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Aden D, Zaheer S. Investigating the FLiRT variants of COVID-19: Is it an emerging concern? Pathol Res Pract 2024; 262:155542. [PMID: 39178510 DOI: 10.1016/j.prp.2024.155542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 08/02/2024] [Accepted: 08/12/2024] [Indexed: 08/26/2024]
Abstract
The ongoing COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to multiple waves of infections globally. As the virus continues to evolve, new variants have emerged, some with concerning changes in transmissibility and virulence. Among these variants, the "FLiRT Variants" have recently gained attention due to their potential to alter the dynamics of transmission and disease severity. According to the Infectious Disease Society of America, the nickname 'FLiRT' is based on the technical names for their mutations. The FLiRT variants, particularly KP.2, seem to exhibit heightened transmissibility in comparison to earlier Omicron sub-variants. Additionally, they demonstrate a capacity to evade immunity conferred by prior infection and vaccines, although the full extent of this evasion is still being investigated. In this article, we review the characteristics of the FLiRT variants, including their genetic mutations, epidemiological features, potential impact on public health measures, and implications for vaccine efficacy. We also discuss strategies for surveillance, prevention, and mitigation efforts to control the spread of this variant and mitigate its impact on global health.
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Affiliation(s)
- Durre Aden
- Department of Pathology, HIMSR, Jamia Hamdard, New Delhi, India
| | - Sufian Zaheer
- Department of Pathology, VMMC and Safdarjang Hospital, New Delhi, India.
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2
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D'Aoust PM, Hegazy N, Ramsay NT, Yang MI, Dhiyebi HA, Edwards E, Servos MR, Ybazeta G, Habash M, Goodridge L, Poon A, Arts E, Brown RS, Payne SJ, Kirkwood A, Simmons D, Desaulniers JP, Ormeci B, Kyle C, Bulir D, Charles T, McKay RM, Gilbride K, Oswald C, Peng H, Pileggi V, Wang ML, Tong A, Orellano D, DeGroot CT, Delatolla R. SARS-CoV-2 viral titer measurements in Ontario, Canada wastewaters throughout the COVID-19 pandemic. Sci Data 2024; 11:656. [PMID: 38906875 PMCID: PMC11192951 DOI: 10.1038/s41597-024-03414-w] [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: 03/14/2024] [Accepted: 05/23/2024] [Indexed: 06/23/2024] Open
Abstract
During the COVID-19 pandemic, the Province of Ontario, Canada, launched a wastewater surveillance program to monitor SARS-CoV-2, inspired by the early work and successful forecasts of COVID-19 waves in the city of Ottawa, Ontario. This manuscript presents a dataset from January 1, 2021, to March 31, 2023, with RT-qPCR results for SARS-CoV-2 genes and PMMoV from 107 sites across all 34 public health units in Ontario, covering 72% of the province's and 26.2% of Canada's population. Sampling occurred 2-7 times weekly, including geographical coordinates, serviced populations, physico-chemical water characteristics, and flowrates. In doing so, this manuscript ensures data availability and metadata preservation to support future research and epidemic preparedness through detailed analyses and modeling. The dataset has been crucial for public health in tracking disease locally, especially with the rise of the Omicron variant and the decline in clinical testing, highlighting wastewater-based surveillance's role in estimating disease incidence in Ontario.
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Affiliation(s)
| | | | | | | | | | | | | | - Gustavo Ybazeta
- Health Sciences North Research Institute, Sudbury, ON, Canada
| | | | | | - Art Poon
- Western University, London, ON, Canada
| | - Eric Arts
- Western University, London, ON, Canada
| | | | | | | | | | | | | | | | | | | | | | | | - Claire Oswald
- Toronto Metropolitan University, Toronto, ON, Canada
| | - Hui Peng
- University of Toronto, Toronto, ON, Canada
| | - Vince Pileggi
- Ontario Ministry of the Environment, Conservation and Parks, Toronto, ON, Canada
| | - Menglu L Wang
- Toronto Metropolitan University, Toronto, ON, Canada
| | - Arthur Tong
- Toronto Metropolitan University, Toronto, ON, Canada
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3
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Olorunfemi AB, Suliman SA, Tran TT, Ayorinde B, Fowora MA, Iwalokun BA, Olowe OA, Opaleye OO, Osman M, Salako BL, Adegbola R, Thomas BN, Pallerla SR, Velavan TP, Ojurongbe O. Whole genome sequencing and phylogenetic analysis of SARS-CoV-2 strains isolated during the COVID-19 pandemic in Nigeria. IJID REGIONS 2024; 10:174-178. [PMID: 38322246 PMCID: PMC10845906 DOI: 10.1016/j.ijregi.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/08/2024]
Abstract
Objectives The emergence and spread of SARS-CoV-2 have stimulated ongoing research into the virus transmission dynamics, circulating variants, and potential mutations. This study was conducted to understand the genomic dynamics of the epidemic in Nigeria. Design Whole genome sequencing was conducted on SARS-CoV-2 samples collected during the first and second outbreaks using the Oxford Nanopore MinION sequencing platform. Phylogenetic analysis was conducted, and genomes were grouped into different pangolin lineages. Results The study revealed four circulating SARS-CoV-2 variants. The Alpha (B.1.1.7) variant was the most prevalent (32.7%), followed by Beta (B.1 B.1.1, L.3, and B.1.1.318) (30.8%), Eta (B.1.525) (28.9%), and Delta (B.1.617, AY.1, AY.109, and AY.36) (7.7%). Phylogenetic analysis revealed three clusters with four Nextstrain clades (20I, 20B, 21D, and 21J). The Alpha lineages (B.1.1.7) clustered with references from Italy. The Beta lineages (Clade 20B) (B.11, B.11318, and L3) and sub-lineage B.11 were distinct. Sub-lineage B.11318 is clustered with references from the USA, whereas sub-lineage L3 is clustered with references from Russia, the Philippines, Australia, and Japan. The 21D and 21J, belonging to two Pango lineages, Eta (B.1525) and Delta (B.1.617 and AY.109), showed high genetic similarity. Conclusion The phylogenetic relatedness of the lineages suggests multiple virus introduction, which could be a source of more virulent, locally adapted variants.
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Affiliation(s)
- Adedolapo B. Olorunfemi
- Center for Emerging and Re-emerging Infectious Diseases, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | | | - Tung T. Tran
- Vietnamese-German Center for Medical Research (VG-CARE), Hanoi, Vietnam
| | - Babatunde Ayorinde
- Molecular Biology & Biotechnology Department, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
- Central Research Laboratory, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Muinah A. Fowora
- Molecular Biology & Biotechnology Department, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
- Central Research Laboratory, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Bamidele A. Iwalokun
- Molecular Biology & Biotechnology Department, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
- Central Research Laboratory, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Olugbenga A. Olowe
- Center for Emerging and Re-emerging Infectious Diseases, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Oluyinka O. Opaleye
- Center for Emerging and Re-emerging Infectious Diseases, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Mohamed Osman
- Institute of Endemic Diseases, University of Khartoum, Sudan
- York Biomedical Research Institute, Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Babatunde L. Salako
- Molecular Biology & Biotechnology Department, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
- Central Research Laboratory, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Richard Adegbola
- Molecular Biology & Biotechnology Department, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
- Central Research Laboratory, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Bolaji N. Thomas
- Department of Biomedical Sciences, College of Health Sciences and Technology, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Srinivas Reddy Pallerla
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Universität Tübingen, Germany
| | - Thirumalaisamy P. Velavan
- Vietnamese-German Center for Medical Research (VG-CARE), Hanoi, Vietnam
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Universität Tübingen, Germany
| | - Olusola Ojurongbe
- Center for Emerging and Re-emerging Infectious Diseases, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
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Yin ZJ, Xiao H, McDonald S, Brusic V, Qiu TY. Dynamically adjustable SVEIR(MH) model of multiwave epidemics: Estimating the effects of public health measures against COVID-19. J Med Virol 2023; 95:e29301. [PMID: 38087460 DOI: 10.1002/jmv.29301] [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: 07/27/2023] [Revised: 10/16/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023]
Abstract
The COVID-19 pandemic was characterized by multiple subsequent, overlapping outbreaks, as well as extremely rapid changes in viral genomes. The information about local epidemics spread and the epidemic control measures was shared on a daily basis (number of cases and deaths) via centralized repositories. The vaccines were developed within the first year of the pandemic. New modes of monitoring and sharing of epidemic data were implemented using Internet resources. We modified the basic SEIR compartmental model to include public health measures, multiwave scenarios, and the variation of viral infectivity and transmissibility reflected by the basic reproduction number R0 of emerging viral variants. SVEIR(MH) model considers the capacity of the medical system, lockdowns, vaccination, and changes in viral reproduction rate on the epidemic spread. The developed model uses daily infection reports for assessing the epidemic dynamics, and daily changes of mobility data from mobile phone networks to assess the lockdown effectiveness. This model was deployed to six European regions Baden-Württemberg (Germany), Belgium, Czechia, Lombardy (Italy), Sweden, and Switzerland for the first 2 years of the pandemic. The correlation coefficients between observed and reported infection data showed good concordance for both years of the pandemic (ρ = 0.84-0.94 for the raw data and ρ = 0.91-0.98 for smoothed 7-day averages). The results show stability across the regions and the different epidemic waves. Optimal control of epidemic waves can be achieved by dynamically adjusting epidemic control measures in real-time. SVEIR(MH) model can simulate different scenarios and inform adjustments to the public health policies to achieve the target outcomes. Because this model is highly representative of actual epidemic situations, it can be used to assess both the public health and socioeconomic effects of the public health measures within the first 7 days of the outbreak.
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Affiliation(s)
- Zuo-Jing Yin
- Institute of Clinical Science, Zhongshan Hospital; Shanghai Institute of Infectious Disease and Biosecurity; Intelligent Medicine Institute, Fudan University, Shanghai, China
| | - Han Xiao
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Stuart McDonald
- Smart Medicine Laboratory, School of Economics, University of Nottingham Ningbo China, Ningbo, China
| | - Vladimir Brusic
- Smart Medicine Laboratory, School of Economics, University of Nottingham Ningbo China, Ningbo, China
| | - Tian-Yi Qiu
- Institute of Clinical Science, Zhongshan Hospital; Shanghai Institute of Infectious Disease and Biosecurity; Intelligent Medicine Institute, Fudan University, Shanghai, China
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5
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Totolian AA, Smirnov VS, Krasnov AA, Ramsay ES, Dedkov VG, Popova AY. COVID-19 Incidence Proportion as a Function of Regional Testing Strategy, Vaccination Coverage, and Vaccine Type. Viruses 2023; 15:2181. [PMID: 38005859 PMCID: PMC10675075 DOI: 10.3390/v15112181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
Introduction: The COVID-19 pandemic has become a serious challenge for humanity almost everywhere globally. Despite active vaccination around the world, the incidence proportion in different countries varies significantly as of May 2022. The reason may be a combination of demographic, immunological, and epidemiological factors. The purpose of this study was to analyze possible relationships between COVID-19 incidence proportion in the population and the types of SARS-CoV-2 vaccines used in different countries globally, taking into account demographic and epidemiological factors. Materials and methods: An initial database was created of demographic and immunoepidemiological information about the COVID-19 situation in 104 countries collected from published official sources and repository data. The baseline included, for each country, population size and density; SARS-CoV-2 testing coverage; vaccination coverage; incidence proportion; and a list of vaccines that were used, including their relative share among all vaccinations. Subsequently, the initial data set was stratified by population and vaccination coverage. The final data set was subjected to statistical processing both in general and taking into account population testing coverage. Results: After formation of the final data set (including 53 countries), it turned out that reported COVID-19 case numbers correlated most strongly with testing coverage and the proportions of vaccine types used, specifically, mRNA (V1); vector (V2); peptide/protein (V3); and whole-virion/inactivated (V4). Due to the fact that an inverse correlation was found between 'reported COVID-19 case numbers' with V2, V3, and V4, these three vaccine types were also combined into one analytic group, 'non-mRNA group' vaccines (Vnmg). When the relationship between vaccine type and incidence proportion was examined, minimum incidence proportion was noted at V1:Vnmg ratios (%:%) from 0:100 to 30:70. Maximum incidence proportion was seen with V1:Vnmg from 80:20 to 100:0. On the other hand, we have shown that the number of reported COVID-19 cases in different countries largely depends on testing coverage. To offset this factor, countries with low and extremely high levels of testing were excluded from the data set; it was then confirmed that the largest number of reported COVID-19 cases occurred in countries with a dominance of V1 vaccines. The fewest reported cases were seen in countries with a dominance of Vnmg vaccines. Conclusion: In this paper, we have shown for the first time that the level of reported COVID-19 incidence proportion depends not only on SARS-CoV-2 testing and vaccination coverage, which is quite logical, but probably also on the vaccine types used. With the same vaccination level and testing coverage, those countries that predominantly use vector and whole-virion vaccines feature incidence proportion that is significantly lower than countries that predominantly use mRNA vaccines.
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Affiliation(s)
- Areg A. Totolian
- Saint Petersburg Pasteur Institute, 197101 St. Petersburg, Russia; (A.A.T.); (V.S.S.); (A.A.K.); (E.S.R.)
| | - Viacheslav S. Smirnov
- Saint Petersburg Pasteur Institute, 197101 St. Petersburg, Russia; (A.A.T.); (V.S.S.); (A.A.K.); (E.S.R.)
| | - Alexei A. Krasnov
- Saint Petersburg Pasteur Institute, 197101 St. Petersburg, Russia; (A.A.T.); (V.S.S.); (A.A.K.); (E.S.R.)
| | - Edward S. Ramsay
- Saint Petersburg Pasteur Institute, 197101 St. Petersburg, Russia; (A.A.T.); (V.S.S.); (A.A.K.); (E.S.R.)
| | - Vladimir G. Dedkov
- Saint Petersburg Pasteur Institute, 197101 St. Petersburg, Russia; (A.A.T.); (V.S.S.); (A.A.K.); (E.S.R.)
| | - Anna Y. Popova
- Federal Service for Supervision of Consumer Rights Protection and Human Welfare, 127994 Moscow, Russia;
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Chala B, Tilaye T, Waktole G. Re-Emerging COVID-19: Controversy of Its Zoonotic Origin, Risks of Severity of Reinfection and Management. Int J Gen Med 2023; 16:4307-4319. [PMID: 37753439 PMCID: PMC10518360 DOI: 10.2147/ijgm.s419789] [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: 05/21/2023] [Accepted: 08/19/2023] [Indexed: 09/28/2023] Open
Abstract
The re-emergence of COVID-19 has sparked controversy around its zoonotic origin, management strategies, risks posed by the virus, and the severity of reinfection. While it is widely accepted that the virus originated from animals, the exact source and transmission pathway remain unclear. This has led to debates regarding the regulation of wildlife markets and trade, as well as the need for more robust surveillance and monitoring systems. Hence, the objective of this review is to provide a brief overview of the disease's biology, preventative strategies, risk factors, degree of reinfection, and epidemiological profile. It offers a thorough examination of the disease's root cause, potential zoonotic transmission, and the most recent preventive measures, like vaccines. In terms of management, there is ongoing debate about the most effective strategies to mitigate the spread of the virus. While public health measures such as social distancing and mask-wearing have been widely implemented, there are differing opinions on the effectiveness of lockdowns and restrictions on public movement. The risks posed by COVID-19 are also a topic of debate, with some arguing that the virus is relatively low-risk for the majority of the population while others highlight the potential for severe illness, particularly among vulnerable populations such as the elderly or those with underlying health conditions. Finally, the possibility of reinfection has raised concerns about the longevity of immunity following infection or vaccination. While some studies have suggested that reinfection may be possible and potentially more severe, the overall risk remains uncertain and further research is needed to fully understand the implications of reinfection.
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Affiliation(s)
- Bayissa Chala
- Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
| | - Tigist Tilaye
- Olanchiti Hospital, Oromia Health Bureau, Oromia Regional State, Ethiopia
| | - Gemechis Waktole
- Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
- Department of Biotechnology, College of Natural and Computational Science, Dambi Dollo University, Dambi Dollo, Ethiopia
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7
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Khalid K, Poh CL. The development of DNA vaccines against SARS-CoV-2. Adv Med Sci 2023; 68:213-226. [PMID: 37364379 PMCID: PMC10290423 DOI: 10.1016/j.advms.2023.05.003] [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: 01/20/2023] [Revised: 04/07/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND The COVID-19 pandemic exerted significant impacts on public health and global economy. Research efforts to develop vaccines at warp speed against SARS-CoV-2 led to novel mRNA, viral vectored, and inactivated vaccines being administered. The current COVID-19 vaccines incorporate the full S protein of the SARS-CoV-2 Wuhan strain but rapidly emerging variants of concern (VOCs) have led to significant reductions in protective efficacies. There is an urgent need to develop next-generation vaccines which could effectively prevent COVID-19. METHODS PubMed and Google Scholar were systematically reviewed for peer-reviewed papers up to January 2023. RESULTS A promising solution to the problem of emerging variants is a DNA vaccine platform since it can be easily modified. Besides expressing whole protein antigens, DNA vaccines can also be constructed to include specific nucleotide genes encoding highly conserved and immunogenic epitopes from the S protein as well as from other structural/non-structural proteins to develop effective vaccines against VOCs. DNA vaccines are associated with low transfection efficiencies which could be enhanced by chemical, genetic, and molecular adjuvants as well as delivery systems. CONCLUSIONS The DNA vaccine platform offers a promising solution to the design of effective vaccines. The challenge of limited immunogenicity in humans might be solved through the use of genetic modifications such as the addition of nuclear localization signal (NLS) peptide gene, strong promoters, MARs, introns, TLR agonists, CD40L, and the development of appropriate delivery systems utilizing nanoparticles to increase uptake by APCs in enhancing the induction of potent immune responses.
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Affiliation(s)
- Kanwal Khalid
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, Malaysia
| | - Chit Laa Poh
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, Malaysia.
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8
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Liu H, Aviszus K, Zelarney P, Liao SY, Gerber AN, Make B, Wechsler ME, Marrack P, Reinhardt RL. Vaccine-elicited B- and T-cell immunity to SARS-CoV-2 is impaired in chronic lung disease patients. ERJ Open Res 2023; 9:00400-2023. [PMID: 37583809 PMCID: PMC10423317 DOI: 10.1183/23120541.00400-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/24/2023] [Indexed: 08/17/2023] Open
Abstract
Background While vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) provides significant protection from coronavirus disease 2019, the protection afforded to individuals with chronic lung disease is less well established. This study seeks to understand how chronic lung disease impacts SARS-CoV-2 vaccine-elicited immunity. Methods Deep immune phenotyping of humoral and cell-mediated responses to the SARS-CoV-2 vaccine was performed in patients with asthma, COPD and interstitial lung disease (ILD) compared to healthy controls. Results 48% of vaccinated patients with chronic lung diseases had reduced antibody titres to the SARS-CoV-2 vaccine antigen relative to healthy controls. Vaccine antibody titres were significantly reduced among asthma (p<0.035), COPD (p<0.022) and a subset of ILD patients as early as 3-4 months after vaccination, correlating with decreased vaccine-specific memory B-cells in circulation. Vaccine-specific memory T-cells were significantly reduced in patients with asthma (CD8+ p<0.004; CD4+ p<0.023) and COPD (CD8+ p<0.008) compared to healthy controls. Impaired T-cell responsiveness was also observed in a subset of ILD patients (CD8+ 21.4%; CD4+ 42.9%). Additional heterogeneity between healthy and disease cohorts was observed among bulk and vaccine-specific follicular T-helper cells. Conclusions Deep immune phenotyping of the SARS-CoV-2 vaccine response revealed the complex nature of vaccine-elicited immunity and highlights the need for more personalised vaccination schemes in patients with underlying lung conditions.
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Affiliation(s)
- Haolin Liu
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, USA
| | - Katja Aviszus
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, USA
| | | | - Shu-Yi Liao
- Department of Medicine, National Jewish Health, Denver, CO, USA
- Division of Environmental and Occupational Health Sciences, National Jewish Health, Denver, CO, USA
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Anthony N. Gerber
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, USA
- Department of Medicine, National Jewish Health, Denver, CO, USA
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO, USA
| | - Barry Make
- Department of Medicine, National Jewish Health, Denver, CO, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO, USA
| | - Michael E. Wechsler
- Department of Medicine, National Jewish Health, Denver, CO, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO, USA
| | - Philippa Marrack
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - R. Lee Reinhardt
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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Chen H, Zhang X, Li J, Xu Z, Luo Y, Chai R, Luo R, Bian Y, Liu Y. Discovering Traditional Chinese Medicine (TCM) Formulas for Complex Diseases Based on a Combination of Reverse Systematic Pharmacology and TCM Meridian Tropism Theory: Taking COVID-19 as an Example. ACS OMEGA 2023; 8:26871-26881. [PMID: 37546617 PMCID: PMC10398703 DOI: 10.1021/acsomega.3c01489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/06/2023] [Indexed: 08/08/2023]
Abstract
OBJECTIVE Infections and death have been a part of our daily lives since the COVID-2019 pandemic outbreak in 2019, and the societal and economic consequences have lingered for an unanticipated duration. Novel and effective treatments are still desperately needed around the world to combat the infection. Here, we discovered a novel traditional Chinese medicine formula (TCMF) to potentially combat COVID-19 through reverse systematic pharmacology (disease → targets → TCMF → disease). METHODS Combining Integrative network pharmacology and the traditional Chinese medicine (TCM) theory, a TCMF for COVID-19 was identified. In silico physiological interactions between herbs and disease hub targets were validated by molecular docking and dynamics simulation. RESULTS Based on disease-related gene/pathway targets and a combination of reverse pharmacology and TCM meridian tropism theory, a COVID-19-associated herb database was constructed. A new TCMF, including Gancao, Baitouweng, Congbai, and Diyu (GBCD), was discovered for anti-COVID-19 therapy. The KEGG and GO analyses of 49 intersecting genes suggested that GBCD could combat COVID-19 through antiviral, antiinflammation, immunoregulation, and cytoprotection activities. Moreover, these possible effects were validated through docking and MD simulation. CONCLUSIONS To the best of our knowledge, this study is the first to combine reverse pharmacology and meridian tropism theories for TCMF development, and a novel herbal combination, GBCD, was discovered for anti-COVID-19 therapy.
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Affiliation(s)
- Hongbo Chen
- School
of Nursing, Tianjin University of Traditional
Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai
District, Tianjin 301617, P. R. China
| | - Xiaohong Zhang
- School
of Nursing, Tianjin University of Traditional
Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai
District, Tianjin 301617, P. R. China
| | - Jiaying Li
- School
of Integrative Medicine, Tianjin University
of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai
District, Tianjin 301617, P. R. China
| | - Zhe Xu
- School
of Integrative Medicine, Tianjin University
of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai
District, Tianjin 301617, P. R. China
| | - Yiwei Luo
- School
of Nursing, Tianjin University of Traditional
Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai
District, Tianjin 301617, P. R. China
| | - Rundong Chai
- School
of Integrative Medicine, Tianjin University
of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai
District, Tianjin 301617, P. R. China
| | - Ruzhen Luo
- School
of Nursing, Tianjin University of Traditional
Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai
District, Tianjin 301617, P. R. China
| | - Yuhong Bian
- School
of Integrative Medicine, Tianjin University
of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai
District, Tianjin 301617, P. R. China
| | - Yanhui Liu
- School
of Nursing, Tianjin University of Traditional
Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai
District, Tianjin 301617, P. R. China
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10
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Beitari S, Duque D, Bavananthasivam J, Hewitt M, Sandhu JK, Hadžisejdić I, Tran A. Cross protection to SARS-CoV-2 variants in hamsters with naturally-acquired immunity. Virol J 2023; 20:167. [PMID: 37507719 PMCID: PMC10386765 DOI: 10.1186/s12985-023-02136-6] [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: 06/08/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Since SARS-CoV-2 was first reported in late 2019, multiple variations of the original virus have emerged. Each variant harbors accumulations of mutations, particularly within the spike glycoprotein, that are associated with increased viral transmissibility and escape immunity. The different mutations in the spike protein of different variants shape the subsequent antibody and T cell responses, such that exposure to different spike proteins can result in reduced or enhanced responses to heterologous variants further down the line. Globally, people have been exposed and re-exposed to multiple variations of the Ancestral strain, including the five variants of concerns. Studies have shown that the protective immune response of an individual is influenced by which strain or combination of strains they are exposed to. The initial exposure to a specific strain may also shape their subsequent immune patterns and response to later infections with a heterologous virus. Most immunological observations were carried out early during the pandemic when the Ancestral strain was circulating. However, SARS-CoV-2 variants exhibit varying patterns of disease severity, waning immunity, immune evasion and sensitivity to therapeutics. Here we investigated the cross-protection in hamsters previously infected with a variant of concern (VOC) and subsequently re-infected with a heterologous variant. We also determined if cross-protection and immunity were dependent on the specific virus to which the hamster was first exposed. We further profiled the host cytokine response induced by each SARS-CoV-2 variants as well as subsequent to re-infection. A comparative analysis of the three VOCs revealed that Alpha variant was the most pathogenic VOC to emerge. We showed that naturally acquired immunity protected hamsters from subsequent re-infection with heterologous SARS-CoV-2 variant, regardless which variant the animal was first exposed to. Our study supports observations that heterologous infection of different SARS-CoV-2 variants do not exacerbate disease in subsequent re-infections. The continual emergence of new SARS-CoV-2 variants mandates a better understanding of cross-protection and immune imprinting in infected individuals. Such information is essential to guide vaccine strategy and public policy to emerging SARS-CoV-2 VOCs and future novel pandemic coronaviruses.
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Affiliation(s)
- Saina Beitari
- Infectious Diseases, Human Health Therapeutics Research Centre, National Research Council Canada, ON, Ottawa, Canada
| | - Diana Duque
- Infectious Diseases, Human Health Therapeutics Research Centre, National Research Council Canada, ON, Ottawa, Canada
| | - Jegarubee Bavananthasivam
- Infectious Diseases, Human Health Therapeutics Research Centre, National Research Council Canada, ON, Ottawa, Canada
| | - Melissa Hewitt
- Preclinical Imaging, Human Health Therapeutics Research Centre, National Research Council Canada, ON, Ottawa, Canada
| | - Jagdeep K Sandhu
- Preclinical Imaging, Human Health Therapeutics Research Centre, National Research Council Canada, ON, Ottawa, Canada
| | - Ita Hadžisejdić
- Clinical Department of Pathology and Cytology, University of Rijeka, Rijeka, Croatia
| | - Anh Tran
- Infectious Diseases, Human Health Therapeutics Research Centre, National Research Council Canada, ON, Ottawa, Canada.
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11
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Khalid K, Poh CL. The Promising Potential of Reverse Vaccinology-Based Next-Generation Vaccine Development over Conventional Vaccines against Antibiotic-Resistant Bacteria. Vaccines (Basel) 2023; 11:1264. [PMID: 37515079 PMCID: PMC10385262 DOI: 10.3390/vaccines11071264] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
The clinical use of antibiotics has led to the emergence of multidrug-resistant (MDR) bacteria, leading to the current antibiotic resistance crisis. To address this issue, next-generation vaccines are being developed to prevent antimicrobial resistance caused by MDR bacteria. Traditional vaccine platforms, such as inactivated vaccines (IVs) and live attenuated vaccines (LAVs), were effective in preventing bacterial infections. However, they have shown reduced efficacy against emerging antibiotic-resistant bacteria, including MDR M. tuberculosis. Additionally, the large-scale production of LAVs and IVs requires the growth of live pathogenic microorganisms. A more promising approach for the accelerated development of vaccines against antibiotic-resistant bacteria involves the use of in silico immunoinformatics techniques and reverse vaccinology. The bioinformatics approach can identify highly conserved antigenic targets capable of providing broader protection against emerging drug-resistant bacteria. Multi-epitope vaccines, such as recombinant protein-, DNA-, or mRNA-based vaccines, which incorporate several antigenic targets, offer the potential for accelerated development timelines. This review evaluates the potential of next-generation vaccine development based on the reverse vaccinology approach and highlights the development of safe and immunogenic vaccines through relevant examples from successful preclinical and clinical studies.
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Affiliation(s)
- Kanwal Khalid
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, Subang Jaya 47500, Malaysia
| | - Chit Laa Poh
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, Subang Jaya 47500, Malaysia
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12
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Marchand G, Masoud AT, Grover S, King A, Brazil G, Ulibarri H, Parise J, Arroyo A, Coriell C, Goetz S, Moir C, Govindan M, Moberly A, Proctor A, Sainz K, Blumrick R. Maternal and neonatal outcomes of COVID-19 vaccination during pregnancy, a systematic review and meta-analysis. NPJ Vaccines 2023; 8:103. [PMID: 37454153 PMCID: PMC10349851 DOI: 10.1038/s41541-023-00698-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 06/27/2023] [Indexed: 07/18/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is associated with increased pregnancy complications. Despite effective vaccination strategies for the general population, the evidence on the safety and efficacy of Coronavirus disease 2019 (COVID-19) vaccinations in pregnancy is limited due to a lack of well-powered studies. The present study compares the maternal, neonatal, and immunological outcomes between vaccinated pregnant and unvaccinated pregnant women using a systematic review and meta-analysis approach. We included 37 studies with a total of 141,107 pregnant women (36.8% vaccinated) spread across all outcomes. Our evidence indicates a higher rate of cesarean section in the 1898 vaccinated pregnant women compared to the 6180 women who did not receive vaccination (OR = 1.20, CI = (1.05, 1.38), P = 0.007, I2 = 45%). Regarding immunological outcomes, the risk of SARS-CoV-2 infection during pregnancy or postpartum was significantly reduced in 6820 vaccinated pregnant women compared to 17,010 unvaccinated pregnant women (OR = 0.25, CI = 0.13-0.48, P < 0.0001, I2 = 61%), as evident from qualitative assessment indicating significantly higher postpartum antibody titers compared to that observed in both unvaccinated mothers and mothers who have recently recovered from a SARS-CoV-2 infection. Our analysis represents high quality evidence showing that COVID-19 vaccination effectively raises antibody titers against SARS-CoV-2. This may confer protection against infection during pregnancy and the postpartum period. In addition to being protective against SARS-CoV-2, the vaccine was associated with decreased odds of preterm delivery. Furthermore, COVID-19 vaccination may also be associated with higher odds of cesarean section.
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Affiliation(s)
- Greg Marchand
- Marchand Institute for Minimally Invasive Surgery, Mesa, AZ, USA.
| | - Ahmed Taher Masoud
- Marchand Institute for Minimally Invasive Surgery, Mesa, AZ, USA
- Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Sandeep Grover
- Center for Human Genetics, Universitatsklinikum Giessen und Marburg, Marburg, Germany
| | - Alexa King
- Marchand Institute for Minimally Invasive Surgery, Mesa, AZ, USA
| | - Giovanna Brazil
- Marchand Institute for Minimally Invasive Surgery, Mesa, AZ, USA
| | - Hollie Ulibarri
- Marchand Institute for Minimally Invasive Surgery, Mesa, AZ, USA
| | - Julia Parise
- Marchand Institute for Minimally Invasive Surgery, Mesa, AZ, USA
| | - Amanda Arroyo
- Marchand Institute for Minimally Invasive Surgery, Mesa, AZ, USA
| | | | - Sydnee Goetz
- Marchand Institute for Minimally Invasive Surgery, Mesa, AZ, USA
| | - Carmen Moir
- Marchand Institute for Minimally Invasive Surgery, Mesa, AZ, USA
| | - Malini Govindan
- Marchand Institute for Minimally Invasive Surgery, Mesa, AZ, USA
| | - Atley Moberly
- Marchand Institute for Minimally Invasive Surgery, Mesa, AZ, USA
| | - Anna Proctor
- University of Iowa, College of Public Health, Iowa City, IA, USA
| | - Katelyn Sainz
- Tucson Medical Center, Department of Pediatrics, Tucson, AZ, USA
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13
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Miteva D, Kitanova M, Batselova H, Lazova S, Chervenkov L, Peshevska-Sekulovska M, Sekulovski M, Gulinac M, Vasilev GV, Tomov L, Velikova T. The End or a New Era of Development of SARS-CoV-2 Virus: Genetic Variants Responsible for Severe COVID-19 and Clinical Efficacy of the Most Commonly Used Vaccines in Clinical Practice. Vaccines (Basel) 2023; 11:1181. [PMID: 37514997 PMCID: PMC10385722 DOI: 10.3390/vaccines11071181] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/22/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Although the chief of the World Health Organization (WHO) has declared the end of the coronavirus disease 2019 (COVID-19) as a global health emergency, the disease is still a global threat. To be able to manage such pandemics in the future, it is necessary to develop proper strategies and opportunities to protect human life. The data on the SARS-CoV-2 virus must be continuously analyzed, and the possibilities of mutation and the emergence of new, more infectious variants must be anticipated, as well as the options of using different preventive and therapeutic techniques. This is because the fast development of severe acute coronavirus 2 syndrome (SARS-CoV-2) variants of concern have posed a significant problem for COVID-19 pandemic control using the presently available vaccinations. This review summarizes data on the SARS-CoV-2 variants that are responsible for severe COVID-19 and the clinical efficacy of the most commonly used vaccines in clinical practice. The consequences after the disease (long COVID or post-COVID conditions) continue to be the subject of studies and research, and affect social and economic life worldwide.
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Affiliation(s)
- Dimitrina Miteva
- Department of Genetics, Faculty of Biology, Sofia University "St. Kliment Ohridski", 8 Dragan Tzankov str., 1164 Sofia, Bulgaria
| | - Meglena Kitanova
- Department of Genetics, Faculty of Biology, Sofia University "St. Kliment Ohridski", 8 Dragan Tzankov str., 1164 Sofia, Bulgaria
| | - Hristiana Batselova
- Department of Epidemiology and Disaster Medicine, University Hospital "Saint George", Medical University, 6000 Plovdiv, Bulgaria
| | - Snezhina Lazova
- Pediatric Department, University Hospital "N. I. Pirogov," 21 "General Eduard I. Totleben" Blvd, 1606 Sofia, Bulgaria
- Department of Healthcare, Faculty of Public Health "Prof. Tsekomir Vodenicharov, MD, DSc", Medical University of Sofia, Bialo More 8 str., 1527 Sofia, Bulgaria
| | - Lyubomir Chervenkov
- Department of Diagnostic Imaging, Medical University Plovdiv, Bul. Vasil Aprilov 15A, 4000 Plovdiv, Bulgaria
| | - Monika Peshevska-Sekulovska
- Department of Gastroenterology, University Hospital Lozenetz, 1407 Sofia, Bulgaria
- Medical Faculty, Sofia University St. Kliment Ohridski, 1407 Sofia, Bulgaria
| | - Metodija Sekulovski
- Medical Faculty, Sofia University St. Kliment Ohridski, 1407 Sofia, Bulgaria
- Department of Anesthesiology and Intensive Care, University Hospital Lozenetz, 1 Kozyak str., 1407 Sofia, Bulgaria
| | - Milena Gulinac
- Department of General and Clinical Pathology, Medical University of Plovdiv, Bul. Vasil Aprilov 15A, 4000 Plovdiv, Bulgaria
| | - Georgi V Vasilev
- Clinic of Endocrinology and Metabolic Disorders, UMHAT "Sv. Georgi", 4000 Plovdiv, Bulgaria
| | - Luchesar Tomov
- Department of Informatics, New Bulgarian University, Montevideo 21 str., 1618 Sofia, Bulgaria
| | - Tsvetelina Velikova
- Medical Faculty, Sofia University St. Kliment Ohridski, 1407 Sofia, Bulgaria
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14
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Palalay H, Vyas R, Tafuto B. Real-world effectiveness of mRNA COVID-19 vaccines in the elderly during the Delta and Omicron variants: Systematic review. World J Meta-Anal 2023; 11:167-180. [PMID: 37575964 PMCID: PMC10421623 DOI: 10.13105/wjma.v11.i5.167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/09/2023] [Accepted: 04/18/2023] [Indexed: 06/16/2023] Open
Abstract
BACKGROUND As of 31 December 2022, there were over 6.6 million coronavirus disease 2019 (COVID-19) deaths and over 651 million cases across 200 countries worldwide. Despite the increase in vaccinations and booster shots, COVID-19 cases and deaths continue to remain high. While the effectiveness of these vaccines has already been established by different manufacturers, the fact remains that these vaccines were created quickly for global emergency use, tested under controlled clinical conditions from voluntary subjects and age groups whose general characteristics may differ from the actual general population. AIM To conduct a systematic review to determine the real-world effectiveness of mRNA COVID-19 vaccines in the elderly during the predominance of Delta and Omicron variants in preventing COVID-19 related infection, hospital, intensive care unit (ICU) admission and intubation, and death. METHODS A combination of Medical Subject Headings and non-Medical Subject Headings was carried out to identify all relevant research articles that meets the inclusion and exclusion criteria from PubMed, Cochrane, CINAHL, Scopus, ProQuest, Embase, Web of Science, and Google Scholar databases, as well as qualified research studies from pre-print servers using medRxiv and Research Square, published from January 1, 2021 - December 31, 2022. RESULTS As per the inclusion and exclusion criteria, the effectiveness of Pfizer-BioNTech and Moderna vaccines were evaluated from an estimated total study population of 26,535,692 using infection, hospital, ICU admission and intubation, and death as outcome measures from studies published between 2021 and 2022, conducted in New York, Finland, Canada, Costa Rica, Qatar, Greece, and Brazil. The risk of bias was evaluated using risk of bias in nonrandomized studies of interventions (ROBINS-I) tool for cohort, case-control, and cross-sectional studies. While clinical trial data on Pfizer-BioNTech and Moderna vaccines demonstrated 94% vaccine effectiveness in the elderly, the results in this study showed that vaccine effectiveness in real-world settings is marginally lower against infection (40%-89%), hospitalization (92%), ICU admission and intubation (98%-85%), and death (77%-87%) with an indication of diminished effectiveness of vaccine over time. Furthermore, 2 doses of mRNA vaccines are inadequate and only provides interim protection. CONCLUSION Because of the natural diminishing effectiveness of the vaccine, the need for booster dose to restore its efficacy is vital. From a research perspective, the use of highly heterogeneous outcome measures inhibits the comparison, contrast, and integration of the results which makes data pooling across different studies problematic. While pharmaceutical intervention like vaccination is important to fight an epidemic, utilizing common outcome measurements or carrying out studies with minimal heterogeneity in outcome measurements, is equally crucial to better understand and respond to an international health crisis.
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Affiliation(s)
- Harvey Palalay
- Department of Health Informatics, Rutgers University, Piscataway, NJ 08854, United States
| | - Riddhi Vyas
- Department of Health Informatics, Rutgers University, Piscataway, NJ 08854, United States
| | - Barbara Tafuto
- Department of Health Informatics, Rutgers University, Piscataway, NJ 08854, United States
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15
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Jiao J, Shi L, Chen H, Wang X, Yang M, Yang J, Liu M, Sun G. Critical national response in coping with Omicron variant in China, Israel, South Africa, and the United States. Front Public Health 2023; 11:1157824. [PMID: 37361174 PMCID: PMC10288025 DOI: 10.3389/fpubh.2023.1157824] [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: 02/03/2023] [Accepted: 05/18/2023] [Indexed: 06/28/2023] Open
Abstract
Objective The aim of this study was to analyze the effectiveness of prevention and control strategies and put forward further measures according to the epidemiological characteristics of Omicron. It summarized the national response during the Omicron epidemic in four countries: China, Israel, South Africa, and the United States. Methods This study summarized prevention and control measures in China, Israel, South Africa, and the United States in their response to the Omicron epidemic, and it also evaluated the effectiveness of these measures. Results After the Omicron variant emerged, China and Israel adopted containment strategies, using the "dynamic zero" policy and country closure measures. Meanwhile, South Africa and the United States adopted mitigation strategies, which virtually abandoned social interventions and only focused on medical measures and vaccines. From the first day of reported Omicron cases to 28 February 2022, the four countries reported the following cases: China reported 9,670 new confirmed cases and no deaths, with total deaths per million of 3.21; Israel reported 2,293,415 new confirmed cases and 2,016 deaths, with total deaths per million of 1,097.21; South Africa reported 731,384 new confirmed cases and 9,509 deaths, with total deaths per million reaching 1,655.708; the United States reported 3,042,743 new confirmed cases and 1,688,851 deaths, with total deaths per million reaching 2,855.052, which was much higher than the other countries. Conclusion Based on this study, it seems that China and Israel adopted containment strategies, while South Africa and the United States adopted mitigation strategies. A rapid response is a powerful weapon against the Omicron epidemic. Vaccines alone will not get any country out of this crisis, and non-pharmacological measures should be used in addition to them. According to the SPO model, future work should consider the strengthening of emergency management capacity, adhering to public health measures, promoting vaccination, and strengthening patient care and close contact management, which are effective measures in coping with Omicron.
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Affiliation(s)
- Jun Jiao
- Department of Health Management, School of Health Management, Southern Medical University, Guangzhou, Guangdong, China
| | - Leiyu Shi
- Department of Health Policy and Management, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Haiqian Chen
- Department of Health Management, School of Health Management, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiaohan Wang
- Department of Health Management, School of Health Management, Southern Medical University, Guangzhou, Guangdong, China
| | - Manfei Yang
- Department of Health Management, School of Health Management, Southern Medical University, Guangzhou, Guangdong, China
| | - Junyan Yang
- Department of Health Management, School of Health Management, Southern Medical University, Guangzhou, Guangdong, China
| | - Meiheng Liu
- Department of Health Management, School of Health Management, Southern Medical University, Guangzhou, Guangdong, China
| | - Gang Sun
- Department of Health Management, School of Health Management, Southern Medical University, Guangzhou, Guangdong, China
- Department of Health Policy and Management, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
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16
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Bono A, Lauria A, La Monica G, Alamia F, Mingoia F, Martorana A. In Silico Design of New Dual Inhibitors of SARS-CoV-2 M PRO through Ligand- and Structure-Based Methods. Int J Mol Sci 2023; 24:ijms24098377. [PMID: 37176082 PMCID: PMC10179319 DOI: 10.3390/ijms24098377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
The viral main protease is one of the most attractive targets among all key enzymes involved in the life cycle of SARS-CoV-2. Considering its mechanism of action, both the catalytic and dimerization regions could represent crucial sites for modulating its activity. Dual-binding the SARS-CoV-2 main protease inhibitors could arrest the replication process of the virus by simultaneously preventing dimerization and proteolytic activity. To this aim, in the present work, we identified two series' of small molecules with a significant affinity for SARS-CoV-2 MPRO, by a hybrid virtual screening protocol, combining ligand- and structure-based approaches with multivariate statistical analysis. The Biotarget Predictor Tool was used to filter a large in-house structural database and select a set of benzo[b]thiophene and benzo[b]furan derivatives. ADME properties were investigated, and induced fit docking studies were performed to confirm the DRUDIT prediction. Principal component analysis and docking protocol at the SARS-CoV-2 MPRO dimerization site enable the identification of compounds 1b,c,i,l and 2i,l as promising drug molecules, showing favorable dual binding site affinity on SARS-CoV-2 MPRO.
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Affiliation(s)
- Alessia Bono
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche "STEBICEF", University of Palermo, Viale delle Scienze, Ed. 17, 90128 Palermo, Italy
| | - Antonino Lauria
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche "STEBICEF", University of Palermo, Viale delle Scienze, Ed. 17, 90128 Palermo, Italy
| | - Gabriele La Monica
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche "STEBICEF", University of Palermo, Viale delle Scienze, Ed. 17, 90128 Palermo, Italy
| | - Federica Alamia
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche "STEBICEF", University of Palermo, Viale delle Scienze, Ed. 17, 90128 Palermo, Italy
| | - Francesco Mingoia
- Istituto per lo Studio dei Materiali Nanostrutturati (ISMN), Consiglio Nazionale delle Ricerche (CNR), Via Ugo La Malfa, 153, 90146 Palermo, Italy
| | - Annamaria Martorana
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche "STEBICEF", University of Palermo, Viale delle Scienze, Ed. 17, 90128 Palermo, Italy
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17
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Liu J, Cang T, Jiang C, Li K, Liu S, Wang H, Wang M, Chen Y, Shao Y, Liu J. CpG 684: an effective adjuvant for the inactivated COVID-19 vaccine in mice. Future Virol 2023; 18:403-410. [PMID: 38051998 PMCID: PMC10241461 DOI: 10.2217/fvl-2022-0172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 04/05/2023] [Indexed: 12/07/2023]
Abstract
Aim This study used CpG 684 as adjuvant of inactivated COVID-19 vaccine to detect a humoral and cellular immune response in mice. Materials & methods We used 10 and 20 µg CpG 684 as adjuvants of an inactivated COVID-19 vaccine to immunize mice. IgG, IgG1, IgG2a, IgG2b and IgM binding antibodies were detected in serum by ELISA. The IFN-γ cytokine was detected by ELISPOT. Results CpG 684 improved spike-specific IgG and IgM subtype binding antibodies and increased the neutralizing antibody titer against prototype, Delta and Beta strains. CpG 684 also improved cellular immune response. Conclusion CpG 684 is an effective adjuvant for inactivated COVID-19 vaccine.
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Affiliation(s)
- Jiandong Liu
- Beijing Minhai Biotechnology Co. Ltd, Beijing, 102600, China
| | - Tianle Cang
- Beijing Minhai Biotechnology Co. Ltd, Beijing, 102600, China
| | - Congli Jiang
- Shenzhen Kangtai Biological Products Co., Ltd, Guangzhou, Shenzhen, 518000, China
| | - Kelei Li
- Beijing Minhai Biotechnology Co. Ltd, Beijing, 102600, China
| | - Siyuan Liu
- Beijing Minhai Biotechnology Co. Ltd, Beijing, 102600, China
| | - Haixin Wang
- Beijing Minhai Biotechnology Co. Ltd, Beijing, 102600, China
| | - Meirong Wang
- Beijing Minhai Biotechnology Co. Ltd, Beijing, 102600, China
| | - Yan Chen
- Jiangsu Taipuriu Biotechnology Co., Ltd, Taizhou Pharmaceutical City, Jiangsu, 225300, China
| | - Yan Shao
- Jiangsu Taipuriu Biotechnology Co., Ltd, Taizhou Pharmaceutical City, Jiangsu, 225300, China
| | - Jiankai Liu
- Beijing Minhai Biotechnology Co. Ltd, Beijing, 102600, China
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18
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Oubahmane M, Hdoufane I, Delaite C, Sayede A, Cherqaoui D, El Allali A. Design of Potent Inhibitors Targeting the Main Protease of SARS-CoV-2 Using QSAR Modeling, Molecular Docking, and Molecular Dynamics Simulations. Pharmaceuticals (Basel) 2023; 16:ph16040608. [PMID: 37111365 PMCID: PMC10146715 DOI: 10.3390/ph16040608] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/08/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a serious global public health threat. The evolving strains of SARS-CoV-2 have reduced the effectiveness of vaccines. Therefore, antiviral drugs against SARS-CoV-2 are urgently needed. The main protease (Mpro) of SARS-CoV-2 is an extremely potent target due to its pivotal role in virus replication and low susceptibility to mutation. In the present study, a quantitative structure-activity relationship (QSAR) study was performed to design new molecules that might have higher inhibitory activity against SARS-CoV-2 Mpro. In this context, a set of 55 dihydrophenanthrene derivatives was used to build two 2D-QSAR models using the Monte Carlo optimization method and the Genetic Algorithm Multi-Linear Regression (GA-MLR) method. From the CORAL QSAR model outputs, the promoters responsible for the increase/decrease in inhibitory activity were extracted and interpreted. The promoters responsible for an increase in activity were added to the lead compound to design new molecules. The GA-MLR QSAR model was used to ensure the inhibitory activity of the designed molecules. For further validation, the designed molecules were subjected to molecular docking analysis and molecular dynamics simulations along with an absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis. The results of this study suggest that the newly designed molecules have the potential to be developed as effective drugs against SARS-CoV-2.
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Affiliation(s)
- Mehdi Oubahmane
- Laboratory of Molecular Chemistry, Department of Chemistry, Faculty of Sciences Semlalia, BP 2390, Marrakech 40000, Morocco
| | - Ismail Hdoufane
- Laboratory of Molecular Chemistry, Department of Chemistry, Faculty of Sciences Semlalia, BP 2390, Marrakech 40000, Morocco
| | - Christelle Delaite
- Laboratoire de Photochimie et d'Ingénierie Macromoléculaires (LPIM), Ecole Nationale Supérieure de Chimie de Mulhouse, Université de Haute-Alsace, 68100 Mulhouse, France
| | - Adlane Sayede
- University Artois, CNRS, Centrale Lille, University Lille, UMR 8181, Unité de Catalyse et Chimie du Solide (UCCS), F-62300 Lens, France
| | - Driss Cherqaoui
- Laboratory of Molecular Chemistry, Department of Chemistry, Faculty of Sciences Semlalia, BP 2390, Marrakech 40000, Morocco
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir 43150, Morocco
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19
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SARS-CoV-2 Vaccines, Vaccine Development Technologies, and Significant Efforts in Vaccine Development during the Pandemic: The Lessons Learned Might Help to Fight against the Next Pandemic. Vaccines (Basel) 2023; 11:vaccines11030682. [PMID: 36992266 DOI: 10.3390/vaccines11030682] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/10/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
We are currently approaching three years since the beginning of the coronavirus disease 2019 (COVID-19) pandemic. SARS-CoV-2 has caused extensive disruptions in everyday life, public health, and the global economy. Thus far, the vaccine has worked better than expected against the virus. During the pandemic, we experienced several things, such as the virus and its pathogenesis, clinical manifestations, and treatments; emerging variants; different vaccines; and the vaccine development processes. This review describes how each vaccine has been developed and approved with the help of modern technology. We also discuss critical milestones during the vaccine development process. Several lessons were learned from different countries during the two years of vaccine research, development, clinical trials, and vaccination. The lessons learned during the vaccine development process will help to fight the next pandemic.
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20
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Felbinger N, Trudil D, Loomis L, Ascione R, Siragusa G, Haba S, Rastogi S, Mucci A, Claycomb M, Snowberger S, Luke B, Francesconi S, Tsang S. Epitope mapping of SARS-CoV-2 spike protein differentiates the antibody binding activity in vaccinated and infected individuals. FRONTIERS IN VIROLOGY 2023. [DOI: 10.3389/fviro.2023.988109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Previous studies have attempted to characterize the antibody response of individuals to the SARS-CoV-2 virus on a linear peptide level by utilizing peptide microarrays. These studies have helped to identify epitopes that have potential to be used for diagnostic tests to identify infected individuals. The immunological responses of individuals who have received the two most popular vaccines available in the US, the Moderna mRNA-1273 or the Pfizer BNT162b2 mRNA vaccines, have not been characterized. We aimed to identify linear peptides of the SARS-CoV-2 spike protein that elicited high IgG or IgA binding activity and to compare the immunoreactivity of infected individuals to those who received both doses of either vaccine by utilizing peptide microarrays. Our results revealed peptide epitopes of significant IgG binding among recently infected individuals. Some of these peptides are located near variable regions of the receptor binding domains as well as the conserved region in the c-terminal of the spike protein implicated in the high infectivity of SARS-CoV-2. Vaccinated individuals lacked a response to these distinct markers despite the overall antibody binding activity being similar.
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21
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Lim CP, Kok BH, Lim HT, Chuah C, Abdul Rahman B, Abdul Majeed AB, Wykes M, Leow CH, Leow CY. Recent trends in next generation immunoinformatics harnessed for universal coronavirus vaccine design. Pathog Glob Health 2023; 117:134-151. [PMID: 35550001 PMCID: PMC9970233 DOI: 10.1080/20477724.2022.2072456] [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] [Indexed: 01/08/2023] Open
Abstract
The ongoing pandemic of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has globally devastated public health, the economies of many countries and quality of life universally. The recent emergence of immune-escaped variants and scenario of vaccinated individuals being infected has raised the global concerns about the effectiveness of the current available vaccines in transmission control and disease prevention. Given the high rate mutation of SARS-CoV-2, an efficacious vaccine targeting against multiple variants that contains virus-specific epitopes is desperately needed. An immunoinformatics approach is gaining traction in vaccine design and development due to the significant reduction in time and cost of immunogenicity studies and increasing reliability of the generated results. It can underpin the development of novel therapeutic methods and accelerate the design and production of peptide vaccines for infectious diseases. Structural proteins, particularly spike protein (S), along with other proteins have been studied intensively as promising coronavirus vaccine targets. Numbers of promising online immunological databases, tools and web servers have widely been employed for the design and development of next generation COVID-19 vaccines. This review highlights the role of immunoinformatics in identifying immunogenic peptides as potential vaccine targets, involving databases, and prediction and characterization of epitopes which can be harnessed for designing future coronavirus vaccines.
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Affiliation(s)
- Chin Peng Lim
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Malaysia.,Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Boon Hui Kok
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Hui Ting Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Candy Chuah
- Faculty of Health Sciences, Universiti Teknologi MARA, Penang, Malaysia
| | | | | | - Michelle Wykes
- Molecular Immunology Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Chiuan Yee Leow
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Malaysia
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22
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Hamad M, AlKhamach DMH, Alsayadi LM, Sarhan SA, Saeed BQ, Sokovic M, Ben Hadda T, Soliman SSM. Alpha to Omicron (Variants of Concern): Mutation Journey, Vaccines, and Therapy. Viral Immunol 2023; 36:83-100. [PMID: 36695729 DOI: 10.1089/vim.2022.0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) initially emerged in December 2019 and has subsequently expanded globally, leading to the ongoing pandemic. The extensive spread of various SARS-CoV-2 variants possesses a serious public health threat. An extensive literature search along with deep analysis was performed to describe and evaluate the characteristics of SARS-CoV-2 variants of concern in relation to the effectiveness of the current vaccines and therapeutics. The obtained results showed that several significant mutations have evolved during the COVID-19 pandemic. The developed variants and their various structural mutations can compromise the effectiveness of several vaccines, escape the neutralizing antibodies, and limit the efficiency of available therapeutics. Furthermore, deep analysis of the available data enables the prediction of the future impact of virus mutations on the ongoing pandemic along with the selection of appropriate vaccines and therapeutics.
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Affiliation(s)
- Mohamad Hamad
- College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Dana M H AlKhamach
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | | | | | | | - Marina Sokovic
- Institute for Biological Research "Siniša Stanković," National Institute of the Republic of Serbia, University of Belgrade, Beograd, Serbia
| | - Taibi Ben Hadda
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, Oujda, Morocco
| | - Sameh S M Soliman
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
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23
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Teli D, Balar P, Patel K, Sharma A, Chavda V, Vora L. Molnupiravir: A Versatile Prodrug against SARS-CoV-2 Variants. Metabolites 2023; 13:309. [PMID: 36837928 PMCID: PMC9962121 DOI: 10.3390/metabo13020309] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
The nucleoside analog β-D-N4-hydroxycytidine is the active metabolite of the prodrug molnupiravir and is accepted as an efficient drug against COVID-19. Molnupiravir targets the RNA-dependent RNA polymerase (RdRp) enzyme, which is responsible for replicating the viral genome during the replication process of certain types of viruses. It works by disrupting the normal function of the RdRp enzyme, causing it to make mistakes during the replication of the viral genome. These mistakes can prevent the viral RNA from being transcribed, converted into a complementary DNA template, translated, or converted into a functional protein. By disrupting these crucial steps in the viral replication process, molnupiravir can effectively inhibit the replication of the virus and reduce its ability to cause disease. This review article sheds light on the impact of molnupiravir and its metabolite on SARS-CoV-2 variants of concern, such as delta, omicron, and hybrid/recombinant variants. The detailed mechanism and molecular interactions using molecular docking and dynamics have also been covered. The safety and tolerability of molnupiravir in patients with comorbidities have also been emphasized.
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Affiliation(s)
- Divya Teli
- Department of Pharmaceutical Chemistry, L. M. College of Pharmacy, Ahmedabad 380009, India
| | - Pankti Balar
- Pharmacy Department, L. M. College of Pharmacy, Ahmedabad 380009, India
| | - Kishan Patel
- Department of Chemistry, University at Buffalo, Buffalo, NY 14260, USA
| | - Anu Sharma
- Department Pharmaceutical Sciences, University of Massachusetts, Boston, MA 02125, USA
| | - Vivek Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L. M. College of Pharmacy, Ahmedabad 380008, India
| | - Lalit Vora
- School of Pharmacy, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
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24
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Liu H, Aviszus K, Zelarney P, Liao SY, Gerber AN, Make B, Wechsler ME, Marrack P, Reinhardt RL. Vaccine-elicited B and T cell immunity to SARS-CoV-2 is impaired in chronic lung disease patients. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.25.23284971. [PMID: 36747750 PMCID: PMC9901055 DOI: 10.1101/2023.01.25.23284971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The protection afforded by vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to individuals with chronic lung disease is not well established. To understand how chronic lung disease impacts SARS-CoV-2 vaccine-elicited immunity we performed deep immunophenotyping of the humoral and cell mediated SARS-CoV-2 vaccine response in an investigative cohort of vaccinated patients with diverse pulmonary conditions including asthma, chronic obstructive pulmonary disease (COPD), and interstitial lung disease (ILD). Compared to healthy controls, 48% of vaccinated patients with chronic lung diseases had reduced antibody titers to the SARS-CoV-2 vaccine antigen as early as 3-4 months after vaccination, correlating with decreased vaccine-specific memory B cells. Vaccine-specific CD4 and CD8 T cells were also significantly reduced in patients with asthma, COPD, and a subset of ILD patients compared to healthy controls. These findings reveal the complex nature of vaccine-elicited immunity in high-risk patients with chronic lung disease.
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Affiliation(s)
- Haolin Liu
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Katja Aviszus
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Pearlanne Zelarney
- Research Informatics Services, National Jewish Health, Denver, CO, 80206, USA
| | - Shu-Yi Liao
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
- Division of Environmental and Occupational Health Sciences, National Jewish Health, Denver CO, 80206, USA
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Anthony N Gerber
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, 80206, USA
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver CO, 80206, USA
| | - Barry Make
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver CO, 80206, USA
| | - Michael E Wechsler
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver CO, 80206, USA
| | - Philippa Marrack
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, 80206, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - R Lee Reinhardt
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, 80206, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
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25
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COVID-19, SARS-CoV-2 Vaccination, and Human Herpesviruses Infections. Vaccines (Basel) 2023; 11:vaccines11020232. [PMID: 36851110 PMCID: PMC9963083 DOI: 10.3390/vaccines11020232] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 01/10/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023] Open
Abstract
There are several human herpesviruses. A common characteristic of infection by these viruses is latency, by which the virus assumes a non-replicative state, subverting the attentions of the host's immune response. In immunocompetent hosts, herpesviruses are immunologically controlled, although periodic virus shedding can occur. In situations where immunological control is lost, herpesviruses can reactivate and produce clinically apparent disease. It is now becoming apparent that COVID-19 or exposure to COVID-19 vaccines can exert several effects on the immune system. The pandemic of COVID-19 shows no sign of abating, with new severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants continuing to evolve. Several COVID-19 vaccines have been developed, and much of the world's population has either experienced COVID-19 or been vaccinated against it. There are an increasing number of reports of associations between herpesvirus infections or reactivations and COVID-19 or COVID-19 vaccination. For instance, a positive cytomegalovirus serostatus may indicate a greater likelihood of severe COVID-19, and herpes simplex virus reactivation may be linked to increased mortality. Epstein-Barr virus reactivation appears to be associated with post-acute sequelae of COVID-19. Finally, herpes zoster has been reported to be associated with COVID-19 vaccination. This brief narrative review will provide several insights into associations between herpesvirus infections or reactivations and COVID-19 or SARS-CoV-2 vaccination.
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Abulsoud AI, El-Husseiny HM, El-Husseiny AA, El-Mahdy HA, Ismail A, Elkhawaga SY, Khidr EG, Fathi D, Mady EA, Najda A, Algahtani M, Theyab A, Alsharif KF, Albrakati A, Bayram R, Abdel-Daim MM, Doghish AS. Mutations in SARS-CoV-2: Insights on structure, variants, vaccines, and biomedical interventions. Biomed Pharmacother 2023; 157:113977. [PMID: 36370519 PMCID: PMC9637516 DOI: 10.1016/j.biopha.2022.113977] [Citation(s) in RCA: 67] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 10/29/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
COVID-19 is a worldwide pandemic caused by SARS-coronavirus-2 (SARS-CoV-2). Less than a year after the emergence of the Covid-19 pandemic, many vaccines have arrived on the market with innovative technologies in the field of vaccinology. Based on the use of messenger RNA (mRNA) encoding the Spike SARS-Cov-2 protein or on the use of recombinant adenovirus vectors enabling the gene encoding the Spike protein to be introduced into our cells, these strategies make it possible to envisage the vaccination in a new light with tools that are more scalable than the vaccine strategies used so far. Faced with the appearance of new variants, which will gradually take precedence over the strain at the origin of the pandemic, these new strategies will allow a much faster update of vaccines to fight against these new variants, some of which may escape neutralization by vaccine antibodies. However, only a vaccination policy based on rapid and massive vaccination of the population but requiring a supply of sufficient doses could make it possible to combat the emergence of these variants. Indeed, the greater the number of infected individuals, the faster the virus multiplies, with an increased risk of the emergence of variants in these RNA viruses. This review will discuss SARS-CoV-2 pathophysiology and evolution approaches in altered transmission platforms and emphasize the different mutations and how they influence the virus characteristics. Also, this article summarizes the common vaccines and the implication of the mutations and genetic variety of SARS-CoV-2 on the COVID-19 biomedical arbitrations.
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Affiliation(s)
- Ahmed I Abulsoud
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt; Department of Biochemistry and Biotechnology, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Hussein M El-Husseiny
- Laboratory of Veterinary Surgery, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai Cho, Fuchu-shi, Tokyo 183-8509, Japan; Department of Surgery, Anesthesiology, and Radiology, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh, Elqaliobiya 13736, Egypt.
| | - Ahmed A El-Husseiny
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt; Department of Biochemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City 11829, Cairo, Egypt
| | - Hesham A El-Mahdy
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Ahmed Ismail
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Samy Y Elkhawaga
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Emad Gamil Khidr
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Doaa Fathi
- Department of Biochemistry and Biotechnology, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Eman A Mady
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai Cho, Fuchu-shi, Tokyo 183-8509, Japan; Department of Animal Hygiene, Behavior and Management, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh, Elqaliobiya 13736, Egypt
| | - Agnieszka Najda
- Department of Vegetable Crops and Medicinal Plants University of Life Sciences, Lublin 50A Doświadczalna Street, 20-280, Lublin, Poland.
| | - Mohammad Algahtani
- Department of Laboratory & Blood Bank, Security Forces Hospital, P.O. Box 14799, Mecca 21955, Saudi Arabia
| | - Abdulrahman Theyab
- Department of Laboratory & Blood Bank, Security Forces Hospital, P.O. Box 14799, Mecca 21955, Saudi Arabia; College of Medicine, Al-Faisal University, P.O. Box 50927, Riyadh 11533, Saudi Arabia
| | - Khalaf F Alsharif
- Department of Clinical Laboratory sciences, College of Applied medical sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ashraf Albrakati
- Department of Human Anatomy, College of Medicine, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Roula Bayram
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Mohamed M Abdel-Daim
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia; Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Ahmed S Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt.
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Karuniawati A, Syam AF, Achmadsyah A, Ibrahim F, Rosa Y, Sudarmono P, Fadilah F, Rasmin M. Case series in Indonesia: B.1.617.2 (delta) variant of SARS-CoV-2 infection after a second dose of vaccine. World J Clin Cases 2022; 10:13216-13226. [PMID: 36683635 PMCID: PMC9851004 DOI: 10.12998/wjcc.v10.i36.13216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/09/2022] [Accepted: 07/31/2022] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The B.1.617.2 (delta) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first discovered in Maharashtra in late 2020 and has rapidly expanded across India and worldwide. It took only 2 mo for this variant to spread in Indonesia, making the country the new epicenter of the delta variant as of July 2021. Despite efforts made by accelerating massive rollouts of current vaccines to protect against infection, cases of fully-vaccinated people infected with the delta variant have been reported.
AIM To describe the demographic statistics and clinical presentation of the delta variant infection after the second dose of vaccine in Indonesia.
METHODS A retrospective, single-centre case series of the general consecutive population that worked or studied at Faculty of Medicine, Universitas Indonesia with confirmed Delta Variant Infection after a second dose of vaccine from 24 June and 25 June 2021. Cases were collected retrospectively based on a combination of author recall, reverse transcription-polymerase chain reaction (RT-PCR), and whole genome sequencing results from the Clinical Microbiology Laboratory, Faculty of Medicine, Universitas Indonesia.
RESULTS Between 24 June and 25 June 2021, 15 subjects were confirmed with the B.1.617.2 (delta) variant infection after a second dose of the vaccine. Fourteen subjects were vaccinated with CoronaVac (Sinovac) and one subject with ChAdOx1 nCoV-19 (Oxford-AstraZeneca). All of the subjects remained in home isolation, with fever being the most common symptom at the onset of illness (n = 10, 66.67%). The mean duration of symptoms was 7.73 d (± 5.444). The mean time that elapsed from the first positive swab to a negative RT-PCR test for SARS-CoV-2 was 17.93 d (± 6.3464). The median time that elapsed from the second dose of vaccine to the first positive swab was 87 d (interquartile range: 86-128).
CONCLUSION Although this case shows that after two doses of vaccine, subjects are still susceptible to the delta variant infection, currently available vaccines remain the most effective protection. They reduce clinical manifestations of COVID-19, decrease recovery time from the first positive swab to negative swab, and lower the probability of hospitalization and mortality rate compared to unvaccinated individuals.
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Affiliation(s)
- Anis Karuniawati
- Department of Clinical Microbiology, Faculty of Medicine, Universitas Indonesia/Cipto Mangunkusumo Jakarta Indonesia, Jakarta 10430, DKI Jaya, Indonesia
| | - Ari F Syam
- Division of Gastroenterology, Department of Internal Medicine, Faculty of Medicine, Universitas Indonesia/Cipto Mangunkusumo Jakarta Indonesia, Jakarta PUsat 10430, DKI Jaya, Indonesia
| | - Armand Achmadsyah
- Faculty of Medicine, Universits Indonesia, Jakarta Pusat 10430, DKI Jaya, Indonesia
| | - Fera Ibrahim
- Department of Clinical Microbiology, Faculty of Medicine, Universitas Indonesia/Cipto Mangunkusumo Jakarta Indonesia, Jakarta 10430, DKI Jaya, Indonesia
| | - Yulia Rosa
- Department of Clinical Microbiology, Faculty of Medicine, Universitas Indonesia/Cipto Mangunkusumo Jakarta Indonesia, Jakarta 10430, DKI Jaya, Indonesia
| | - Pratiwi Sudarmono
- Department of Clinical Microbiology, Faculty of Medicine, Universitas Indonesia/Cipto Mangunkusumo Jakarta Indonesia, Jakarta 10430, DKI Jaya, Indonesia
| | - Fadilah Fadilah
- Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Jakarta Indonesia , Faculty of Medicine, Universitas Indonesia, Jakarta 10430, DKI Jaya, Indonesia
| | - Menaldi Rasmin
- Department of Pulmonology and Respiratory Medicine, Faculty of Medicine, Universitas Indonesia/Persahabatan Hospital, Jakarta Indonesia, Jakarta Pusat 10430, DKI Jaya, Indonesia
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Kumar A, Sharma A, Tirpude NV, Padwad Y, Hallan V, Kumar S. Plant-derived immuno-adjuvants in vaccines formulation: a promising avenue for improving vaccines efficacy against SARS-CoV-2 virus. Pharmacol Rep 2022; 74:1238-1254. [PMID: 36125739 PMCID: PMC9487851 DOI: 10.1007/s43440-022-00418-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 12/13/2022]
Abstract
The SARS-CoV-2 outbreak has posed a plethora of problems for the global healthcare system and socioeconomic burden. Despite valiant efforts to contain the COVID-19 outbreak, the situation has deteriorated to the point that there are no viable preventive therapies to treat this disease. The case count has skyrocketed globally due to the newly evolved variants. Despite vaccination drives, the re-occurrence of recent pandemic waves has reinforced the importance of innovation/utilization of immune-booster to achieve appropriate long-term vaccine protection. Plant-derived immuno-adjuvants, which have multifaceted functions, can impede infections by boosting the immune system. Many previous studies have shown that formulation of vaccines using plant-derived adjuvant results in long-lasting immunity may overcome the natural tendency of coronavirus immunity to wane quickly. Plant polysaccharides, glycosides, and glycoprotein extracts have reportedly been utilized as enticing adjuvants in experimental vaccines, such as Advax, Matrix-M, and Mistletoe lectin, which have been shown to be highly immunogenic and safe. When employed in vaccine formulation, Advax and Matrix-M generate long-lasting antibodies, a balanced robust Th1/Th2 cytokine profile, and the stimulation of cytotoxic T cells. Thus, the use of adjuvants derived from plants may increase the effectiveness of vaccines, resulting in the proper immunological response required to combat COVID-19. A few have been widely used in epidemic outbreaks, including SARS and H1N1 influenza, and their use could also improve the efficacy of COVID-19 vaccines. In this review, the immunological adjuvant properties of plant compounds as well as their potential application in anti-COVID-19 therapy are thoroughly discussed.
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Affiliation(s)
- Arbind Kumar
- COVID-19 Testing facility, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Aashish Sharma
- COVID-19 Testing facility, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Narendra Vijay Tirpude
- Dietetics and Nutrition Technology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Yogendra Padwad
- Dietetics and Nutrition Technology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Vipin Hallan
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Sanjay Kumar
- CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
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29
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Bian L, Liu J, Gao F, Gao Q, He Q, Mao Q, Wu X, Xu M, Liang Z. Research progress on vaccine efficacy against SARS-CoV-2 variants of concern. Hum Vaccin Immunother 2022; 18:2057161. [PMID: 35438600 PMCID: PMC9115786 DOI: 10.1080/21645515.2022.2057161] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 03/08/2022] [Accepted: 03/21/2022] [Indexed: 01/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to circulate worldwide and a variety of variants have emerged. Variants of concern (VOC) designated by the World Health Organization (WHO) have triggered epidemic waves due to their strong infectivity or pathogenicity and potential immune escape, among other reasons. Although large-scale vaccination campaigns undertaken globally have contributed to the improved control of SARS-CoV-2, the efficacies of current vaccines against VOCs have declined to various degrees. In particular, the highly infectious Delta and Omicron variants have caused recent epidemics and prompted concerns about control measures. This review summarizes current VOCs, the protective efficacy of vaccines against VOCs, and the shortcomings in methods for evaluating vaccine efficacy. In addition, strategies for responding to variants are proposed for future epidemic prevention and control as well as for vaccine research and development.
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Affiliation(s)
- Lianlian Bian
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Jianyang Liu
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Fan Gao
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Qiushuang Gao
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Qian He
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Qunying Mao
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Xing Wu
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Miao Xu
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Zhenglun Liang
- Institute of Biological Products, Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China
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30
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Tarragó‐Gil R, Gil‐Mosteo MJ, Aza‐Pascual‐Salcedo M, Alvarez MJL, Ainaga RR, Gimeno NL, Viñuales RF, Fernández YM, Marco JM, Bolsa EA, Sancho JB, Cajo SA, Perez‐Zsolt D, Raïch‐Regué D, Muñoz‐Basagoiti J, Izquierdo‐Useros N, Pociello VB, León R, Peris DS. Randomized clinical trial to assess the impact of oral intervention with cetylpyridinium chloride to reduce salivary SARS-CoV-2 viral load. J Clin Periodontol 2022; 50:288-294. [PMID: 36345827 PMCID: PMC9877833 DOI: 10.1111/jcpe.13746] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 10/25/2022] [Accepted: 11/03/2022] [Indexed: 11/11/2022]
Abstract
AIM Aerosols released from the oral cavity help spread the SARS-CoV-2 virus. The use of a mouthwash formulated with an antiviral agent could reduce the viral load in saliva, helping to lower the spread of the virus. The aim of this study was to assess the efficacy of a mouthwash with 0.07% cetylpyridinium chloride (CPC) to reduce the viral load in the saliva of Coronavirus disease 2019 (COVID-19) patients. MATERIALS AND METHODS In this multi-centre, single-blind, randomized, parallel group clinical trial, 80 COVID-19 patients were enrolled and randomized to two groups, namely test (n = 40) and placebo (n = 40). Saliva samples were collected at baseline and 2 h after rinsing. The samples were analysed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and an enzyme-linked immunosorbent assay test specific for the nucleocapsid (N) protein of SARS-CoV-2. RESULTS With RT-qPCR, no significant differences were observed between the placebo group and the test group. However, 2 h after a single rinse, N protein concentration in saliva was significantly higher in the test group, indicating an increase in lysed virus. CONCLUSIONS The use of 0.07% CPC mouthwash induced a significant increase in N protein detection in the saliva of COVID-19 patients. Lysis of the virus in the mouth could help reduce the transmission of SARS-CoV-2. However, more studies are required to prove this.
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Affiliation(s)
- Rosa Tarragó‐Gil
- Seminario Primary Care Health CentreAragon Health ServiceZaragozaSpain,Institute of Health Research of Aragón (IIS Aragón)ZaragozaSpain
| | - María José Gil‐Mosteo
- Seminario Primary Care Health CentreAragon Health ServiceZaragozaSpain,Institute of Health Research of Aragón (IIS Aragón)ZaragozaSpain
| | - Mercedes Aza‐Pascual‐Salcedo
- Institute of Health Research of Aragón (IIS Aragón)ZaragozaSpain,Zaragoza III Primary Care Health DirectionAragon Health ServiceZaragozaSpain
| | - María Jesús Lallana Alvarez
- Institute of Health Research of Aragón (IIS Aragón)ZaragozaSpain,Zaragoza III Primary Care Health DirectionAragon Health ServiceZaragozaSpain
| | - Raquel Refusta Ainaga
- Institute of Health Research of Aragón (IIS Aragón)ZaragozaSpain,San José Primary Care Health CentreAragon Health ServiceZaragozaSpain
| | - Natalia Lázaro Gimeno
- Seminario Primary Care Health CentreAragon Health ServiceZaragozaSpain,Institute of Health Research of Aragón (IIS Aragón)ZaragozaSpain
| | - Roberto Fuentes Viñuales
- Institute of Health Research of Aragón (IIS Aragón)ZaragozaSpain,Sagasta Primary Care Health CentreAragon Health ServiceZaragozaSpain
| | - Yolanda Millán Fernández
- Seminario Primary Care Health CentreAragon Health ServiceZaragozaSpain,Institute of Health Research of Aragón (IIS Aragón)ZaragozaSpain
| | - Jesica Montero Marco
- Institute of Health Research of Aragón (IIS Aragón)ZaragozaSpain,Lozano Blesa University Clinic HospitalZaragozaSpain
| | - Elena Altarribas Bolsa
- Institute of Health Research of Aragón (IIS Aragón)ZaragozaSpain,Lozano Blesa University Clinic HospitalZaragozaSpain
| | - Jessica Bueno Sancho
- Institute of Health Research of Aragón (IIS Aragón)ZaragozaSpain,Lozano Blesa University Clinic HospitalZaragozaSpain
| | - Sonia Algarate Cajo
- Institute of Health Research of Aragón (IIS Aragón)ZaragozaSpain,Lozano Blesa University Clinic HospitalZaragozaSpain
| | | | | | | | - Nuria Izquierdo‐Useros
- IrsiCaixa AIDS Research InstituteBadalonaSpain,Germans Trias i Pujol Research Institute (IGTP)BadalonaSpain
| | | | - Rubén León
- Dentaid Research CenterCerdanyola del VallèsSpain
| | - Diana Serrano Peris
- Institute of Health Research of Aragón (IIS Aragón)ZaragozaSpain,Zaragoza III Primary Care Health DirectionAragon Health ServiceZaragozaSpain
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Ben Fredj S, Ghammem R, Zammit N, Maatouk A, Haddad N, Haddad N, Kachroudi M, Rebai S, Laadhari H, Ghodhbani MM, Maatoug J, Ghannem H. Risk factors for severe Covid-19 breakthrough infections: an observational longitudinal study. BMC Infect Dis 2022; 22:894. [DOI: 10.1186/s12879-022-07859-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 11/08/2022] [Indexed: 11/29/2022] Open
Abstract
Abstract
Background
The drive to vaccinate large populations is nowadays the main instrument for combating the pandemic and preventing serious disease and death. However, breakthrough infection (post-vaccination infection) still happens after vaccination among fully vaccinated people. We aimed to assess the severity outcomes and to determine its associated factors among vaccinated COVID-19 cases in the governorate of Sousse, Tunisia.
Methods
We carried out a five-month observational longitudinal study including all the population of Sousse. Confirmed infections of SARS-CoV-2 and the vaccination status are recorded in the daily COVID- 19 database of the Regional Office of the Tunisian Ministry of Health. We included all post-vaccination COVID-19 cases for the analysis of the COVID-19 serious outcomes. Data were collected via 15-min telephonic call interviews conducted by trained interviewers. Descriptive analysis with calculating incidence rates of confirmed COVID-19 cases per 100,000 inhabitants was conducted. In binary logistic regression, adjusted odds ratios along with 95% intervals confidence were performed to determine factors related to severe or critical COVID-19.
Results
As of 31 July 2021, 107,545 persons over 19 years old have received at least one dose of COVID-19 vaccination. Among the vaccinated population, we traced and included 765 breakthrough infection cases, and the incidence rate was 711.3 per week. The majority were female (sex-ratio = 0.8), and the average age of the overall cases was 55.7 years. The prevalence of severe or critical cases in vaccinated COVID-19 patients occurs in 10.8% of cases. Patients with a medical history of cardiovascular diseases had more than two times increased odds to have a severe or critical disease. We also found the highest self-estimation of adherence to preventive measures was inversely correlated to serious cases and having an incomplete vaccination schema was strongly associated with complications.
Conclusions
We tried to provide evidence about the breakthrough infections to improve measures of prevention and control of COVID-19. Boosting immunity for vulnerable patients added to maintaining and promoting preventive measures are not only essential to prevent severe cases of breakthrough infections of COVID-19, but also other influenza-like diseases.
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32
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Valenzuela-Fernández A, Cabrera-Rodriguez R, Ciuffreda L, Perez-Yanes S, Estevez-Herrera J, González-Montelongo R, Alcoba-Florez J, Trujillo-González R, García-Martínez de Artola D, Gil-Campesino H, Díez-Gil O, Lorenzo-Salazar JM, Flores C, Garcia-Luis J. Nanomaterials to combat SARS-CoV-2: Strategies to prevent, diagnose and treat COVID-19. Front Bioeng Biotechnol 2022; 10:1052436. [PMID: 36507266 PMCID: PMC9732709 DOI: 10.3389/fbioe.2022.1052436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/09/2022] [Indexed: 11/26/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the associated coronavirus disease 2019 (COVID-19), which severely affect the respiratory system and several organs and tissues, and may lead to death, have shown how science can respond when challenged by a global emergency, offering as a response a myriad of rapid technological developments. Development of vaccines at lightning speed is one of them. SARS-CoV-2 outbreaks have stressed healthcare systems, questioning patients care by using standard non-adapted therapies and diagnostic tools. In this scenario, nanotechnology has offered new tools, techniques and opportunities for prevention, for rapid, accurate and sensitive diagnosis and treatment of COVID-19. In this review, we focus on the nanotechnological applications and nano-based materials (i.e., personal protective equipment) to combat SARS-CoV-2 transmission, infection, organ damage and for the development of new tools for virosurveillance, diagnose and immune protection by mRNA and other nano-based vaccines. All the nano-based developed tools have allowed a historical, unprecedented, real time epidemiological surveillance and diagnosis of SARS-CoV-2 infection, at community and international levels. The nano-based technology has help to predict and detect how this Sarbecovirus is mutating and the severity of the associated COVID-19 disease, thereby assisting the administration and public health services to make decisions and measures for preparedness against the emerging variants of SARS-CoV-2 and severe or lethal COVID-19.
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Affiliation(s)
- Agustín Valenzuela-Fernández
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Romina Cabrera-Rodriguez
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Laura Ciuffreda
- Research Unit, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Silvia Perez-Yanes
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Judith Estevez-Herrera
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | | | - Julia Alcoba-Florez
- Servicio de Microbiología, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Rodrigo Trujillo-González
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
- Departamento de Análisis Matemático, Facultad de Ciencias, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | | | - Helena Gil-Campesino
- Servicio de Microbiología, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Oscar Díez-Gil
- Servicio de Microbiología, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - José M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Carlos Flores
- Research Unit, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Jonay Garcia-Luis
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
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33
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La Monica G, Bono A, Lauria A, Martorana A. Targeting SARS-CoV-2 Main Protease for Treatment of COVID-19: Covalent Inhibitors Structure-Activity Relationship Insights and Evolution Perspectives. J Med Chem 2022; 65:12500-12534. [PMID: 36169610 PMCID: PMC9528073 DOI: 10.1021/acs.jmedchem.2c01005] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Indexed: 02/07/2023]
Abstract
The viral main protease is one of the most attractive targets among all key enzymes involved in the SARS-CoV-2 life cycle. Covalent inhibition of the cysteine145 of SARS-CoV-2 MPRO with selective antiviral drugs will arrest the replication process of the virus without affecting human catalytic pathways. In this Perspective, we analyzed the in silico, in vitro, and in vivo data of the most representative examples of covalent SARS-CoV-2 MPRO inhibitors reported in the literature to date. In particular, the studied molecules were classified into eight different categories according to their reactive electrophilic warheads, highlighting the differences between their reversible/irreversible mechanism of inhibition. Furthermore, the analyses of the most recurrent pharmacophoric moieties and stereochemistry of chiral carbons were reported. The analyses of noncovalent and covalent in silico protocols, provided in this Perspective, would be useful for the scientific community to discover new and more efficient covalent SARS-CoV-2 MPRO inhibitors.
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Affiliation(s)
| | | | - Antonino Lauria
- Dipartimento di Scienze e
Tecnologie Biologiche Chimiche e Farmaceutiche, University of Palermo, Viale delle Scienze, Ed. 17, I-90128 Palermo, Italy
| | - Annamaria Martorana
- Dipartimento di Scienze e
Tecnologie Biologiche Chimiche e Farmaceutiche, University of Palermo, Viale delle Scienze, Ed. 17, I-90128 Palermo, Italy
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34
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Suddhapas K, Choi MH, Shortreed MR, Timperman A. Evaluation of Variant-Specific Peptides for Detection of SARS-CoV-2 Variants of Concern. J Proteome Res 2022; 21:2443-2452. [PMID: 36108102 PMCID: PMC10318299 DOI: 10.1021/acs.jproteome.2c00325] [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] [Indexed: 11/28/2022]
Abstract
The SARS-CoV-2 omicron variant presented significant challenges to the global effort to counter the pandemic. SARS-CoV-2 is predicted to remain prevalent for the foreseeable future, making the ability to identify SARS-CoV-2 variants imperative in understanding and controlling the pandemic. The predominant variant discovery method, genome sequencing, is time-consuming, insensitive, and expensive. Ultraperformance liquid chromatography-mass spectrometry (UPLC-MS) offers an exciting alternative detection modality provided that variant-containing peptide markers are sufficiently detectable from their tandem mass spectra (MS/MS). We have synthesized model tryptic peptides of SARS-CoV-2 variants alpha, beta, gamma, delta, and omicron and evaluated their signal intensity, HCD spectra, and reverse phase retention time. Detection limits of 781, 781, 65, and 65 amol are obtained for the molecular ions of the proteotypic peptides, beta (QIAPGQTGNIADYNYK), gamma (TQLPSAYTNSFTR), delta (VGGNYNYR), and omicron (TLVKQLSSK), from neat solutions. These detection limits are on par with the detection limits of a previously reported proteotypic peptide from the SARS-CoV-2 spike protein, HTPINLVR. This study demonstrates the potential to differentiate SARS-CoV-2 variants through their proteotypic peptides with an approach that is broadly applicable across a wide range of pathogens.
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Affiliation(s)
- Kantaphon Suddhapas
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - M Hannah Choi
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - AaronT Timperman
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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35
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Chavda VP, Yao Q, Vora LK, Apostolopoulos V, Patel CA, Bezbaruah R, Patel AB, Chen ZS. Fast-track development of vaccines for SARS-CoV-2: The shots that saved the world. Front Immunol 2022; 13:961198. [PMID: 36263030 PMCID: PMC9574046 DOI: 10.3389/fimmu.2022.961198] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
In December 2019, an outbreak emerged of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which leads to coronavirus disease 2019 (COVID-19). The World Health Organisation announced the outbreak a global health emergency on 30 January 2020 and by 11 March 2020 it was declared a pandemic. The spread and severity of the outbreak took a heavy toll and overburdening of the global health system, particularly since there were no available drugs against SARS-CoV-2. With an immediate worldwide effort, communication, and sharing of data, large amounts of funding, researchers and pharmaceutical companies immediately fast-tracked vaccine development in order to prevent severe disease, hospitalizations and death. A number of vaccines were quickly approved for emergency use, and worldwide vaccination rollouts were immediately put in place. However, due to several individuals being hesitant to vaccinations and many poorer countries not having access to vaccines, multiple SARS-CoV-2 variants quickly emerged that were distinct from the original variant. Uncertainties related to the effectiveness of the various vaccines against the new variants as well as vaccine specific-side effects have remained a concern. Despite these uncertainties, fast-track vaccine approval, manufacturing at large scale, and the effective distribution of COVID-19 vaccines remain the topmost priorities around the world. Unprecedented efforts made by vaccine developers/researchers as well as healthcare staff, played a major role in distributing vaccine shots that provided protection and/or reduced disease severity, and deaths, even with the delta and omicron variants. Fortunately, even for those who become infected, vaccination appears to protect against major disease, hospitalisation, and fatality from COVID-19. Herein, we analyse ongoing vaccination studies and vaccine platforms that have saved many deaths from the pandemic.
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Affiliation(s)
- Vivek P. Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, LM College of Pharmacy, Ahmedabad, Gujarat, India
| | - Qian Yao
- Graduate School, University of St. La Salle, Bacolod City, Philippines
| | | | | | - Chirag A. Patel
- Department of Pharmacology, LM College of Pharmacy, Ahmedabad, Gujarat, India
| | - Rajashri Bezbaruah
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India
| | - Aayushi B. Patel
- Pharmacy Section, LM. College of Pharmacy, Ahmedabad, Gujarat, India
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Science, College of Pharmacy and Health Sciences, St. John’s University, New York, NY, United States
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36
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Huang X, Kon E, Han X, Zhang X, Kong N, Mitchell MJ, Peer D, Tao W. Nanotechnology-based strategies against SARS-CoV-2 variants. NATURE NANOTECHNOLOGY 2022; 17:1027-1037. [PMID: 35982317 DOI: 10.1038/s41565-022-01174-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has already infected more than 500 million people globally (as of May 2022), creating the coronavirus disease 2019 (COVID-19) pandemic. Nanotechnology has played a pivotal role in the fight against SARS-CoV-2 in various aspects, with the successful development of the two highly effective nanotechnology-based messenger RNA vaccines being the most profound. Despite the remarkable efficacy of mRNA vaccines against the original SARS-CoV-2 strain, hopes for quickly ending this pandemic have been dampened by the emerging SARS-CoV-2 variants, which have brought several new pandemic waves. Thus, novel strategies should be proposed to tackle the crisis presented by existing and emerging SARS-CoV-2 variants. Here, we discuss the SARS-CoV-2 variants from biological and immunological perspectives, and the rational design and development of novel and potential nanotechnology-based strategies to combat existing and possible future SARS-CoV-2 variants. The lessons learnt and design strategies developed from this battle against SARS-CoV-2 variants could also inspire innovation in the development of nanotechnology-based strategies for tackling other global infectious diseases and their future variants.
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Affiliation(s)
- Xiangang Huang
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Edo Kon
- Laboratory of Precision Nanomedicine, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
- Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
- Cancer Biology Research Center, Tel Aviv University, Tel Aviv, Israel
| | - Xuexiang Han
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Xingcai Zhang
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Na Kong
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael J Mitchell
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Dan Peer
- Laboratory of Precision Nanomedicine, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
- Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel.
- Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel.
- Cancer Biology Research Center, Tel Aviv University, Tel Aviv, Israel.
| | - Wei Tao
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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Jamal Z, Haider M, Ikram A, Salman M, Rana MS, Rehman Z, Haider SA, Ammar M, Nisar N, Umair M. Breakthrough cases of Omicron and Delta variants of SARS-CoV-2 during the fifth wave in Pakistan. Front Public Health 2022; 10:987452. [PMID: 36249252 PMCID: PMC9557048 DOI: 10.3389/fpubh.2022.987452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/02/2022] [Indexed: 01/26/2023] Open
Abstract
COVID-19 pandemic has severely affected Pakistan with 1,557,134 cases as of August 4, 2022. However, the data regarding breakthrough infections in Pakistan is scant. Hence, the objective was to analyze SARS-CoV-2 breakthrough infections with respect to vaccines and variants during the fifth wave in Pakistan. Therefore, the Department of Virology (NIH, Pakistan) genotyped 2,467 randomly selected individuals between November 2021 and February 2022 using the SNPsig® SARS-CoV-2 (EscapePLEX) kit (PrimerDesign, UK). P681R and K417N mutations were used to distinguish delta and omicron. Data on the patient's age, gender, date of collection, variant, and vaccination status were analyzed using Statistical Package for Social Sciences (SPSS) software. Among 2,467 genotyped samples, Omicron was detected in 58.6% (n = 1445), Delta in 40.4% (n = 998) and undetermined/wildtype variant in 24 samples. The vaccination status of omicron-positive patients showed (49.7%; n = 718/1445) and Delta-positive patients (39.67%; n = 396/998) to be fully vaccinated. Of note, a high percentage 85% of breakthrough cases (n = 947) were identified among fully vaccinated individuals (n = 1114). Among them, 85.9% (n = 617/718) belonged to omicron and 83.3% (n = 330/396) to delta. Moreover, 76.7% (n = 855) of vaccinated individuals (n = 1114) received Sinopharm (n = 432) and Sinovac (n = 423) vaccines. The majority of breakthrough subjects who contracted Omicron were vaccinated with Sinopharm (93.0%, n = 256) and delta with Cansino (100%, n = 44). Individuals vaccinated with Sinovac showed the most frequent breakthrough cases for both Omicron and Delta variant between the 4th and 6th months (n = 278) after primary vaccination as compared to the 7th to 9th months (n = 24) category. While in case of Sinopharm, maximum breakthrough cases occurred between 7th to 9th months (n = 234) as compared to the 4th to 6th months (n = 120) after primary vaccination. Omicron and Delta breakthrough cases in men (n = 364 and 193) are more frequently seen than women (n = 253 and 138) respectively and breakthrough majority cases (n = 392) occurred in individuals aged 18-33 years. Breakthrough cases limiting monitoring in Pakistan impose a substantial constraint on policymakers' ability to take timely effective decisions. Since the current study consists of only a 2,467-genotyped sample, comprehensive data should be analyzed.
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Rudi E, Martin Aispuro P, Zurita E, Gonzalez Lopez Ledesma M, Bottero D, Malito J, Gabrielli M, Gaillard E, Stuible M, Durocher Y, Gamarnik A, Wigdorovitz A, Hozbor D. Immunological study of COVID-19 vaccine candidate based on recombinant spike trimer protein from different SARS-CoV-2 variants of concern. Front Immunol 2022; 13:1020159. [PMID: 36248791 PMCID: PMC9560800 DOI: 10.3389/fimmu.2022.1020159] [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: 08/15/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
The emergency of new SARS-CoV-2 variants that feature increased immune escape marks an urgent demand for better vaccines that will provide broader immunogenicity. Here, we evaluated the immunogenic capacity of vaccine candidates based on the recombinant trimeric spike protein (S) of different SARS-CoV-2 variants of concern (VOC), including the ancestral Wuhan, Beta and Delta viruses. In particular, we assessed formulations containing either single or combined S protein variants. Our study shows that the formulation containing the single S protein from the ancestral Wuhan virus at a concentration of 2µg (SW2-Vac 2µg) displayed in the mouse model the highest IgG antibody levels against all the three (Wuhan, Beta, and Delta) SARS-CoV-2 S protein variants tested. In addition, this formulation induced significantly higher neutralizing antibody titers against the three viral variants when compared with authorized Gam-COVID-Vac-rAd26/rAd5 (Sputnik V) or ChAdOx1 (AstraZeneca) vaccines. SW2-Vac 2µg was also able to induce IFN-gamma and IL-17, memory CD4 populations and follicular T cells. Used as a booster dose for schedules performed with different authorized vaccines, SW2-Vac 2µg vaccine candidate also induced higher levels of total IgG and IgG isotypes against S protein from different SARS-CoV-2 variants in comparison with those observed with homologous 3-dose schedule of Sputnik V or AstraZeneca. Moreover, SW2-Vac 2µg booster induced broadly strong neutralizing antibody levels against the three tested SARS-CoV-2 variants. SW2-Vac 2µg booster also induced CD4+ central memory, CD4+ effector and CD8+ populations. Overall, the results demonstrate that SW2-Vac 2 µg is a promising formulation for the development of a next generation COVID-19 vaccine.
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Affiliation(s)
- Erika Rudi
- Laboratorio VacSal, Instituto de Biotecnología y Biología Molecular (IBBM), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico Tecnológico – Consejo Nacional de Investigaciones Científicas y Técnicas (CCT-CONICET), La Plata, Argentina
| | - Pablo Martin Aispuro
- Laboratorio VacSal, Instituto de Biotecnología y Biología Molecular (IBBM), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico Tecnológico – Consejo Nacional de Investigaciones Científicas y Técnicas (CCT-CONICET), La Plata, Argentina
| | - Eugenia Zurita
- Laboratorio VacSal, Instituto de Biotecnología y Biología Molecular (IBBM), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico Tecnológico – Consejo Nacional de Investigaciones Científicas y Técnicas (CCT-CONICET), La Plata, Argentina
| | | | - Daniela Bottero
- Laboratorio VacSal, Instituto de Biotecnología y Biología Molecular (IBBM), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico Tecnológico – Consejo Nacional de Investigaciones Científicas y Técnicas (CCT-CONICET), La Plata, Argentina
| | - Juan Malito
- INCUINTA INTA, CONICET, HURLINGHAM, INTA Castelar, Buenos Aires, Argentina
| | - Magali Gabrielli
- Laboratorio VacSal, Instituto de Biotecnología y Biología Molecular (IBBM), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico Tecnológico – Consejo Nacional de Investigaciones Científicas y Técnicas (CCT-CONICET), La Plata, Argentina
| | - Emilia Gaillard
- Laboratorio VacSal, Instituto de Biotecnología y Biología Molecular (IBBM), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico Tecnológico – Consejo Nacional de Investigaciones Científicas y Técnicas (CCT-CONICET), La Plata, Argentina
| | - Matthew Stuible
- Human Health Therapeutics Research Center, National Research Council Canada, Montreal, QC, Canada
| | - Yves Durocher
- Human Health Therapeutics Research Center, National Research Council Canada, Montreal, QC, Canada
| | | | - Andrés Wigdorovitz
- INCUINTA INTA, CONICET, HURLINGHAM, INTA Castelar, Buenos Aires, Argentina
| | - Daniela Hozbor
- Laboratorio VacSal, Instituto de Biotecnología y Biología Molecular (IBBM), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico Tecnológico – Consejo Nacional de Investigaciones Científicas y Técnicas (CCT-CONICET), La Plata, Argentina
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Khorattanakulchai N, Srisutthisamphan K, Shanmugaraj B, Manopwisedjaroen S, Rattanapisit K, Panapitakkul C, Kemthong T, Suttisan N, Malaivijitnond S, Thitithanyanont A, Jongkaewwattana A, Phoolcharoen W. A recombinant subunit vaccine candidate produced in plants elicits neutralizing antibodies against SARS-CoV-2 variants in macaques. FRONTIERS IN PLANT SCIENCE 2022; 13:901978. [PMID: 36247553 PMCID: PMC9555276 DOI: 10.3389/fpls.2022.901978] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Since the outbreak of the coronavirus disease (COVID) pandemic in 2019, the development of effective vaccines to combat the infection has been accelerated. With the recent emergence of highly transmissible severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC), there are concerns regarding the immune escape from vaccine-induced immunity. Hence an effective vaccine against VOC with a potent immune response is required. Our previous study confirmed that the two doses of the plant-produced receptor-binding domain (RBD) of SARS-CoV-2 fused with the Fc region of human IgG1, namely Baiya SARS-CoV-2 Vax 1, showed high immunogenicity in mice and monkeys. Here, we aimed to evaluate the immunogenicity of a three-dose intramuscular injection of Baiya SARS-CoV-2 Vax 1 on days 0, 21, and 133 in cynomolgus monkeys. At 14 days after immunization, blood samples were collected to determine RBD-specific antibody titer, neutralizing antibody, and pseudovirus neutralizing antibody titers. Immunized monkeys developed significantly high levels of antigen-specific antibodies against SARS-CoV-2 compared to the control group. Interestingly, the sera collected from immunized monkeys also showed a neutralizing antibody response against the SARS-CoV-2 VOCs; Alpha, Beta, Gamma, Delta, and Omicron. These findings demonstrate that a three-dose regimen of Baiya SARS-CoV-2 Vax 1 vaccine elicits neutralizing immune response against SARS-CoV-2 variants.
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Affiliation(s)
- Narach Khorattanakulchai
- Center of Excellence in Plant-produced Pharmaceuticals, Chulalongkorn University, Bangkok, Thailand
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Kanjana Srisutthisamphan
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | | | | | | | - Chalisa Panapitakkul
- Center of Excellence in Plant-produced Pharmaceuticals, Chulalongkorn University, Bangkok, Thailand
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Taratorn Kemthong
- National Primate Research Center of Thailand-Chulalongkorn University, Saraburi, Thailand
| | - Nutchanat Suttisan
- National Primate Research Center of Thailand-Chulalongkorn University, Saraburi, Thailand
| | | | | | - Anan Jongkaewwattana
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Waranyoo Phoolcharoen
- Center of Excellence in Plant-produced Pharmaceuticals, Chulalongkorn University, Bangkok, Thailand
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
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40
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Miles B, Chacko J, Zaidan M. The Impact of Elexacaftor/Ivacaftor/Tezacaftor on Cystic Fibrosis Patients Who Acquire COVID-19 Infection. Cureus 2022; 14:e29276. [PMID: 36277555 PMCID: PMC9578654 DOI: 10.7759/cureus.29276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2022] [Indexed: 11/17/2022] Open
Abstract
The combination of medication containing elexacaftor, ivacaftor, and tezacaftor (EIT) has dramatically impacted the treatment and prognosis for patients with cystic fibrosis (CF). Lung function, weight, and self-reported quality of life have improved for many of these patients, but little is known about whether this treatment will have a beneficial effect in preventing morbidity and/or mortality from respiratory infections such as COVID-19. EIT received Food and Drug Administration (FDA) approval shortly before the first cases of COVID-19 appeared in the United States. We performed an analysis using the TriNetX (Cambridge, MA, USA) research database to determine if patients being treated with EIT who became infected with COVID-19 experienced significantly different outcomes compared to patients who were not receiving it.
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41
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Liu D, An C, Bai Y, Li K, Liu J, Wang Q, He Q, Song Z, Zhang J, Song L, Cui B, Mao Q, Jiang W, Liang Z. A Novel Single-Stranded RNA-Based Adjuvant Improves the Immunogenicity of the SARS-CoV-2 Recombinant Protein Vaccine. Viruses 2022; 14:v14091854. [PMID: 36146661 PMCID: PMC9504790 DOI: 10.3390/v14091854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/19/2022] [Accepted: 08/20/2022] [Indexed: 11/17/2022] Open
Abstract
The research and development (R&D) of novel adjuvants is an effective measure for improving the immunogenicity of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) recombinant protein vaccine. Toward this end, we designed a novel single-stranded RNA-based adjuvant, L2, from the SARS-CoV-2 prototype genome. L2 could initiate retinoic acid-inducible gene-I signaling pathways to effectively activate the innate immunity. ZF2001, an aluminum hydroxide (Al) adjuvanted SARS-CoV-2 recombinant receptor binding domain (RBD) subunit vaccine with emergency use authorization in China, was used for comparison. L2, with adjuvant compatibility with RBD, elevated the antibody response to a level more than that achieved with Al, CpG 7909, or poly(I:C) as adjuvants in mice. L2 plus Al with composite adjuvant compatibility with RBD markedly improved the immunogenicity of ZF2001; in particular, neutralizing antibody titers increased by about 44-fold for Omicron, and the combination also induced higher levels of antibodies than CpG 7909/poly(I:C) plus Al in mice. Moreover, L2 and L2 plus Al effectively improved the Th1 immune response, rather than the Th2 immune response. Taken together, L2, used as an adjuvant, enhanced the immune response of the SARS-CoV-2 recombinant RBD protein vaccine in mice. These findings should provide a basis for the R&D of novel RNA-based adjuvants.
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Affiliation(s)
- Dong Liu
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
- Changchun Institute of Biological Products Co., Ltd., Changchun 130062, China
| | - Chaoqiang An
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
- Beijing Minhai Biotechnology Co., Ltd., Beijing 102629, China
| | - Yu Bai
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
| | - Kelei Li
- Beijing Minhai Biotechnology Co., Ltd., Beijing 102629, China
| | - Jianyang Liu
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
| | - Qian Wang
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
| | - Qian He
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
| | - Ziyang Song
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
| | - Jialu Zhang
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
| | - Lifang Song
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
| | - Bopei Cui
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
| | - Qunying Mao
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
| | - Wei Jiang
- Changchun Institute of Biological Products Co., Ltd., Changchun 130062, China
- Correspondence: (W.J.); (Z.L.)
| | - Zhenglun Liang
- Division of Hepatitis and Enterovirus Vaccines, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
- Correspondence: (W.J.); (Z.L.)
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He Q, Mao Q, Zhang J, Gao F, Bai Y, Cui B, Liu J, An C, Wang Q, Yan X, Yang J, Song L, Song Z, Liu D, Yuan Y, Sun J, Zhao J, Bian L, Wu X, Huang W, Li C, Wang J, Liang Z, Xu M. Heterologous immunization with adenovirus vectored and inactivated vaccines effectively protects against SARS-CoV-2 variants in mice and macaques. Front Immunol 2022; 13:949248. [PMID: 36059554 PMCID: PMC9428284 DOI: 10.3389/fimmu.2022.949248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
To cope with the decline in COVID-19 vaccine-induced immunity caused by emerging SARS-CoV-2 variants, a heterologous immunization regimen using chimpanzee adenovirus vectored vaccine expressing SARS-CoV-2 spike (ChAd-S) and an inactivated vaccine (IV) was tested in mice and non-human primates (NHPs). Heterologous regimen successfully enhanced or at least maintained antibody and T cell responses and effectively protected against SARS-CoV-2 variants in mice and NHPs. An additional heterologous booster in mice further improved and prolonged the spike-specific antibody response and conferred effective neutralizing activity against the Omicron variant. Interestingly, priming with ChAd-S and boosting with IV reduced the lung injury risk caused by T cell over activation in NHPs compared to homologous ChAd-S regimen, meanwhile maintained the flexibility of antibody regulation system to react to virus invasion by upregulating or preserving antibody levels. This study demonstrated the satisfactory compatibility of ChAd-S and IV in prime-boost vaccination in animal models.
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Affiliation(s)
- Qian He
- Division of Hepatitis and Enterovirus Vaccines, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Qunying Mao
- Division of Hepatitis and Enterovirus Vaccines, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Jialu Zhang
- Division of Hepatitis and Enterovirus Vaccines, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Fan Gao
- Division of Hepatitis and Enterovirus Vaccines, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Yu Bai
- Division of Hepatitis and Enterovirus Vaccines, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Bopei Cui
- Division of Hepatitis and Enterovirus Vaccines, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Jianyang Liu
- Division of Hepatitis and Enterovirus Vaccines, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Chaoqiang An
- Division of Hepatitis and Enterovirus Vaccines, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Qian Wang
- Division of Hepatitis and Enterovirus Vaccines, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Xujia Yan
- Division of Hepatitis and Enterovirus Vaccines, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Jinghuan Yang
- Division of Hepatitis and Enterovirus Vaccines, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Lifang Song
- Division of Hepatitis and Enterovirus Vaccines, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Ziyang Song
- Division of Hepatitis and Enterovirus Vaccines, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Dong Liu
- Division of Hepatitis and Enterovirus Vaccines, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Yadi Yuan
- Division of Hepatitis and Enterovirus Vaccines, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Jing Sun
- Guangzhou Laboratory, Guangzhou, China
| | | | - Lianlian Bian
- Division of Hepatitis and Enterovirus Vaccines, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Xing Wu
- Division of Hepatitis and Enterovirus Vaccines, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Weijin Huang
- Division of Hepatitis and Enterovirus Vaccines, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Changgui Li
- Division of Hepatitis and Enterovirus Vaccines, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Junzhi Wang
- Division of Hepatitis and Enterovirus Vaccines, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
- *Correspondence: Junzhi Wang, ; Zhenglun Liang, ; Miao Xu,
| | - Zhenglun Liang
- Division of Hepatitis and Enterovirus Vaccines, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
- *Correspondence: Junzhi Wang, ; Zhenglun Liang, ; Miao Xu,
| | - Miao Xu
- Division of Hepatitis and Enterovirus Vaccines, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
- *Correspondence: Junzhi Wang, ; Zhenglun Liang, ; Miao Xu,
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Nguyen DC, Dao TL, Truong TMD, Nguyen TH, Phan TN, Nguyen HM, Pham TD, Nguyen XB, Nguyen TB, Hoang VT. Short-Term Adverse Effects Immediately after the Start of COVID-19 Booster Vaccination in Vietnam. Vaccines (Basel) 2022; 10:vaccines10081325. [PMID: 36016213 PMCID: PMC9414515 DOI: 10.3390/vaccines10081325] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 12/20/2022] Open
Abstract
Background: Risk communication is necessary to improve the booster vaccination rate, but Vietnam does not have a system to collect and disclose such information. Therefore, the purpose of this study was to clarify adverse reactions and their frequency in the early period after booster vaccination, and to obtain primary data for improving the booster vaccination rate. Methods: A cross-sectional survey was conducted among adults aged ≥18 years. Clinical data were collected 14 days after booster vaccination by using a standard questionnaire. Results: A total of 1322 participants were included with median age = 23 and sex ratio (Male/Female) = 0.53. AstraZeneca was the most commonly used vaccine for the first and second doses, while Pfizer was the most commonly used vaccine for booster shots. Injection site pain, fatigue, and myalgia were the most common side effect reported (71.9%, 28.1%, and 21.8%, respectively). Compared to previous COVID-19 vaccine injections, 81.9% of participants reported that their symptoms were similar or milder after receiving the booster dose. They were more likely to present injection site pain (OR = 1.43, p < 0.0001) and lymphadenopathy (OR = 4.76, p < 0.0001) after receiving the booster shot. Fever (OR = 0.33, p < 0.0001) and fatigue (OR = 0.77, p = 0.002) were less often reported after booster shots compared to the first and second injections. The severity of symptoms occurring after booster dose versus first and second doses increased significantly with each additional year of age and among participants receiving the Pfizer and Moderna vaccines. Conclusion: Adverse reactions to booster vaccination are minor and their incidence is the same as for the first or the second vaccination. Multicenter studies with larger sample sizes on the side effects and safety of COVID-19 vaccine booster shots need to be conducted to make the population less worried, in order to increase the vaccination rate, to protect individuals’ and communities’ health.
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Kumar A, Ladha A, Choudhury A, Ikbal AMA, Bhattacharjee B, Das T, Gupta G, Sharma C, Sarbajna A, Mandal SC, Choudhury MD, Ali N, Slama P, Rezaei N, Palit P, Tiwari ON. The chimera of S1 and N proteins of SARS-CoV-2: can it be a potential vaccine candidate for COVID-19? Expert Rev Vaccines 2022; 21:1071-1086. [PMID: 35604776 DOI: 10.1080/14760584.2022.2081156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has emerged as one of the biggest global health issues. Spike protein (S) and nucleoprotein (N), the major immunogenic components of SARS-CoV-2, have been shown to be involved in the attachment and replication of the virus inside the host cell. AREAS COVERED Several investigations have shown that the SARS-CoV-2 nucleoprotein can elicit a cell-mediated immune response capable of regulating viral replication and lowering viral burden. However, the development of an effective vaccine that can stop the transmission of SARS-CoV-2 remains a matter of concern. Literature was retrieved using the keywords COVID-19 vaccine, role of nucleoprotein as vaccine candidate, spike protein, nucleoprotein immune responses against SARS-CoV-2, and chimera vaccine in PubMed, Google Scholar, and Google. EXPERT OPINION We have focussed on the use of chimera protein, consisting of N and S-1 protein components of SARS-CoV-2, as a potential vaccine candidate. This may act as a polyvalent mixed recombinant protein vaccine to elicit a strong T and B cell immune response, which will be capable of neutralizing the wild and mutated variants of SARS-CoV-2, and also restricting its attachment, replication, and budding in the host cell.
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Affiliation(s)
- Amresh Kumar
- Department of Life Sciences and Bioinformatics, Assam University, Silchar, India
| | - Amit Ladha
- Area of Biotechnology and Bioinformatics, NIIT University, Neemrana, India
| | - Ankita Choudhury
- Department of Pharmaceutical Sciences, Allama TR College of Pharmacy, Hospital Rd, Srigouri, India
| | - Abu Md Ashif Ikbal
- Department of Pharmacy, Tripura University (A Central University), Suryamaninagar, Tripura (W), India
| | - Bedanta Bhattacharjee
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, India
| | - Tanmay Das
- Department of Business Administration, Assam University Silchar, India
| | - Gaurav Gupta
- Area of Biotechnology and Bioinformatics, NIIT University, Neemrana, India.,Department of Immunology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Chhavi Sharma
- Area of Biotechnology and Bioinformatics, NIIT University, Neemrana, India
| | - Adity Sarbajna
- Department of Zoology, Surendranath College, Kolkata, India
| | - Subhash C Mandal
- Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | | | - Nahid Ali
- Division of Immunology, Department of Infectious Diseases, INDIAN INSTITUTE OF CHEMICAL BIOLOGY, Kolkata, India
| | - Petr Slama
- Laboratory of Animal Immunology and Biotechnology, Department of Animal Morphology, Physiology and Genetics, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, Brno, Czech Republic
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Stockholm, Sweden
| | - Partha Palit
- Department of Pharmaceutical Sciences Drug Discovery research Laboratory, Assam University, Silchar, India
| | - Onkar Nath Tiwari
- Centre for Conservation and Utilisation of Blue Green Algae (CCUBGA), Division of Microbiology, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, India
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Sassi MB, Ferjani S, Mkada I, Arbi M, Safer M, Elmoussi A, Abid S, Souiai O, Gharbi A, Tejouri A, Gaies E, Eljabri H, Ayed S, Hechaichi A, Daghfous R, Gouider R, Khelil JB, Kharrat M, Kacem I, Alya NB, Benkahla A, Trabelsi S, Boubaker IBB. Phylogenetic and amino acid signature analysis of the SARS-CoV-2s lineages circulating in Tunisia. INFECTION, GENETICS AND EVOLUTION 2022; 102:105300. [PMID: 35552003 PMCID: PMC9085353 DOI: 10.1016/j.meegid.2022.105300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 05/01/2022] [Accepted: 05/05/2022] [Indexed: 11/19/2022]
Abstract
Since the beginning of the Coronavirus disease-2019 pandemic, there has been a growing interest in exploring SARS-CoV-2 genetic variation to understand the origin and spread of the pandemic, improve diagnostic methods and develop the appropriate vaccines. The objective of this study was to identify the SARS-CoV-2s lineages circulating in Tunisia and to explore their amino acid signature in order to follow their genome dynamics. Whole genome sequencing and genetic analyses of fifty-eight SARS-CoV-2 samples collected during one-year between March 2020 and March 2021 from the National Influenza Center were performed using three sampling strategies.. Multiple lineage introductions were noted during the initial phase of the pandemic, including B.4, B.1.1, B.1.428.2, B.1.540 and B.1.1.189. Subsequently, lineages B1.160 (24.2%) and B1.177 (22.4%) were dominant throughout the year. The Alpha variant (B.1.1.7 lineage) was identified in February 2021 and firstly observed in the center of our country. In addition, A clear diversity of lineages was observed in the North of the country. A total of 335 mutations including 10 deletions were found. The SARS-CoV-2 proteins ORF1ab, Spike, ORF3a, and Nucleocapsid were observed as mutation hotspots with a mutation frequency exceeding 20%. The 2 most frequent mutations, D614G in S protein and P314L in Nsp12 appeared simultaneously and are often associated with increased viral infectivity. Interestingly, deletions in coding regions causing consequent deletions of amino acids and frame shifts were identified in NSP3, NSP6, S, E, ORF7a, ORF8 and N proteins. These findings contribute to define the COVID-19 outbreak in Tunisia. Despite the country's limited resources, surveillance of SARS-CoV-2 genomic variation should be continued to control the occurrence of new variants.
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Affiliation(s)
- Mouna Ben Sassi
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Boulevard 9 Dr Zouhier Essafi, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR16SP02, 1007 Tunis, Tunisia
| | - Sana Ferjani
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09, 1007 Tunis, Tunisia.
| | - Imen Mkada
- Department of Neurology, LR18SP03, Razi Universitary Hospital, 1 rue des orangers Manouba, 2010 Tunis, Tunisia; Clinical Investigation Centre (CIC) "Neurosciences and Mental Health", Razi Universitary Hospital, 1 rue des orangers Manouba, 2010, Tunis, Tunisia
| | - Marwa Arbi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis, Tunisia
| | - Mouna Safer
- Ministry of Health, National Observatory of New and Emerging Diseases, 1006 Tunis, Tunisia
| | - Awatef Elmoussi
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia
| | - Salma Abid
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia
| | - Oussema Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis, Tunisia
| | - Alya Gharbi
- Department of Neurology, LR18SP03, Razi Universitary Hospital, 1 rue des orangers Manouba, 2010 Tunis, Tunisia; Clinical Investigation Centre (CIC) "Neurosciences and Mental Health", Razi Universitary Hospital, 1 rue des orangers Manouba, 2010, Tunis, Tunisia; Faculty of Medicine of Tunis, University of Tunis El Manar, 15, Rue DjebelAkhdhar - La Rabta - 1007, Tunis, Tunisia
| | - Asma Tejouri
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES10 Human Genetics Laboratory, 1007 Tunis, Tunisia
| | - Emna Gaies
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Boulevard 9 Dr Zouhier Essafi, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR16SP02, 1007 Tunis, Tunisia
| | - Hanene Eljabri
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Boulevard 9 Dr Zouhier Essafi, Tunis 1006, Tunisia
| | - Samia Ayed
- Faculty of Medicine of Tunis, University of Tunis El Manar, 15, Rue DjebelAkhdhar - La Rabta - 1007, Tunis, Tunisia; Abderrahmen Mami Hospital, Department of Medical Intensive Care, 2080 Ariana, Tunisia
| | - Aicha Hechaichi
- Ministry of Health, National Observatory of New and Emerging Diseases, 1006 Tunis, Tunisia
| | - Riadh Daghfous
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Boulevard 9 Dr Zouhier Essafi, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR16SP02, 1007 Tunis, Tunisia
| | - Riadh Gouider
- Department of Neurology, LR18SP03, Razi Universitary Hospital, 1 rue des orangers Manouba, 2010 Tunis, Tunisia; Clinical Investigation Centre (CIC) "Neurosciences and Mental Health", Razi Universitary Hospital, 1 rue des orangers Manouba, 2010, Tunis, Tunisia; Faculty of Medicine of Tunis, University of Tunis El Manar, 15, Rue DjebelAkhdhar - La Rabta - 1007, Tunis, Tunisia
| | - Jalila Ben Khelil
- Faculty of Medicine of Tunis, University of Tunis El Manar, 15, Rue DjebelAkhdhar - La Rabta - 1007, Tunis, Tunisia; Abderrahmen Mami Hospital, Department of Medical Intensive Care, 2080 Ariana, Tunisia
| | - Maher Kharrat
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES10 Human Genetics Laboratory, 1007 Tunis, Tunisia
| | - Imen Kacem
- Department of Neurology, LR18SP03, Razi Universitary Hospital, 1 rue des orangers Manouba, 2010 Tunis, Tunisia; Clinical Investigation Centre (CIC) "Neurosciences and Mental Health", Razi Universitary Hospital, 1 rue des orangers Manouba, 2010, Tunis, Tunisia; Faculty of Medicine of Tunis, University of Tunis El Manar, 15, Rue DjebelAkhdhar - La Rabta - 1007, Tunis, Tunisia
| | - Nissaf Ben Alya
- Ministry of Health, National Observatory of New and Emerging Diseases, 1006 Tunis, Tunisia
| | - Alia Benkahla
- Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis, Tunisia
| | - Sameh Trabelsi
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Boulevard 9 Dr Zouhier Essafi, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR16SP02, 1007 Tunis, Tunisia
| | - Ilhem Boutiba-Ben Boubaker
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09, 1007 Tunis, Tunisia
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Zhang Y, Zheng X, Sheng W, Liang H, Zhao Y, Zhu X, Yang R, Zhang Y, Dong X, Li W, Pei F, Ding L, Chang Z, Deng L, Yuan G, Yang Z, Zhu D, Yang X, Wang H. Alum/CpG Adjuvanted Inactivated COVID-19 Vaccine with Protective Efficacy against SARS-CoV-2 and Variants. Vaccines (Basel) 2022; 10:vaccines10081208. [PMID: 36016098 PMCID: PMC9413105 DOI: 10.3390/vaccines10081208] [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: 06/08/2022] [Revised: 07/20/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Abstract
Since the beginning of the COVID-19 pandemic, numerous variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have emerged, including five variants of concern (VOC) strains listed by the WHO: Alpha, Beta, Gamma, Delta and Omicron. Extensive studies have shown that most of these VOC strains, especially the currently dominant variant Omicron, can escape the host immune response induced by existing COVID-19 vaccines to different extents, which poses considerable risk to the health of human beings around the world. In the present study, we developed a vaccine based on inactivated SARS-CoV-2 and an adjuvant consisting of aluminum hydroxide (alum) and CpG. The immunogenicity and safety of the vaccine were investigated in rats. The candidate vaccine elicited high titers of SARS-CoV-2-spike-specific IgG antibody and neutralizing antibody in immunized rats, which not only neutralize the original SARS-CoV-2, but also showed great cross-neutralization activity against the Beta, Delta and Omicron variants.
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Affiliation(s)
- Yuntao Zhang
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China; (Y.Z.); (X.Z.); (H.L.); (Y.Z.); (X.Z.); (R.Y.); (Y.Z.); (X.D.); (W.L.); (F.P.); (L.D.); (Z.C.); (L.D.); (G.Y.); (Z.Y.); (D.Z.)
- China National Biotec Group Company Limited, Beijing 100024, China
| | - Xiaotong Zheng
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China; (Y.Z.); (X.Z.); (H.L.); (Y.Z.); (X.Z.); (R.Y.); (Y.Z.); (X.D.); (W.L.); (F.P.); (L.D.); (Z.C.); (L.D.); (G.Y.); (Z.Y.); (D.Z.)
| | - Wang Sheng
- College of Life Sciences and Biotechnology, Beijing University of Technology, Beijing 100021, China;
| | - Hongyang Liang
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China; (Y.Z.); (X.Z.); (H.L.); (Y.Z.); (X.Z.); (R.Y.); (Y.Z.); (X.D.); (W.L.); (F.P.); (L.D.); (Z.C.); (L.D.); (G.Y.); (Z.Y.); (D.Z.)
| | - Yuxiu Zhao
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China; (Y.Z.); (X.Z.); (H.L.); (Y.Z.); (X.Z.); (R.Y.); (Y.Z.); (X.D.); (W.L.); (F.P.); (L.D.); (Z.C.); (L.D.); (G.Y.); (Z.Y.); (D.Z.)
| | - Xiujuan Zhu
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China; (Y.Z.); (X.Z.); (H.L.); (Y.Z.); (X.Z.); (R.Y.); (Y.Z.); (X.D.); (W.L.); (F.P.); (L.D.); (Z.C.); (L.D.); (G.Y.); (Z.Y.); (D.Z.)
| | - Rong Yang
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China; (Y.Z.); (X.Z.); (H.L.); (Y.Z.); (X.Z.); (R.Y.); (Y.Z.); (X.D.); (W.L.); (F.P.); (L.D.); (Z.C.); (L.D.); (G.Y.); (Z.Y.); (D.Z.)
| | - Yadan Zhang
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China; (Y.Z.); (X.Z.); (H.L.); (Y.Z.); (X.Z.); (R.Y.); (Y.Z.); (X.D.); (W.L.); (F.P.); (L.D.); (Z.C.); (L.D.); (G.Y.); (Z.Y.); (D.Z.)
| | - Xiaofei Dong
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China; (Y.Z.); (X.Z.); (H.L.); (Y.Z.); (X.Z.); (R.Y.); (Y.Z.); (X.D.); (W.L.); (F.P.); (L.D.); (Z.C.); (L.D.); (G.Y.); (Z.Y.); (D.Z.)
| | - Weidong Li
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China; (Y.Z.); (X.Z.); (H.L.); (Y.Z.); (X.Z.); (R.Y.); (Y.Z.); (X.D.); (W.L.); (F.P.); (L.D.); (Z.C.); (L.D.); (G.Y.); (Z.Y.); (D.Z.)
| | - Fei Pei
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China; (Y.Z.); (X.Z.); (H.L.); (Y.Z.); (X.Z.); (R.Y.); (Y.Z.); (X.D.); (W.L.); (F.P.); (L.D.); (Z.C.); (L.D.); (G.Y.); (Z.Y.); (D.Z.)
| | - Ling Ding
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China; (Y.Z.); (X.Z.); (H.L.); (Y.Z.); (X.Z.); (R.Y.); (Y.Z.); (X.D.); (W.L.); (F.P.); (L.D.); (Z.C.); (L.D.); (G.Y.); (Z.Y.); (D.Z.)
| | - Zhen Chang
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China; (Y.Z.); (X.Z.); (H.L.); (Y.Z.); (X.Z.); (R.Y.); (Y.Z.); (X.D.); (W.L.); (F.P.); (L.D.); (Z.C.); (L.D.); (G.Y.); (Z.Y.); (D.Z.)
| | - Li Deng
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China; (Y.Z.); (X.Z.); (H.L.); (Y.Z.); (X.Z.); (R.Y.); (Y.Z.); (X.D.); (W.L.); (F.P.); (L.D.); (Z.C.); (L.D.); (G.Y.); (Z.Y.); (D.Z.)
| | - Guangying Yuan
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China; (Y.Z.); (X.Z.); (H.L.); (Y.Z.); (X.Z.); (R.Y.); (Y.Z.); (X.D.); (W.L.); (F.P.); (L.D.); (Z.C.); (L.D.); (G.Y.); (Z.Y.); (D.Z.)
| | - Zhaona Yang
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China; (Y.Z.); (X.Z.); (H.L.); (Y.Z.); (X.Z.); (R.Y.); (Y.Z.); (X.D.); (W.L.); (F.P.); (L.D.); (Z.C.); (L.D.); (G.Y.); (Z.Y.); (D.Z.)
| | - Di Zhu
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China; (Y.Z.); (X.Z.); (H.L.); (Y.Z.); (X.Z.); (R.Y.); (Y.Z.); (X.D.); (W.L.); (F.P.); (L.D.); (Z.C.); (L.D.); (G.Y.); (Z.Y.); (D.Z.)
| | - Xiaoming Yang
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China; (Y.Z.); (X.Z.); (H.L.); (Y.Z.); (X.Z.); (R.Y.); (Y.Z.); (X.D.); (W.L.); (F.P.); (L.D.); (Z.C.); (L.D.); (G.Y.); (Z.Y.); (D.Z.)
- China National Biotec Group Company Limited, Beijing 100024, China
- Correspondence: (X.Y.); (H.W.)
| | - Hui Wang
- Beijing Institute of Biological Products Company Limited, Beijing 100176, China; (Y.Z.); (X.Z.); (H.L.); (Y.Z.); (X.Z.); (R.Y.); (Y.Z.); (X.D.); (W.L.); (F.P.); (L.D.); (Z.C.); (L.D.); (G.Y.); (Z.Y.); (D.Z.)
- Correspondence: (X.Y.); (H.W.)
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47
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Garg I, Sheikh AB, Pal S, Shekhar R. Mix-and-Match COVID-19 Vaccinations (Heterologous Boost): A Review. Infect Dis Rep 2022; 14:537-546. [PMID: 35893476 PMCID: PMC9326526 DOI: 10.3390/idr14040057] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/08/2022] [Accepted: 07/13/2022] [Indexed: 12/10/2022] Open
Abstract
Various safe and effective COVID-19 vaccines utilizing different platforms (mRNA, adenovirus vector, inactivated virus-based) are available against SARS-CoV-2 infection. A prime-boost regimen (administration of two doses) is recommended to induce an adequate and sustained immune response. Most of these vaccines follow a homologous regimen (the same type of vaccine as priming and booster doses). However, there is a growing interest in a heterologous prime-boost vaccination regimen to potentially help address concerns posed by fluctuating vaccine supplies, serious adverse effects (anaphylaxis and thromboembolic episodes following adenovirus-based vaccines), new emerging virulent strains, inadequate immune response in immunocompromised individuals, and waning immunity. Various studies have demonstrated that heterologous prime-boost vaccination may induce comparable or higher antibody (spike protein) titers and a similar reactogenicity profile to the homologous prime-boost regimen. Based on these considerations, the Center for Disease Control and Prevention has issued guidance supporting the "mix-and-match" heterologous boost COVID-19 vaccine strategy.
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Affiliation(s)
- Ishan Garg
- Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87106, USA; (A.B.S.); (S.P.)
| | | | | | - Rahul Shekhar
- Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87106, USA; (A.B.S.); (S.P.)
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48
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Chavda VP, Patel AB, Vaghasiya DD. SARS-CoV-2 variants and vulnerability at the global level. J Med Virol 2022; 94:2986-3005. [PMID: 35277864 PMCID: PMC9088647 DOI: 10.1002/jmv.27717] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 12/24/2022]
Abstract
Numerous variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic have evolved. Viral variants may evolve with harmful susceptibility to the immunity established with the existing COVID-19 vaccination. These variants are more transmissible, induce relatively extreme illness, have evasive immunological features, decrease neutralization using antibodies from vaccinated persons, and are more susceptible to re-infection. The Centers for Disease Control and Prevention (CDC) has categorized SARS-CoV-2 mutations as variants of interest (VOI), variants of concern (VOC), and variants of high consequence (VOHC). At the moment, four VOC and many variants of interest have been defined and require constant observation. This review article summarizes various variants of SARS-CoV-2 surfaced with special emphasis on VOCs that are spreading across the world, as well as several viral mutational impacts and how these modifications alter the properties of the virus.
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Affiliation(s)
- Vivek P. Chavda
- Department of Pharmaceutics and Pharmaceutical TechnologyL.M. College of PharmacyAhmedabadGujaratIndia
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Wang Z, Cryar A, Lemke O, Tober-Lau P, Ludwig D, Helbig ET, Hippenstiel S, Sander LE, Blake D, Lane CS, Sayers RL, Mueller C, Zeiser J, Townsend S, Demichev V, Mülleder M, Kurth F, Sirka E, Hartl J, Ralser M. A multiplex protein panel assay for severity prediction and outcome prognosis in patients with COVID-19: An observational multi-cohort study. EClinicalMedicine 2022; 49:101495. [PMID: 35702332 PMCID: PMC9181834 DOI: 10.1016/j.eclinm.2022.101495] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/11/2022] [Accepted: 05/17/2022] [Indexed: 12/15/2022] Open
Abstract
Background Global healthcare systems continue to be challenged by the COVID-19 pandemic, and there is a need for clinical assays that can help optimise resource allocation, support treatment decisions, and accelerate the development and evaluation of new therapies. Methods We developed a multiplexed proteomics assay for determining disease severity and prognosis in COVID-19. The assay quantifies up to 50 peptides, derived from 30 known and newly introduced COVID-19-related protein markers, in a single measurement using routine-lab compatible analytical flow rate liquid chromatography and multiple reaction monitoring (LC-MRM). We conducted two observational studies in patients with COVID-19 hospitalised at Charité - Universitätsmedizin Berlin, Germany before (from March 1 to 26, 2020, n=30) and after (from April 4 to November 19, 2020, n=164) dexamethasone became standard of care. The study is registered in the German and the WHO International Clinical Trials Registry (DRKS00021688). Findings The assay produces reproducible (median inter-batch CV of 10.9%) absolute quantification of 47 peptides with high sensitivity (median LLOQ of 143 ng/ml) and accuracy (median 96.8%). In both studies, the assay reproducibly captured hallmarks of COVID-19 infection and severity, as it distinguished healthy individuals, mild, moderate, and severe COVID-19. In the post-dexamethasone cohort, the assay predicted survival with an accuracy of 0.83 (108/130), and death with an accuracy of 0.76 (26/34) in the median 2.5 weeks before the outcome, thereby outperforming compound clinical risk assessments such as SOFA, APACHE II, and ABCS scores. Interpretation Disease severity and clinical outcomes of patients with COVID-19 can be stratified and predicted by the routine-applicable panel assay that combines known and novel COVID-19 biomarkers. The prognostic value of this assay should be prospectively assessed in larger patient cohorts for future support of clinical decisions, including evaluation of sample flow in routine setting. The possibility to objectively classify COVID-19 severity can be helpful for monitoring of novel therapies, especially in early clinical trials. Funding This research was funded in part by the European Research Council (ERC) under grant agreement ERC-SyG-2020 951475 (to M.R) and by the Wellcome Trust (IA 200829/Z/16/Z to M.R.). The work was further supported by the Ministry of Education and Research (BMBF) as part of the National Research Node 'Mass Spectrometry in Systems Medicine (MSCoresys)', under grant agreements 031L0220 and 161L0221. J.H. was supported by a Swiss National Science Foundation (SNSF) Postdoc Mobility fellowship (project number 191052). This study was further supported by the BMBF grant NaFoUniMedCOVID-19 - NUM-NAPKON, FKZ: 01KX2021. The study was co-funded by the UK's innovation agency, Innovate UK, under project numbers 75594 and 56328.
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Affiliation(s)
- Ziyue Wang
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Am Chariteplatz 1, 10117 Berlin, Germany
| | - Adam Cryar
- Inoviv, Mappin House, 4 Winsley St, London, United Kingdom
| | - Oliver Lemke
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Am Chariteplatz 1, 10117 Berlin, Germany
| | - Pinkus Tober-Lau
- Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Daniela Ludwig
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Am Chariteplatz 1, 10117 Berlin, Germany
| | - Elisa Theresa Helbig
- Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Stefan Hippenstiel
- Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Leif-Erik Sander
- Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
- Berlin Institute of Health at the Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | | | | | - Christoph Mueller
- Agilent Technologies Sales & Services GmbH & Co. KG, Waldbronn, Germany
| | - Johannes Zeiser
- Agilent Technologies Sales & Services GmbH & Co. KG, Waldbronn, Germany
| | - StJohn Townsend
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Am Chariteplatz 1, 10117 Berlin, Germany
| | - Vadim Demichev
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Am Chariteplatz 1, 10117 Berlin, Germany
| | - Michael Mülleder
- Core Facility – High-Throughput Mass Spectrometry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Am Chariteplatz 1, 10117 Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, and Department of Medicine I, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Ernestas Sirka
- Inoviv, Mappin House, 4 Winsley St, London, United Kingdom
| | - Johannes Hartl
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Am Chariteplatz 1, 10117 Berlin, Germany
| | - Markus Ralser
- Department of Biochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Am Chariteplatz 1, 10117 Berlin, Germany
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
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50
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Gogolewski K, Miasojedow B, Sadkowska-Todys M, Stepień M, Demkow U, Lech A, Szczurek E, Rabczenko D, Rosińska M, Gambin A. Data-driven case fatality rate estimation for the primary lineage of SARS-CoV-2 in Poland. Methods 2022; 203:584-593. [PMID: 35085741 PMCID: PMC8785264 DOI: 10.1016/j.ymeth.2022.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 12/05/2021] [Accepted: 01/18/2022] [Indexed: 12/28/2022] Open
Abstract
After more than one and a half year since the COVID-19 pandemics outbreak the scientific world is constantly trying to understand its dynamics. In this paper of the case fatality rates (CFR) for COVID-19 we study the historic data regarding mortality in Poland during the first six months of pandemic, when no SARS-CoV-2 variants of concern were present among infected. To this end, we apply competing risk models to perform both uni- and multivariate analyses on specific subpopulations selected by different factors including the key indicators: age, sex, hospitalization. The study explores the case fatality rate to find out its decreasing trend in time. Furthermore, we describe the differences in mortality among hospitalized and other cases indicating a sudden increase of mortality among hospitalized cases at the end of the 2020 spring season. Exploratory and multivariate analysis revealed the real impact of each variable and besides the expected factors indicating increased mortality (age, comorbidities) we track more non-obvious indicators. Recent medical care as well as the identification of the source contact, independently of the comorbidities, significantly impact an individual mortality risk. As a result, the study provides a twofold insight into the COVID-19 mortality in Poland. On one hand we explore mortality in different groups with respect to different variables, on the other we indicate novel factors that may be crucial in reducing mortality. The later can be coped, e.g. by more efficient contact tracing and proper organization and management of the health care system to accompany those who need medical care independently of comorbidities or COVID-19 infection.
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Affiliation(s)
- Krzysztof Gogolewski
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Błażej Miasojedow
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Małgorzata Sadkowska-Todys
- Department of Infectious Disease Epidemiology and Surveillance, National Institute of Public Health NIH - National Research Institute, Warsaw, Poland
| | - Małgorzata Stepień
- Department of Infectious Disease Epidemiology and Surveillance, National Institute of Public Health NIH - National Research Institute, Warsaw, Poland
| | - Urszula Demkow
- Department of Laboratory Diagnostics and Clinical Immunology of Developmental Age, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Lech
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland
| | - Ewa Szczurek
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Daniel Rabczenko
- Department for Monitoring and Analysis of Population Health Status, National Institute of Public Health NIH - National Research Institute, Warsaw, Poland
| | - Magdalena Rosińska
- Department of Infectious Disease Epidemiology and Surveillance, National Institute of Public Health NIH - National Research Institute, Warsaw, Poland
| | - Anna Gambin
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
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