interest (VOI)”, and “Variants of High Consequence (VOHC)”, respectively, and contain no variants classified currently under these categories. The surge in VBM and VOC poses a significant threat to public health globally as they exhibit altered virulence, transmissibility, diagnostic or therapeutic escape, and the ability to evade the host immune response. Studies have shown that certain mutations increase the infectivity and pathogenicity of the virus as demonstrated in the case of SARS-CoV-2, the Omicron variant. It is reported that the Omicron variant has >60 mutations with at least 30 mutations in the Spike protein (“S” protein) and 15 mutations in the receptor-binding domain (RBD), resulting in rapid attachment to target cells and immune evasion. The spread of VBM and VOCs has affected the actual protective efficacy of the first-generation vaccines (ChAdOx1, Ad26.COV2.S, NVX-CoV2373, BNT162b2). Currently, the data on the effectiveness of existing vaccines against newer variants of SARS-CoV-2 are very scanty; hence additional studies are immediately warranted. To this end, recent studies have initiated investigations to elucidate the structural features of crucial proteins of SARS-CoV-2 variants and their involvement in pathogenesis. In addition, intense research is in progress to develop better preventive and therapeutic strategies to halt the spread of COVID-19 caused by variants. This review summarizes the structure and life cycle of SARS-CoV-2, provides background information on several variants of SARS-CoV-2 and mutations associated with these variants, and reviews recent studies on the safety and efficacy of major vaccines/vaccine candidates approved against SARS-CoV-2, and its variants.
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Affiliation(s)
- SubbaRao V. Tulimilli
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR) Laboratory (DST-FIST Supported Center), Department of Biochemistry (DST-FIST Supported Department), JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru 570004, Karnataka, India
| | - Siva Dallavalasa
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR) Laboratory (DST-FIST Supported Center), Department of Biochemistry (DST-FIST Supported Department), JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru 570004, Karnataka, India
| | - Chaithanya G. Basavaraju
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR) Laboratory (DST-FIST Supported Center), Department of Biochemistry (DST-FIST Supported Department), JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru 570004, Karnataka, India
| | - Vinay Kumar Rao
- Department of Medical Genetics, JSS Medical College & Hospital, JSS Academy of Higher Education & Research (JSS AHER), Mysore 570015, Karnataka, India
| | - Prashanth Chikkahonnaiah
- Department of Pulmonary Medicine, Mysore Medical College and Research Institute, Mysuru 570001, Karnataka, India
| | - SubbaRao V. Madhunapantula
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR) Laboratory (DST-FIST Supported Center), Department of Biochemistry (DST-FIST Supported Department), JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru 570004, Karnataka, India
- Special Interest Group in Cancer Biology and Cancer Stem Cells (SIG-CBCSC), JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru 570004, Karnataka, India
| | - Ravindra P. Veeranna
- Department of Biochemistry, Council of Scientific and Industrial Research (CSIR)-Central Food Technological Research Institute (CFTRI), Mysuru 570020, Karnataka, India
- Correspondence:
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Chavda VP, Yao Q, Vora LK, Apostolopoulos V, Patel CA, Bezbaruah R, Patel AB, Chen ZS. Fast-track development of vaccines for SARS-CoV-2: The shots that saved the world. Front Immunol 2022; 13:961198. [PMID: 36263030 PMCID: PMC9574046 DOI: 10.3389/fimmu.2022.961198] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
In December 2019, an outbreak emerged of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which leads to coronavirus disease 2019 (COVID-19). The World Health Organisation announced the outbreak a global health emergency on 30 January 2020 and by 11 March 2020 it was declared a pandemic. The spread and severity of the outbreak took a heavy toll and overburdening of the global health system, particularly since there were no available drugs against SARS-CoV-2. With an immediate worldwide effort, communication, and sharing of data, large amounts of funding, researchers and pharmaceutical companies immediately fast-tracked vaccine development in order to prevent severe disease, hospitalizations and death. A number of vaccines were quickly approved for emergency use, and worldwide vaccination rollouts were immediately put in place. However, due to several individuals being hesitant to vaccinations and many poorer countries not having access to vaccines, multiple SARS-CoV-2 variants quickly emerged that were distinct from the original variant. Uncertainties related to the effectiveness of the various vaccines against the new variants as well as vaccine specific-side effects have remained a concern. Despite these uncertainties, fast-track vaccine approval, manufacturing at large scale, and the effective distribution of COVID-19 vaccines remain the topmost priorities around the world. Unprecedented efforts made by vaccine developers/researchers as well as healthcare staff, played a major role in distributing vaccine shots that provided protection and/or reduced disease severity, and deaths, even with the delta and omicron variants. Fortunately, even for those who become infected, vaccination appears to protect against major disease, hospitalisation, and fatality from COVID-19. Herein, we analyse ongoing vaccination studies and vaccine platforms that have saved many deaths from the pandemic.
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Affiliation(s)
- Vivek P. Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, LM College of Pharmacy, Ahmedabad, Gujarat, India
| | - Qian Yao
- Graduate School, University of St. La Salle, Bacolod City, Philippines
| | | | | | - Chirag A. Patel
- Department of Pharmacology, LM College of Pharmacy, Ahmedabad, Gujarat, India
| | - Rajashri Bezbaruah
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India
| | - Aayushi B. Patel
- Pharmacy Section, LM. College of Pharmacy, Ahmedabad, Gujarat, India
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Science, College of Pharmacy and Health Sciences, St. John’s University, New York, NY, United States
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89
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Pitsillou E, Liang JJ, Beh RC, Hung A, Karagiannis TC. Molecular dynamics simulations highlight the altered binding landscape at the spike-ACE2 interface between the Delta and Omicron variants compared to the SARS-CoV-2 original strain. Comput Biol Med 2022; 149:106035. [PMID: 36055162 PMCID: PMC9420038 DOI: 10.1016/j.compbiomed.2022.106035] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 08/15/2022] [Accepted: 08/20/2022] [Indexed: 11/21/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.529 variant (Omicron), represents a significant deviation in genetic makeup and function compared to previous variants. Following the BA.1 sublineage, the BA.2 and BA.3 Omicron subvariants became dominant, and currently the BA.4 and BA.5, which are quite distinct variants, have emerged. Using molecular dynamics simulations, we investigated the binding characteristics of the Delta and Omicron (BA.1) variants in comparison to wild-type (WT) at the interface of the spike protein receptor binding domain (RBD) and human angiotensin converting enzyme-2 (ACE2) ectodomain. The primary aim was to compare our molecular modelling systems with previously published observations, to determine the robustness of our approach for rapid prediction of emerging future variants. Delta and Omicron were found to bind to ACE2 with similar affinities (−39.4 and −43.3 kcal/mol, respectively) and stronger than WT (−33.5 kcal/mol). In line with previously published observations, the energy contributions of the non-mutated residues at the interface were largely retained between WT and the variants, with F456, F486, and Y489 having the strongest energy contributions to ACE2 binding. Further, residues N440K, Q498R, and N501Y were predicted to be energetically favourable in Omicron. In contrast to Omicron, which had the E484A and K417N mutations, intermolecular bonds were detected for the residue pairs E484:K31 and K417:D30 in WT and Delta, in accordance with previously published findings. Overall, our simplified molecular modelling approach represents a step towards predictive model systems for rapidly analysing arising variants of concern.
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90
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Dhawan M, Saied AA, Mitra S, Alhumaydhi FA, Emran TB, Wilairatana P. Omicron variant (B.1.1.529) and its sublineages: What do we know so far amid the emergence of recombinant variants of SARS-CoV-2? Biomed Pharmacother 2022; 154:113522. [PMID: 36030585 PMCID: PMC9376347 DOI: 10.1016/j.biopha.2022.113522] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 12/19/2022] Open
Abstract
Since the start of the COVID-19 pandemic, numerous variants of SARS-CoV-2 have been reported worldwide. The advent of variants of concern (VOCs) raises severe concerns amid the serious containment efforts against COVID-19 that include physical measures, pharmacological repurposing, immunization, and genomic/community surveillance. Omicron variant (B.1.1.529) has been identified as a highly modified, contagious, and crucial variant among the five VOCs of SARS-CoV-2. The increased affinity of the spike protein (S-protein), and host receptor, angiotensin converting enzyme-2 (ACE-2), due to a higher number of mutations in the receptor-binding domain (RBD) of the S-protein has been proposed as the primary reason for the decreased efficacy of majorly available vaccines against the Omicron variant and the increased transmissible nature of the Omicron variant. Because of its significant competitive advantage, the Omicron variant and its sublineages swiftly surpassed other variants to become the dominant circulating lineages in a number of nations. The Omicron variant has been identified as a prevalent strain in the United Kingdom and South Africa. Furthermore, the emergence of recombinant variants through the conjunction of the Omicron variant with other variants or by the mixing of the Omicron variant's sublineages/subvariants poses a major threat to humanity. This raises various issues and hazards regarding the Omicron variant and its sublineages, such as an Omicron variant breakout in susceptible populations among fully vaccinated persons. As a result, understanding the features and genetic implications of this variant is crucial. Hence, we explained in depth the evolution and features of the Omicron variant and analyzed the repercussions of spike mutations on infectiousness, dissemination ability, viral entry mechanism, and immune evasion. We also presented a viewpoint on feasible strategies for precluding and counteracting any future catastrophic emergence and spread of the omicron variant and its sublineages that could result in a detrimental wave of COVID-19 cases.
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Affiliation(s)
- Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana 141004, Punjab, India; Trafford College, Altrincham, Manchester WA14 5PQ, UK.
| | - AbdulRahman A Saied
- National Food Safety Authority (NFSA), Aswan Branch, Aswan 81511, Egypt; Ministry of Tourism and Antiquities, Aswan Office, Aswan 81511, Egypt
| | - Saikat Mitra
- Department of Pharmacy, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh
| | - Fahad A Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 52571, Saudi Arabia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh; Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh.
| | - Polrat Wilairatana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand.
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91
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Shaheen N, Mohamed A, Attalla A, Diab RA, Swed S, Nashwan AJ, Rababah AA, Hefnawy MT, Soliman Y, Abdelwahab OA, Desouki MT, Khaity A, Shaheen A, Ramadan A, Meshref M. Could the New BA.2.75 Sub-Variant Cause the Emergence of a Global Epidemic of COVID-19? A Scoping Review. Infect Drug Resist 2022; 15:6317-6330. [PMID: 36345537 PMCID: PMC9635999 DOI: 10.2147/idr.s387551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/19/2022] [Indexed: 11/05/2022] Open
Abstract
With over 58 million cases and 6 million deaths by August 2022, the Coronavirus disease 2019 (COVID-19), causing severe acute respiratory syndrome coronavirus 2 (SARs-CoV-2), has had an insurmountable impact on the world’s population. This is one of the worst health crises since 1918’s influenza pandemic. There are four subvariants of Omicron; BA.1, BA.1.1, BA.2 and BA.3. As a result of new mutations in its spike protein, most of which occur in its receptor binding site, the Omicron variant appears to be more transmissible and less resistant to vaccination and antibody response. Understanding Omicron’s virology and mutations is essential to developing diagnostic and therapeutic methods. A thorough assessment of control measures, as well as timely adjustment of control measures, requires addressing such issues as re-infection risk, vaccine response, booster vaccine doses, and the increased rate of Omicron infections. This review article aims to look at the current information about the different types of SARs-CoV-2, focusing on the new subtype BA.2.75.
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Affiliation(s)
- Nour Shaheen
- Alexandria Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | | | | | - Rehab Adel Diab
- Faculty of Medicine, Al-Azhar University, Cairo, Egypt, Medical Research Group of Egypt, Cairo, Egypt
| | - Sarya Swed
- Aleppo University, Faculty of Medicine, Aleppo, Syria
| | - Abdulqadir J Nashwan
- Hamad Medical Corporation, Doha, Qatar
- Correspondence: Abdulqadir J Nashwan, Hamad Medical Corporation, PO Box 3050, Doha, Qatar, Email
| | | | - Mahmoud Tarek Hefnawy
- Faculty of Medicine, Zagazig University, Egypt, Medical Research Group of Egypt, Cairo, Egypt
| | | | - Omar Ahmed Abdelwahab
- Faculty of Medicine, Al-Azhar University, Cairo, Egypt, Medical Research Group of Egypt, Cairo, Egypt
| | | | | | - Ahmed Shaheen
- Alexandria Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | | | - Mostafa Meshref
- Neurology Department, Faculty of Medicine, Al-Azhar University, Cairo, Egypt
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92
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Feng XL, Yu D, Zhang M, Li X, Zou QC, Ma W, Han JB, Xu L, Yang C, Qu W, Deng ZH, Long J, Long Y, Li M, Yao YG, Dong XQ, Zeng J, Li MH. Characteristics of replication and pathogenicity of SARS-CoV-2 Alpha and Delta isolates. Virol Sin 2022; 37:804-812. [PMID: 36167254 PMCID: PMC9507998 DOI: 10.1016/j.virs.2022.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/20/2022] [Indexed: 01/19/2023] Open
Abstract
The continuously arising of SARS-CoV-2 variants has been posting a great threat to public health safety globally, from B.1.17 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta) to B.1.1.529 (Omicron). The emerging or re-emerging of the SARS-CoV-2 variants of concern is calling for the constant monitoring of their epidemics, pathogenicity and immune escape. In this study, we aimed to characterize replication and pathogenicity of the Alpha and Delta variant strains isolated from patients infected in Laos. The amino acid mutations within the spike fragment of the isolates were determined via sequencing. The more efficient replication of the Alpha and Delta isolates was documented than the prototyped SARS-CoV-2 in Calu-3 and Caco-2 cells, while such features were not observed in Huh-7, Vero E6 and HPA-3 cells. We utilized both animal models of human ACE2 (hACE2) transgenic mice and hamsters to evaluate the pathogenesis of the isolates. The Alpha and Delta can replicate well in multiple organs and cause moderate to severe lung pathology in these animals. In conclusion, the spike protein of the isolated Alpha and Delta variant strains was characterized, and the replication and pathogenicity of the strains in the cells and animal models were also evaluated.
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Affiliation(s)
- Xiao-Li Feng
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Dandan Yu
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, and KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China,National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Mi Zhang
- Department of Infectious Diseases, Yunnan Provincial Infectious Diseases Hospital, Kunming, 650301, China
| | - Xiaohong Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, and KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Qing-Cui Zou
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Wentai Ma
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, 100101, China,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian-Bao Han
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Ling Xu
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, and KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China,National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Cuixian Yang
- Department of Infectious Diseases, Yunnan Provincial Infectious Diseases Hospital, Kunming, 650301, China
| | - Wang Qu
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Zhong-Hua Deng
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Junyi Long
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Yanghaopeng Long
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Mingkun Li
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, 100101, China,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yong-Gang Yao
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, and KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China,National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Xing-Qi Dong
- Department of Infectious Diseases, Yunnan Provincial Infectious Diseases Hospital, Kunming, 650301, China,Corresponding authors.
| | - Jianxiong Zeng
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, and KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China,National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China,Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China,Corresponding authors.
| | - Ming-Hua Li
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China,Corresponding authors.
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93
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Rana R, Kant R, Huirem RS, Bohra D, Ganguly NK. Omicron variant: Current insights and future directions. Microbiol Res 2022; 265:127204. [PMID: 36152612 PMCID: PMC9482093 DOI: 10.1016/j.micres.2022.127204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/22/2022] [Accepted: 09/13/2022] [Indexed: 01/08/2023]
Abstract
The global COVID-19 outbreak has returned with the identification of the SARS-CoV-2 Omicron variant (B.1.1.529) after appearing to be persistently spreading for the more than past two years. In comparison to prior SARS-CoV-2 variants, this new variant revealed a significant amount of mutation. This novel variety may have a greater rate of transmissibility which might impede the effectiveness of current diagnostic equipment as well as vaccination efficacy and also impede immunotherapies (Antibody / monoclonal antibody based). WHO designated B.1.1.529 as a variant of concern on November 26, 2021, identified as Omicron. The Omicron variant transmission method and severity, on the other hand, are well defined. The global spread of Omicron, which has now seized many nations, has resulted in numerous speculations regarding its origin and degree of infectivity. The following sections will go over its potential for transmission, omicron structure, and impact on COVID-19 vaccines, how it is different from delta variant and diagnostics.
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Affiliation(s)
- Rashmi Rana
- Department of Research, Sir Ganga Ram Hospital, Delhi, India.
| | - Ravi Kant
- Department of Research, Sir Ganga Ram Hospital, Delhi, India
| | | | - Deepika Bohra
- Department of Research, Sir Ganga Ram Hospital, Delhi, India
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94
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Berno G, Fabeni L, Matusali G, Gruber CEM, Rueca M, Giombini E, Garbuglia AR. SARS-CoV-2 Variants Identification: Overview of Molecular Existing Methods. Pathogens 2022; 11:1058. [PMID: 36145490 PMCID: PMC9504725 DOI: 10.3390/pathogens11091058] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/30/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Since the beginning of COVID-19 pandemic the Real Time sharing of genome sequences of circulating virus supported the diagnostics and surveillance of SARS-CoV-2 and its transmission dynamics. SARS-CoV-2 straightaway showed its tendency to mutate and adapt to the host, culminating in the emergence of variants; so it immediately became of crucial importance to be able to detect them quickly but also to be able to monitor in depth the changes on the whole genome to early identify the new possibly emerging variants. In this scenario, this manuscript aims to provide an overview of the existing methods for the identification of SARS-CoV-2 variants (from rapid method based on identification of one or more specific mutations to Whole Genome sequencing approach-WGS), taking into account limitations, advantages and applications of them in the field of diagnosis and surveillance of SARS-CoV-2.
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Affiliation(s)
| | | | | | | | | | | | - Anna Rosa Garbuglia
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy
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95
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Yamacli S, Avci M. Computation of the Binding Energies between Human ACE2 and Spike RBDs of the Original Strain, Delta and Omicron Variants of the SARS-CoV-2: A DFT Simulation Approach. ADVANCED THEORY AND SIMULATIONS 2022; 5:2200337. [PMID: 36248211 PMCID: PMC9538088 DOI: 10.1002/adts.202200337] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/31/2022] [Indexed: 11/09/2022]
Abstract
The receptor binding domain (RBD) of SARS-CoV-2 binds to human ACE2 leading to infection. In this study, the complexes that are formed by the attachment of the SARS-CoV-2 spike RBDs of the original strain, delta and omicron variants to the human ACE2 are investigated via density functional theory (DFT) simulations to obtain binding energies. The DFT computations are performed without fragmenting the interfaces to involve longer-range interactions for improved accuracy, which is one of the primary features of the approach used in this study. Basis set superposition error corrections and van der Waals dispersions are also included in the DFT simulations. The binding energies of the SARS-CoV-2 spike RBDs of the original strain, delta and omicron variants to the human ACE2 are computed as -4.76, -6.68, and -11.77 eV, respectively. These binding energy values indicate that the binding of the omicron variant to the ACE2 is much more favorable than the binding of the original strain and the delta variant, which constitute a molecular reason for the takeover of the omicron variant. The binding energies and the decomposition of these energies found in this study are expected to aid in the development of neutralizing agents.
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Affiliation(s)
- Serhan Yamacli
- Department of Electrical‐Electronics EngineeringNuh Naci Yazgan UniversityKayseri38090Turkey
| | - Mutlu Avci
- Department of Biomedical EngineeringCukurova UniversityAdana01330Turkey
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96
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Johnson R, Mangwana N, Sharma JR, Muller CJF, Malemela K, Mashau F, Dias S, Ramharack P, Kinnear C, Glanzmann B, Viraragavin A, Louw J, Surujlal-Naicker S, Nkambule S, Webster C, Mdhluli M, Gray G, Mathee A, Preiser W, Vorster A, Dalvie S, Street R. Delineating the spread and prevalence of SARS-CoV-2 Omicron sub-lineages (BA.1- BA.5) and Deltacron using wastewater in the Western Cape, South Africa. J Infect Dis 2022; 226:1418-1427. [PMID: 36017801 PMCID: PMC9574669 DOI: 10.1093/infdis/jiac356] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/24/2022] [Indexed: 11/26/2022] Open
Abstract
This study was one of the first to detect Omicron sublineages BA.4 and BA.5 in wastewater from South Africa. Spearman rank correlation analysis confirmed a strong positive correlation between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral RNA in wastewater samples and clinical cases (r = 0.7749, P < .0001). SARS-CoV-2 viral load detected in wastewater, resulting from the Delta-driven third wave, was significantly higher than during the Omicron-driven fourth wave. Whole-genome sequencing confirmed presence of Omicron lineage defining mutations in wastewater with the first occurrence reported 23 November 2021 (BA.1 predominant). The variant spread rapidly, with prevalence of Omicron-positive wastewater samples rising to >80% by 10 January 2022 with BA.2 as the predominant sublineage by 10 March 2022, whilst on 18 April 2022 BA.4 and BA.5 were detected in selected wastewater sites. These findings demonstrate the value of wastewater-based epidemiology to monitor the spatiotemporal spread and potential origin of new Omicron sublineages.
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Affiliation(s)
- Rabia Johnson
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa.,Centre for Cardio-metabolic Research in Africa, Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa
| | - Noluxabiso Mangwana
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa
| | - Jyoti R Sharma
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa.,Centre for Cardio-metabolic Research in Africa, Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa
| | - Christo J F Muller
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa.,Centre for Cardio-metabolic Research in Africa, Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa.,Department of Biochemistry and Microbiology, University of Zululand, Kwa-Dlangezwa, South Africa
| | - Kholofelo Malemela
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa
| | - Funanani Mashau
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa
| | - Stephanie Dias
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa
| | - Pritika Ramharack
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa.,Pharmaceutical Sciences, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Craig Kinnear
- Genomics Centre, South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa.,DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Brigitte Glanzmann
- Pharmaceutical Sciences, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Amsha Viraragavin
- Genomics Centre, South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa
| | - Johan Louw
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa.,Department of Biochemistry and Microbiology, University of Zululand, Kwa-Dlangezwa, South Africa
| | - Swastika Surujlal-Naicker
- Scientific Services, Water and Sanitation Department, City of Cape Town Metropolitan Municipality, Cape Town, South Africa
| | - Sizwe Nkambule
- Environment & Health Research Unit, South African Medical Research Council (SAMRC), Durban, South Africa
| | - Candice Webster
- Environment & Health Research Unit, South African Medical Research Council (SAMRC), JohannesburgSouth Africa
| | - Mongezi Mdhluli
- Chief Research Operations Office, South African Medical Research Council, Tygerberg 7050, South Africa
| | - Glenda Gray
- Office of the President, South African Medical Research Council, Tygerberg 7050, South Africa
| | - Angela Mathee
- Environment & Health Research Unit, South African Medical Research Council (SAMRC), JohannesburgSouth Africa
| | - Wolfgang Preiser
- Division of Medical Virology at NHLS Tygerberg Hospital and Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Alvera Vorster
- Central Analytical Facilities, Stellenbosch University, South Africa
| | - Shareefa Dalvie
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa.,SAMRC, Unit on Risk & Resilience in Mental Disorders, Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Renee Street
- Environment & Health Research Unit, South African Medical Research Council (SAMRC), Durban, South Africa
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97
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Barozi V, Edkins AL, Tastan Bishop Ö. Evolutionary progression of collective mutations in Omicron sub-lineages towards efficient RBD-hACE2: Allosteric communications between and within viral and human proteins. Comput Struct Biotechnol J 2022; 20:4562-4578. [PMID: 35989699 PMCID: PMC9384468 DOI: 10.1016/j.csbj.2022.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/06/2022] [Accepted: 08/07/2022] [Indexed: 11/23/2022] Open
Abstract
The interaction between the Spike (S) protein of SARS-CoV-2 and the human angiotensin converting enzyme 2 (hACE2) is essential for infection, and is a target for neutralizing antibodies. Consequently, selection of mutations in the S protein is expected to be driven by the impact on the interaction with hACE2 and antibody escape. Here, for the first time, we systematically characterized the collective effects of mutations in each of the Omicron sub-lineages (BA.1, BA.2, BA.3 and BA.4) on both the viral S protein receptor binding domain (RBD) and the hACE2 protein using post molecular dynamics studies and dynamic residue network (DRN) analysis. Our analysis suggested that Omicron sub-lineage mutations result in altered physicochemical properties that change conformational flexibility compared to the reference structure, and may contribute to antibody escape. We also observed changes in the hACE2 substrate binding groove in some sub-lineages. Notably, we identified unique allosteric communication paths in the reference protein complex formed by the DRN metrics betweenness centrality and eigencentrality hubs, originating from the RBD core traversing the receptor binding motif of the S protein and the N-terminal domain of the hACE2 to the active site. We showed allosteric changes in residue network paths in both the RBD and hACE2 proteins due to Omicron sub-lineage mutations. Taken together, these data suggest progressive evolution of the Omicron S protein RBD in sub-lineages towards a more efficient interaction with the hACE2 receptor which may account for the increased transmissibility of Omicron variants.
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Affiliation(s)
- Victor Barozi
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda/Grahamstown 6139, South Africa
| | - Adrienne L. Edkins
- The Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Rhodes University, Makhanda/Grahamstown 6139, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda/Grahamstown 6139, South Africa
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98
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Chaudhari AM, Joshi M, Kumar D, Patel A, Lokhande KB, Krishnan A, Hanack K, Filipek S, Liepmann D, Renugopalakrishnan V, Paulmurugan R, Joshi C. Evaluation of immune evasion in SARS-CoV-2 Delta and Omicron variants. Comput Struct Biotechnol J 2022; 20:4501-4516. [PMID: 35965661 PMCID: PMC9359593 DOI: 10.1016/j.csbj.2022.08.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/04/2022] [Accepted: 08/04/2022] [Indexed: 12/18/2022] Open
Abstract
Emerging SARS-CoV-2 variants with higher transmissibility and immune escape remain a persistent threat across the globe. This is evident from the recent outbreaks of the Delta (B.1.617.2) and Omicron variants. These variants have originated from different continents and spread across the globe. In this study, we explored the genomic and structural basis of these variants for their lineage defining mutations of the spike protein through computational analysis, protein modeling, and molecular dynamic (MD) simulations. We further experimentally validated the importance of these deletion mutants for their immune escape using a pseudovirus-based neutralization assay, and an antibody (4A8) that binds directly to the spike protein's NTD. Delta variant with the deletion and mutations in the NTD revealed a better rigidity and reduced flexibility as compared to the wild-type spike protein (Wuhan isolate). Furthermore, computational studies of 4A8 monoclonal antibody (mAb) revealed a reduced binding of Delta variant compared to the wild-type strain. Similarly, the MD simulation data and virus neutralization assays revealed that the Omicron also exhibits immune escape, as antigenic beta-sheets appear to be disrupted. The results of the present study demonstrate the higher possibility of immune escape and thereby achieved better fitness advantages by the Delta and Omicron variants, which warrants further demonstrations through experimental evidences. Our study, based on in-silico computational modelling, simulations, and pseudovirus-based neutralization assay, highlighted and identified the probable mechanism through which the Delta and Omicron variants are more pathogenically evolved with higher transmissibility as compared to the wild-type strain.
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Affiliation(s)
- Armi M Chaudhari
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar 382011, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar 382011, India
| | - Dinesh Kumar
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar 382011, India
| | - Amrutlal Patel
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar 382011, India
| | - Kiran Bharat Lokhande
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar 382011, India
| | - Anandi Krishnan
- Cellular Pathway Imaging Laboratory (CPIL), Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94304, United States
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA 94304, United States
| | - Katja Hanack
- Immunotechnology Group, Department of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Slawomir Filipek
- Faculty of Chemistry & Biological and Chemical Research, Centre, University of Warsaw, ul, Pasteura 1, 02-093 Warsaw, Poland
| | - Dorian Liepmann
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Venkatesan Renugopalakrishnan
- Department of Chemistry, Northeastern University, Boston Children's Hospital, Harvard Medical School, Boston, MGB Center for COVID Innovation, MA 02115, United States
| | - Ramasamy Paulmurugan
- Cellular Pathway Imaging Laboratory (CPIL), Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94304, United States
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar 382011, India
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99
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Implications of the SARS-CoV-2 subvariants BA.4 and BA.5. Int J Surg 2022; 104:106806. [PMID: 35926828 PMCID: PMC9343086 DOI: 10.1016/j.ijsu.2022.106806] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 07/27/2022] [Indexed: 11/25/2022]
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100
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Potent and broad neutralization of SARS-CoV-2 variants of concern (VOCs) including omicron sub-lineages BA.1 and BA.2 by biparatopic human VH domains. iScience 2022; 25:104798. [PMID: 35875685 PMCID: PMC9296231 DOI: 10.1016/j.isci.2022.104798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/08/2022] [Accepted: 07/14/2022] [Indexed: 12/24/2022] Open
Abstract
The emergence of SARS-CoV-2 variants of concern (VOCs) requires the development of next-generation biologics with high neutralization breadth. Here, we characterized a human VH domain, F6, which we generated by sequentially panning large phage-displayed VH libraries against receptor binding domains (RBDs) containing VOC mutations. Cryo-EM analyses reveal that F6 has a unique binding mode that spans a broad surface of the RBD and involves the antibody framework region. Attachment of an Fc region to a fusion of F6 and ab8, a previously characterized VH domain, resulted in a construct (F6-ab8-Fc) that broadly and potently neutralized VOCs including Omicron. Additionally, prophylactic treatment using F6-ab8-Fc reduced live Beta (B.1.351) variant viral titers in the lungs of a mouse model. Our results provide a new potential therapeutic against SARS-CoV-2 variants including Omicron and highlight a vulnerable epitope within the spike that may be exploited to achieve broad protection against circulating variants.
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