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Alkafaas SS, Abdallah AM, Hussien AM, Bedair H, Abdo M, Ghosh S, Elkafas SS, Apollon W, Saki M, Loutfy SA, Onyeaka H, Hessien M. A study on the effect of natural products against the transmission of B.1.1.529 Omicron. Virol J 2023; 20:191. [PMID: 37626376 PMCID: PMC10464336 DOI: 10.1186/s12985-023-02160-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND The recent outbreak of the Coronavirus pandemic resulted in a successful vaccination program launched by the World Health Organization. However, a large population is still unvaccinated, leading to the emergence of mutated strains like alpha, beta, delta, and B.1.1.529 (Omicron). Recent reports from the World Health Organization raised concerns about the Omicron variant, which emerged in South Africa during a surge in COVID-19 cases in November 2021. Vaccines are not proven completely effective or safe against Omicron, leading to clinical trials for combating infection by the mutated virus. The absence of suitable pharmaceuticals has led scientists and clinicians to search for alternative and supplementary therapies, including dietary patterns, to reduce the effect of mutated strains. MAIN BODY This review analyzed Coronavirus aetiology, epidemiology, and natural products for combating Omicron. Although the literature search did not include keywords related to in silico or computational research, in silico investigations were emphasized in this study. Molecular docking was implemented to compare the interaction between natural products and Chloroquine with the ACE2 receptor protein amino acid residues of Omicron. The global Omicron infection proceeding SARS-CoV-2 vaccination was also elucidated. The docking results suggest that DGCG may bind to the ACE2 receptor three times more effectively than standard chloroquine. CONCLUSION The emergence of the Omicron variant has highlighted the need for alternative therapies to reduce the impact of mutated strains. The current review suggests that natural products such as DGCG may be effective in binding to the ACE2 receptor and combating the Omicron variant, however, further research is required to validate the results of this study and explore the potential of natural products to mitigate COVID-19.
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Affiliation(s)
- Samar Sami Alkafaas
- Molecular Cell Biology Unit, Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, 31527, Egypt.
| | - Abanoub Mosaad Abdallah
- Narcotic Research Department, National Center for Social and Criminological Research (NCSCR), Giza, 11561, Egypt
| | - Aya Misbah Hussien
- Biotechnology Department at Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Heba Bedair
- Botany Department, Faculty of Science, Tanta University, Tanta, Egypt
| | - Mahmoud Abdo
- Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Soumya Ghosh
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, 9301, South Africa.
| | - Sara Samy Elkafas
- Production Engineering and Mechanical Design Department, Faculty of Engineering, Menofia University, Menofia, Egypt
| | - Wilgince Apollon
- Department of Agricultural and Food Engineering, Faculty of Agronomy, Universidad Autónoma de Nuevo León, Francisco Villa S/N, Ex-Hacienda El Canadá, 66050, General Escobedo, Nuevo León, Mexico
| | - Morteza Saki
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Samah A Loutfy
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
- Nanotechnology Research Center, British University, Cairo, Egypt
| | - Helen Onyeaka
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - Mohamed Hessien
- Molecular Cell Biology Unit, Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, 31527, Egypt
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Giron CC, Laaksonen A, Barroso da Silva FL. Differences between Omicron SARS-CoV-2 RBD and other variants in their ability to interact with cell receptors and monoclonal antibodies. J Biomol Struct Dyn 2023; 41:5707-5727. [PMID: 35815535 DOI: 10.1080/07391102.2022.2095305] [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: 03/23/2022] [Accepted: 06/23/2022] [Indexed: 12/23/2022]
Abstract
SARS-CoV-2 remains a health threat with the continuous emergence of new variants. This work aims to expand the knowledge about the SARS-CoV-2 receptor-binding domain (RBD) interactions with cell receptors and monoclonal antibodies (mAbs). By using constant-pH Monte Carlo simulations, the free energy of interactions between the RBD from different variants and several partners (Angiotensin-Converting Enzyme-2 (ACE2) polymorphisms and various mAbs) were predicted. Computed RBD-ACE2-binding affinities were higher for two ACE2 polymorphisms (rs142984500 and rs4646116) typically found in Europeans which indicates a genetic susceptibility. This is amplified for Omicron (BA.1) and its sublineages BA.2 and BA.3. The antibody landscape was computationally investigated with the largest set of mAbs so far in the literature. From the 32 studied binders, groups of mAbs were identified from weak to strong binding affinities (e.g. S2K146). These mAbs with strong binding capacity and especially their combination are amenable to experimentation and clinical trials because of their high predicted binding affinities and possible neutralization potential for current known virus mutations and a universal coronavirus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Carolina Corrêa Giron
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- Universidade Federal do Triângulo Mineiro, Hospital de Clínicas, Uberaba, MG, Brazil
| | - Aatto Laaksonen
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
- State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing, PR China
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Iasi, Romania
- Department of Engineering Sciences and Mathematics, Division of Energy Science, Luleå University of Technology, Luleå, Sweden
- Department of Chemical and Geological Sciences, University of Cagliari, Monserrato, Italy
| | - Fernando Luís Barroso da Silva
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
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Doke PP, Mhaske ST, Oka G, Kulkarni R, Muley V, Mishra AC, Arankalle VA. SARS-CoV-2 breakthrough infections during the second wave of COVID-19 at Pune, India. Front Public Health 2023; 10:1040012. [PMID: 36711329 PMCID: PMC9877521 DOI: 10.3389/fpubh.2022.1040012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/19/2022] [Indexed: 01/13/2023] Open
Abstract
Breakthrough infections following SARS-CoV-2 vaccination remain the global concern. The current study was conducted during the second wave of COVID-19 (1st March-7th July 2021) in Pune, India, at two tertiary care hospitals. Of the 6,159 patients diagnosed as COVID-19, 372/2,210 (16.8%) were breakthrough infections. Of these, 81.1 and 18.8% received one or two doses of Covishield or Covaxin, respectively. Of note, 30.7% patients were with comorbidities, hypertension being the commonest (12.44%). The majority of infections were mild (81.2%). Forty-three patients with breakthrough infections were hospitalized with severe (n = 27, 62.8%) or moderate (n = 16, 37.2%) disease. The receptor binding domain (RBD) sequences from vaccinated (n = 126) and non-vaccinated (n = 168) samples were used for variant analysis. The delta variant was predominant followed by kappa in both vaccinated and non-vaccinated groups. Viral load (qRT-PCR) was not different among these categories. Full-genome comparisons of sequences in relation to vaccination status did not identify any mutation characteristic of the vaccinated group. Irrespective of the number of doses, neutralizing antibody titers (PRNT50) during the first week of clinical disease were higher in the vaccinated patients than the unvaccinated category. In conclusion, though not completely, SARS-CoV-2 vaccines used for country-wide immunization did reduce disease severity among the individuals without any comorbidity by inducing rapid immune response against distinctly different delta and kappa variants. The utility against emerging variants with further mutations need to be carefully examined.
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Affiliation(s)
- Prakash P. Doke
- Department of Community Medicine, Bharati Vidyapeeth (Deemed to be University) Medical College, Pune, India
| | - Suhas T. Mhaske
- Department of Communicable Diseases, Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth (Deemed to be University), Pune, India
| | - Gauri Oka
- Department of Community Medicine, Bharati Vidyapeeth (Deemed to be University) Medical College, Pune, India
| | - Ruta Kulkarni
- Department of Communicable Diseases, Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth (Deemed to be University), Pune, India
| | - Vrishali Muley
- Department of Microbiology, Smt. Kashibai Navale Medical College, Pune, India
| | - Akhilesh Chandra Mishra
- Department of Communicable Diseases, Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth (Deemed to be University), Pune, India
| | - Vidya A. Arankalle
- Department of Communicable Diseases, Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth (Deemed to be University), Pune, India
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Neamtu A, Mocci F, Laaksonen A, Barroso da Silva FL. Towards an optimal monoclonal antibody with higher binding affinity to the receptor-binding domain of SARS-CoV-2 spike proteins from different variants. Colloids Surf B Biointerfaces 2023; 221:112986. [PMID: 36375294 PMCID: PMC9617679 DOI: 10.1016/j.colsurfb.2022.112986] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/13/2022] [Accepted: 10/27/2022] [Indexed: 11/13/2022]
Abstract
A highly efficient and robust multiple scales in silico protocol, consisting of atomistic Molecular Dynamics (MD), coarse-grain (CG) MD, and constant-pH CG Monte Carlo (MC), has been developed and used to study the binding affinities of selected antigen-binding fragments of the monoclonal antibody (mAbs) CR3022 and several of its here optimized versions against 11 SARS-CoV-2 variants including the wild type. Totally 235,000 mAbs structures were initially generated using the RosettaAntibodyDesign software, resulting in top 10 scored CR3022-like-RBD complexes with critical mutations and compared to the native one, all having the potential to block virus-host cell interaction. Of these 10 finalists, two candidates were further identified in the CG simulations to be the best against all SARS-CoV-2 variants. Surprisingly, all 10 candidates and the native CR3022 exhibited a higher affinity for the Omicron variant despite its highest number of mutations. The multiscale protocol gives us a powerful rational tool to design efficient mAbs. The electrostatic interactions play a crucial role and appear to be controlling the affinity and complex building. Studied mAbs carrying a more negative total net charge show a higher affinity. Structural determinants could be identified in atomistic simulations and their roles are discussed in detail to further hint at a strategy for designing the best RBD binder. Although the SARS-CoV-2 was specifically targeted in this work, our approach is generally suitable for many diseases and viral and bacterial pathogens, leukemia, cancer, multiple sclerosis, rheumatoid, arthritis, lupus, and more.
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Affiliation(s)
- Andrei Neamtu
- Department of Physiology, "Grigore T. Popa" University of Medicine and Pharmacy of Iasi, Str. Universitatii nr. 16, 700051 Iasi, România; TRANSCEND Centre - Regional Institute of Oncology (IRO) Iasi, Str. General Henri Mathias Berthelot, Nr. 2-4 Iași, România
| | - Francesca Mocci
- University of Cagliari, Department of Chemical and Geological Sciences, Campus Monserrato, SS 554 bivio per Sestu, 09042 Monserrato, Italy
| | - Aatto Laaksonen
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, PetruPoni Institute of Macromolecular Chemistry Aleea Grigore Ghica-Voda, 41 A, 700487 Iasi, Romania; University of Cagliari, Department of Chemical and Geological Sciences, Campus Monserrato, SS 554 bivio per Sestu, 09042 Monserrato, Italy; Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden; State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing 210009, PR China; Department of Engineering Sciences and Mathematics, Division of Energy Science, Luleå University of Technology, SE-97187 Luleå, Sweden
| | - Fernando L Barroso da Silva
- Universidade de São Paulo, Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Av. café, s/no - campus da USP, BR-14040-903 Ribeirão Preto, SP, Brazil; Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA.
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Sarkar MS, Madabhavi I. SARS-CoV-2 variants of concern: a review. Monaldi Arch Chest Dis 2022. [DOI: 10.4081/monaldi.2022.2337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2022] Open
Abstract
The virus that causes severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) belongs to the genus Beta coronavirus and the family Coronaviridae. The SARS-CoV-2 virus is a positive sense, non-segmented single-strand RNA virus that causes coronavirus disease 2019 (COVID-19), which was first reported in December 2019 in Wuhan, China. COVID-19 is now a worldwide pandemic. Globally, several newer variants have been identified; however, only a few of them are of concern (VOCs). VOCs differ in terms of infectivity, transmissibility, disease severity, drug efficacy, and neutralization efficacy by monoclonal antibodies, convalescent sera, or vaccines. VOCs reported from various parts of the world include B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617/B.1.617.2 (Delta), P.1 (Gamma), and B.1.1.529 (Omicron). These VOCs are the result of mutations, with some based on spike proteins. Mutations may also cause molecular diagnostic tests to fail to detect the few VOCs, leading to a delayed diagnosis, increased community spread, and delayed treatment. We searched PubMed, EMBASE, Covariant, Stanford variants database, and CINAHL from December 2019 to February 2022 using the following search terms: Variant of Concern, SARS-CoV-2, Omicron, etc. All types of research were chosen. All research methods were considered. This review discusses the various VOCs, as well as their mutations, infectivity, transmissibility, and neutralization efficacy.
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Morris CP, Eldesouki RE, Fall A, Gaston DC, Norton JM, Gallagher ND, Luo CH, Abdullah O, Klein EY, Mostafa HH. SARS-CoV-2 reinfections during the Delta and Omicron waves. JCI Insight 2022; 7:e162007. [PMID: 36048527 PMCID: PMC9714778 DOI: 10.1172/jci.insight.162007] [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: 05/25/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUNDIncreased SARS-CoV-2 reinfection rates have been reported recently, with some locations basing reinfection on a second positive PCR test at least 90 days after initial infection. In this study, we used Johns Hopkins SARS-CoV-2 genomic surveillance data to evaluate the frequency of sequencing-validated, confirmed, and inferred reinfections between March 2020 and July 2022.METHODSPatients who had 2 or more positive SARS-CoV-2 tests in our system, with samples sequenced as a part of our surveillance efforts, were identified as the cohort for our study. SARS-CoV-2 genomes of patients' initial and later samples were compared.RESULTSA total of 755 patients (920 samples) had a positive test at least 90 days after the initial test, with a median time between tests of 377 days. Sequencing was attempted on 231 samples and was successful in 127. Rates of successful sequencing spiked during the Omicron surge; there was a higher median number of days from initial infection in these cases compared with those with failed sequences. A total of 122 (98%) patients showed evidence of reinfection; 45 of these patients had sequence-validated reinfection and 77 had inferred reinfections (later sequencing showed a clade that was not circulating when the patient was initially infected). Of the 45 patients with sequence-validated reinfections, 43 (96%) had reinfections that were caused by the Omicron variant, 41 (91%) were symptomatic, 32 (71%) were vaccinated prior to the second infection, 6 (13%) were immunosuppressed, and only 2 (4%) were hospitalized.CONCLUSIONSequence-validated reinfections increased with the Omicron surge but were generally associated with mild infections.FUNDINGFunding was provided by the Johns Hopkins Center of Excellence in Influenza Research and Surveillance (HHSN272201400007C), CDC (75D30121C11061), Johns Hopkins University President's Fund Research Response, Johns Hopkins Department of Pathology, and the Maryland Department of Health.
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Affiliation(s)
- C. Paul Morris
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- National Institute of Allergy and Infectious Disease, NIH, Bethesda, Maryland, USA
| | - Raghda E. Eldesouki
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Genetics Unit, Histology Department, School of Medicine, Suez Canal University, Ismailia, Egypt
| | - Amary Fall
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - David C. Gaston
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Julie M. Norton
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Nicholas D. Gallagher
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Chun Huai Luo
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Omar Abdullah
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Eili Y. Klein
- Department of Emergency Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Center for Disease Dynamics, Economics, and Policy, Washington, DC, USA
| | - Heba H. Mostafa
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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D’Apice L, Trovato M, Gramigna G, Colavita F, Francalancia M, Matusali G, Meschi S, Lapa D, Bettini A, Mizzoni K, Aurisicchio L, Di Caro A, Castilletti C, De Berardinis P. Comparative analysis of the neutralizing activity against SARS-CoV-2 Wuhan-Hu-1 strain and variants of concern: Performance evaluation of a pseudovirus-based neutralization assay. Front Immunol 2022; 13:981693. [PMID: 36225911 PMCID: PMC9549111 DOI: 10.3389/fimmu.2022.981693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectivesEmergence of new variants of SARS-CoV-2 might affect vaccine efficacy. Therefore, assessing the capacity of sera to neutralize variants of concern (VOCs) in BSL-2 conditions will help evaluating the immune status of population following vaccination or infection.MethodsPseudotyped viruses bearing SARS-CoV-2 spike protein from Wuhan-Hu-1/D614G strains (wild type, WT), B.1.617.2 (Delta), or B.1.1.529 (Omicron) VOCs were generated to assess the neutralizing antibodies (nAbs) activity by a pseudovirus-based neutralization assay (PVNA). PVNA performance was assessed in comparison to the micro-neutralization test (MNT) based on live viruses. Sera collected from COVID-19 convalescents and vaccinees receiving mRNA (BNT16b2 or mRNA-1273) or viral vector (AZD1222 or Ad26.COV2.S) vaccines were used to measure nAbs elicited by two-dose BNT16b2, mRNA-1273, AZD1222 or one-dose Ad26.CO2.S, at different times from completed vaccination, ~ 1.5 month and ~ 4-6 months. Sera from pre-pandemic and unvaccinated individuals were analyzed as controls. Neutralizing activity following booster vaccinations against VOCs was also determined.ResultsPVNA titers correlated with the gold standard MNT assay, validating the reliability of PVNA. Sera analyzed late from the second dose showed a reduced neutralization activity compared to sera collected earlier. Ad26.CO2.S vaccination led to very low or absent nAbs. Neutralization of Delta and Omicron BA.1 VOCs showed significant reduction of nAbs respect to WT strain. Importantly, booster doses enhanced Omicron BA.1 nAbs, with persistent levels at 3 months from boosting.ConclusionsPVNA is a reliable tool for assessing anti-SARS-CoV-2 nAbs helping the establishment of a correlate of protection and the management of vaccination strategies.
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Affiliation(s)
- Luciana D’Apice
- Institute of Biochemistry and Cell Biology, Consiglio Nazionale delle Ricerche (CNR), Naples, Italy
- *Correspondence: Luciana D’Apice, ; Francesca Colavita,
| | - Maria Trovato
- Institute of Biochemistry and Cell Biology, Consiglio Nazionale delle Ricerche (CNR), Naples, Italy
| | - Giulia Gramigna
- National Institute for Infectious Diseases “L. Spallanzani” Istituto Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Francesca Colavita
- National Institute for Infectious Diseases “L. Spallanzani” Istituto Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- *Correspondence: Luciana D’Apice, ; Francesca Colavita,
| | - Massimo Francalancia
- National Institute for Infectious Diseases “L. Spallanzani” Istituto Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Giulia Matusali
- National Institute for Infectious Diseases “L. Spallanzani” Istituto Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Silvia Meschi
- National Institute for Infectious Diseases “L. Spallanzani” Istituto Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Daniele Lapa
- National Institute for Infectious Diseases “L. Spallanzani” Istituto Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Aurora Bettini
- National Institute for Infectious Diseases “L. Spallanzani” Istituto Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Klizia Mizzoni
- National Institute for Infectious Diseases “L. Spallanzani” Istituto Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | | | - Antonino Di Caro
- National Institute for Infectious Diseases “L. Spallanzani” Istituto Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Concetta Castilletti
- National Institute for Infectious Diseases “L. Spallanzani” Istituto Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
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Ali AM, Tofiq AM, Rostam HM, Ali KM, Tawfeeq HM. Disease severity and efficacy of homologous vaccination among patients infected with SARS-CoV-2 Delta or Omicron VOCs, compared to unvaccinated using main biomarkers. J Med Virol 2022; 94:5867-5876. [PMID: 36029103 PMCID: PMC9538273 DOI: 10.1002/jmv.28098] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/12/2022] [Accepted: 08/25/2022] [Indexed: 01/08/2023]
Abstract
From March 2021, various countries including Iraq issued prompted recommendations for increased COVID-19 vaccine protection in individuals especially those at risk of catching the virus (i.e., lifestyle, health sector workers, and chronic diseases). It is critically important to understand the impact of COVID-19 vaccinations with the most commonly used vaccines (Pfizer and AstraZeneca) among populations either on the severity of the disease or the transmissibility of SARS-CoV-2 variants of concern (VOCs) and in sequential waves. This study was conducted to establish the clinical severity of COVID-19 caused by Delta and Omicron SARS-CoV-2 variants among patients who either attended or were admitted to hospitals and to compare the effectiveness of Pfizer and AstraZeneca COVID-19 vaccines (single or double doses) at least to prevent hospitalizations if not eradicating the pandemic. A case-control study was done of 570 hospitalized patients; including 328 COVID-19 confirmed patients (166 males, 160 females) who received homologous vaccinations and 242 unvaccinated patients (128 males, 114 females) during the studied waves. The study showed that unvaccinated COVID-19 patients in both waves had expressed significantly a higher number and longer periods of symptoms than vaccinated ones. Additionally, there was no significant effect of vaccine types, Pfizer and AstraZeneca or vaccine shot numbers on the PCR-Ct in the last (Omicron) wave of the pandemic. However, in the previous (Delta) wave of the pandemic, fully vaccinated (double doses) COVID-19 patients had higher PCR-Ct values. Whether among vaccinated or unvaccinated patients, lower CRP levels recorded during the Omicron wave than that of the Delta wave, and regardless of the vaccine type or shot numbers, there were no significant differences between the two waves. Lower WBCs were observed in patients (vaccinated and unvaccinated) infected with the Delta variant in comparison to those infected with the Omicron variant and without any remarkable effect of the vaccine type or shot numbers. This is the first molecular and investigational study of the Delta variant and circulated Omicron in Iraq, regarding the severity of these two waves of SARS-CoV-2 pandemic and the efficacy of homologous vaccination, indicating the insufficiency of two doses and the demand for booster dose(s) as the most effective way of keeping on the safe-side against SARS-CoV-2.
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Affiliation(s)
- Ayad M. Ali
- Department of ChemistryUniversity of GarmianKalarKurdistan RegionIraq
| | - Ahmed M. Tofiq
- Department of Biology, College of EducationHead of International Academic Relations (IRO) University of GarmianKalarKurdistan RegionIraq
| | - Hassan M. Rostam
- Immunology & Immuno‐Bioengineering Group, Infections, Immunity and Microbes Division, School of Life Sciences, Faculty of Medicine & Health SciencesUniversity of NottinghamNottinghamUK,Department of Medicine, College of MedicineUniversity of GarmianKalarKurdistan RegionIraq
| | - Kameran M. Ali
- Medical Lab Technology Department, Kalar Technical CollegeSulaimani Polytechnic UniversityKalarKurdistan RegionIraq
| | - Hassan M. Tawfeeq
- Medical Lab Technology Department, Kalar Technical CollegeSulaimani Polytechnic UniversityKalarKurdistan RegionIraq
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Sun K, Tempia S, Kleynhans J, von Gottberg A, McMorrow ML, Wolter N, Bhiman JN, Moyes J, du Plessis M, Carrim M, Buys A, Martinson NA, Kahn K, Tollman S, Lebina L, Wafawanaka F, du Toit JD, Gómez-Olivé FX, Mkhencele T, Viboud C, Cohen C. SARS-CoV-2 transmission, persistence of immunity, and estimates of Omicron's impact in South African population cohorts. Sci Transl Med 2022; 14:eabo7081. [PMID: 35638937 PMCID: PMC9161370 DOI: 10.1126/scitranslmed.abo7081] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 05/25/2022] [Indexed: 12/14/2022]
Abstract
Understanding the build-up of immunity with successive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and the epidemiological conditions that favor rapidly expanding epidemics will help facilitate future pandemic control. We analyzed high-resolution infection and serology data from two longitudinal household cohorts in South Africa to reveal high cumulative infection rates and durable cross-protective immunity conferred by prior infection in the pre-Omicron era. Building on the history of past exposures to different SARS-CoV-2 variants and vaccination in the cohort most representative of South Africa's high urbanization rate, we used mathematical models to explore the fitness advantage of the Omicron variant and its epidemic trajectory. Modeling suggests that the Omicron wave likely infected a large fraction (44 to 81%) of the population, leaving a complex landscape of population immunity primed and boosted with antigenically distinct variants. We project that future SARS-CoV-2 resurgences are likely under a range of scenarios of viral characteristics, population contacts, and residual cross-protection.
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Affiliation(s)
- Kaiyuan Sun
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892-2220, United States of America
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, 30333, United States of America
| | - Jackie Kleynhans
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Meredith L McMorrow
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, 30333, United States of America
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Jinal N. Bhiman
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Jocelyn Moyes
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Maimuna Carrim
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Amelia Buys
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
| | - Neil A Martinson
- Perinatal HIV Research Unit, University of the Witwatersrand, 1864, South Africa
- Johns Hopkins University Center for TB Research, Baltimore, Maryland, 21287, United States of America
| | - Kathleen Kahn
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Limakatso Lebina
- Perinatal HIV Research Unit, University of the Witwatersrand, 1864, South Africa
| | - Floidy Wafawanaka
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Jacques D. du Toit
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Francesc Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Thulisa Mkhencele
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
| | - Cécile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892-2220, United States of America
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, 2131, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
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10
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Santra D, Maiti S. Molecular dynamic simulation suggests stronger interaction of Omicron-spike with ACE2 than wild but weaker than Delta SARS-CoV-2 can be blocked by engineered S1-RBD fraction. Struct Chem 2022; 33:1755-1769. [PMID: 35966763 PMCID: PMC9362541 DOI: 10.1007/s11224-022-02022-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/26/2022] [Indexed: 11/30/2022]
Abstract
The SARS-CoV-2 claimed millions of lives, globally. Occurring from Wuhan (wild type) in December, 2019, it constantly mutated to Omicron (B.1.1.529), the predecessor to Delta. Omicron having ~ 32 spike mutations has variable infectivity-multiplicity-immuno-invasive properties. Understanding of its mutational effect on ACE2-binding/disease severity and developing preventive/therapeutic strategies are important. The binding affinities of Wuhan/Delta/Omicron spikes (PDB/GISAID/SWISS-MODEL) were docked (HADDOCK2.4) with ACE2 and compared by competitive-docking (PRODIGY). The protein structural stability was verified by kinetic-data/Ramachandran-plot (Zlab/UMassMedBioinfo). After several trials, a 59 amino acid (453ARG-510VAL) peptide-cut (Expasy-server) of the wild-type spike RBD with some desired mutants (THR500SER/THR500GLY/THR500ALA/THR500CYS) was blindly/competitively docked (PyMOL-V2.2.2) to block the Omicron-ACE2 binding. We examined molecular dynamic simulation (iMOD-server, with 9000 cycles/300 k-heating/1 atm pressure for system equilibration for 50 ns-run) of ACE2 and two CUTs with different SARS-CoV-2 variants. The binding-affinity of Omicron-ACE2 is slightly higher than the rest two in competitive docking setup. During individual (1:1) docking, Omicron showed little higher than wild type but much weaker binding affinity than Delta. Competitive docking suggests ten H-bonding (1.3–2.4 Å) with highly favorable energy values/Van-der-Walls-force/Haddock score for more stable-binding of Omicron-RBD with ACE2. Blind docking of different CUTs (wild/mutants) and Omicron to ACE2 completely rejected the Omicron-RBD from ACE2-target. The best blocking/binding affinity of −16.4 and −13 kcal/mole were observed in the case of THR500SER and THR500GLY, respectively, with multiple H-bonding 1.9–2.2 Å. These are supported by the MD-simulation results. So, the spike binding affinities were Delta > Omicron > wild in 1:1 docking with ACE2. Considering the wild type is non-existing nowadays, Omicron showed less ACE2 binding properties. The 59 cut of spike-RBD and its mutant THR500SER/THR500GLY may be further screened as universal blockers of this virus.
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Affiliation(s)
- Dipannita Santra
- Department of Biochemistry and Biotechnology, Cell and Molecular Therapeutics Laboratory, Oriental Institute of Science and Technology, Midnapore, India
| | - Smarajit Maiti
- Department of Biochemistry and Biotechnology, Cell and Molecular Therapeutics Laboratory, Oriental Institute of Science and Technology, Midnapore, India
- Agricure Biotech Research Society, Epidemiology and Human Health Division, Midnapore, 721101 India
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11
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Torresi J, Edeling MA, Nolan T, Godfrey DI. A Complementary Union of SARS-CoV2 Natural and Vaccine Induced Immune Responses. Front Immunol 2022; 13:914167. [PMID: 35911696 PMCID: PMC9326230 DOI: 10.3389/fimmu.2022.914167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/13/2022] [Indexed: 12/27/2022] Open
Abstract
Our understanding of the immune responses that follow SARS-CoV-2 infection and vaccination has progressed considerably since the COVID-19 pandemic was first declared on the 11th of March in 2020. Recovery from infection is associated with the development of protective immune responses, although over time these become less effective against new emerging SARS-CoV-2 variants. Consequently, reinfection with SARS-CoV-2 variants is not infrequent and has contributed to the ongoing pandemic. COVID-19 vaccines have had a tremendous impact on reducing infection and particularly the number of deaths associated with SARS-CoV-2 infection. However, waning of vaccine induced immunity plus the emergence of new variants has necessitated the use of boosters to maintain the benefits of vaccination in reducing COVID-19 associated deaths. Boosting is also beneficial for individuals who have recovered from COVID-19 and developed natural immunity, also enhancing responses immune responses to SARS-CoV-2 variants. This review summarizes our understanding of the immune responses that follow SARS-CoV-2 infection and vaccination, the risks of reinfection with emerging variants and the very important protective role vaccine boosting plays in both vaccinated and previously infected individuals.
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Affiliation(s)
- Joseph Torresi
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Melissa A. Edeling
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Terry Nolan
- Department of Infectious Diseases, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - Dale I. Godfrey
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
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12
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Scadding GK. A New Grand Challenge in Rhinology: An Intranasal COVID Vaccine. FRONTIERS IN ALLERGY 2022; 3:881118. [PMID: 35769553 PMCID: PMC9234858 DOI: 10.3389/falgy.2022.881118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/19/2022] [Indexed: 12/16/2022] Open
Affiliation(s)
- Glenis Kathleen Scadding
- University College London Hospitals NHS Foundation Trust, London, United Kingdom
- Division of Immunity and Infection, University College London, London, United Kingdom
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13
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Morris CP, Eldesouki RE, Fall A, Gaston DC, Norton JM, Gallagher N, Luo CH, Abdullah O, Klein EY, Mostafa HH. Sequence Proven Reinfections with SARS-CoV-2 at a Large Academic Center. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.05.17.22275210. [PMID: 35665008 PMCID: PMC9164520 DOI: 10.1101/2022.05.17.22275210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Background Increased reinfection rates with SARS-CoV-2 have recently been reported, with some locations basing reinfection on a second positive PCR test at least 90 days after initial infection. Methods We identified cases where patients had two positive tests for SARS-CoV-2 and evaluated which of these had been sequenced as part of our surveillance efforts, and evaluated sequencing and clinical data. Results 750 patients (920 samples) had a positive test at least 90 days after the initial test. The median time between tests was 377 days, and 724 (79%) of the post 90-day positives were collected after the emergence of the Omicron variant in November 2021. Sequencing was attempted on 231 samples and successful in 127. Successful sequencing spiked during the Omicron surge and showed higher median days from initial infection compared to failed sequences (median 398 days compared to 276 days, p<0.0005). A total of 122 (98%) patients showed evidence of reinfection, 45 of which had sequence proven reinfection and 77 had inferred reinfections (later sequence showed a clade that was not circulating when the patient was initially infected). Children accounted for only 4% of reinfections. 43 (96%) of 45 infections with sequence proven reinfection were caused by the Omicron variant, 41 (91%) were symptomatic, 32 (71%), were vaccinated prior to the second infection, and 6 (13%) were Immunosuppressed. Only 2 (4%) were hospitalized, and both had underlying conditions. Conclusion Sequence proven reinfections increased with the Omicron variant but generally caused mild infections.
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Affiliation(s)
- C. Paul Morris
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Raghda E. Eldesouki
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Genetics Unit Histology Department, School of Medicine, Suez Canal University, Egypt
| | - Amary Fall
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - David C. Gaston
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Julie M. Norton
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Nicholas Gallagher
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Chun Huai Luo
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Omar Abdullah
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Eili Y. Klein
- Department of Emergency Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Center for Disease Dynamics, Economics, and Policy, Washington DC
| | - Heba H. Mostafa
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
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14
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Lotz C, Herrmann J, Hübsch ME, Notz Q, Meybohm P. [Measurement of Anti-SARS CoV-2 Antibodies following Vaccination: Valuable Monitoring or Irrelevant Tool?]. Anasthesiol Intensivmed Notfallmed Schmerzther 2022; 57:302-306. [PMID: 35451036 DOI: 10.1055/a-1783-3932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Vaccination against severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) provides effective protection against infection or severe coronavirus disease 2019 (COVID-19). Moreover, it is regarded as the single most important measure to end the pandemic. Individual vaccination effectiveness is often judged via measurement of anti-SARS-CoV-2 antibodies. However, considering the complexity of the humoral and cellular immune response the question arises whether the relation of anti-SARS-CoV-2 antibody titers and COVID-19 vaccine effectiveness is a myth or a fact? The current article aims to answer this question and provide a short review of the immunological mechanisms of SARS-CoV-2 vaccination. Recommendations for clinical practice are given based on the current evidence and known problems of anti-SARS-CoV-2 antibody measurements after vaccination.
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15
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Projecting the Pandemic Trajectory through Modeling the Transmission Dynamics of COVID-19. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19084541. [PMID: 35457409 PMCID: PMC9032231 DOI: 10.3390/ijerph19084541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 12/13/2022]
Abstract
The course of the COVID-19 pandemic has given rise to many disease trends at various population scales, ranging from local to global. Understanding these trends and the epidemiological phenomena that lead to the changing dynamics associated with disease progression is critical for public health officials and the global community to rein in further spread of this and other virulent diseases. Classic epidemiological modeling based on dynamical systems are powerful tools used for modeling and understanding diseases, but often necessitate modifications to the classic compartmental models to reflect empirical observations. In this paper, we present a collection of extensions to the classic SIRS model to support public health decisions associated with viral pandemics. Specifically, we present models that reflect different levels of disease severity among infected individuals, capture the effect of vaccination on different population groups, capture the effect of different vaccines with different levels of effectiveness, and model the impact of a vaccine with varying number of doses. Further, our mathematical models support the investigation of a pandemic’s trend under the emergence of new variants and the associated reduction in vaccine effectiveness. Our models are supported through numerical simulations, which we use to illustrate phenomena that have been observed in the COVID-19 pandemic. Our findings also confirm observations that the mild infectious group accounts for the majority of infected individuals, and that prompt immunization results in weaker pandemic waves across all levels of infection as well as a lower number of disease-caused deaths. Finally, using our models, we demonstrate that, when dealing with a single variant and having access to a highly effective vaccine, a three-dose vaccine has a strong ability to reduce the infectious population. However, when a new variant with higher transmissibility and lower vaccine efficiency emerges, it becomes the dominant circulating variant, as was observed in the recent emergence of the Omicron variant.
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16
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Medigeshi GR, Batra G, Murugesan DR, Thiruvengadam R, Chattopadhyay S, Das B, Gosain M, Ayushi, Singh J, Anbalagan A, Shaman H, Pargai K, Mehdi F, Das SJ, Kahlon N, Singh S, Kshetrapal P, Wadhwa N, Pandey AK, Bhatnagar S, Garg PK. Sub-optimal neutralisation of omicron (B.1.1.529) variant by antibodies induced by vaccine alone or SARS-CoV-2 Infection plus vaccine (hybrid immunity) post 6-months. EBioMedicine 2022; 78:103938. [PMID: 35305396 PMCID: PMC8923830 DOI: 10.1016/j.ebiom.2022.103938] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/23/2022] [Accepted: 03/01/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Rapid spread of the omicron SARS-CoV-2 variant despite extensive vaccination suggests immune escape. The neutralising ability of different vaccines alone or with natural SARS-CoV-2 infection against omicron is not well-known. METHODS In this cross-sectional study, we tested the ability of vaccine and natural infection induced antibodies to neutralise omicron variant in a live virus neutralisation assay in four groups of individuals: (i) ChAdOx1 nCoV-19 vaccination, (ii) ChAdOx1 nCoV-19 vaccination plus prior SARS-CoV-2 infection, (iii) vaccination with inactivated virus vaccine (BBV152), and (iv) BBV152 vaccination plus prior SARS-CoV-2 infection. Primary outcome was fold-change in virus neutralisation titre against omicron compared with ancestral virus. FINDINGS We included 80 subjects. The geometric mean titre (GMT) of the 50% focus reduction neutralisation test (FRNT50) was 380·4 (95% CI: 221·1, 654·7) against the ancestral virus with BBV152 vaccination and 379·3 (95% CI: 185·6, 775·2) with ChAdOx1 nCov-19 vaccination alone. GMT for vaccination plus infection groups were 806·1 (95% CI: 478·5, 1357·8) and 1526·2 (95% CI: 853·2, 2730·0), respectively. Against omicron variant, only 5 out of 20 in both BBV152 and ChAdOx1 nCoV-19 vaccine only groups, 6 out of 20 in BBV152 plus prior SARS-CoV-2 infection group, and 9 out of 20 in ChAdOx1 nCoV-19 plus prior SARS-CoV-2 infection group exhibited neutralisation titres above the lower limit of quantification (1:20) suggesting better neutralisation with prior infection. A reduction of 26·6 and 25·7 fold in FRNT50 titres against Omicron compared to ancestral SARS-CoV-2 strain was observed for individuals without prior SARS-CoV-2 infection vaccinated with BBV152 and ChAdOx1 nCoV-19, respectively. The corresponding reduction was 57·1 and 58·1 fold, respectively, for vaccinated individuals with prior infection. The 50% neutralisation titre against omicron demonstrated moderate correlation with serum anti-RBD IgG levels [Spearman r: 0·58 (0·41, 0·71)]. INTERPRETATION Significant reduction in the neutralising ability of both vaccine-induced and vaccine plus infection-induced antibodies was observed for omicron variant which might explain immune escape. FUNDING Department of Biotechnology, India; Bill & Melinda Gates Foundation, USA.
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Affiliation(s)
| | - Gaurav Batra
- Translational Health Science and Technology Institute, Faridabad, Haryana 120001, India
| | | | | | - Souvick Chattopadhyay
- Translational Health Science and Technology Institute, Faridabad, Haryana 120001, India
| | - Bhabatosh Das
- Translational Health Science and Technology Institute, Faridabad, Haryana 120001, India
| | - Mudita Gosain
- Translational Health Science and Technology Institute, Faridabad, Haryana 120001, India
| | - Ayushi
- Translational Health Science and Technology Institute, Faridabad, Haryana 120001, India
| | - Janmejay Singh
- Translational Health Science and Technology Institute, Faridabad, Haryana 120001, India
| | - Anantharaj Anbalagan
- Translational Health Science and Technology Institute, Faridabad, Haryana 120001, India
| | - Heena Shaman
- Translational Health Science and Technology Institute, Faridabad, Haryana 120001, India
| | - Kamal Pargai
- Translational Health Science and Technology Institute, Faridabad, Haryana 120001, India
| | - Farha Mehdi
- Translational Health Science and Technology Institute, Faridabad, Haryana 120001, India
| | - Soon Jyoti Das
- Translational Health Science and Technology Institute, Faridabad, Haryana 120001, India
| | - Namrata Kahlon
- ESIC Medical College and Hospital, Faridabad, Haryana, India
| | - Savita Singh
- Translational Health Science and Technology Institute, Faridabad, Haryana 120001, India
| | - Pallavi Kshetrapal
- Translational Health Science and Technology Institute, Faridabad, Haryana 120001, India
| | - Nitya Wadhwa
- Translational Health Science and Technology Institute, Faridabad, Haryana 120001, India
| | - Anil K Pandey
- ESIC Medical College and Hospital, Faridabad, Haryana, India
| | - Shinjini Bhatnagar
- Translational Health Science and Technology Institute, Faridabad, Haryana 120001, India
| | - Pramod Kumar Garg
- Translational Health Science and Technology Institute, Faridabad, Haryana 120001, India.
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17
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Ding K, Jiang W, Xiong C, Lei M. Turning point: A new global COVID-19 wave or a signal of the beginning of the end of the global COVID-19 pandemic? Immun Inflamm Dis 2022; 10:e606. [PMID: 35349754 PMCID: PMC8962637 DOI: 10.1002/iid3.606] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 12/23/2022] Open
Abstract
A new variant named Omicron (B.1.1.529), first identified in South Africa, has become of considerable interest to the World Health Organization. This variant differs from the other known major variants, as it carries a large number of unusual mutations, particularly in the spinous process protein and receptor binding domains. Some specific mutation sites make it vaccine resistant, highly infectious, and highly pathogenic. The world fears that the Omicron variant could be even more harmful than the previous major variant, given that it has emerged amid fierce competition to trigger a new global pandemic peak as infections in South Africa rise. However, some epidemiological evidence has emerged that the Omicron variant may produce milder patient symptoms. We speculate if the virulence of the Omicron variant will diminish as transmissibility increases, thereby signaling the beginning of the end for the global COVID-19 pandemic. Based on this view, we make recommendations for COVID-19 mitigation in the present and future. However, it will take a few weeks to determine the true threat posed by the Omicron variant and we need to be fully prepared for future outbreaks, regardless of their severity.
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Affiliation(s)
- Kaixi Ding
- Hospital of Chengdu University of Traditional Chinese MedicineChengduChina
| | - Wei Jiang
- Hospital of Chengdu University of Traditional Chinese MedicineChengduChina
| | - Chunping Xiong
- Hospital of Chengdu University of Traditional Chinese MedicineChengduChina
| | - Ming Lei
- Hospital of Chengdu University of Traditional Chinese MedicineChengduChina
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18
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Affiliation(s)
- Etienne Simon-Loriere
- Institut Pasteur, Université de Paris, G5 Evolutionary Genomics of RNA viruses, Paris, France.
| | - Olivier Schwartz
- Institut Pasteur, Université de Paris, CNRS UMR3569, Virus and Immunity Unit, Paris, France.
- Vaccine Research Institute, Créteil, France.
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19
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Abas AH, Marfuah S, Idroes R, Kusumawaty D, Fatimawali, Park MN, Siyadatpanah A, Alhumaydhi FA, Mahmud S, Tallei TE, Emran TB, Kim B. Can the SARS-CoV-2 Omicron Variant Confer Natural Immunity against COVID-19? Molecules 2022; 27:2221. [PMID: 35408618 PMCID: PMC9000495 DOI: 10.3390/molecules27072221] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 02/06/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is still ongoing, with no signs of abatement in sight. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of this pandemic and has claimed over 5 million lives, is still mutating, resulting in numerous variants. One of the newest variants is Omicron, which shows an increase in its transmissibility, but also reportedly reduces hospitalization rates and shows milder symptoms, such as in those who have been vaccinated. As a result, many believe that Omicron provides a natural vaccination, which is the first step toward ending the COVID-19 pandemic. Based on published research and scientific evidence, we review and discuss how the end of this pandemic is predicted to occur as a result of Omicron variants being surpassed in the community. In light of the findings of our research, we believe that it is most likely true that the Omicron variant is a natural way of vaccinating the masses and slowing the spread of this deadly pandemic. While the mutation that causes the Omicron variant is encouraging, subsequent mutations do not guarantee that the disease it causes will be less severe. As the virus continues to evolve, humans must constantly adapt by increasing their immunity through vaccination.
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Affiliation(s)
- Abdul Hawil Abas
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia; (A.H.A.); (S.M.)
| | - Siti Marfuah
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia; (A.H.A.); (S.M.)
| | - Rinaldi Idroes
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Universitas Syiah Kuala, Kopelma Darussalam, Banda Aceh 23111, Aceh, Indonesia;
| | - Diah Kusumawaty
- Department of Biology, Faculty of Mathematics and Natural Sciences Education, Universitas Pendidikan Indonesia, Bandung 40154, West Java, Indonesia;
| | - Fatimawali
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia;
| | - Moon Nyeo Park
- College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemungu, Seoul 05253, Korea;
| | - Abolghasem Siyadatpanah
- Ferdows School of Paramedical and Health, Birjand University of Medical Sciences, Birjand 97178-53577, Iran;
| | - Fahad A. Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 52571, Saudi Arabia;
| | - Shafi Mahmud
- Department of Genome Science, John Curtin School of Medical Research, Australian National University, Canberra, ACT 0200, Australia;
| | - Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia; (A.H.A.); (S.M.)
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
| | - Bonglee Kim
- College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemungu, Seoul 05253, Korea;
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20
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Minka SO, Minka FH. A tabulated summary of the evidence on humoral and cellular responses to the SARS-CoV-2 Omicron VOC, as well as vaccine efficacy against this variant. Immunol Lett 2022; 243:38-43. [PMID: 35131373 PMCID: PMC8815275 DOI: 10.1016/j.imlet.2022.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/23/2022] [Accepted: 02/03/2022] [Indexed: 12/16/2022]
Abstract
INTRODUCTION SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is the virus responsible for COVID-19. It is one of the most mutating virus in the world. These mutations are responsible for the appearance of new variants, the most recent of which is Omicron (line B.1.1.529). This new variant was first identified in South Africa in November 2021. The main fear with this variant is that of an immune escape and ineffectiveness of vaccines currently available. OBJECTIVE We studied the response of our immune system and the effectiveness of current vaccines against SARS-CoV-2 Omicron VOC. METHODS We carried out a narrative review from 32 scientific articles from databases: MEDLINE (PubMed), Embase, BioRxiv and MedRxiv. RESULTS Faced with SARS-CoV-2 Omicron VOC: The humoral immune response decreased, while the cellular immune response was preserved. The booster vaccine provided protection against symptomatic or non-symptomatic infections, transmission, and serious forms. CONCLUSION In the end, according to these data, the 3rd dose appears to be the solution to be able to defeat SARS-CoV-2 Omicron VOC. But the health authorities must not forget to insist on the primary vaccination of individuals not yet vaccinated, as well as on an "equal" distribution of vaccines against COVID-19 throughout the world.
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Affiliation(s)
- S O Minka
- Emergency Department, Bichat Hospital, Public Assistance of Parisian Hospitals, Faculty of Medicine, University of Paris, 46 Rue Henri Huchard, 75018 Paris, France.
| | - F H Minka
- Emergency Department, Lariboisière Hospital, Public Assistance of Parisian Hospitals, Faculty of Medicine, University of Paris, 2 Rue Ambroise Pare, 75010 Paris, France
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21
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Cheng SMS, Mok CKP, Leung YWY, Ng SS, Chan KCK, Ko FW, Chen C, Yiu K, Lam BHS, Lau EHY, Chan KKP, Luk LLH, Li JKC, Tsang LCH, Poon LLM, Hui DSC, Peiris M. Neutralizing antibodies against the SARS-CoV-2 Omicron variant BA.1 following homologous and heterologous CoronaVac or BNT162b2 vaccination. Nat Med 2022; 28:486-489. [PMID: 35051989 PMCID: PMC8940714 DOI: 10.1038/s41591-022-01704-7] [Citation(s) in RCA: 253] [Impact Index Per Article: 126.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 01/18/2022] [Indexed: 11/09/2022]
Abstract
The Omicron variant is rapidly becoming the dominant SARS-CoV-2 virus circulating globally. It is important to define reductions in virus neutralizing activity in the serum of convalescent or vaccinated individuals to understand potential loss of protection against infection by Omicron. We previously established that a 50% plaque reduction neutralization antibody titer (PRNT50) ≥25.6 in our live virus assay corresponded to the threshold for 50% protection from infection against wild-type (WT) SARS-CoV-2. Here we show markedly reduced serum antibody titers against the Omicron variant (geometric mean titer (GMT) < 10) compared to WT virus 3-5 weeks after two doses of BNT162b2 (GMT = 218.8) or CoronaVac vaccine (GMT = 32.5). A BNT162b2 booster dose elicited Omicron PRNT50 titers ≥25.6 in 88% of individuals (22 of 25) who previously received 2 doses of BNT162b2 and 80% of individuals (24 of 30) who previously received CoronaVac. However, few (3%) previously infected individuals (1 of 30) or those vaccinated with three doses of CoronaVac (1 of 30) met this threshold. Our findings suggest that countries primarily using CoronaVac vaccines should consider messenger RNA vaccine boosters in response to the spread of Omicron. Studies evaluating the effectiveness of different vaccines against the Omicron variant are urgently needed.
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Affiliation(s)
- Samuel M S Cheng
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China
| | - Chris Ka Pun Mok
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, P. R. China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, P. R. China
| | - Yonna W Y Leung
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China
| | - Susanna S Ng
- Department of Medicine & Therapeutics, Faculty of Medicine, The Chinese University of Hong, Kong, Hong Kong, P. R. China
| | - Karl C K Chan
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China
| | - Fanny W Ko
- Department of Medicine & Therapeutics, Faculty of Medicine, The Chinese University of Hong, Kong, Hong Kong, P. R. China
| | - Chunke Chen
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, P. R. China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, P. R. China
| | - Karen Yiu
- Department of Medicine & Therapeutics, Faculty of Medicine, The Chinese University of Hong, Kong, Hong Kong, P. R. China
| | - Bosco H S Lam
- Department of Pathology, North Lantau Hospital, Hong Kong, P. R. China
| | - Eric H Y Lau
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China
- Laboratory of Data Discovery for Health Limited, Hong Kong Science Park, Hong Kong, P. R. China
| | - Ken K P Chan
- Department of Medicine & Therapeutics, Faculty of Medicine, The Chinese University of Hong, Kong, Hong Kong, P. R. China
| | - Leo L H Luk
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China
| | - John K C Li
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China
| | - Leo C H Tsang
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China
| | - Leo L M Poon
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong, P. R. China
| | - David S C Hui
- Department of Medicine & Therapeutics, Faculty of Medicine, The Chinese University of Hong, Kong, Hong Kong, P. R. China.
- Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, P. R. China.
| | - Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China.
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong, P. R. China.
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22
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Tsui WNT, Hamill V, Noll L, Lu N, Porter EP, Harbidge D, Cox E, Richardson C, Gray M, Sebhatu T, Goerl K, Brown S, Hanzlicek G, Retallick J, Bai J. Molecular detverection of SARS-CoV-2 and differentiation of Omicron and Delta variant strains. Transbound Emerg Dis 2022; 69:e1618-e1631. [PMID: 35218683 PMCID: PMC9115370 DOI: 10.1111/tbed.14497] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 12/04/2022]
Abstract
The SARS‐CoV‐2 virus is the causative agent of COVID‐19 and has undergone continuous mutations throughout the pandemic. The more transmissible Omicron variant has quickly spread and is replacing the Delta variant as the most prevalent strain globally, including in the United States. A new molecular assay that can detect and differentiate both the Delta and Omicron variants was developed. A collection of 660,035 SARS‐CoV‐2 full‐ or near‐full genomes, including 169,454 Delta variant and 24,202 Omicron variant strains, were used for primer and probe designs. In silico data analysis predicted an assay coverage of >99% of all strains, including >99% of the Delta and >99% of Omicron strains. The Omicron variant differential test was designed based on the Δ31‐33 aa deletion in the N‐gene, which is present in the original B.1.1.529 main genotype, BA.1, as well as in BA.2 and BA.3 subtypes. Therefore, the assay should detect the majority of all Omicron variant strains. Standard curves generated with human clinical samples indicated that the PCR amplification efficiencies were 104%, 90.7% and 90.4% for the Omicron, Delta, and non‐Delta/non‐Omicron wild‐type genotypes, respectively. Correlation coefficients of the standard curves were all >0.99. The detection limit of the assay was 14.3, 32.0, and 21.5 copies per PCR reaction for Omicron, Delta, and wild‐type genotypes, respectively. The assay was designed to specifically detect SAR‐CoV‐2 strains. Selected samples with Omicron, Delta and wild‐type genotypes identified by the RT‐qPCR assay were also confirmed by sequencing. The assay did not detect any animal coronavirus‐positive samples that were tested. Human nasal swab samples that previously tested positive (n = 182) or negative (n = 42) for SARS‐CoV‐2 by the ThermoFisher TaqPath COVID‐19 Combo Kit, produced the same result with the new assay. Among positive samples, 55.5% (101/182), 23.1% (42/182), and 21.4% (39/182) were identified as Omicron, Delta, and non‐Omicron/non‐Delta wild‐type genotypes, respectively.
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Affiliation(s)
- Wai Ning Tiffany Tsui
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Vaughn Hamill
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Lance Noll
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States.,Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, United States
| | - Nanyan Lu
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States.,Division of Biology, Kansas State University, Manhattan, KS 66506, United States
| | - Elizabeth Poulsen Porter
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Donald Harbidge
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Emily Cox
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Claire Richardson
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Mark Gray
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Tesfaalem Sebhatu
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Kyle Goerl
- Lafene Health Center, Kansas State University, Manhattan, KS 66506, United States
| | - Susan Brown
- Division of Biology, Kansas State University, Manhattan, KS 66506, United States
| | - Gregg Hanzlicek
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States.,Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, United States
| | - Jamie Retallick
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States.,Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, United States
| | - Jianfa Bai
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States.,Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, United States
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23
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Glocker MO, Opuni KFM, Thiesen HJ. From Free Binding Energy Calculations of SARS-CoV-2-Receptor Interactions to Cellular Immune Responses. MEDICINA (KAUNAS, LITHUANIA) 2022; 58:226. [PMID: 35208550 PMCID: PMC8876798 DOI: 10.3390/medicina58020226] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/21/2022] [Accepted: 01/31/2022] [Indexed: 11/16/2022]
Abstract
Our study focuses on free energy calculations of SARS-CoV-2 spike protein receptor binding motives (RBMs) from wild type and variants of concern (VOCs), with emphasis on SARS-CoV-2 Omicron. Our computational analysis underlines the occurrence of positive selection processes that specify Omicron host adaption and bring changes on the molecular level into context with clinically relevant observations. Our free energy calculation studies regarding the interaction of Omicron's RBM with human angiotensin converting enzyme 2 (hACE2) indicate weaker binding to the receptor than Alpha's or Delta's RBMs. Upon weaker binding, fewer viruses are predicted to be generated in time per infected cell, resulting in a delayed induction of danger signals as a trade-off. Along with delayed immunogenicity and pathogenicity, more viruses may be produced in the upper respiratory tract, explaining enhanced transmissibility. Since in interdependence on the human leukocyte antigen type (HLA type), more SARS-CoV-2 Omicron viruses are assumed to be required to initiate inflammatory immune responses, and because of pre-existing partial immunity through previous infections and/or vaccinations, which mostly guard the lower respiratory tract, overall disease severity is expected to be reduced.
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Affiliation(s)
- Michael O. Glocker
- Proteome Center Rostock, University Medicine Rostock, University of Rostock, Schillingallee 69, 18059 Rostock, Germany
| | - Kwabena F. M. Opuni
- Department of Pharmaceutical Chemistry, School of Pharmacy, College of Health Science, University of Ghana, Legon, Accra P.O. Box LG43, Ghana;
| | - Hans-Juergen Thiesen
- Institute of Immunology, University Medicine Rostock, Schillingallee 69, 18059 Rostock, Germany;
- Gesellschaft für Individualisierte Medizin mbH (IndyMed), Industriestrasse 15, 18069 Rostock, Germany
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24
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Abstract
At the population level we are seeing milder disease during the Omicron wave of the SARS-CoV-2 pandemic. Is this due to the virus or pre-existing immunity, and what should we expect next?
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Affiliation(s)
- Alex Sigal
- Africa Health Research Institute, Durban, South Africa.
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
- Max Planck Institute for Infection Biology, Berlin, Germany.
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25
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Hossen ML, Baral P, Sharma T, Gerstman BS, Chapagain P. Significance of the RBD mutations in the SARS-CoV-2 Omicron: from spike opening to antibody escape and cell attachment. Phys Chem Chem Phys 2022; 24:9123-9129. [DOI: 10.1039/d2cp00169a] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We computationally investigated the role of the Omicron RBD mutations on its structure and interactions with surrounding domains in the spike trimer as well as with ACE2. Our results suggest...
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26
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Yang Z, Zhang S, Tang YP, Yue SJ, Xu DQ, Fu RJ, Zhang S, Liu QL. Will New Variants Emerge after Delta and Omicron? Aging Dis 2022; 13:1317-1322. [PMID: 36186131 PMCID: PMC9466981 DOI: 10.14336/ad.2022.0307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/07/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
- Zhen Yang
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi’an, Shaanxi, China.
- School of Public Health, Shaanxi University of Chinese Medicine, Xi’an, Shaanxi, China.
| | - Shuo Zhang
- School of Clinical Medicine (Guang’anmen Hospital), Beijing University of Chinese Medicine, Beijing, China.
| | - Yu-Ping Tang
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi’an, Shaanxi, China.
- Correspondence should be addressed to: Dr. Yu-Ping Tang, Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, Shaanxi University of Chinese Medicine, Shaanxi Province, China. ; Dr. Qi-Ling Liu, School of Public Health, Shaanxi University of Chinese Medicine, Xi’an, Shaanxi, China. .
| | - Shi-Jun Yue
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi’an, Shaanxi, China.
| | - Ding-Qiao Xu
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi’an, Shaanxi, China.
| | - Rui-Jia Fu
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi’an, Shaanxi, China.
| | - Sai Zhang
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi’an, Shaanxi, China.
| | - Qi-Ling Liu
- School of Public Health, Shaanxi University of Chinese Medicine, Xi’an, Shaanxi, China.
- Correspondence should be addressed to: Dr. Yu-Ping Tang, Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, Shaanxi University of Chinese Medicine, Shaanxi Province, China. ; Dr. Qi-Ling Liu, School of Public Health, Shaanxi University of Chinese Medicine, Xi’an, Shaanxi, China. .
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