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Chelly S, Jaziri S, Ammar A, Ezzi O, Douss N, Saffar S, Tritar M, Njah M, Mahjoub M. Safety and efficiency of COVID-19 vaccine in North Africa. Hum Vaccin Immunother 2024; 20:2306703. [PMID: 38304972 PMCID: PMC10841012 DOI: 10.1080/21645515.2024.2306703] [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: 10/17/2023] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Background In the absence of a specific treatment for COVID-19, preventive measures have been implemented to control this pandemic and vaccination is one of them. However, it is crucial to verify the safety and efficiency of every vaccine. The aim was to determinate the predictive factors of side effects and reinfection after COVID-19 vaccine. Methods A cross-sectional study was conducted in February 2022 among Tunisians infected with COVID-19 between March 2020 and February 2022, using an online self-administered questionnaire. We conducted univariate and multivariate analyses using binary stepwise logistic regression. Results A total of 1541 was selected from 1911 individuals. Comorbidities affected a quarter of the population (22.3%). Before the initial infection, 39.3% had received full vaccination, and 8.7% had received partial vaccination. By February 2022, the majority (82.9%) had received at least two vaccine doses. The reinfection rate was 30.6%. All vaccines prior to the first infection was identified as a protective factor against reinfection. Inactivated virus vaccinations were less likely to induce adverse effects. Conclusion ach vaccine has its own set of advantages and disadvantages: mRNA-based vaccines had a higher incidence of side effects but all vaccines provided better protection against reinfection.
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Affiliation(s)
- Souhir Chelly
- Faculty of Medicine of Sousse, Infection Prevention and Control Department, Farhat Hached University Hospital, University of Sousse, Sousse, Tunisia
| | - Shayma Jaziri
- Faculty of Medicine of Sousse, Infection Prevention and Control Department, Farhat Hached University Hospital, University of Sousse, Sousse, Tunisia
| | - Asma Ammar
- Faculty of Medicine of Sousse, Infection Prevention and Control Department, Farhat Hached University Hospital, University of Sousse, Sousse, Tunisia
| | - Olfa Ezzi
- Faculty of Medicine of Sousse, Infection Prevention and Control Department, Farhat Hached University Hospital, University of Sousse, Sousse, Tunisia
| | - Nour Douss
- Faculty of Medicine of Sousse, Infection Prevention and Control Department, Farhat Hached University Hospital, University of Sousse, Sousse, Tunisia
| | - Sonia Saffar
- Faculty of Medicine of Sousse, Infection Prevention and Control Department, Farhat Hached University Hospital, University of Sousse, Sousse, Tunisia
| | - Marouen Tritar
- Faculty of Medicine of Sousse, Infection Prevention and Control Department, Farhat Hached University Hospital, University of Sousse, Sousse, Tunisia
| | - Mansour Njah
- Faculty of Medicine of Sousse, Infection Prevention and Control Department, Farhat Hached University Hospital, University of Sousse, Sousse, Tunisia
| | - Mohamed Mahjoub
- Faculty of Medicine of Sousse, Infection Prevention and Control Department, Farhat Hached University Hospital, University of Sousse, Sousse, Tunisia
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Lytton SD, Ghosh AK. SARS-CoV-2 Variants and COVID-19 in Bangladesh-Lessons Learned. Viruses 2024; 16:1077. [PMID: 39066238 PMCID: PMC11281597 DOI: 10.3390/v16071077] [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: 04/23/2024] [Revised: 06/27/2024] [Accepted: 07/01/2024] [Indexed: 07/28/2024] Open
Abstract
The coronavirus infectious disease-2019 (COVID-19) in Bangladesh is a paradigm for how one of the most densely populated countries in the world, with 1270 people per square kilometer, managed to cope with the COVID-19 pandemic under extraordinary circumstances. This review highlights the SARS-CoV-2 variants in Bangladesh and the timeline of their detection in the context of the global experience with the management of vaccination and natural SARS-CoV-2 infection. The motivation to overcome the COVID-19 vaccine dilemma and track Bangladeshi SARS-CoV-2 sub-variants underscores the potential for a low-income country to excel in international medical science, despite having stressed health care services and limited availability of resources for SARS-CoV-2 testing and gene sequencing.
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Affiliation(s)
| | - Asish Kumar Ghosh
- Department of Virology, Dhaka Medical College Hospital, Dhaka 1000, Bangladesh;
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3
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Hattab D, Amer MFA, Al-Alami ZM, Bakhtiar A. SARS-CoV-2 journey: from alpha variant to omicron and its sub-variants. Infection 2024; 52:767-786. [PMID: 38554253 PMCID: PMC11143066 DOI: 10.1007/s15010-024-02223-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/22/2024] [Indexed: 04/01/2024]
Abstract
The COVID-19 pandemic has affected hundreds of millions of individuals and caused more than six million deaths. The prolonged pandemic duration and the continual inter-individual transmissibility have contributed to the emergence of a wide variety of SARS-CoV-2 variants. Genomic surveillance and phylogenetic studies have shown that substantial mutations in crucial supersites of spike glycoprotein modulate the binding affinity of the evolved SARS-COV-2 lineages to ACE2 receptors and modify the binding of spike protein with neutralizing antibodies. The immunological spike mutations have been associated with differential transmissibility, infectivity, and therapeutic efficacy of the vaccines and the immunological therapies among the new variants. This review highlights the diverse genetic mutations assimilated in various SARS-CoV-2 variants. The implications of the acquired mutations related to viral transmission, infectivity, and COVID-19 severity are discussed. This review also addresses the effectiveness of human neutralizing antibodies induced by SARS-CoV-2 infection or immunization and the therapeutic antibodies against the ascended variants.
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Affiliation(s)
- Dima Hattab
- School of Pharmacy, The University of Jordan, Queen Rania Street, Amman, Jordan
| | - Mumen F A Amer
- Faculty of Pharmacy, Applied Science Private University, Amman, Jordan
| | - Zina M Al-Alami
- Department of Basic Medical Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman, Jordan
| | - Athirah Bakhtiar
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia.
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4
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Lytton SD, Ghosh AK, Bulbul RH, Nasifa T, Mamunur R, Meier C, Landt O, Kaiser M. The severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) omicron sub-variants in Bangladesh cause mild COVID-19 and associate with similar antibody responses irrespective of natural infection or vaccination history. Heliyon 2024; 10:e31011. [PMID: 38770337 PMCID: PMC11103536 DOI: 10.1016/j.heliyon.2024.e31011] [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: 09/16/2023] [Revised: 05/09/2024] [Accepted: 05/09/2024] [Indexed: 05/22/2024] Open
Abstract
Objective Genomic surveillance and seroprevalence of severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) in Bangladesh is paramount for COVID-19 pandemic preparedness yet lagging the high-income countries due to limited resources. Methods SARS-CoV-2 variants, COVID-19 symptoms, and serology were prospectively evaluated in a cross-sectional study of Bangladeshi adults testing RT-PCR positive in 2021 and 2022. Results SARS CoV-2 Omicron variants of asymptomatic or mild COVID-19 in 2022 replaced Delta variant infections requiring hospitalization and oxygen support. The omicron XBB became predominant in July 2022 and associated with cough, headache or body ache and loss of smell; 47 of 68 (69 %), 30 of 68 (44 %) and 27 of 68 (40 %) respectively at higher frequency than BA.1/BA.2; 16 of 88 (18 %), 13 of 88 (15 %) and 0 of 88 (0 %) p < 0.01, p < 0.01 and p < 0.0001. Linear regression analysis reveals no associations between the number of previous infections and the number of symptoms, r = -0.084, p = 0.68. The anti-nucleoprotein (N)-protein IgG post COVID-19 and anti-Spike (S) protein IgG post-COVID-19 vaccination were similar between BA.2, BA.4/BA.5 and XBB and significantly lower than the levels in delta variant infections (p < 0.001). Conclusions Omicron XBB subvariants emerged in Bangladesh two months prior to previous reports and include unique patterns of S-protein mutations not assigned in PANGO lineage. The SARS CoV-2 omicron break-through infections persist in the presence of sustained antibody responses and vaccinations, underscoring the importance of molecular surveillance in low-income countries.
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Affiliation(s)
| | - Asish Kumar Ghosh
- Department of Virology, Dhaka Medical College Hospital, Dhaka, 1000, Bangladesh
| | | | - Tasnim Nasifa
- National Institute of Laboratory Medicine and Referral Center, Sher E-Bangla Nagar, Dhaka, 1207, Bangladesh
| | - Rashid Mamunur
- Bangladesh Institute Tropical Infectious Disease (BITID), Fouzderhat, Chittagong, 4317, Bangladesh
| | - Christian Meier
- TIB Molbiol GmbH, Eresburgstraße 22-23, 12103, Berlin, Germany
| | - Olfert Landt
- TIB Molbiol GmbH, Eresburgstraße 22-23, 12103, Berlin, Germany
| | - Marco Kaiser
- TIB Molbiol GmbH, Eresburgstraße 22-23, 12103, Berlin, Germany
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5
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Bouchnita A, Bi K, Fox SJ, Meyers LA. Projecting Omicron scenarios in the US while tracking population-level immunity. Epidemics 2024; 46:100746. [PMID: 38367285 DOI: 10.1016/j.epidem.2024.100746] [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: 06/27/2023] [Revised: 12/16/2023] [Accepted: 01/23/2024] [Indexed: 02/19/2024] Open
Abstract
Throughout the COVID-19 pandemic, changes in policy, shifts in behavior, and the emergence of new SARS-CoV-2 variants spurred multiple waves of transmission. Accurate assessments of the changing risks were vital for ensuring adequate healthcare capacity, designing mitigation strategies, and communicating effectively with the public. Here, we introduce a model of COVID-19 transmission and vaccination that provided rapid and reliable projections as the BA.1, BA.4 and BA.5 variants emerged and spread across the US. For example, our three-week ahead national projection of the early 2021 peak in COVID-19 hospitalizations was only one day later and 11.6-13.3% higher than the actual peak, while our projected peak in mortality was two days earlier and 0.22-4.7% higher than reported. We track population-level immunity from prior infections and vaccination in terms of the percent reduction in overall susceptibility relative to a completely naive population. As of October 1, 2022, we estimate that the US population had a 36.52% reduction in overall susceptibility to the BA.4/BA.5 variants, with 61.8%, 15.06%, and 23.54% of immunity attributable to infections, primary series vaccination, and booster vaccination, respectively. We retrospectively projected the potential impact of expanding booster coverage starting on July 15, 2022, and found that a five-fold increase in weekly boosting rates would have resulted in 70% of people over 65 vaccinated by Oct 10, 2022 and averted 25,000 (95% CI: 14,400-35,700) deaths during the BA.4/BA.5 surge. Our model provides coherent variables for tracking population-level immunity in the increasingly complex landscape of variants and vaccines and enables robust simulations of plausible scenarios for the emergence and mitigation of novel COVID variants.
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Affiliation(s)
- Anass Bouchnita
- Department of Mathematical Sciences, The University of Texas at El Paso, El Paso, TX 79968, USA
| | - Kaiming Bi
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Spencer J Fox
- Department of Epidemiology & Biostatistics, University of Georgia, Athens, GA 30602, USA; Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Lauren Ancel Meyers
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA.
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6
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Van Dusen J, LeBlanc H, Nastasi N, Panescu J, Shamblin A, Smith JW, Sovic MG, Williams A, Quam MBM, Faith S, Dannemiller KC. Identification of SARS-CoV-2 variants in indoor dust. PLoS One 2024; 19:e0297172. [PMID: 38335205 PMCID: PMC10857703 DOI: 10.1371/journal.pone.0297172] [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: 09/12/2023] [Accepted: 12/30/2023] [Indexed: 02/12/2024] Open
Abstract
Environmental surveillance of pathogens underlying infectious disease is critical to ensure public health. Recent efforts to track SARS-CoV-2 have utilized wastewater sampling to infer community trends in viral abundance and variant composition. Indoor dust has also been used for building-level inferences, though to date no sequencing data providing variant-scale resolution have been reported from dust samples, and strategies to monitor circulating variants in dust are needed to help inform public health decisions. In this study, we demonstrate that SARS-CoV-2 lineages can be detected and sequenced from indoor bulk dust samples. We collected 93 vacuum bags from April 2021 to March 2022 from buildings on The Ohio State University's (OSU) Columbus campus, and the dust was used to develop and apply an amplicon-based whole-genome sequencing protocol to identify the variants present and estimate their relative abundances. Three variants of concern were detected in the dust: Alpha, Delta, and Omicron. Alpha was found in our earliest sample in April 2021 with an estimated frequency of 100%. Delta was the primary variant present from October of 2021 to January 2022, with an average estimated frequency of 91% (±1.3%). Omicron became the primary variant in January 2022 and was the dominant strain in circulation through March with an estimated frequency of 87% (±3.2%). The detection of these variants on OSU's campus correlates with the circulation of these variants in the surrounding population (Delta p<0.0001 and Omicron p = 0.02). Overall, these results support the hypothesis that dust can be used to track COVID-19 variants in buildings.
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Affiliation(s)
- John Van Dusen
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Haley LeBlanc
- Genetic Counseling Program, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Nicholas Nastasi
- Environmental Sciences Graduate Program, The Ohio State University, Columbus, Ohio, United States of America
- Department of Civil, Environmental & Geodetic Engineering, College of Engineering, The Ohio State University, Columbus, Ohio, United States of America
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, Ohio, United States of America
| | - Jenny Panescu
- Department of Civil, Environmental & Geodetic Engineering, College of Engineering, The Ohio State University, Columbus, Ohio, United States of America
| | - Austin Shamblin
- Applied Microbiology Services Lab, The Ohio State University, Columbus, Ohio, United States of America
| | - Jacob W. Smith
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Michael G. Sovic
- Applied Microbiology Services Lab, The Ohio State University, Columbus, Ohio, United States of America
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Amanda Williams
- Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Mikkel B. M. Quam
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, United States of America
- Division of Epidemiology, College of Public Health, The Ohio State University, Columbus, Ohio, United States of America
- Section of Sustainable Health, Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Seth Faith
- Applied Microbiology Services Lab, The Ohio State University, Columbus, Ohio, United States of America
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Karen C. Dannemiller
- Department of Civil, Environmental & Geodetic Engineering, College of Engineering, The Ohio State University, Columbus, Ohio, United States of America
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, Ohio, United States of America
- Sustainability Institute, The Ohio State University, Columbus, Ohio, United States of America
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7
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Gu Y, Shunmuganathan B, Qian X, Gupta R, Tan RSW, Kozma M, Purushotorman K, Murali TM, Tan NYJ, Preiser PR, Lescar J, Nasir H, Somani J, Tambyah PA, Smith KGC, Renia L, Ng LFP, Lye DC, Young BE, MacAry PA. Employment of a high throughput functional assay to define the critical factors that influence vaccine induced cross-variant neutralizing antibodies for SARS-CoV-2. Sci Rep 2023; 13:21810. [PMID: 38071323 PMCID: PMC10710454 DOI: 10.1038/s41598-023-49231-w] [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: 05/21/2023] [Accepted: 12/06/2023] [Indexed: 12/18/2023] Open
Abstract
The scale and duration of neutralizing antibody responses targeting SARS-CoV-2 viral variants represents a critically important serological parameter that predicts protective immunity for COVID-19. In this study, we describe the development and employment of a new functional assay that measures neutralizing antibodies for SARS-CoV-2 and present longitudinal data illustrating the impact of age, sex and comorbidities on the kinetics and strength of vaccine-induced antibody responses for key variants in an Asian volunteer cohort. We also present an accurate quantitation of serological responses for SARS-CoV-2 that exploits a unique set of in-house, recombinant human monoclonal antibodies targeting the viral Spike and nucleocapsid proteins and demonstrate a reduction in neutralizing antibody titres across all groups 6 months post-vaccination. We also observe a marked reduction in the serological binding activity and neutralizing responses targeting recently newly emerged Omicron variants including XBB 1.5 and highlight a significant increase in cross-protective neutralizing antibody responses following a third dose (boost) of vaccine. These data illustrate how key virological factors such as immune escape mutations combined with host demographic factors such as age and sex of the vaccinated individual influence the strength and duration of cross-protective serological immunity for COVID-19.
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Affiliation(s)
- Yue Gu
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUH-Cambridge Immune Phenotyping Centre, National University of Singapore, Singapore, Singapore
| | - Bhuvaneshwari Shunmuganathan
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xinlei Qian
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Rashi Gupta
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Rebecca S W Tan
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Mary Kozma
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Kiren Purushotorman
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tanusya M Murali
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Nikki Y J Tan
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Peter R Preiser
- Antimicrobial Resistance Interdisciplinary Research Group (AMR-IRG), Singapore-MIT Alliance in Research and Technology (SMART), Singapore, 138602, Singapore
- School of Biological Science (SBS), Nanyang Technological University (NTU), 60 Nanyang Dr, Singapore, 637551, Singapore
| | - Julien Lescar
- School of Biological Science (SBS), Nanyang Technological University (NTU), 60 Nanyang Dr, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore
| | - Haziq Nasir
- Division of Infectious Disease, University Medicine Cluster, National University Hospital, Singapore, Singapore
| | - Jyoti Somani
- Division of Infectious Disease, University Medicine Cluster, National University Hospital, Singapore, Singapore
| | - Paul A Tambyah
- Division of Infectious Disease, University Medicine Cluster, National University Hospital, Singapore, Singapore
| | - Kenneth G C Smith
- NUH-Cambridge Immune Phenotyping Centre, National University of Singapore, Singapore, Singapore
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, CB2 0AW, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Laurent Renia
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Lisa F P Ng
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - David C Lye
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Barnaby E Young
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Paul A MacAry
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore.
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- NUH-Cambridge Immune Phenotyping Centre, National University of Singapore, Singapore, Singapore.
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8
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Zaman N, Parvaiz N, Gul F, Yousaf R, Gul K, Azam SS. Dynamics of water-mediated interaction effects on the stability and transmission of Omicron. Sci Rep 2023; 13:20894. [PMID: 38017052 PMCID: PMC10684572 DOI: 10.1038/s41598-023-48186-2] [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: 11/24/2022] [Accepted: 11/23/2023] [Indexed: 11/30/2023] Open
Abstract
SARS-Cov-2 Omicron variant and its highly transmissible sublineages amidst news of emerging hybrid variants strengthen the evidence of its ability to rapidly spread and evolve giving rise to unprecedented future waves. Owing to the presence of isolated RBD, monomeric and trimeric Cryo-EM structures of spike protein in complex with ACE2 receptor, comparative analysis of Alpha, Beta, Gamma, Delta, and Omicron assist in a rational assessment of their probability to evolve as new or hybrid variants in future. This study proposes the role of hydration forces in mediating Omicron function and dynamics based on a stronger interplay between protein and solvent with each Covid wave. Mutations of multiple hydrophobic residues into hydrophilic residues underwent concerted interactions with water leading to variations in charge distribution in Delta and Omicron during molecular dynamics simulations. Moreover, comparative analysis of interacting moieties characterized a large number of mutations lying at RBD into constrained, homologous and low-affinity groups referred to as mutational drivers inferring that the probability of future mutations relies on their function. Furthermore, the computational findings reveal a significant difference in angular distances among variants of concern due 3 amino acid insertion (EPE) in Omicron variant that not only facilitates tight domain organization but also seems requisite for characterization of mutational processes. The outcome of this work signifies the possible relation between hydration forces, their impact on conformation and binding affinities, and viral fitness that will significantly aid in understanding dynamics of drug targets for Covid-19 countermeasures. The emerging scenario is that hydration forces and hydrophobic interactions are crucial variables to probe in mutational analysis to explore conformational landscape of macromolecules and reveal the molecular origins of protein behaviors.
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Affiliation(s)
- Naila Zaman
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Nousheen Parvaiz
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Fouzia Gul
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Rimsha Yousaf
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Kainat Gul
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan.
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9
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Ellis LP, Hess O, Huynh KLA, Bearman G, Kang L, Doern CD. A comparison of severity of illness between the SARS-CoV-2 Omicron variant and Delta variant. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2023; 3:e188. [PMID: 38028915 PMCID: PMC10654945 DOI: 10.1017/ash.2023.453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 12/01/2023]
Abstract
Background The COVID-19 pandemic has disproportionally affected traditionally marginalized groups. Both the Delta and Omicron variants raised concern amongst public health officials due to potentially higher infectivity rates and disease severity than prior variants. This study sought to compare disease severity between adults infected with the Omicron variant and adults infected with the Delta variant who presented to the Emergency Department at an academic, safety-net hospital in Virginia. Methods This retrospective cohort study used electronic medical record data of patients who presented to the Emergency Department and received a positive SARS-CoV-2 test between September 1, 2021, and January 31, 2022. Positive tests were stratified by genotypic variant through whole genome sequencing. Participants with the Omicron variant were propensity scores matched with individuals with the Delta variant. Results Among 500 Delta and 500 Omicron participants, 279 propensity score-matched pairs were identified. Participants were predominantly unvaccinated, with medical comorbidities, and self-identified as Black. Individuals infected with the Delta variant had more severe disease compared to those with the Omicron variant, regardless of vaccination status. Patients with kidney, liver, and respiratory disease, as well as cancer, are at higher risk for severe disease. Patients with 2 doses of COVID-19 immunization trended toward less severe disease. Conclusions Overall, these data further support the literature regarding the disproportionate effects of the COVID-19 pandemic on vulnerable patient populations - such as those with limited access to care, people of color, and those with chronic medical conditions - and can be used to inform public health interventions.
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Affiliation(s)
- Laura Peyton Ellis
- Obstetrics and Gynecology Residency Program, University of Connecticut, Farmington, CT, USA
| | - Olivia Hess
- School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Khoa Le Anh Huynh
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
| | - Gonzalo Bearman
- Richard P. Wenzel Professor of Medicine, Chair, Division of Infectious Diseases, Virginia Commonwealth University, Richmond, VA, USA
- Antimicrobial Stewardship and Healthcare Epidemiology, Cambridge University Press, Cambridge, UK
| | - Le Kang
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
| | - Christopher D. Doern
- Microbiology & Pathology and Pediatrics, Virginia Commonwealth University, Richmond, VA, USA
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10
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Testino G, Pellicano R. COVID-19 and alcohol consumption: recommendations in the Omicron era. Minerva Gastroenterol (Torino) 2023; 69:423-432. [PMID: 35511656 DOI: 10.23736/s2724-5985.22.03194-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In the early stages of the pandemic, the first reports began that alcohol consumption could increase the risk of becoming infected and worsening the prognosis disease. This is for two reasons: behavioral and socio-economic factors that characterize a part of this population can be the cause of viral spread and a direct or indirect negative action of ethanol on the immune system. The data used for the preparation of these recommendations are based on a detailed analysis of the scientific literature published before March 31, 2022 (Web of Science, Scopus, Google Scholar). Furthermore, in the process of developing this work, we consulted the guidelines/position papers of the Italian Society on Alcohol and of the World Health Organization. It has been confirmed that AC is in COVID-19 era a risky behavior and that AUD and substance use disorder (SUD) patients are certainly at greater risk of contracting infection and also of having a worse course. In light of what has been said, some recommendations can be made: correctly inform the general population that AC negatively interacts with COVID-19 infection; reducing the COVID-19 risk by advocating healthy lifestyle habits (smoke, diet, physical exercise, etc.) and preferential policies in population with comorbidities; implement actions that reduce the average consumption of alcohol by avoiding hazardous/harmful consumption. Abstention is better; identify alcohol consumption through a more in-depth alcohol history, using the AUDIT; AUDs patients are frail patients deserving a complete vaccination course; suggest a period of alcoholic abstention of at least thirty days before vaccination to be maintained for the following fifteen days; promoting health education campaigns for young people in order to promote vaccination culture and correct lifestyles.
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Affiliation(s)
- Gianni Testino
- Unit of Addiction and Hepatology/Alcohological Regional Centre, ASL3 c/o San Martino Polyclinic Hospital, Genoa, Italy -
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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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Al-Hatamleh MA, Abusalah MA, Hatmal MM, Alshaer W, Ahmad S, Mohd-Zahid MH, Rahman ENSE, Yean CY, Alias IZ, Uskoković V, Mohamud R. Understanding the challenges to COVID-19 vaccines and treatment options, herd immunity and probability of reinfection. J Taibah Univ Med Sci 2023; 18:600-638. [PMID: 36570799 PMCID: PMC9758618 DOI: 10.1016/j.jtumed.2022.11.007] [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: 08/20/2022] [Revised: 10/29/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
Unlike pandemics in the past, the outbreak of coronavirus disease 2019 (COVID-19), which rapidly spread worldwide, was met with a different approach to control and measures implemented across affected countries. The lack of understanding of the fundamental nature of the outbreak continues to make COVID-19 challenging to manage for both healthcare practitioners and the scientific community. Challenges to vaccine development and evaluation, current therapeutic options, convalescent plasma therapy, herd immunity, and the emergence of reinfection and new variants remain the major obstacles to combating COVID-19. This review discusses these challenges in the management of COVID-19 at length and highlights the mechanisms needed to provide better understanding of this pandemic.
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Affiliation(s)
- Mohammad A.I. Al-Hatamleh
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Mai A. Abusalah
- Department of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Zarqa University, Zarqa, Jordan
| | - Ma'mon M. Hatmal
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, The Hashemite University, Zarqa, Jordan
| | - Walhan Alshaer
- Cell Therapy Center (CTC), The University of Jordan, Amman, Jordan
| | - Suhana Ahmad
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Manali H. Mohd-Zahid
- Department of Chemical Pathology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Engku Nur Syafirah E.A. Rahman
- Department of Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Chan Y. Yean
- Department of Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Iskandar Z. Alias
- Department of Chemical Pathology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | | | - Rohimah Mohamud
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
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Meister T, Kolde A, Fischer K, Pisarev H, Kolde R, Kalda R, Suija K, Tisler A, Uusküla A. A retrospective cohort study of incidence and risk factors for severe SARS-CoV-2 breakthrough infection among fully vaccinated people. Sci Rep 2023; 13:8531. [PMID: 37237050 DOI: 10.1038/s41598-023-35591-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/20/2023] [Indexed: 05/28/2023] Open
Abstract
SARS-CoV-2 vaccination is currently the mainstay in combating the COVID-19 pandemic. However, there are still people among vaccinated individuals suffering from severe forms of the disease. We conducted a retrospective cohort study based on data from nationwide e-health databases. The study included 184,132 individuals who were SARS-CoV-2 infection-naive and had received at least a primary series of COVID-19 vaccination. The incidence of BTI (breakthrough infection) was 8.03 (95% CI [confidence interval] 7.95⎼8.13/10,000 person-days), and for severe COVID-19 it was 0.093 (95% CI 0.084⎼ 0.104/10,000 person-days). The protective effect of vaccination against severe COVID-19 remained constant for up to six months, and the booster dose offered an additional pronounced benefit (hospitalization aHR 0.32, 95% CI 0.19⎼0.54). The risk of severe COVID-19 was higher among those ≥ 50 years of age (aHR [adjusted hazard ratio] 2.06, 95% CI 1.25⎼3.42) and increased constantly with every decade of life. Male sex (aHR 1.32, 95% CI 1.16⎼1.45), CCI (The Charlson Comorbidity Index) score ≥ 1 (aHR 2.09, 95% CI 1.54⎼2.83), and a range of comorbidities were associated with an increased risk of COVID-19 hospitalization. There are identifiable subgroups of COVID-19-vaccinated individuals at high risk of hospitalization due to SARS-CoV-2 infection. This information is crucial to driving vaccination programs and planning treatment strategies.
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Affiliation(s)
- Tatjana Meister
- Institute of Family Medicine and Public Health, Faculty of Medicine, University of Tartu, Tartu, Estonia.
| | - Anastassia Kolde
- Institute of Mathematics and Statistics, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
- Institute of Genomics, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Krista Fischer
- Institute of Mathematics and Statistics, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
- Institute of Genomics, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Heti Pisarev
- Institute of Family Medicine and Public Health, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Raivo Kolde
- Institute of Computer Science, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Ruth Kalda
- Institute of Family Medicine and Public Health, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Kadri Suija
- Institute of Family Medicine and Public Health, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Anna Tisler
- Institute of Family Medicine and Public Health, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Anneli Uusküla
- Institute of Family Medicine and Public Health, Faculty of Medicine, University of Tartu, Tartu, Estonia
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Rando HM, Lordan R, Kolla L, Sell E, Lee AJ, Wellhausen N, Naik A, Kamil JP, Gitter A, Greene CS. The Coming of Age of Nucleic Acid Vaccines during COVID-19. mSystems 2023; 8:e0092822. [PMID: 36861992 PMCID: PMC10134841 DOI: 10.1128/msystems.00928-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
In the 21st century, several emergent viruses have posed a global threat. Each pathogen has emphasized the value of rapid and scalable vaccine development programs. The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has made the importance of such efforts especially clear. New biotechnological advances in vaccinology allow for recent advances that provide only the nucleic acid building blocks of an antigen, eliminating many safety concerns. During the COVID-19 pandemic, these DNA and RNA vaccines have facilitated the development and deployment of vaccines at an unprecedented pace. This success was attributable at least in part to broader shifts in scientific research relative to prior epidemics: the genome of SARS-CoV-2 was available as early as January 2020, facilitating global efforts in the development of DNA and RNA vaccines within 2 weeks of the international community becoming aware of the new viral threat. Additionally, these technologies that were previously only theoretical are not only safe but also highly efficacious. Although historically a slow process, the rapid development of vaccines during the COVID-19 crisis reveals a major shift in vaccine technologies. Here, we provide historical context for the emergence of these paradigm-shifting vaccines. We describe several DNA and RNA vaccines in terms of their efficacy, safety, and approval status. We also discuss patterns in worldwide distribution. The advances made since early 2020 provide an exceptional illustration of how rapidly vaccine development technology has advanced in the last 2 decades in particular and suggest a new era in vaccines against emerging pathogens. IMPORTANCE The SARS-CoV-2 pandemic has caused untold damage globally, presenting unusual demands on but also unique opportunities for vaccine development. The development, production, and distribution of vaccines are imperative to saving lives, preventing severe illness, and reducing the economic and social burdens caused by the COVID-19 pandemic. Although vaccine technologies that provide the DNA or RNA sequence of an antigen had never previously been approved for use in humans, they have played a major role in the management of SARS-CoV-2. In this review, we discuss the history of these vaccines and how they have been applied to SARS-CoV-2. Additionally, given that the evolution of new SARS-CoV-2 variants continues to present a significant challenge in 2022, these vaccines remain an important and evolving tool in the biomedical response to the pandemic.
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Affiliation(s)
- Halie M. Rando
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz School of Medicine, Aurora, Colorado, USA
- Center for Health AI, University of Colorado Anschutz School of Medicine, Aurora, Colorado, USA
- Department of Biomedical Informatics, University of Colorado Anschutz School of Medicine, Aurora, Colorado, USA
| | - Ronan Lordan
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Likhitha Kolla
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elizabeth Sell
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Alexandra J. Lee
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nils Wellhausen
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Amruta Naik
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jeremy P. Kamil
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center Shreveport, Shreveport, Louisiana, USA
| | - COVID-19 Review Consortium
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz School of Medicine, Aurora, Colorado, USA
- Center for Health AI, University of Colorado Anschutz School of Medicine, Aurora, Colorado, USA
- Department of Biomedical Informatics, University of Colorado Anschutz School of Medicine, Aurora, Colorado, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center Shreveport, Shreveport, Louisiana, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Philadelphia, Pennsylvania, USA
| | - Anthony Gitter
- Department of Biostatistics and Medical Informatics, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Casey S. Greene
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz School of Medicine, Aurora, Colorado, USA
- Center for Health AI, University of Colorado Anschutz School of Medicine, Aurora, Colorado, USA
- Department of Biomedical Informatics, University of Colorado Anschutz School of Medicine, Aurora, Colorado, USA
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Philadelphia, Pennsylvania, USA
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Khalid ET, Salah Khalefa M, Yassen W, Adil Yassin A. Omicron virus emotions understanding system based on deep learning architecture. JOURNAL OF AMBIENT INTELLIGENCE AND HUMANIZED COMPUTING 2023; 14:9497-9507. [PMID: 37288131 PMCID: PMC10113983 DOI: 10.1007/s12652-023-04615-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 04/04/2023] [Indexed: 06/09/2023]
Abstract
Emotions understanding has acquired a significant interest in the last few years because it has introduced remarkable services in many aspects regarding public opinion mining and recognition in the field of marketing, seeking product reviews, reviews of movies, and healthcare issues based on sentiment understanding. This conducted research has utilized the issue of Omicron virus as a case study to implement a emotions analysis framework to explore the global attitude and sentiment toward Omicron variant as an expression of Positive feeling, Neutral, and Negative feeling. Because since December 2021. Omicron variant has gained obvious attention and wide discussions on social media platforms that revealed lots of fears and anxiety feeling, due to its rapid spreading and infection ability between humans that could exceed the Delta variant infection. Therefore, this paper proposes to develop a framework utilizes techniques of natural languages processing (NLP) in deep learning methods using neural network model of Bidirectional-Long-Short-Term-Memory (Bi-LSTM) and deep neural network (DNN) to achieve accurate results. This study utilizes textual data collected and pulled from the Twitter platform (users' tweets) for the time interval from 11-Dec.-2021 to 18-Dec.-2021. Consequently, the overall achieved accuracy for the developed model is 0.946%. The produced results from carrying out the proposed framework for sentiment understanding have recorded Negative sentiment at 42.3%, Positive sentiment at 35.8%, and Neutral sentiment at 21.9% of overall extracted tweets. The acquired accuracy using data of validation for the deployed model is 0.946%.
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Affiliation(s)
- Eman Thabet Khalid
- Department of Computer Sciences, College of Education for Pure Sciences, University of Basrah, Basrah, 6100 Iraq
| | - Mustafa Salah Khalefa
- Department of Computer Sciences, College of Education for Pure Sciences, University of Basrah, Basrah, 6100 Iraq
| | - Wijdan Yassen
- Department of Computer Sciences, College of Education for Pure Sciences, University of Basrah, Basrah, 6100 Iraq
| | - Ali Adil Yassin
- Department of Computer Sciences, College of Education for Pure Sciences, University of Basrah, Basrah, 6100 Iraq
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Safety and efficacy of COVID-19 prime-boost vaccinations: Homologous BBIBP-CorV versus heterologous BNT162b2 boosters in BBIBP-CorV-primed individuals. Vaccine 2023; 41:1925-1933. [PMID: 36725431 PMCID: PMC9868355 DOI: 10.1016/j.vaccine.2023.01.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/12/2022] [Accepted: 01/16/2023] [Indexed: 01/24/2023]
Abstract
BACKGROUND Booster vaccine doses against SARS-CoV-2 have been advocated to address evidence of waning immunity, breakthrough infection, and the emergence of immune-evasive variants. A heterologous prime-boost vaccine strategy may offer advantages over a homologous approach, but the safety and efficacy of this approach with the mRNA vaccine BNT162b2 (BNT: Pfizer) and inactivated BBIBP-CorV (BBIBT: Sinopharm) vaccines have not been studied. METHODS We conducted a non-randomized, non-blinded phase II observational community trial acrossBahrain, investigating the reactogenic and immunogenic responseof participants who had previously received two doses of BBIBP, followed by a third booster dose of either BBIBP (homologous booster) or BNT (heterologous booster). Immunogenicity through serological statuswas determined at baseline and on the following 8thweek. Reactogenicity data (safety and adverse events) were collected throughout study period, in addition to participant-led electronic journaling. RESULTS 305 participants (152 BBIBP and 153 BNT booster) were enrolled in the study,with 246 (127 BBIBP and 119 BNT booster) included in the final analysis. There was a significant increase in anti-SARS-CoV-2 antibody levels post booster administration in both groups; however, the heterologous BNT arm demonstrated a significantly larger mean increase in the level of spike (S) antigen-specific antibodies (32.7-fold increase versus 2.6, p < 0.0001) and sVNT neutralising antibodies (3.4-fold increase versus 1.8, p < 0.0001), whereas the homologous arm demonstrated a significant increase in the levels of nucleocapsid (N) antigen-specific antibodies (3.8-fold increase versus none). Non-serious adverse events (injection site pain, fever, and fatigue) were more commonly reported in the heterologous arm, but no serious adverse events occurred. CONCLUSION Heterologous prime-boost vaccination with the mRNA BNT162b2 (Pfizer) vaccine in those who had received two doses of inactivated virus BBIBP-CorV (Sinopharm) vaccine demonstrated a more robust immune response against SARS-CoV-2 than the homologous BBIBP booster and appears safe and well tolerated. Clinical Trial Registry Number (ClinicalTrials.gov): NCT04993560.
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Onyeaghala AA, Anyiam AF, Husaini DC, Onyeaghala EO, Obi E. Herbal Supplements as Treatment Options for COVID-19: A call for Clinical Development of Herbal Supplements for Emerging and Re-Emerging Viral Threats in Sub-Saharan Africa. SCIENTIFIC AFRICAN 2023; 20:e01627. [PMID: 36974333 PMCID: PMC9985929 DOI: 10.1016/j.sciaf.2023.e01627] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 02/10/2023] [Accepted: 03/02/2023] [Indexed: 03/07/2023] Open
Abstract
The advent of Corona virus Disease 2019 (COVID-19) distorted health systems of many countries. Efforts have been made to either develop new treatment solutions such as vaccines or repurpose previously adopted drugs. Challenges in accessing available treatment, inadequate, non-existent, or overstretched healthcare facilities, long COVID disease, cultural practices and beliefs about vaccination, vaccine hesitancy, availability, accessibility and perceived safety of herbal supplements seem to be major factors propelling individuals to use herbal supplements. Published reports advocating for clinical development of herbal supplements for COVID-19 and other emerging and re-emerging viral diseases are sparse. This paper aims to review the pathogenesis of COVID-19, use of herbal products during the pandemic and make case for clinical development of herbal supplements through the adoption of modern and acceptable technologies and research processes. This was a scoping review. Database searches of Google Scholar, PubMed and ResearchGate among others were performed using related keywords to identify relevant journals and lists of primary articles. Clinical trial databases:-Clinicaltrial.gov, Pan African Clinical Trial Registry (PACTR) and WHO international clinical trial registry (ICTRP) were reviewed to extract data. The use of herbal supplements during COVID-19 was not only peculiar to individuals living in Sub-Saharan Africa, but a global practice. Herbal supplements recommended to manage COVID-19 have not been validated using clinical trials. Available data showed that the number of herbal supplements undergoing clinical trial for COVID-19 indication in Africa was low. The availability of medicinal plants in Sub-Saharan Africa if well explored has great potentials to address various emerging and re-emerging viral diseases confronting the region. The economic potential of clinically validated herbal supplements are huge, and tapping into this opportunity created by preference of population to herbal supplement could increase export of herbal supplement and gross domestic product (GDP) of respective countries in Africa.
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Affiliation(s)
- Augustine Anayochukwu Onyeaghala
- Unit of Clinical Chemistry, Department of Medical Laboratory Science, University College Hospital, Ibadan,Unit of Clinical Chemistry, Department of Medical Laboratory Science, Chrisland University, Owode, Abeokuta, Ogun State,Corresponding Author
| | - Arinze Favour Anyiam
- Department of Medical Laboratory Science, Thomas Adewumi University, Oko, Kwara State
| | - Danladi Chiroma Husaini
- Department of Allied Health (Pharmacy), Faculty of Health Sciences, University of Belize, Belize, Central America
| | | | - Ejeatuluchukwu Obi
- Department of Pharmacology and Therapeutics, Faculty of Basic Clinical Science, College of Health Science, Nnamdi Azikiwe University, Nnewi, Campus, Nnewi
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18
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Kislaya I, Peralta‐Santos A, Borges V, Vieira L, Sousa C, Ferreira B, Pelerito A, Gomes JP, Leite PP, Nunes B. Comparative complete scheme and booster effectiveness of COVID-19 vaccines in preventing SARS-CoV-2 infections with SARS-CoV-2 Omicron (BA.1) and Delta (B.1.617.2) variants: A case-case study based on electronic health records. Influenza Other Respir Viruses 2023; 17:e13121. [PMID: 36935845 PMCID: PMC10014519 DOI: 10.1111/irv.13121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 03/17/2023] Open
Abstract
Background Information on vaccine effectiveness in a context of novel variants of concern (VOC) emergence is of key importance to inform public health policies. This study aimed to estimate a measure of comparative vaccine effectiveness between Omicron (BA.1) and Delta (B.1.617.2 and sub-lineages) VOC according to vaccination exposure (primary or booster). Methods We developed a case-case study using data on RT-PCR SARS-CoV-2-positive cases notified in Portugal during Weeks 49-51, 2021. To obtain measure of comparative vaccine effectiveness, we compared the odds of vaccination in Omicron cases versus Delta using logistic regression adjusted for age group, sex, region, week of diagnosis, and laboratory of origin. Results Higher odds of vaccination were observed in cases infected by Omicron VOC compared with Delta VOC cases for both complete primary vaccination (odds ratio [OR] = 2.1; 95% confidence interval [CI]: 1.8 to 2.4) and booster dose (OR = 5.2; 95% CI: 3.1 to 8.8), equivalent to reduction of vaccine effectiveness from 44.7% and 92.8%, observed against infection with Delta, to -6.0% (95% CI: 29.2% to 12.7%) and 62.7% (95% CI: 35.7% to 77.9%), observed against infection with Omicron, for complete primary vaccination and booster dose, respectively. Conclusion Consistent reduction in vaccine-induced protection against infection with Omicron was observed. Complete primary vaccination may not be protective against SARS-CoV-2 infection in regions where Omicron variant is dominant.
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Affiliation(s)
- Irina Kislaya
- Department of EpidemiologyNational Institute of Health Doutor Ricardo JorgeLisbonPortugal
- Public Health Research Centre, NOVA National School of Public HealthUniversidade NOVA de LisboaLisbonPortugal
- Comprehensive Health Research Centre (CHRC)Universidade NOVA de LisboaLisbonPortugal
| | - André Peralta‐Santos
- Public Health Research Centre, NOVA National School of Public HealthUniversidade NOVA de LisboaLisbonPortugal
- Comprehensive Health Research Centre (CHRC)Universidade NOVA de LisboaLisbonPortugal
- Direção de Serviços de Informação e AnáliseDireção‐Geral da SaúdeLisbonPortugal
| | - Vítor Borges
- Genomic and Bioinformatics Unit, Department of Infectious DiseasesNational Institute of Health Doutor Ricardo JorgeLisbonPortugal
| | - Luís Vieira
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo JorgeUnidade de Tecnologia e InovaçãoLisbonPortugal
| | | | - Bibiana Ferreira
- Algarve Biomedical Center Research Institute (ABC‐RI)FaroPortugal
- Faculty of Medicine and Biomedical Sciences (FMCB), Campus de GambelasUniversity of AlgarveFaroPortugal
| | | | - João Paulo Gomes
- Genomic and Bioinformatics Unit, Department of Infectious DiseasesNational Institute of Health Doutor Ricardo JorgeLisbonPortugal
| | - Pedro Pinto Leite
- Direção de Serviços de Informação e AnáliseDireção‐Geral da SaúdeLisbonPortugal
| | - Baltazar Nunes
- Department of EpidemiologyNational Institute of Health Doutor Ricardo JorgeLisbonPortugal
- Public Health Research Centre, NOVA National School of Public HealthUniversidade NOVA de LisboaLisbonPortugal
- Comprehensive Health Research Centre (CHRC)Universidade NOVA de LisboaLisbonPortugal
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19
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Rouet R, Henry JY, Johansen MD, Sobti M, Balachandran H, Langley DB, Walker GJ, Lenthall H, Jackson J, Ubiparipovic S, Mazigi O, Schofield P, Burnett DL, Brown SHJ, Martinello M, Hudson B, Gilroy N, Post JJ, Kelleher A, Jäck HM, Goodnow CC, Turville SG, Rawlinson WD, Bull RA, Stewart AG, Hansbro PM, Christ D. Broadly neutralizing SARS-CoV-2 antibodies through epitope-based selection from convalescent patients. Nat Commun 2023; 14:687. [PMID: 36755042 PMCID: PMC9907207 DOI: 10.1038/s41467-023-36295-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 01/25/2023] [Indexed: 02/10/2023] Open
Abstract
Emerging variants of concern (VOCs) are threatening to limit the effectiveness of SARS-CoV-2 monoclonal antibodies and vaccines currently used in clinical practice; broadly neutralizing antibodies and strategies for their identification are therefore urgently required. Here we demonstrate that broadly neutralizing antibodies can be isolated from peripheral blood mononuclear cells of convalescent patients using SARS-CoV-2 receptor binding domains carrying epitope-specific mutations. This is exemplified by two human antibodies, GAR05, binding to epitope class 1, and GAR12, binding to a new epitope class 6 (located between class 3 and 5). Both antibodies broadly neutralize VOCs, exceeding the potency of the clinical monoclonal sotrovimab (S309) by orders of magnitude. They also provide prophylactic and therapeutic in vivo protection of female hACE2 mice against viral challenge. Our results indicate that exposure to SARS-CoV-2 induces antibodies that maintain broad neutralization against emerging VOCs using two unique strategies: either by targeting the divergent class 1 epitope in a manner resistant to VOCs (ACE2 mimicry, as illustrated by GAR05 and mAbs P2C-1F11/S2K14); or alternatively, by targeting rare and highly conserved epitopes, such as the new class 6 epitope identified here (as illustrated by GAR12). Our results provide guidance for next generation monoclonal antibody development and vaccine design.
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Affiliation(s)
- Romain Rouet
- Garvan Institute of Medical Research, Sydney, NSW, Australia. .,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia.
| | - Jake Y Henry
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Matt D Johansen
- Center for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, NSW, Australia
| | - Meghna Sobti
- UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia.,Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
| | - Harikrishnan Balachandran
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia.,Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | - David B Langley
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Gregory J Walker
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia.,Kirby Institute, UNSW Sydney, Sydney, NSW, Australia.,Prince of Wales Hospital, Sydney, NSW, Australia
| | - Helen Lenthall
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Jennifer Jackson
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Stephanie Ubiparipovic
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Ohan Mazigi
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Peter Schofield
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Deborah L Burnett
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Simon H J Brown
- Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia
| | - Marianne Martinello
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia.,Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | | | | | | | - Anthony Kelleher
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia.,Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Friedrich-Alexander University Erlangen-Nürnberg and University Hospital Erlangen, Erlangen-Nürnberg, Germany
| | - Christopher C Goodnow
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Stuart G Turville
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia.,Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | - William D Rawlinson
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia.,Prince of Wales Hospital, Sydney, NSW, Australia
| | - Rowena A Bull
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia.,Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | - Alastair G Stewart
- UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia.,Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
| | | | - Daniel Christ
- Garvan Institute of Medical Research, Sydney, NSW, Australia. .,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia.
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20
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Zeng L, Lu Y, Yan W, Yang Y. A Protein Co-Conservation Network Model Characterizes Mutation Effects on SARS-CoV-2 Spike Protein. Int J Mol Sci 2023; 24:ijms24043255. [PMID: 36834664 PMCID: PMC9960056 DOI: 10.3390/ijms24043255] [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: 01/19/2023] [Revised: 02/03/2023] [Accepted: 02/04/2023] [Indexed: 02/10/2023] Open
Abstract
The emergence of numerous variants of SARS-CoV-2 has presented challenges to the global efforts to control the COVID-19 pandemic. The major mutation is in the SARS-CoV-2 viral envelope spike protein that is responsible for virus attachment to the host, and is the main target for host antibodies. It is critically important to study the biological effects of the mutations to understand the mechanisms of how mutations alter viral functions. Here, we propose a protein co-conservation weighted network (PCCN) model only based on the protein sequence to characterize the mutation sites by topological features and to investigate the mutation effects on the spike protein from a network view. Frist, we found that the mutation sites on the spike protein had significantly larger centrality than the non-mutation sites. Second, the stability changes and binding free energy changes in the mutation sites were positively significantly correlated with their neighbors' degree and the shortest path length separately. The results indicate that our PCCN model provides new insights into mutations on spike proteins and reflects the mutation effects on protein function alternations.
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Affiliation(s)
- Lianjie Zeng
- School of Computer Science & Technology, Soochow University, Suzhou 215000, China
- Collaborative Innovation Center of Novel Software Technology and Industrialization, Nanjing 210000, China
| | - Yitan Lu
- Department of Bioinformatics, School of Biology and Basic Medical Sciences, Medical College of Soochow University, Suzhou 215123, China
| | - Wenying Yan
- Department of Bioinformatics, School of Biology and Basic Medical Sciences, Medical College of Soochow University, Suzhou 215123, China
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Suzhou 215123, China
- Correspondence: (W.Y.); (Y.Y.)
| | - Yang Yang
- School of Computer Science & Technology, Soochow University, Suzhou 215000, China
- Collaborative Innovation Center of Novel Software Technology and Industrialization, Nanjing 210000, China
- Correspondence: (W.Y.); (Y.Y.)
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21
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Mohammed H, Pham-Tran DD, Yeoh ZYM, Wang B, McMillan M, Andraweera PH, Marshall HS. A Systematic Review and Meta-Analysis on the Real-World Effectiveness of COVID-19 Vaccines against Infection, Symptomatic and Severe COVID-19 Disease Caused by the Omicron Variant (B.1.1.529). Vaccines (Basel) 2023; 11:vaccines11020224. [PMID: 36851102 PMCID: PMC9965204 DOI: 10.3390/vaccines11020224] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/12/2023] [Accepted: 01/14/2023] [Indexed: 01/20/2023] Open
Abstract
Real-world data on the effectiveness of COVID-19 vaccines against the Omicron variant (B.1.1.529) is limited. This systematic review aimed to investigate the real-world effectiveness and durability of protection conferred by primary course and booster vaccines against confirmed Omicron infection, and severe outcomes. We systematically searched literature up to 1 August 2022. Meta-analysis was performed with the DerSimonian-Laird random-effects model to estimate the pooled vaccine effectiveness (VE). Overall, 28 studies were included representing 11 million individuals. The pooled VE against Omicron infection was 20.4% (95%CI: 12.1-28.7%) and 23.4% (95%CI: 13.5-33.3%) against symptomatic infection with variation based on vaccine type and age groups. VE sharply declined from 28.1% (95%CI: 19.1-37.1%) at three months to 3.9% (95%CI: -24.8-32.7%) at six months. Similar trends were observed for symptomatic Omicron infection. A booster dose restored protection against Omicron infection up to 51.1% (95%CI: 43.8-58.3%) and 57.3% (95%CI: 54.0-60.5%) against symptomatic infection within three months; however, this waned to 32.8% (95%CI: 16.8-48.7%) within six months. VE against severe Omicron infection following the primary course was 63.6% (95%CI: 57.5-69.7%) at three months, decreased to 49% (95%CI: 35.7-63.4%) within six months, and increased to 86% after the first or second booster dose.
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Affiliation(s)
- Hassen Mohammed
- Vaccinology and Immunology Research Trials Unit, Women’s and Children’s Health Network, Adelaide, SA 5006, Australia
- Robinson Research Institute and Adelaide Medical School, the University of Adelaide, Adelaide, SA 5006, Australia
- Correspondence: ; Tel.: +61-8-8161-9157
| | - Dan Duy Pham-Tran
- Robinson Research Institute and Adelaide Medical School, the University of Adelaide, Adelaide, SA 5006, Australia
| | - Zi Yi Michelle Yeoh
- Robinson Research Institute and Adelaide Medical School, the University of Adelaide, Adelaide, SA 5006, Australia
| | - Bing Wang
- Vaccinology and Immunology Research Trials Unit, Women’s and Children’s Health Network, Adelaide, SA 5006, Australia
- Robinson Research Institute and Adelaide Medical School, the University of Adelaide, Adelaide, SA 5006, Australia
| | - Mark McMillan
- Vaccinology and Immunology Research Trials Unit, Women’s and Children’s Health Network, Adelaide, SA 5006, Australia
- Robinson Research Institute and Adelaide Medical School, the University of Adelaide, Adelaide, SA 5006, Australia
| | - Prabha H. Andraweera
- Vaccinology and Immunology Research Trials Unit, Women’s and Children’s Health Network, Adelaide, SA 5006, Australia
- Robinson Research Institute and Adelaide Medical School, the University of Adelaide, Adelaide, SA 5006, Australia
| | - Helen S. Marshall
- Vaccinology and Immunology Research Trials Unit, Women’s and Children’s Health Network, Adelaide, SA 5006, Australia
- Robinson Research Institute and Adelaide Medical School, the University of Adelaide, Adelaide, SA 5006, Australia
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22
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Using survey data to estimate the impact of the omicron variant on vaccine efficacy against COVID-19 infection. Sci Rep 2023; 13:900. [PMID: 36650230 PMCID: PMC9844193 DOI: 10.1038/s41598-023-27951-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Symptoms-based detection of SARS-CoV-2 infection is not a substitute for precise diagnostic tests but can provide insight into the likely level of infection in a given population. This study uses symptoms data collected in the Global COVID-19 Trends and Impact Surveys (UMD Global CTIS), and data on variants sequencing from GISAID. This work, conducted in January of 2022 during the emergence of the Omicron variant (subvariant BA.1), aims to improve the quality of infection detection from the available symptoms and to use the resulting estimates of infection levels to assess the changes in vaccine efficacy during a change of dominant variant; from the Delta dominant to the Omicron dominant period. Our approach produced a new symptoms-based classifier, Random Forest, that was compared to a ground-truth subset of cases with known diagnostic test status. This classifier was compared with other competing classifiers and shown to exhibit an increased performance with respect to the ground-truth data. Using the Random Forest classifier, and knowing the vaccination status of the subjects, we then proceeded to analyse the evolution of vaccine efficacy towards infection during different periods, geographies and dominant variants. In South Africa, where the first significant wave of Omicron occurred, a significant reduction of vaccine efficacy is observed from August-September 2021 to December 2021. For instance, the efficacy drops from 0.81 to 0.30 for those vaccinated with 2 doses (of Pfizer/BioNTech), and from 0.51 to 0.09 for those vaccinated with one dose (of Pfizer/BioNTech or Johnson & Johnson). We also extended the study to other countries in which Omicron has been detected, comparing the situation in October 2021 (before Omicron) with that of December 2021. While the reduction measured is smaller than in South Africa, we still found, for instance, an average drop in vaccine efficacy from 0.53 to 0.45 among those vaccinated with two doses. Moreover, we found a significant negative (Pearson) correlation of around - 0.6 between the measured prevalence of Omicron in several countries and the vaccine efficacy in those same countries. This prediction, in January of 2022, of the decreased vaccine efficacy towards Omicron is in line with the subsequent increase of Omicron infections in the first half of 2022.
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23
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Wang BG, Wang ZC, Wu Y, Xiong Y, Zhang J, Ma Z. A mathematical model reveals the influence of NPIs and vaccination on SARS-CoV-2 Omicron Variant. NONLINEAR DYNAMICS 2023; 111:3937-3952. [PMID: 36339320 PMCID: PMC9628561 DOI: 10.1007/s11071-022-07985-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 09/19/2022] [Indexed: 05/10/2023]
Abstract
An SVEIR SARS-CoV-2 Omicron variant model is proposed to provide some insights to coordinate non-pharmaceutical interventions (NPIs) and vaccination. Mathematically, we define the basic reproduction number R 0 and the effective reproduction number R e to measure the infection potential of Omicron variant and formulate an optimal disease control strategy. Our inversion results imply that the sick period of Omicron variant in the United States is longer than that of Delta variant in India. The decrease in the infectious period of the infection with infectiousness implies that the risk of hospitalization is reduced; but the increasing period of the infection with non-infectiousness signifies that Omicron variant lengthens the period of nucleic acid test being negative. Optimistically, Omicron's death rate is only a quarter of Delta's. Moreover, we forecast that the cumulative cases will exceed 100 million in the United States on February 28, 2022, and the daily confirmed cases will reach a peak on February 2, 2022. The results of parameters sensitivity analysis imply that NPIs are helpful to reduce the number of confirmed cases. In particular, NPIs are indispensable even if all the people were vaccinated when the efficiency of vaccine is relatively low. By simulating the relationships of the effective reproduction number R e , the vaccination rate and the efficacy of vaccine, we find that it is impossible to achieve the herd immunity without NPIs while the efficiency of vaccine is lower than 88.7 % . Therefore, the herd immunity area is defined by the evolution of relationships between the vaccination rate and the efficacy of vaccine. Finally, we present that the disease-induced mortality rate demonstrates the periodic oscillation and an almost periodic function is deduced to match the curve. A discussion completes the paper.
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Affiliation(s)
- Bin-Guo Wang
- School of Mathematics and Statistics, Lanzhou University, Lanzhou, Gansu 730000 People’s Republic of China
| | - Zhi-Cheng Wang
- School of Mathematics and Statistics, Lanzhou University, Lanzhou, Gansu 730000 People’s Republic of China
| | - Yan Wu
- School of Mathematics and Statistics, Lanzhou University, Lanzhou, Gansu 730000 People’s Republic of China
| | - Yongping Xiong
- School of Mathematics and Statistics, Lanzhou University, Lanzhou, Gansu 730000 People’s Republic of China
| | - Jiangqian Zhang
- School of Mathematics and Statistics, Lanzhou University, Lanzhou, Gansu 730000 People’s Republic of China
| | - Zhuihui Ma
- School of Mathematics and Statistics, Lanzhou University, Lanzhou, Gansu 730000 People’s Republic of China
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24
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Landaverde L, Turcinovic J, Doucette-Stamm L, Gonzales K, Platt J, Connor JH, Klapperich C. Comparison of BinaxNOW and SARS-CoV-2 qRT-PCR Detection of the Omicron Variant from Matched Anterior Nares Swabs. Microbiol Spectr 2022; 10:e0130722. [PMID: 36255297 PMCID: PMC9769721 DOI: 10.1128/spectrum.01307-22] [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: 04/12/2022] [Accepted: 09/22/2022] [Indexed: 01/05/2023] Open
Abstract
The COVID-19 pandemic has increased use of rapid diagnostic tests (RDTs). In winter 2021 to 2022, the Omicron variant surge made it apparent that although RDTs are less sensitive than quantitative reverse transcription-PCR (qRT-PCR), the accessibility, ease of use, and rapid readouts made them a sought after and often sold-out item at local suppliers. Here, we sought to qualify the Abbott BinaxNOW RDT for use in our university testing program as a method to rule in positive or rule out negative individuals quickly at our priority qRT-PCR testing site. To perform this qualification study, we collected additional swabs from individuals attending this site. All swabs were tested using BinaxNOW. Initially as part of a feasibility study, test period 1 (n = 110) samples were stored cold before testing. In test period 2 (n = 209), samples were tested immediately. Combined, 102/319 samples tested severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive via qRT-PCR. All sequenced samples were Omicron (n = 92). We calculated 53.9% sensitivity, 100% specificity, a 100% positive predictive value, and an 82.2% negative predictive value for BinaxNOW (n = 319). Sensitivity would be improved (75.3%) by changing the qRT-PCR positivity threshold from a threshold cycle (CT) value of 40 to a CT value of 30. The receiver operating characteristic (ROC) curve shows that for qRT-PCR-positive CT values of between 24 and 40, the BinaxNOW test is of limited value diagnostically. Results suggest BinaxNOW could be used in our setting to confirm SARS-CoV-2 infection in individuals with substantial viral load, but a significant fraction of infected individuals would be missed if we used RDTs exclusively to rule out infection. IMPORTANCE Our results suggest BinaxNOW can rule in SARS-CoV-2 infection but would miss infections if RDTs were exclusively used.
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Affiliation(s)
- Lena Landaverde
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Clinical Testing Laboratory, Boston University, Boston, Massachusetts, USA
- Precision Diagnostics Center, Boston University, Boston, Massachusetts, USA
| | - Jacquelyn Turcinovic
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Program in Bioinformatics, Boston University, Boston, Massachusetts, USA
| | | | - Kevin Gonzales
- Student Health Services, Healthway, Boston University, Boston, Massachusetts, USA
- Office of Research, Boston University, Boston, Massachusetts, USA
| | - Judy Platt
- Student Health Services, Healthway, Boston University, Boston, Massachusetts, USA
| | - John H. Connor
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Program in Bioinformatics, Boston University, Boston, Massachusetts, USA
- Center for Emerging Infectious Disease Research and Policy, Boston University, Boston, Massachusetts, USA
| | - Catherine Klapperich
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Clinical Testing Laboratory, Boston University, Boston, Massachusetts, USA
- Precision Diagnostics Center, Boston University, Boston, Massachusetts, USA
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25
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Chernyaeva EN, Ayginin AA, Bulusheva IA, Vinogradov KS, Stetsenko IF, Romanova SV, Tsypkina AV, Matsvay AD, Savochkina YA, Shipulin GA. Genomic Variability of SARS-CoV-2 Omicron Variant Circulating in the Russian Federation during Early December 2021 and Late January 2022. Pathogens 2022; 11:pathogens11121461. [PMID: 36558796 PMCID: PMC9786029 DOI: 10.3390/pathogens11121461] [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: 11/16/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Analysis of genomic variability of pathogens associated with heightened public health concerns is an opportunity to track transmission routes of the disease and helps to develop more effective vaccines and specific diagnostic tests. We present the findings of a detailed genomic analysis of the genomic variability of the SARS-CoV-2 Omicron variant that spread in Russia between 8 December 2021 and 30 January 2022. We performed phylogenetic analysis of Omicron viral isolates collected in Moscow (n = 589) and downloaded from GISAID (n = 397), and identified that the BA.1 lineage was predominant in Russia during this period. The BA.2 lineage was also identified early in December 2021. We identified three cases of BA.1/BA.2 coinfections and one case of Delta/Omicron coinfection. A comparative genomic analysis of SARS-CoV-2 viral variants that spread in other countries allowed us to identify possible cases of transmission. We also found that some mutations that are quite rare in the Global Omicron dataset have a higher incidence rate, and identified genetic markers that could be associated with ways of Omicron transmission in Russia. We give the genomic variability of single nucleotide variations across the genome and give a characteristic of haplotype variability of Omicron strains in both Russia and around the world, and we also identify them.
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26
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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] [MESH Headings] [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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27
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Yu X, Qi X, Cao Y, Li P, Lu L, Wang P, Feng Y, Yang J, Wei H, Guo L, Sun M, Liu Q, Lv J, Feng Y. Three doses of an inactivation-based COVID-19 vaccine induces cross-neutralizing immunity against the SARS CoV-2 Omicron variant. Emerg Microbes Infect 2022; 11:749-752. [PMID: 35176972 PMCID: PMC8903785 DOI: 10.1080/22221751.2022.2044271] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/15/2022] [Indexed: 11/03/2022]
Abstract
The immunity potency upon natural infection or vaccination is the main concern for the vaccine strategy of severe acute respiratory syndrome coronavirus 2 (SARS COV-2 variant), especially the recently reported Omicron variant (B.1.1.529). In this study, 200 recipients immunized with three doses of a COVID-19-inactivated vaccine were enrolled, whose serum samples were collected within 2 months after the third immunization. The neutralizing activity of sera against the pseudotyped Omicron variant, prototype, and Delta variant was determined. Our results demonstrated that the positive neutralization activity was 95.5% for the Omicron variant, 99.5% for the prototype, and 98.5% for the Delta variant. The geometric mean titers (GMT) for the Omicron variant was 49 and maintained sustained immune levels for 2 months, which decreased by 4.9-fold and 3.0-fold compared with the prototype (GMT, 239) and Delta variant (GMT, 148), respectively. In summary, our study demonstrated that three doses of a COVID-19-inactivated vaccine effectively yielded potent cross-neutralizing activity against the Omicron variant at 2 months after the third vaccination.
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Affiliation(s)
- Xiaoling Yu
- Gobond Testing Technology (Beijing) Co., Ltd., Beijing, People’s Republic of China
| | - Xiangrong Qi
- Gobond Testing Technology (Beijing) Co., Ltd., Beijing, People’s Republic of China
| | - Yu Cao
- Department of Science and Development, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Peiyao Li
- Gobond Testing Technology (Beijing) Co., Ltd., Beijing, People’s Republic of China
| | - Li Lu
- Yearth Biotechnology Co. Ltd., Changsha, People’s Republic of China
| | - Pingping Wang
- Gobond Testing Technology (Beijing) Co., Ltd., Beijing, People’s Republic of China
| | - Yuchen Feng
- Gobond Testing Technology (Beijing) Co., Ltd., Beijing, People’s Republic of China
| | - Jie Yang
- Gobond Testing Technology (Beijing) Co., Ltd., Beijing, People’s Republic of China
| | - Huihui Wei
- Gobond Testing Technology (Beijing) Co., Ltd., Beijing, People’s Republic of China
| | - Lixian Guo
- Gobond Testing Technology (Beijing) Co., Ltd., Beijing, People’s Republic of China
| | - Mingyue Sun
- Gobond Testing Technology (Beijing) Co., Ltd., Beijing, People’s Republic of China
| | - Qiang Liu
- Gobond Testing Technology (Beijing) Co., Ltd., Beijing, People’s Republic of China
| | - Jing Lv
- Gobond Testing Technology (Beijing) Co., Ltd., Beijing, People’s Republic of China
| | - Yingmei Feng
- Department of Science and Development, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
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28
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Zhao H, Lu L, Peng Z, Chen LL, Meng X, Zhang C, Ip JD, Chan WM, Chu AWH, Chan KH, Jin DY, Chen H, Yuen KY, To KKW. SARS-CoV-2 Omicron variant shows less efficient replication and fusion activity when compared with Delta variant in TMPRSS2-expressed cells. Emerg Microbes Infect 2022; 11:277-283. [PMID: 34951565 PMCID: PMC8774049 DOI: 10.1080/22221751.2021.2023329] [Citation(s) in RCA: 252] [Impact Index Per Article: 126.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 12/22/2021] [Indexed: 02/07/2023]
Abstract
The novel SARS-CoV-2 Omicron variant (B.1.1.529), first found in early November 2021, has sparked considerable global concern and it has >50 mutations, many of which are known to affect transmissibility or cause immune escape. In this study, we sought to investigate the virological characteristics of the Omicron variant and compared it with the Delta variant which has dominated the world since mid-2021. Omicron variant replicated more slowly than the Delta variant in transmembrane serine protease 2 (TMPRSS2)-overexpressing VeroE6 (VeroE6/TMPRSS2) cells. Notably, the Delta variant replicated well in Calu3 cell line which has robust TMPRSS2 expression, while the Omicron variant replicated poorly in this cell line. Competition assay showed that Delta variant outcompeted Omicron variant in VeroE6/TMPRSS2 and Calu3 cells. To confirm the difference in entry pathway between the Omicron and Delta variants, we assessed the antiviral effect of bafilomycin A1, chloroquine (inhibiting endocytic pathway), and camostat (inhibiting TMPRSS2 pathway). Camostat potently inhibited the Delta variant but not the Omicron variant, while bafilomycin A1 and chloroquine could inhibit both Omicron and Delta variants. Moreover, the Omicron variant also showed weaker cell-cell fusion activity when compared with Delta variant in VeroE6/TMPRSS2 cells. Collectively, our results suggest that Omicron variant infection is not enhanced by TMPRSS2 but is largely mediated via the endocytic pathway. The difference in entry pathway between Omicron and Delta variants may have an implication on the clinical manifestations or disease severity.
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Affiliation(s)
- Hanjun Zhao
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Lu Lu
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Zheng Peng
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Lin-Lei Chen
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Xinjin Meng
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Chuyuan Zhang
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Jonathan Daniel Ip
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Wan-Mui Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Allen Wing-Ho Chu
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Kwok-Hung Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Dong-Yan Jin
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Honglin Chen
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Kwok-Yung Yuen
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, People’s Republic of China
| | - Kelvin Kai-Wang To
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, People’s Republic of China
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Chen Q, Zhu K, Liu X, Zhuang C, Huang X, Huang Y, Yao X, Quan J, Lin H, Huang S, Su Y, Wu T, Zhang J, Xia N. The Protection of Naturally Acquired Antibodies Against Subsequent SARS-CoV-2 Infection: A Systematic Review and Meta-Analysis. Emerg Microbes Infect 2022; 11:793-803. [PMID: 35195494 PMCID: PMC8920404 DOI: 10.1080/22221751.2022.2046446] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/21/2022] [Indexed: 01/18/2023]
Abstract
The specific antibodies induced by SARS-CoV-2 infection may provide protection against a subsequent infection. However, the efficacy and duration of protection provided by naturally acquired immunity against subsequent SARS-CoV-2 infection remain controversial. We systematically searched for the literature describing COVID-19 reinfection published before 07 February 2022. The outcomes were the pooled incidence rate ratio (IRR) for estimating the risk of subsequent infection. The Newcastle-Ottawa Scale (NOS) was used to assess the quality of the included studies. Statistical analyses were conducted using the R programming language 4.0.2. We identified 19 eligible studies including more than 3.5 million individuals without the history of COVID-19 vaccination. The efficacy of naturally acquired antibodies against reinfection was estimated at 84% (pooled IRR = 0.16, 95% CI: 0.14-0.18), with higher efficacy against symptomatic COVID-19 cases (pooled IRR = 0.09, 95% CI = 0.07-0.12) than asymptomatic infection (pooled IRR = 0.28, 95% CI = 0.14-0.54). In the subgroup analyses, the pooled IRRs of COVID-19 infection in health care workers (HCWs) and the general population were 0.22 (95% CI = 0.16-0.31) and 0.14 (95% CI = 0.12-0.17), respectively, with a significant difference (P = 0.02), and those in older (over 60 years) and younger (under 60 years) populations were 0.26 (95% CI = 0.15-0.48) and 0.16 (95% CI = 0.14-0.19), respectively. The risk of subsequent infection in the seropositive population appeared to increase slowly over time. In conclusion, naturally acquired antibodies against SARS-CoV-2 can significantly reduce the risk of subsequent infection, with a protection efficacy of 84%.Registration number: CRD42021286222.
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Affiliation(s)
- Qi Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People’s Republic of China
| | - Kongxin Zhu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People’s Republic of China
| | - Xiaohui Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People’s Republic of China
| | - Chunlan Zhuang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People’s Republic of China
| | - Xingcheng Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People’s Republic of China
| | - Yue Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People’s Republic of China
| | - Xingmei Yao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People’s Republic of China
| | - Jiali Quan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People’s Republic of China
| | - Hongyan Lin
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People’s Republic of China
| | - Shoujie Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People’s Republic of China
| | - Yingying Su
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People’s Republic of China
| | - Ting Wu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People’s Republic of China
| | - Jun Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People’s Republic of China
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People’s Republic of China
- The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, Xiamen City, Fujian Province, People's Republic of China
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30
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Rui J, Zheng JX, Chen J, Wei H, Yu S, Zhao Z, Wang XY, Chen MX, Xia S, Zhou Y, Chen T, Zhou XN. Optimal control strategies of SARS-CoV-2 Omicron supported by invasive and dynamic models. Infect Dis Poverty 2022; 11:115. [PMID: 36435792 PMCID: PMC9701379 DOI: 10.1186/s40249-022-01039-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/28/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND There is a raising concern of a higher infectious Omicron BA.2 variant and the latest BA.4, BA.5 variant, made it more difficult in the mitigation process against COVID-19 pandemic. Our study aimed to find optimal control strategies by transmission of dynamic model from novel invasion theory. METHODS Based on the public data sources from January 31 to May 31, 2022, in four cities (Nanjing, Shanghai, Shenzhen and Suzhou) of China. We segmented the theoretical curves into five phases based on the concept of biological invasion. Then, a spatial autocorrelation analysis was carried out by detecting the clustering of the studied areas. After that, we choose a mathematical model of COVID-19 based on system dynamics methodology to simulate numerous intervention measures scenarios. Finally, we have used publicly available migration data to calculate spillover risk. RESULTS Epidemics in Shanghai and Shenzhen has gone through the entire invasion phases, whereas Nanjing and Suzhou were all ended in the establishment phase. The results indicated that Rt value and public health and social measures (PHSM)-index of the epidemics were a negative correlation in all cities, except Shenzhen. The intervention has come into effect in different phases of invasion in all studied cities. Until the May 31, most of the spillover risk in Shanghai remained above the spillover risk threshold (18.81-303.84) and the actual number of the spillovers (0.94-74.98) was also increasing along with the time. Shenzhen reported Omicron cases that was only above the spillover risk threshold (17.92) at the phase of outbreak, consistent with an actual partial spillover. In Nanjing and Suzhou, the actual number of reported cases did not exceed the spillover alert value. CONCLUSIONS Biological invasion is positioned to contribute substantively to understanding the drivers and mechanisms of the COVID-19 spread and outbreaks. After evaluating the spillover risk of cities at each invasion phase, we found the dynamic zero-COVID strategy implemented in four cities successfully curb the disease epidemic peak of the Omicron variant, which was highly correlated to the way to perform public health and social measures in the early phases right after the invasion of the virus.
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Affiliation(s)
- Jia Rui
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, People's Republic of China
| | - Jin-Xin Zheng
- Department of Nephrology, Institute of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Jin Chen
- National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, NHC Key Laboratory of Parasites and Vectors Biology of China, Shanghai, 200025, People's Republic of China
| | - Hongjie Wei
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, People's Republic of China
| | - Shanshan Yu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, People's Republic of China
| | - Zeyu Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, People's Republic of China
| | - Xin-Yi Wang
- National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, NHC Key Laboratory of Parasites and Vectors Biology of China, Shanghai, 200025, People's Republic of China
| | - Mu-Xin Chen
- National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, NHC Key Laboratory of Parasites and Vectors Biology of China, Shanghai, 200025, People's Republic of China
| | - Shang Xia
- National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, NHC Key Laboratory of Parasites and Vectors Biology of China, Shanghai, 200025, People's Republic of China
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Ying Zhou
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China.
| | - Tianmu Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, People's Republic of China.
| | - Xiao-Nong Zhou
- National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, NHC Key Laboratory of Parasites and Vectors Biology of China, Shanghai, 200025, People's Republic of China.
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China.
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31
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Chia TRT, Young BE, Chia PY. The Omicron-transformer: Rise of the subvariants in the age of vaccines. ANNALS OF THE ACADEMY OF MEDICINE, SINGAPORE 2022. [DOI: 10.47102/annals-acadmedsg.2022294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Introduction: Omicron is the latest SARS-CoV-2 variant of concern, the pathogen that causes COVID-19. Since its emergence in late 2021, Omicron has displaced other circulating variants and caused successive waves of infection worldwide throughout 2022. Omicron is characterised by the rapid emergence of many subvariants and high rates of infection in people with vaccine- and/or infection-induced immunity. This review article will consolidate current knowledge regarding Omicron subvariants, the role of boosters, and future vaccine development. Method: This narrative review is based on a literature search using PubMed. Search terms related to Omicron were used and priority was given to published peer-reviewed articles over pre-prints. Results: Studies indicate that vaccinations and boosters are important to reduce disease severity, hospitalisation and death from Omicron. A variety of factors, such as differing host factors, circulating variants, and forces of infection, can influence the benefit of repeated booster administration. Next-generation bivalent vaccines have now been approved in some countries including Singapore and have demonstrated the ability to induce broad variant protection. Future third-generation vaccines involving mucosal vaccines and/or pan-sarbecovirus vaccines may provide broader and longer-lasting protection. Conclusion: Due to current high levels of vaccine- and infection-induced immunity, it is likely that rates of severe illness, hospitalisation, and death due to Omicron will continue to moderate. Nevertheless, the virus is ever-changing, and public health policies, especially those related to vaccinations, will also have to continually evolve and adapt as COVID-19 transitions to endemicity.
Keywords: Booster, COVID-19, infectious diseases, Omicron, vaccine
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Affiliation(s)
| | | | - Po Ying Chia
- National Centre for Infectious Diseases, Singapore
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32
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Ait Mahiout L, Mozokhina A, Tokarev A, Volpert V. Virus replication and competition in a cell culture: Application to the SARS-CoV-2 variants. APPLIED MATHEMATICS LETTERS 2022; 133:108217. [PMID: 35669092 PMCID: PMC9155187 DOI: 10.1016/j.aml.2022.108217] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 05/23/2022] [Accepted: 05/23/2022] [Indexed: 05/29/2023]
Abstract
Viral replication in a cell culture is described by a delay reaction-diffusion system. It is shown that infection spreads in cell culture as a reaction-diffusion wave, for which the speed of propagation and viral load can be determined both analytically and numerically. Competition of two virus variants in the same cell culture is studied, and it is shown that the variant with larger individual wave speed out-competes another one, and eliminates it. This approach is applied to the Delta and Omicron variants of the SARS-CoV-2 infection in the cultures of human epithelial and lung cells, allowing characterization of infectivity and virulence of each variant, and their comparison.
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Affiliation(s)
- L Ait Mahiout
- Laboratoire d'équations aux dérivées partielles non linéaires et histoire des mathématiques Ecole Normale Supérieure, B.P. 92, Vieux Kouba, 16050 Algiers, Algeria
| | - A Mozokhina
- Peoples Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St, Moscow, 117198, Russia
| | - A Tokarev
- Peoples Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St, Moscow, 117198, Russia
- Semenov Institute of Chemical Physics RAS, Kosygin St., 4, 119991 Moscow, Russia
| | - V Volpert
- Institut Camille Jordan, UMR 5208 CNRS, University Lyon 1, 69622 Villeurbanne, France
- Peoples Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St, Moscow, 117198, Russia
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33
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Kubale J, Gleason C, Carreño JM, Srivastava K, Singh G, Gordon A, Krammer F, Simon V. SARS-CoV-2 Spike-Binding Antibody Longevity and Protection from Reinfection with Antigenically Similar SARS-CoV-2 Variants. mBio 2022; 13:e0178422. [PMID: 35997286 PMCID: PMC9600418 DOI: 10.1128/mbio.01784-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 07/25/2022] [Indexed: 11/20/2022] Open
Abstract
The PARIS (Protection Associated with Rapid Immunity to SARS-CoV-2) cohort follows health care workers with and without documented coronavirus disease 2019 (COVID-19) since April 2020. We report our findings regarding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike-binding antibody stability and protection from infection in the pre-variant era. We analyzed data from 400 health care workers (150 seropositive and 250 seronegative at enrollment) for a median of 84 days. The SARS-CoV-2 spike-binding antibody titers were highly variable with antibody levels decreasing over the first 3 months, followed by a relative stabilization. We found that both more advanced age (>40 years) and female sex were associated with higher antibody levels (1.6-fold and 1.4-fold increases, respectively). Only six percent of the initially seropositive participants "seroreverted." We documented a total of 11 new SARS-CoV-2 infections (10 naive participants and 1 previously infected participant without detectable antibodies; P < 0.01), indicating that spike antibodies limit the risk of reinfection. These observations, however, only apply to SARS-CoV-2 variants antigenically similar to the ancestral SARS-CoV-2 ones. In conclusion, SARS-CoV-2 antibody titers mounted upon infection are stable over several months and provide protection from infection with antigenically similar viruses. IMPORTANCE SARS-CoV-2 is the cause of one of the largest noninfluenza pandemics of this century. This exceptional public health crisis highlights the urgent need for better understanding of the correlates of protection from infection and severe COVID-19. We established the PARIS cohort to determine durability and effectiveness of SARS-CoV-2 immune responses. Here, we report on the kinetics of SARS-CoV-2 spike-binding antibody after SARS-CoV-2 infection as well as reinfection rates using data collected between April 2020 and August 2021. We found that antibody levels stabilized at individual steady state levels after an initial decrease with seroreversion being found in only 6% of the convalescent participants. SARS-CoV-2 infections only occurred in participants without detectable spike-binding antibodies, indicating significant protection from reinfection with antigenically similar viruses. Our data indicate the importance of spike-binding antibody titers in protection prior to vaccination and the wide circulation of antigenically diverse variants of concern.
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Affiliation(s)
- John Kubale
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Charles Gleason
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Komal Srivastava
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Gagandeep Singh
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - PARIS Study Team
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Aubree Gordon
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Chassalevris T, Chaintoutis SC, Koureas M, Petala M, Moutou E, Beta C, Kyritsi M, Hadjichristodoulou C, Kostoglou M, Karapantsios T, Papadopoulos A, Papaioannou N, Dovas CI. SARS-CoV-2 wastewater monitoring using a novel PCR-based method rapidly captured the Delta-to-Omicron ΒΑ.1 transition patterns in the absence of conventional surveillance evidence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022. [PMID: 35753493 DOI: 10.1101/2022.01.28.21268186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Conventional SARS-CoV-2 surveillance based on genotyping of clinical samples is characterized by challenges related to the available sequencing capacity, population sampling methodologies, and is time, labor, and resource-demanding. Wastewater-based variant surveillance constitutes a valuable supplementary practice, since it does not require extensive sampling, and provides information on virus prevalence in a timely and cost-effective manner. Consequently, we developed a sensitive real-time RT-PCR-based approach that exclusively amplifies and quantifies SARS-CoV-2 genomic regions carrying the S:Δ69/70 deletion, indicative of the Omicron BA.1 variant, in wastewater. The method was incorporated in the analysis of composite daily samples taken from the main Wastewater Treatment Plant of Thessaloniki, Greece, from 1 December 2021. The applicability of the methodology is dependent on the epidemiological situation. During Omicron BA.1 global emergence, Thessaloniki was experiencing a massive epidemic wave attributed solely to the Delta variant, according to genomic surveillance data. Since Delta does not possess the S:Δ69/70, the emergence of Omicron BA.1 could be monitored via the described methodology. Omicron BA.1 was detected in sewage samples on 19 December 2021 and a rapid increase of its viral load was observed in the following 10-day period, with an estimated early doubling time of 1.86 days. The proportion of the total SARS-CoV-2 load attributed to BA.1 reached 91.09 % on 7 January, revealing a fast Delta-to-Omicron transition pattern. The detection of Omicron BA.1 subclade in wastewater preceded the outburst of reported (presumable) Omicron cases in the city by approximately 7 days. The proposed wastewater surveillance approach based on selective PCR amplification of a genomic region carrying a deletion signature enabled rapid, real-time data acquisition on Omicron BA.1 prevalence and dynamics during the slow remission of the Delta wave. Timely provision of these results to State authorities readily influences the decision-making process for targeted public health interventions, including control measures, awareness, and preparedness.
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Affiliation(s)
- Taxiarchis Chassalevris
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Serafeim C Chaintoutis
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Michalis Koureas
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Maria Petala
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Evangelia Moutou
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Christina Beta
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Maria Kyritsi
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Christos Hadjichristodoulou
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Margaritis Kostoglou
- Laboratory of Chemical and Environmental Technology, School of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Thodoris Karapantsios
- Laboratory of Chemical and Environmental Technology, School of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Agis Papadopoulos
- EYATH S.A., Thessaloniki Water Supply and Sewerage Company S.A., 54636 Thessaloniki, Greece
| | - Nikolaos Papaioannou
- Laboratory of Pathology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Chrysostomos I Dovas
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece.
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Chassalevris T, Chaintoutis SC, Koureas M, Petala M, Moutou E, Beta C, Kyritsi M, Hadjichristodoulou C, Kostoglou M, Karapantsios T, Papadopoulos A, Papaioannou N, Dovas CI. SARS-CoV-2 wastewater monitoring using a novel PCR-based method rapidly captured the Delta-to-Omicron ΒΑ.1 transition patterns in the absence of conventional surveillance evidence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 844:156932. [PMID: 35753493 PMCID: PMC9225927 DOI: 10.1016/j.scitotenv.2022.156932] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/09/2022] [Accepted: 06/20/2022] [Indexed: 05/21/2023]
Abstract
Conventional SARS-CoV-2 surveillance based on genotyping of clinical samples is characterized by challenges related to the available sequencing capacity, population sampling methodologies, and is time, labor, and resource-demanding. Wastewater-based variant surveillance constitutes a valuable supplementary practice, since it does not require extensive sampling, and provides information on virus prevalence in a timely and cost-effective manner. Consequently, we developed a sensitive real-time RT-PCR-based approach that exclusively amplifies and quantifies SARS-CoV-2 genomic regions carrying the S:Δ69/70 deletion, indicative of the Omicron BA.1 variant, in wastewater. The method was incorporated in the analysis of composite daily samples taken from the main Wastewater Treatment Plant of Thessaloniki, Greece, from 1 December 2021. The applicability of the methodology is dependent on the epidemiological situation. During Omicron BA.1 global emergence, Thessaloniki was experiencing a massive epidemic wave attributed solely to the Delta variant, according to genomic surveillance data. Since Delta does not possess the S:Δ69/70, the emergence of Omicron BA.1 could be monitored via the described methodology. Omicron BA.1 was detected in sewage samples on 19 December 2021 and a rapid increase of its viral load was observed in the following 10-day period, with an estimated early doubling time of 1.86 days. The proportion of the total SARS-CoV-2 load attributed to BA.1 reached 91.09 % on 7 January, revealing a fast Delta-to-Omicron transition pattern. The detection of Omicron BA.1 subclade in wastewater preceded the outburst of reported (presumable) Omicron cases in the city by approximately 7 days. The proposed wastewater surveillance approach based on selective PCR amplification of a genomic region carrying a deletion signature enabled rapid, real-time data acquisition on Omicron BA.1 prevalence and dynamics during the slow remission of the Delta wave. Timely provision of these results to State authorities readily influences the decision-making process for targeted public health interventions, including control measures, awareness, and preparedness.
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Affiliation(s)
- Taxiarchis Chassalevris
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Serafeim C Chaintoutis
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Michalis Koureas
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Maria Petala
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Evangelia Moutou
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Christina Beta
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Maria Kyritsi
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Christos Hadjichristodoulou
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Margaritis Kostoglou
- Laboratory of Chemical and Environmental Technology, School of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Thodoris Karapantsios
- Laboratory of Chemical and Environmental Technology, School of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Agis Papadopoulos
- EYATH S.A., Thessaloniki Water Supply and Sewerage Company S.A., 54636 Thessaloniki, Greece
| | - Nikolaos Papaioannou
- Laboratory of Pathology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Chrysostomos I Dovas
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece.
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Chen WC, Lin YP, Cheng CM, Shen CF, Li CW, Wang YK, Shih TY, Hong C, Chang TC, Shen CJ. Detection of SARS-CoV-2 Neutralizing Antibodies in Vaccinated Pregnant Women and Neonates by Using a Lateral Flow Immunoassay Coupled with a Spectrum-Based Reader. BIOSENSORS 2022; 12:bios12100891. [PMID: 36291029 PMCID: PMC9599695 DOI: 10.3390/bios12100891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/11/2022] [Accepted: 10/16/2022] [Indexed: 06/02/2023]
Abstract
The focus of this study was to investigate the detection of neutralizing antibodies (Nabs) in maternal serum and cord blood as the targeted samples by employing a lateral flow immunoassay combined with a spectrum reader (LFI-SR) and the correlation of Nab protection against different types of SARS-CoV-2. We enrolled 20 pregnant women who were vaccinated with the Moderna (mRNA-1273) vaccine during pregnancy and collected 40 samples during delivery. We used an LFI-SR for the level of spike protein receptor binding domain antibody (SRBD IgG) as Nabs and examined the correlation of the SRBD IgG concentration and Nab inhibition rates (NabIR) via enzyme-linked immunosorbent assays (ELISA). The LFI-SR had high confidence for the SRBD IgG level (p < 0.0001). Better NabIR were found in wild-type SARS-CoV-2 (WT) compared to Delta-type (DT) and Omicron-type (OT). Women with two-dose vaccinations demonstrated greater NabIR than those with a single dose. The cut-off value of the SRBD IgG level by the LFI-SR for NabIR to DT (≥30%; ≥70%) was 60.15 and 150.21 ng/mL for mothers (both p = 0.005), and 156.31 (p = 0.011) and 230.20 ng/mL (p = 0.006) for babies, respectively. An additional vaccine booster may be considered for those mothers with SRBD IgG levels < 60.15 ng/mL, and close protection should be given for those neonates with SRBD IgG levels < 150.21 ng/mL, since there is no available vaccine for them.
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Affiliation(s)
- Wei-Chun Chen
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital at Linkou, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Department of Obstetrics and Gynecology, New Taipei City Municipal Tucheng Hospital, New Taipei City 236, Taiwan
| | - Yen-Pin Lin
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Chao-Min Cheng
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Ching-Fen Shen
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | | | | | | | | | - Ting-Chang Chang
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital at Linkou, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Ching-Ju Shen
- Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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Vitiello A, La Porta R, Trama U, Ferrara F, Zovi A, Auti AM, Di Domenico M, Boccellino M. Pandemic COVID-19, an update of current status and new therapeutic strategies. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2022; 395:1159-1165. [PMID: 35779085 DOI: 10.1007/s00210-022-02265-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/14/2022] [Indexed: 12/15/2022]
Abstract
The global COVID-19 pandemic is underway. In recent weeks, several countries throughout the globe, and particularly in Europe, have experienced an exponential increase in the number of individuals infected with COVID-19, probably induced by a new variant of SARS-CoV-2, called the "Omicron variant." Mass vaccination against COVID-19 continues worldwide. Are authorized mRNA vaccines effective against the new Omicron variant? Recently, several pharmaceutical companies have developed oral antiviral pills against SARS-CoV-2, i.e., molnupiravir and paxlovid, that inhibit SARS-CoV-2 viral replication by acting on the RNA polymerase of SARS-CoV. In pre-registration clinical trials, molnupiravir and paxlovid have shown excellent clinical efficacy results, but what impact will these new oral antiviral agents have against pandemic COVID-19? In what specific clinical situations are they preferred over other antivirals such as remdesivir? In this brief review, we explore these important aspects.
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Affiliation(s)
- Antonio Vitiello
- Pharmaceutical Department, Usl Umbria 1, Via XIV Settembre, 06132, Perugia, Italy
| | - Raffaele La Porta
- Clinical Pathologist, Pathology Department, ASUR Marche, Area Vasta 1, Urbino, Italy
| | - Ugo Trama
- Directorate General for Healthcare and Coordination of the Regional Healthcare System, Naples, Italy
| | - Francesco Ferrara
- Pharmaceutical Department, Asl Napoli 3 Sud, Via Dell'amicizia 22, 80035, Naples, Nola, Italy.
| | - Andrea Zovi
- Ministry of Health, Viale Giorgio Ribotta 5, 00144, Rome, Italy
| | - Amogh Milind Auti
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | - Marina Di Domenico
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, USA
| | - Mariarosaria Boccellino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
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The Receptor Binding Domain of SARS-CoV-2 Lambda Variant Has a Better Chance Than the Delta Variant in Evading BNT162b2 COVID-19 mRNA Vaccine-Induced Humoral Immunity. Int J Mol Sci 2022; 23:ijms231911325. [PMID: 36232627 PMCID: PMC9569855 DOI: 10.3390/ijms231911325] [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: 07/19/2022] [Revised: 09/07/2022] [Accepted: 09/20/2022] [Indexed: 12/04/2022] Open
Abstract
The SARS-CoV-2 Delta and Lambda variants had been named variants of concern (VOC) and variants of interest (VOI), respectively, by the World Health Organization (WHO). Both variants have two mutations in the spike receptor binding domain (RBD) region, with L452R and T478K mutations in the Delta variant, and L452Q and F490S mutations in the Lambda variant. We used surface plasmon resonance (SPR)-based technology to evaluate the effect of these mutations on human angiotensin-converting enzyme 2 (ACE2) and Bamlanivimab binding. The affinity for the RBD ligand, ACE2, of the Delta RBD is approximately twice as strong as that of the wild type RBD, an increase that accounts for the increased infectivity of the Delta variant. On the other hand, in spite of its amino acid changes, the Lambda RBD has similar affinity to ACE2 as the wild type RBD. The protective anti-wild type RBD antibody Bamlanivimab binds very poorly to the Delta RBD and not at all to the Lambda RBD. Nevertheless, serum antibodies from individuals immunized with the BNT162b2 vaccine were found to bind well to the Delta RBD, but less efficiently to the Lambda RBD in contrast. As a result, the blocking ability of ACE2 binding by serum antibodies was decreased more by the Lambda than the Delta RBD. Titers of sera from BNT162b2 mRNA vaccinated individuals dropped 3-fold within six months of vaccination regardless of whether the target RBD was wild type, Delta or Lambda. This may account partially for the fall off with time in the protective effect of vaccines against any variant.
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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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Candido KL, Eich CR, de Fariña LO, Kadowaki MK, da Conceição Silva JL, Maller A, Simão RDCG. Spike protein of SARS-CoV-2 variants: a brief review and practical implications. Braz J Microbiol 2022; 53:1133-1157. [PMID: 35397075 PMCID: PMC8994061 DOI: 10.1007/s42770-022-00743-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/21/2022] [Indexed: 12/24/2022] Open
Abstract
The scientific community has been alarmed by the possible immunological evasion, higher infectivity, and severity of disease caused by the newest variants of SARS-CoV-2. The spike protein has an important role in the cellular invasion of viruses and is the target of several vaccines and therapeutic resources, such as monoclonal antibodies. In addition, some of the most relevant mutations in the different variants are on the spike (S) protein gene sequence that leads to structural alterations in the predicted protein, thus causing concern about the protection mediated by vaccines against these new strains. The present review highlights the most recent knowledge about COVID-19 and vaccines, emphasizing the different spike protein structures of SARS-CoV-2 and updating the reader about the emerging viral variants and their classifications, the more common viral mutations described and their distribution in Brazil. It also compiles a table with the most recent knowledge about all of the Omicron spike mutations.
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Affiliation(s)
- Kattlyn Laryssa Candido
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Caio Ricardo Eich
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Luciana Oliveira de Fariña
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Marina Kimiko Kadowaki
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - José Luis da Conceição Silva
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Alexandre Maller
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Rita de Cássia Garcia Simão
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
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41
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Shrestha LB, Foster C, Rawlinson W, Tedla N, Bull RA. Evolution of the SARS-CoV-2 omicron variants BA.1 to BA.5: Implications for immune escape and transmission. Rev Med Virol 2022; 32:e2381. [PMID: 35856385 PMCID: PMC9349777 DOI: 10.1002/rmv.2381] [Citation(s) in RCA: 250] [Impact Index Per Article: 125.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/01/2022] [Accepted: 07/11/2022] [Indexed: 12/15/2022]
Abstract
The first dominant SARS-CoV-2 Omicron variant BA.1 harbours 35 mutations in its Spike protein from the original SARS-CoV-2 variant that emerged late 2019. Soon after its discovery, BA.1 rapidly emerged to become the dominant variant worldwide and has since evolved into several variants. Omicron is of major public health concern owing to its high infectivity and antibody evasion. This review article examines the theories that have been proposed on the evolution of Omicron including zoonotic spillage, infection in immunocompromised individuals and cryptic spread in the community without being diagnosed. Added to the complexity of Omicron's evolution are the multiple reports of recombination events occurring between co-circulating variants of Omicron with Delta and other variants such as XE. Current literature suggests that the combination of the novel mutations in Omicron has resulted in the variant having higher infectivity than the original Wuhan-Hu-1 and Delta variant. However, severity is believed to be less owing to the reduced syncytia formation and lower multiplication in the human lung tissue. Perhaps most challenging is that several studies indicate that the efficacy of the available vaccines have been reduced against Omicron variant (8-127 times reduction) as compared to the Wuhan-Hu-1 variant. The administration of booster vaccine, however, compensates with the reduction and improves the efficacy by 12-35 fold. Concerningly though, the broadly neutralising monoclonal antibodies, including those approved by FDA for therapeutic use against previous SARS-CoV-2 variants, are mostly ineffective against Omicron with the exception of Sotrovimab and recent reports suggest that the Omicron BA.2 is also resistant to Sotrovimab. Currently two new Omicron variants BA.4 and BA.5 are emerging and are reported to be more transmissible and resistant to immunity generated by previous variants including Omicron BA.1 and most monoclonal antibodies. As new variants of SARS-CoV-2 will likely continue to emerge it is important that the evolution, and biological consequences of new mutations, in existing variants be well understood.
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Affiliation(s)
- Lok Bahadur Shrestha
- School of Medical SciencesFaculty of MedicineUNSWSydneyNew South WalesAustralia
- The Kirby InstituteUNSWSydneyNew South WalesAustralia
| | - Charles Foster
- School of Medical SciencesFaculty of MedicineUNSWSydneyNew South WalesAustralia
- Serology and Virology DivisionDepartment of MicrobiologyNew South Wales Health PathologySydneyNew South WalesAustralia
| | - William Rawlinson
- School of Medical SciencesFaculty of MedicineUNSWSydneyNew South WalesAustralia
- Serology and Virology DivisionDepartment of MicrobiologyNew South Wales Health PathologySydneyNew South WalesAustralia
| | - Nicodemus Tedla
- School of Medical SciencesFaculty of MedicineUNSWSydneyNew South WalesAustralia
| | - Rowena A. Bull
- School of Medical SciencesFaculty of MedicineUNSWSydneyNew South WalesAustralia
- The Kirby InstituteUNSWSydneyNew South WalesAustralia
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Durmaz V, Köchl K, Krassnigg A, Parigger L, Hetmann M, Singh A, Nutz D, Korsunsky A, Kahler U, König C, Chang L, Krebs M, Bassetto R, Pavkov-Keller T, Resch V, Gruber K, Steinkellner G, Gruber CC. Structural bioinformatics analysis of SARS-CoV-2 variants reveals higher hACE2 receptor binding affinity for Omicron B.1.1.529 spike RBD compared to wild type reference. Sci Rep 2022; 12:14534. [PMID: 36008461 PMCID: PMC9406262 DOI: 10.1038/s41598-022-18507-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 08/08/2022] [Indexed: 01/16/2023] Open
Abstract
To date, more than 263 million people have been infected with SARS-CoV-2 during the COVID-19 pandemic. In many countries, the global spread occurred in multiple pandemic waves characterized by the emergence of new SARS-CoV-2 variants. Here we report a sequence and structural-bioinformatics analysis to estimate the effects of amino acid substitutions on the affinity of the SARS-CoV-2 spike receptor binding domain (RBD) to the human receptor hACE2. This is done through qualitative electrostatics and hydrophobicity analysis as well as molecular dynamics simulations used to develop a high-precision empirical scoring function (ESF) closely related to the linear interaction energy method and calibrated on a large set of experimental binding energies. For the latest variant of concern (VOC), B.1.1.529 Omicron, our Halo difference point cloud studies reveal the largest impact on the RBD binding interface compared to all other VOC. Moreover, according to our ESF model, Omicron achieves a much higher ACE2 binding affinity than the wild type and, in particular, the highest among all VOCs except Alpha and thus requires special attention and monitoring.
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Affiliation(s)
| | | | | | | | - Michael Hetmann
- Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria
- Austrian Centre of Industrial Biotechnology, 8010, Graz, Austria
| | - Amit Singh
- Innophore GmbH, 8010, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria
| | | | | | | | | | - Lee Chang
- AWS Diagnostic Development Initiative-Global Social Impact, Seattle, WA, 98109, USA
| | - Marius Krebs
- Amazon Web Services EMEA SARL, 80807, Muenchen, Germany
| | | | - Tea Pavkov-Keller
- Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria
| | | | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria
- Field of Excellence BioHealth-University of Graz, 8010, Graz, Austria
| | - Georg Steinkellner
- Innophore GmbH, 8010, Graz, Austria.
- Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria.
| | - Christian C Gruber
- Innophore GmbH, 8010, Graz, Austria.
- Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria.
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43
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Andeweg SP, de Gier B, Eggink D, van den Ende C, van Maarseveen N, Ali L, Vlaemynck B, Schepers R, Hahné SJM, Reusken CBEM, de Melker HE, van den Hof S, Knol MJ. Protection of COVID-19 vaccination and previous infection against Omicron BA.1, BA.2 and Delta SARS-CoV-2 infections. Nat Commun 2022; 13:4738. [PMID: 35961956 PMCID: PMC9373894 DOI: 10.1038/s41467-022-31838-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/04/2022] [Indexed: 02/05/2023] Open
Abstract
Given the emergence of the SARS-CoV-2 Omicron BA.1 and BA.2 variants and the roll-out of booster COVID-19 vaccination, evidence is needed on protection conferred by primary vaccination, booster vaccination and previous SARS-CoV-2 infection by variant. We employed a test-negative design on S-gene target failure data from community PCR testing in the Netherlands from 22 November 2021 to 31 March 2022 (n = 671,763). Previous infection, primary vaccination or both protected well against Delta infection. Protection against Omicron BA.1 infection was much lower compared to Delta. Protection was similar against Omicron BA.1 compared to BA.2 infection after previous infection, primary and booster vaccination. Higher protection was observed against all variants in individuals with both vaccination and previous infection compared with either one. Protection against all variants decreased over time since last vaccination or infection. We found that primary vaccination with current COVID-19 vaccines and previous SARS-CoV-2 infections offered low protection against Omicron BA.1 and BA.2 infection. Booster vaccination considerably increased protection against Omicron infection, but decreased rapidly after vaccination.
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Affiliation(s)
- Stijn P Andeweg
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Brechje de Gier
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Dirk Eggink
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Caroline van den Ende
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Noortje van Maarseveen
- Saltro Diagnostic Center for Primary Care, Utrecht, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Lubna Ali
- Saltro Diagnostic Center for Primary Care, Utrecht, The Netherlands
| | | | | | - Susan J M Hahné
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Chantal B E M Reusken
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Hester E de Melker
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Susan van den Hof
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Mirjam J Knol
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.
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Wilhelm A, Widera M, Grikscheit K, Toptan T, Schenk B, Pallas C, Metzler M, Kohmer N, Hoehl S, Marschalek R, Herrmann E, Helfritz FA, Wolf T, Goetsch U, Ciesek S. Limited neutralisation of the SARS-CoV-2 Omicron subvariants BA.1 and BA.2 by convalescent and vaccine serum and monoclonal antibodies. EBioMedicine 2022; 82:104158. [PMID: 35834885 DOI: 10.1101/2021.12.07.21267432] [Citation(s) in RCA: 160] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 06/23/2022] [Accepted: 06/28/2022] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND In recent months, Omicron variants of SARS-CoV-2 have become dominant in many regions of the world, and case numbers with Omicron subvariants BA.1 and BA.2 continue to increase. Due to numerous mutations in the spike protein, the efficacy of currently available vaccines, which are based on Wuhan-Hu 1 isolate of SARS-CoV-2, is reduced, leading to breakthrough infections. Efficacy of monoclonal antibody therapy is also likely impaired. METHODS In our in vitro study using A549-AT cells constitutively expressing ACE2 and TMPRSS2, we determined and compared the neutralizing capacity of vaccine-elicited sera, convalescent sera and monoclonal antibodies against authentic SARS-CoV-2 Omicron BA.1 and BA.2 compared with Delta. FINDINGS Almost no neutralisation of Omicron BA.1 and BA.2 was observed using sera from individuals vaccinated with two doses 6 months earlier, regardless of the type of vaccine taken. Shortly after the booster dose, most sera from triple BNT162b2-vaccinated individuals were able to neutralise both Omicron variants. In line with waning antibody levels three months after the booster, only weak residual neutralisation was observed for BA.1 (26%, n = 34, 0 median NT50) and BA.2 (44%, n = 34, 0 median NT50). In addition, BA.1 but not BA.2 was resistant to the neutralising monoclonal antibodies casirivimab/imdevimab, while BA.2 exhibited almost a complete evasion from the neutralisation induced by sotrovimab. INTERPRETATION Both SARS-CoV-2 Omicron subvariants BA.1 and BA.2 escape antibody-mediated neutralisation elicited by vaccination, previous infection with SARS-CoV-2, and monoclonal antibodies. Waning immunity renders the majority of tested sera obtained three months after booster vaccination negative in BA.1 and BA.2 neutralisation. Omicron subvariant specific resistance to the monoclonal antibodies casirivimab/imdevimab and sotrovimab emphasizes the importance of genotype-surveillance and guided application. FUNDING This study was supported in part by the Goethe-Corona-Fund of the Goethe University Frankfurt (M.W.) and the Federal Ministry of Education and Research (COVIDready; grant 02WRS1621C (M.W.).
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Affiliation(s)
- Alexander Wilhelm
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany.
| | - Katharina Grikscheit
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Tuna Toptan
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Barbara Schenk
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Christiane Pallas
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Melinda Metzler
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Niko Kohmer
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Sebastian Hoehl
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology, Goethe University, Frankfurt am Main, Germany
| | - Eva Herrmann
- Institute of Biostatistics and Mathematical Modelling, Goethe University Frankfurt, 60596 Frankfurt, Germany
| | - Fabian A Helfritz
- Bürgerhospital Frankfurt, Nibelungenallee 37-41, 60318 Frankfurt am Main, Germany
| | - Timo Wolf
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Udo Goetsch
- Health Protection Authority of the City of Frankfurt am Main, 60313 Frankfurt am Main, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany; German Centre for Infection Research (DZIF), partner site Frankfurt, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology, Branch Translational Medicine and Pharmacology, 60596 Frankfurt am Main, Germany.
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45
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Cao Y, Wang X, Li S, Dong Y, Liu Y, Li J, Zhao Y, Feng Y. A third high dose of inactivated COVID-19 vaccine induces higher neutralizing antibodies in humans against the Delta and Omicron variants: a Randomized, Double-Blinded Clinical Trial. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1677-1679. [PMID: 35441932 PMCID: PMC9020148 DOI: 10.1007/s11427-022-2110-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Yu Cao
- Department of Science and Technology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Xiaoli Wang
- Beijing Center for Disease Prevention and Control, Beijing, 100013, China
| | - Siqi Li
- Beijing Center for Disease Prevention and Control, Beijing, 100013, China
| | - Yuan Dong
- Department of Science and Technology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Yonghong Liu
- Beijing Center for Disease Prevention and Control, Beijing, 100013, China
| | - Jing Li
- Sinovac Biotech Co, Ltd, Beijing, Beijing, 100085, China
| | - Yanqing Zhao
- Sinovac Biotech Co, Ltd, Beijing, Beijing, 100085, China
| | - Yingmei Feng
- Department of Science and Technology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China.
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46
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Zahmatkesh S, Sillanpaa M, Rezakhani Y, Wang C. Review of concerned SARS-CoV-2 variants like Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529), as well as novel methods for reducing and inactivating SARS-CoV-2 mutants in wastewater treatment facilities. JOURNAL OF HAZARDOUS MATERIALS ADVANCES 2022; 7:100140. [PMID: 37520798 PMCID: PMC9349052 DOI: 10.1016/j.hazadv.2022.100140] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/23/2022] [Accepted: 08/03/2022] [Indexed: 12/23/2022]
Abstract
The coronavirus known as COVID-19, which causes pandemics, is causing a global epidemic at a critical stage today. Furthermore, novel mutations in the SARS-CoV-2 spike protein have been discovered in an entirely new strain, impacting the clinical and epidemiological features of COVID-19. Variants of these viruses can increase the transmission in wastewater, lead to reinfection, and reduce immunity provided by monoclonal antibodies and vaccinations. According to the research, a large quantity of viral RNA was discovered in wastewater, suggesting that wastewater can be a crucial source of epidemiological data and health hazards. The purpose of this paper is to introduce a few basic concepts regarding wastewater surveillance as a starting point for comprehending COVID-19's epidemiological aspects. Next, the observation of Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529) in wastewater is discussed in detail. Secondly, the essential information for the initial, primary, and final treating sewage in SARS-CoV-2 is introduced. Following that, a thorough examination is provided to highlight the newly developed methods for eradicating SARS-CoV-2 using a combination of solar water disinfection (SODIS) and ultraviolet radiation A (UVA (315-400 nm)), ultraviolet radiation B (UVB (280-315 nm)), and ultraviolet radiation C (UVC (100-280 nm)) processes. SARS-CoV-2 eradication requires high temperatures (above 56°C) and UVC. However, SODIS technologies are based on UVA and operate at cooler temperatures (less than 45°C). Hence, it is not appropriate for sewage treatment (or water consumption) to be conducted using SODIS methods in the current pandemic. Finally, SARS-CoV-2 may be discovered in sewage utilizing the wastewater-based epidemiology (WBE) monitoring method.
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Affiliation(s)
- Sasan Zahmatkesh
- Department of Chemical Engineering, University of Science and Technology of Mazandaran, P.O. Box 48518-78195, Behshahr, Iran
| | - Mika Sillanpaa
- Faculty of Science and Technology, School of Applied Physics, University Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- International Research Centre of Nanotechnology for Himalayan Sustainability (IRCNHS), Shoolini University, Solan, 173212, Himachal Pradesh, India
- Department of Chemical Engineering, School of Mining, Metallurgy and Chemical Engineering, University of Johannesburg, P. O. Box 17011, Doornfontein 2028, South Africa
| | - Yousof Rezakhani
- Department of Civil Engineer in g, Pardis Branch, Islamic Azad University, Pardis, Iran
| | - Chongqing Wang
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
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47
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Rajpal VR, Sharma S, Kumar A, Chand S, Joshi L, Chandra A, Babbar S, Goel S, Raina SN, Shiran B. "Is Omicron mild"? Testing this narrative with the mutational landscape of its three lineages and response to existing vaccines and therapeutic antibodies. J Med Virol 2022; 94:3521-3539. [PMID: 35355267 PMCID: PMC9088584 DOI: 10.1002/jmv.27749] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/10/2022] [Accepted: 03/28/2022] [Indexed: 11/12/2022]
Abstract
SARS-CoV-2 Omicron with its lineages BA.1, BA.2, and BA.3 has triggered a fresh wave of Covid-19 infections. Though, Omicron has, so far, produced mild symptoms, its genome contains 60 mutations including 37 in the spike protein and 15 in the receptor-binding domain. Thirteen sites conserved in previous SARS-CoV-2 variants carry mutations in Omicron. Many mutations have shown evolution under positive selection. Omicron's giant mutational leap has raised concerns as there are signs of higher virus infectivity rate, pathogenesis, reinfection, and immune evasion. Preliminary studies have reported waning of immunity after two-dose primary vaccine regime, need for the boosters, folds reduction in vaccine effectiveness and neutralizing antibodies even after boosting and significant neutralization resistance with the therapeutic monoclonal, polyclonal, and convalescent antibodies against Omicron. The narrative that "Omicron is mild," therefore, needs time to be tested with a deeper, scientific dwelling into the facts.
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Affiliation(s)
| | - Shashi Sharma
- Division of VirologyDefence Research and Development EstablishmentGwaliorMadhya PradeshIndia
| | - Avinash Kumar
- Department of BotanyVinoba Bhave UniversityHazaribagJharkhandIndia
| | - Shweta Chand
- Department of BotanyHansraj College, University of DelhiDelhiIndia
| | - Lata Joshi
- Department of BotanyHansraj College, University of DelhiDelhiIndia
| | - Atika Chandra
- Department of BotanyMaitreyi College, University of DelhiDelhiIndia
| | - Sadhna Babbar
- Department of BotanySwami Shraddhanand College, University of DelhiDelhiIndia
| | | | - Soom Nath Raina
- Department of BiotechnologyAmity Institute of Biotechnology, Amity University Uttar PradeshNoidaUttar PradeshIndia
| | - Behrouz Shiran
- Department of Plant Breeding and BiotechnologyShahrekord UniversityShahrekordIran
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48
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Lee WL, Armas F, Guarneri F, Gu X, Formenti N, Wu F, Chandra F, Parisio G, Chen H, Xiao A, Romeo C, Scali F, Tonni M, Leifels M, Chua FJD, Kwok GW, Tay JY, Pasquali P, Thompson J, Alborali GL, Alm EJ. Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater. WATER RESEARCH 2022; 221:118809. [PMID: 35841797 PMCID: PMC9250349 DOI: 10.1016/j.watres.2022.118809] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/18/2022] [Accepted: 07/01/2022] [Indexed: 05/06/2023]
Abstract
On November 26, 2021, the B.1.1.529 COVID-19 variant was classified as the Omicron variant of concern (VOC). Reports of higher transmissibility and potential immune evasion triggered flight bans and heightened health control measures across the world to stem its distribution. Wastewater-based surveillance has demonstrated to be a useful complement for clinical community-based tracking of SARS-CoV-2 variants. Using design principles of our previous assays that detect SARS-CoV-2 variants (Alpha and Delta), we developed an allele-specific RT-qPCR assay which simultaneously targets the stretch of mutations from Q493R to Q498R for quantitative detection of the Omicron variant in wastewater. We report their validation against 10-month longitudinal samples from the influent of a wastewater treatment plant in Italy. SARS-CoV-2 RNA concentrations and variant frequencies in wastewater determined using these variant assays agree with clinical cases, revealing rapid displacement of the Delta variant by the Omicron variant within three weeks. These variant trends, when mapped against vaccination rates, support clinical studies that found the rapid emergence of SARS-CoV-2 Omicron variant being associated with an infection advantage over Delta in vaccinated persons. These data reinforce the versatility, utility and accuracy of these open-sourced methods using allele-specific RT-qPCR for tracking the dynamics of variant displacement in communities through wastewater for informed public health responses.
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Affiliation(s)
- Wei Lin Lee
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Federica Armas
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Flavia Guarneri
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Xiaoqiong Gu
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Nicoletta Formenti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Fuqing Wu
- Center for Infectious Disease, Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas School of Public Health, Houston, TX, USA
| | - Franciscus Chandra
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Giovanni Parisio
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Hongjie Chen
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Amy Xiao
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, USA; Department of Biological Engineering, Massachusetts Institute of Technology, USA
| | - Claudia Romeo
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Federico Scali
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Matteo Tonni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Mats Leifels
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Feng Jun Desmond Chua
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Germaine Wc Kwok
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Joey Yr Tay
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Paolo Pasquali
- Dipartimento di Sicurezza Alimentare, Nutrizione e Sanità Pubblica Veterinaria, Istituto Superiore di Sanità, Italy
| | - Janelle Thompson
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; Asian School of the Environment, Nanyang Technological University, Singapore.
| | - Giovanni Loris Alborali
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Eric J Alm
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, USA; Department of Biological Engineering, Massachusetts Institute of Technology, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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49
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Moss P, Berenbaum F, Curigliano G, Grupper A, Berg T, Pather S. Benefit-risk evaluation of COVID-19 vaccination in special population groups of interest. Vaccine 2022; 40:4348-4360. [PMID: 35718592 PMCID: PMC9135663 DOI: 10.1016/j.vaccine.2022.05.067] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/06/2022] [Accepted: 05/22/2022] [Indexed: 11/29/2022]
Abstract
Several population groups display an increased risk of severe disease and mortality following SARS-CoV-2 infection. These include those who are immunocompromised (IC), have a cancer diagnosis, human immunodeficiency virus (HIV) infection or chronic inflammatory disease including autoimmune disease, primary immunodeficiencies, and those with kidney or liver disease. As such, improved understanding of the course of COVID-19 disease, as well as the efficacy, safety, and benefit-risk profiles of COVID-19 vaccines in these vulnerable groups is paramount in order to inform health policy makers and identify evidence-based vaccination strategies. In this review, we seek to summarize current data, including recommendations by national health authorities, on the impact and benefit-risk profiles of COVID-19 vaccination in these populations. Moving forward, although significant efforts have been made to elucidate and characterize COVID-19 disease course and vaccine responses in these groups, further larger-scale and longer-term evaluation will be instrumental to help further guide management and vaccination strategies, particularly given concerns about waning of vaccine-induced immunity and the recent surge of transmission with SARS-CoV-2 variants of concern.
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Affiliation(s)
- Paul Moss
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK; Queen Elizabeth Hospital, University Hospitals Birmingham, Birmingham B15 2TH, UK
| | - Francis Berenbaum
- Sorbonne University, INSERM, AP-HP Saint-Antoine Hospital, Paris, France
| | - Giuseppe Curigliano
- Istituto Europeo di Oncologia, IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Ayelet Grupper
- Department of Nephrology, Tel-Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Thomas Berg
- Division of Hepatology, Department of Medicine II, Leipzig University Medical Center, 04103 Leipzig, Germany
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50
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Eales O, de Oliveira Martins L, Page AJ, Wang H, Bodinier B, Tang D, Haw D, Jonnerby J, Atchison C, Ashby D, Barclay W, Taylor G, Cooke G, Ward H, Darzi A, Riley S, Elliott P, Donnelly CA, Chadeau-Hyam M. Dynamics of competing SARS-CoV-2 variants during the Omicron epidemic in England. Nat Commun 2022; 13:4375. [PMID: 35902613 PMCID: PMC9330949 DOI: 10.1038/s41467-022-32096-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/14/2022] [Indexed: 12/15/2022] Open
Abstract
The SARS-CoV-2 pandemic has been characterised by the regular emergence of genomic variants. With natural and vaccine-induced population immunity at high levels, evolutionary pressure favours variants better able to evade SARS-CoV-2 neutralising antibodies. The Omicron variant (first detected in November 2021) exhibited a high degree of immune evasion, leading to increased infection rates worldwide. However, estimates of the magnitude of this Omicron wave have often relied on routine testing data, which are prone to several biases. Using data from the REal-time Assessment of Community Transmission-1 (REACT-1) study, a series of cross-sectional surveys assessing prevalence of SARS-CoV-2 infection in England, we estimated the dynamics of England's Omicron wave (from 9 September 2021 to 1 March 2022). We estimate an initial peak in national Omicron prevalence of 6.89% (5.34%, 10.61%) during January 2022, followed by a resurgence in SARS-CoV-2 infections as the more transmissible Omicron sub-lineage, BA.2 replaced BA.1 and BA.1.1. Assuming the emergence of further distinct variants, intermittent epidemics of similar magnitudes may become the 'new normal'.
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Affiliation(s)
- Oliver Eales
- School of Public Health, Imperial College London, London, UK.
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, Imperial College London, London, UK.
| | | | | | - Haowei Wang
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, Imperial College London, London, UK
| | - Barbara Bodinier
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - David Tang
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - David Haw
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, Imperial College London, London, UK
| | - Jakob Jonnerby
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, Imperial College London, London, UK
| | | | - Deborah Ashby
- School of Public Health, Imperial College London, London, UK
| | - Wendy Barclay
- Department of Infectious Disease, Imperial College London, London, UK
| | - Graham Taylor
- Department of Infectious Disease, Imperial College London, London, UK
| | - Graham Cooke
- Department of Infectious Disease, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK
| | - Helen Ward
- School of Public Health, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK
| | - Ara Darzi
- Imperial College Healthcare NHS Trust, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK
- Institute of Global Health Innovation, Imperial College London, London, UK
| | - Steven Riley
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, Imperial College London, London, UK
| | - Paul Elliott
- School of Public Health, Imperial College London, London, UK.
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, Imperial College London, London, UK.
- Imperial College Healthcare NHS Trust, London, UK.
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK.
- Health Data Research (HDR) UK, Imperial College London, London, UK.
- UK Dementia Research Institute Centre at Imperial, Imperial College London, London, UK.
| | - Christl A Donnelly
- School of Public Health, Imperial College London, London, UK.
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, Imperial College London, London, UK.
- Department of Statistics, University of Oxford, Oxford, UK.
| | - Marc Chadeau-Hyam
- School of Public Health, Imperial College London, London, UK.
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK.
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