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Lu J, Tan S, Gu H, Liu K, Huang W, Yu Z, Lu G, Wu Z, Gao X, Zhao J, Yao Z, Yi F, Yang Y, Wang H, Hu X, Lu M, Li W, Zhou H, Yu H, Shan C, Lin J. Effectiveness of a broad-spectrum bivalent mRNA vaccine against SARS-CoV-2 variants in preclinical studies. Emerg Microbes Infect 2024; 13:2321994. [PMID: 38377136 PMCID: PMC10906132 DOI: 10.1080/22221751.2024.2321994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/16/2024] [Indexed: 02/22/2024]
Abstract
Vaccines utilizing modified messenger RNA (mRNA) technology have shown robust protective efficacy against SARS-CoV-2 in humans. As the virus continues to evolve in both human and non-human hosts, risk remains that the performance of the vaccines can be compromised by new variants with strong immune escape abilities. Here we present preclinical characterizations of a novel bivalent mRNA vaccine RQ3025 for its safety and effectiveness in animal models. The mRNA sequence of the vaccine is designed to incorporate common mutations on the SARS-CoV-2 spike protein that have been discovered along the evolutionary paths of different variants. Broad-spectrum, high-titer neutralizing antibodies against multiple variants were induced in mice (BALB/c and K18-hACE2), hamsters and rats upon injections of RQ3025, demonstrating advantages over the monovalent mRNA vaccines. Effectiveness in protection against several newly emerged variants is also evident in RQ3025-vaccinated rats. Analysis of splenocytes derived cytokines in BALB/c mice suggested that a Th1-biased cellular immune response was induced by RQ3025. Histological analysis of multiple organs in rats following injection of a high dose of RQ3025 showed no evidence of pathological changes. This study proves the safety and effectiveness of RQ3025 as a broad-spectrum vaccine against SARS-CoV-2 variants in animal models and lays the foundation for its potential clinical application in the future.
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Affiliation(s)
- Jing Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, People’s Republic of China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, People’s Republic of China
- Center for mRNA Translational Research, Fudan University, Shanghai, People’s Republic of China
- Shanghai RNACure Biopharma Co., Ltd, Shanghai, People’s Republic of China
| | - Shudan Tan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, People’s Republic of China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, People’s Republic of China
- Center for mRNA Translational Research, Fudan University, Shanghai, People’s Republic of China
- Shanghai RNACure Biopharma Co., Ltd, Shanghai, People’s Republic of China
| | - Hao Gu
- Shanghai RNACure Biopharma Co., Ltd, Shanghai, People’s Republic of China
| | - Kunpeng Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
- University of the Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Wei Huang
- Shanghai RNACure Biopharma Co., Ltd, Shanghai, People’s Republic of China
| | - Zhaoli Yu
- Shanghai RNACure Biopharma Co., Ltd, Shanghai, People’s Republic of China
| | - Guoliang Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, People’s Republic of China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, People’s Republic of China
- Center for mRNA Translational Research, Fudan University, Shanghai, People’s Republic of China
| | - Zihan Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, People’s Republic of China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, People’s Republic of China
- Center for mRNA Translational Research, Fudan University, Shanghai, People’s Republic of China
| | - Xiaobo Gao
- Shanghai RNACure Biopharma Co., Ltd, Shanghai, People’s Republic of China
| | - Jinghua Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, People’s Republic of China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, People’s Republic of China
- Center for mRNA Translational Research, Fudan University, Shanghai, People’s Republic of China
- Shanghai RNACure Biopharma Co., Ltd, Shanghai, People’s Republic of China
| | - Zongting Yao
- Shanghai RNACure Biopharma Co., Ltd, Shanghai, People’s Republic of China
| | - Feng Yi
- Shanghai RNACure Biopharma Co., Ltd, Shanghai, People’s Republic of China
| | - Yantao Yang
- Shanghai RNACure Biopharma Co., Ltd, Shanghai, People’s Republic of China
| | - Hu Wang
- Shanghai RNACure Biopharma Co., Ltd, Shanghai, People’s Republic of China
| | - Xue Hu
- Shanghai RNACure Biopharma Co., Ltd, Shanghai, People’s Republic of China
| | - Mingqing Lu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
- University of the Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Wei Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, People’s Republic of China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, People’s Republic of China
- Center for mRNA Translational Research, Fudan University, Shanghai, People’s Republic of China
| | - Hui Zhou
- Shanghai RNACure Biopharma Co., Ltd, Shanghai, People’s Republic of China
| | - Hang Yu
- Shanghai RNACure Biopharma Co., Ltd, Shanghai, People’s Republic of China
| | - Chao Shan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
- University of the Chinese Academy of Sciences, Beijing, People’s Republic of China
- Hubei Jiangxia Laboratory, Wuhan, People’s Republic of China
| | - Jinzhong Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, People’s Republic of China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, People’s Republic of China
- Center for mRNA Translational Research, Fudan University, Shanghai, People’s Republic of China
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Calistri A, Francesco Roggero P, Palù G. Chaos theory in the understanding of COVID-19 pandemic dynamics. Gene 2024; 912:148334. [PMID: 38458366 DOI: 10.1016/j.gene.2024.148334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/28/2024] [Indexed: 03/10/2024]
Abstract
The chaos theory, a field of study in mathematics and physics, offers a unique lens through which to understand the dynamics of the COVID-19 pandemic. This theory, which deals with complex systems whose behavior is highly sensitive to initial conditions, can provide insights into the unpredictable and seemingly random nature of the pandemic's spread. In this review, we will discuss some literature data with the aim of showing how chaos theory could provide valuable perspectives in understanding the complex and dynamic nature of the COVID-19 pandemic. In particular, we will emphasize how the chaos theory can help in dissecting the unpredictable, non- linear progression of the disease, the importance of initial conditions, and the complex interactions between various factors influencing its spread. These insights are crucial for developing effective strategies to manage and mitigate the impact of the pandemic.
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Affiliation(s)
- Arianna Calistri
- Department of Molecular Medicine, University of Padova, Via A. Gabelli 63, 35121 Padova, Italy.
| | - Pier Francesco Roggero
- Department of Molecular Medicine, University of Padova, Via A. Gabelli 63, 35121 Padova, Italy.
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Via A. Gabelli 63, 35121 Padova, Italy.
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Schmitz T, Freuer D, Goßlau Y, Warm TD, Hyhlik-Dürr A, Linseisen J, Meisinger C, Kirchberger I. Can inflammatory plasma proteins predict Long COVID or Fatigue severity after SARS-CoV-2 infection? Virus Res 2024; 344:199363. [PMID: 38508399 PMCID: PMC10979265 DOI: 10.1016/j.virusres.2024.199363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 03/22/2024]
Abstract
OBJECTIVE To investigate whether specific immune response plasma proteins can predict an elevated risk of developing Long COVID symptoms or fatigue severity after SARS-CoV-2 infection. METHODS This study was based on 257 outpatients with test-confirmed SARS-CoV-2 infection between February 2020 and January 2021. At least 12 weeks after the acute infection, 92 plasma proteins were measured using the Olink Target 96 immune response panel (median time between acute infection and venous blood sampling was 38.8 [IQR: 24.0-48.0] weeks). The presence of Long COVID symptoms and fatigue severity was assessed 115.8 [92.5-118.6] weeks after the acute infection by a follow-up postal survey. Long COVID (yes/no) was defined as having one or more of the following symptoms: fatigue, shortness of breath, concentration or memory problems. The severity of fatigue was assessed using the Fatigue Assessment Scale (FAS). In multivariable-adjusted logistic and linear regression models the associations between each plasma protein (exposure) and Long COVID (yes/no) or severity of fatigue were investigated. RESULTS Nine plasma proteins were significantly associated with Long COVID before, but not after adjusting for multiple testing (FDR-adjustment): DFFA, TRIM5, TRIM21, HEXIM1, SRPK2, PRDX5, PIK3AP1, IFNLR1 and HCLS1. Moreover, a total of 10 proteins were significantly associated with severity of fatigue before FDR-adjustment: SRPK2, ITGA6, CLEC4G, HEXIM1, PPP1R9B, PLXNA4, PRDX5, DAPP1, STC1 and HCLS1. Only SRPK2 and ITGA6 remained significantly associated after FDR-adjustment. CONCLUSIONS This study demonstrates that certain immune response plasma proteins might play an important role in the pathophysiology of Long COVID and severity of fatigue after SARS-CoV-2 infection.
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Affiliation(s)
- Timo Schmitz
- Epidemiology, Medical Faculty, University of Augsburg, Augsburg, Germany.
| | - Dennis Freuer
- Epidemiology, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Yvonne Goßlau
- Vascular Surgery, Faculty of Medicine, University of Augsburg, Stenglinstr. 2, 86156, Augsburg, Germany
| | - Tobias Dominik Warm
- Vascular Surgery, Faculty of Medicine, University of Augsburg, Stenglinstr. 2, 86156, Augsburg, Germany
| | - Alexander Hyhlik-Dürr
- Vascular Surgery, Faculty of Medicine, University of Augsburg, Stenglinstr. 2, 86156, Augsburg, Germany
| | - Jakob Linseisen
- Epidemiology, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Christa Meisinger
- Epidemiology, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Inge Kirchberger
- Epidemiology, Medical Faculty, University of Augsburg, Augsburg, Germany
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Luo L, Lv J. An evolutionary theory on virus mutation in COVID-19. Virus Res 2024; 344:199358. [PMID: 38508401 PMCID: PMC10979259 DOI: 10.1016/j.virusres.2024.199358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/16/2024] [Accepted: 03/17/2024] [Indexed: 03/22/2024]
Abstract
With the rapid evolution of SARS-CoV-2, the emergence of new strains is an intriguing question. This paper presents an evolutionary theory to analyze the mutations of the virus and identify the conditions that lead to the generation of new strains. We represent the virus variants using a 4-letter sequence based on amino acid mutations on the spike protein and employ an n-distance algorithm to derive a variant phylogenetic tree. We show that the theoretically-derived tree aligns with experimental data on virus evolution. Additionally, we propose an A-X model, utilizing the set of existing mutation sites (A) and a set of randomly generated sites (X), to calculate the emergence of new strains. Our findings demonstrate that a sufficient number of random iterations can predict the generation of new macro-lineages when the number of sites in X is large enough. These results provide a crucial theoretical basis for understanding the evolution of SARS-CoV-2.
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Affiliation(s)
- Liaofu Luo
- Faculty of Physical Science and Technology, Inner Mongolia University, 235 West College Road, Hohhot 010021, China.
| | - Jun Lv
- College of Science, Inner Mongolia University of Technology, 49 Aymin Street, Hohhot 010051, China.
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Xiong D, Zhang X, Xu B, Shi M, Chen M, Dong Z, Zhong J, Gong R, Wu C, Li J, Wei H, Yu J. PHDtools: A platform for pathogen detection and multi-dimensional genetic signatures decoding to realize pathogen genomics data analyses online. Gene 2024; 909:148306. [PMID: 38408616 DOI: 10.1016/j.gene.2024.148306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/06/2024] [Accepted: 02/20/2024] [Indexed: 02/28/2024]
Abstract
OBJECTIVES Facing the emerging diseases, rapid identification of the pathogen and multi-dimensional characterization of the genomic features at both isolate-level and population-level through high-throughput sequencing data can provide invaluable information to guide the development of antiviral agents and strategies. However, a user-friendly program is in urgent need for clinical laboratories without bioinformatics background to decode the complex big genomics data. METHODS In this study, we developed an interactive online platform named PHDtools with a total of 15 functions to analyze metagenomics data to identify the potential pathogen and decode multi-dimensional genetic signatures including intra-/inter-host variations and lineage-level variations. The platform was applied to analyze the meta-genomic data of the samples collected from the 172 imported COVID-19 cases. RESULTS According to the analytical results of mNGS, 27 patients were found to have the co-infections of SARS-CoV-2 with either influenza virus (n = 9) or human picobirnavirus (n = 19). Enough coverages of all the assembled SARS-CoV-2 genomes provided the sub-lineages of Omicron variant, and the number of mutations in the non-structural genes and M gene was increased, as well as the intra-host variations occurred in E and M gene were under positive selection (Ka/Ks > 1). These findings of increased or changed mutations in the SARS-CoV-2 genome characterized the current adaptive evolution patterns of Omicron sub-lineages, and revealed the evolution speed of these sub-lineages might increase. CONCLUSIONS Consequently, the application of PHDtools has proved that this platform is accurate, user-friendly and convenient for clinical users who are deficient in bioinformatics, and the clinical monitor of SARS-CoV-2 genomes by PHDtools also highlighted the potential evolution features of current SARS-CoV-2 and indicated that the development of anti-SARS-CoV-2 agents and new-designed vaccines should incorporate the gene variations other than S gene.
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Affiliation(s)
- Dongyan Xiong
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China; Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China; Department of Chemical Pathology, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Xiaoxu Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Bohan Xu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengjuan Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuo Dong
- Hubei International Travel Healthcare Center (Wuhan Customs Port Outpatient Department), Wuhan 430070, China
| | - Jie Zhong
- Hubei International Travel Healthcare Center (Wuhan Customs Port Outpatient Department), Wuhan 430070, China
| | - Rui Gong
- Hubei International Travel Healthcare Center (Wuhan Customs Port Outpatient Department), Wuhan 430070, China
| | - Chang Wu
- Hubei International Travel Healthcare Center (Wuhan Customs Port Outpatient Department), Wuhan 430070, China
| | - Ji Li
- Hubei International Travel Healthcare Center (Wuhan Customs Port Outpatient Department), Wuhan 430070, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Junping Yu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Zhang X, Lam SJA, Ip JD, Fong CHY, Chu AWH, Chan WM, Lai YSY, Tsoi HW, Chan BPC, Chen LL, Meng X, Yuan S, Zhao H, Cheng VCC, Yuen JKY, Yuen KY, Zhou J, To KKW. Characterizing fitness and immune escape of SARS-CoV-2 EG.5 sublineage using elderly serum and nasal organoid. iScience 2024; 27:109706. [PMID: 38660398 PMCID: PMC11039328 DOI: 10.1016/j.isci.2024.109706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/23/2024] [Accepted: 04/06/2024] [Indexed: 04/26/2024] Open
Abstract
SARS-CoV-2 Omicron variant has evolved into sublineages. Here, we compared the neutralization susceptibility and viral fitness of EG.5.1 and XBB.1.9.1. Serum neutralization antibody titer against EG.5.1 was 1.71-fold lower than that for XBB.1.9.1. However, there was no significant difference in virus replication between EG.5.1 and XBB.1.9.1 in human nasal organoids and TMPRSS2/ACE2 over-expressing A549 cells. No significant difference was observed in competitive fitness and cytokine/chemokine response between EG.5.1 and XBB.1.9.1. Both EG.5.1 and XBB.1.9.1 replicated more robustly in the nasal organoid from a younger adult than that from an older adult. Our findings suggest that enhanced immune escape contributes to the dominance of EG.5.1 over earlier sublineages. The combination of population serum susceptibility testing and viral fitness evaluation with nasal organoids may hold promise in risk assessment of upcoming variants. Utilization of serum specimens and nasal organoid derived from older adults provides a targeted risk assessment for this vulnerable population.
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Affiliation(s)
- Xiaojuan Zhang
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Stephanie Joy-Ann Lam
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Jonathan Daniel Ip
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Carol Ho-Yan Fong
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Allen Wing-Ho Chu
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Wan-Mui Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yoyo Suet-Yiu Lai
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Hoi-Wah Tsoi
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Brian Pui-Chun Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Lin-Lei Chen
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Xinjie Meng
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Shuofeng Yuan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Hanjun Zhao
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Vincent Chi-Chung Cheng
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jacqueline Kwan Yuk Yuen
- Division of Geriatric Medicine, Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kwok-Yung Yuen
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Jie Zhou
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Kelvin Kai-Wang To
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
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Wiriyachaiporn N, Kongrueng J, Sukkuea K, Tanrattanawong R, Vanichtanankul J, Saeyang T, Jantra T, Japrung D, Maneeprakorn W, Bamrungsap S, Janchompoo P, Pasomsub E. Characterizing a visual lateral flow device for rapid SARS-CoV-2 virus protein detection: pre-clinical and system assessment. Anal Methods 2024; 16:2740-2750. [PMID: 38634326 DOI: 10.1039/d3ay02075d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections have affected more than 769 million individuals worldwide over the last few years. Although the pandemic is transitioning into an endemic, the COVID-19 outbreak is still a global concern. A rapid screening platform is needed for effective preventive and control measures. Herein, a visual rapid lateral flow platform for SARS-CoV-2 nucleocapsid protein detection is developed. Under optimal conditions, the system demonstrated good detection sensitivity and selectivity against tested respiratory viruses. The system provides direct visual detection with a limit of 0.7 ng of the nucleocapsid protein per mL of a sample (0.7 ng mL-1) within 15 minutes. Further, a correlation between direct visual detection and semi-quantitative analysis using a reader showed a similar detection limit (R2 = 0.9571). The repeatability and reproducibility studies highlighted the potential of the system for the rapid screening of SARS-CoV-2 infection, with variations within 5% and 10% at high and low protein concentrations, respectively. Subsequent pre-clinical validation to correlate the performance with the standard molecular approach (RT-PCR) using 170 nasopharyngeal swabs demonstrated 98% estimated sensitivity (95% CI, 89.35-99.95%) and 100% specificity (95% CI, 96.38-100%). The positive and negative predictive values were reported to be 100% and 99%, respectively, with an accuracy of 99.3%. With high viral load samples (Ct value ≤25, n = 47), the system demonstrated 100% detection sensitivity and specificity. The proposed technique provides a valuable platform for potential use in rapid screening, particularly during pandemics, where diagnostic capacity and mass screening are crucial.
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Affiliation(s)
- Natpapas Wiriyachaiporn
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
| | - Jetnapang Kongrueng
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
| | - Kannika Sukkuea
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
| | - Rattana Tanrattanawong
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
| | - Jarunee Vanichtanankul
- National Center of Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Thanaya Saeyang
- National Center of Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Tararat Jantra
- National Center of Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Deanpen Japrung
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
| | - Weerakanya Maneeprakorn
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
| | - Suwussa Bamrungsap
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
| | - Pareena Janchompoo
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Ekawat Pasomsub
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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8
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Colson P, Chaudet H, Delerce J, Pontarotti P, Levasseur A, Fantini J, La Scola B, Devaux C, Raoult D. Role of SARS-CoV-2 mutations in the evolution of the COVID-19 pandemic. J Infect 2024; 88:106150. [PMID: 38570164 DOI: 10.1016/j.jinf.2024.106150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 03/12/2024] [Accepted: 03/27/2024] [Indexed: 04/05/2024]
Abstract
OBJECTIVES The SARS-CoV-2 pandemic and large-scale genomic surveillance provided an exceptional opportunity to analyze mutations that appeared over three years in viral genomes. Here we studied mutations and their epidemic consequences for SARS-CoV-2 genomes from our center. METHODS We analyzed 61,397 SARS-CoV-2 genomes we sequenced from respiratory samples for genomic surveillance. Mutations frequencies were calculated using Nextclade, Microsoft Excel, and an in-house Python script. RESULTS A total of 22,225 nucleotide mutations were identified, 220 (1.0%) being each at the root of ≥836 genomes, classifying mutations as 'hyperfertile'. Two seeded the European pandemic: P323L in RNA polymerase, associated with an increased mutation rate, and D614G in spike that improved fitness. Most 'hyperfertile' mutations occurred in areas not predicted with increased virulence. Their mean number was 8±6 (0-22) per 1000 nucleotides per gene. They were 3.7-times more frequent in accessory than informational genes (13.8 versus 3.7/1000 nucleotides). Particularly, they were 4.1-times more frequent in ORF8 than in the RNA polymerase gene. Interestingly, stop codons were present in 97 positions, almost only in accessory genes, including ORF8 (21/100 codons). CONCLUSIONS most 'hyperfertile' mutations did not predict emergence of a new epidemic, and some were stop codons indicating the existence of so-named 'non-virulence' genes.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005 Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 Rue Saint-Pierre, 13005 Marseille, France
| | - Hervé Chaudet
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 Rue Saint-Pierre, 13005 Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Vecteurs, Infections Tropicales et Méditerranéennes (VITROME), 27 Boulevard Jean Moulin, 13005 Marseille, France; French Armed Forces Center for Epidemiology and Public Health (CESPA), Camp de Sainte Marthe, Marseille, France
| | - Jérémy Delerce
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005 Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 Rue Saint-Pierre, 13005 Marseille, France
| | - Pierre Pontarotti
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Department of Biological Sciences, Centre National de la Recherche Scientifique (CNRS)-SNC5039, Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005 Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 Rue Saint-Pierre, 13005 Marseille, France
| | - Jacques Fantini
- "Aix-Marseille Université, INSERM UMR UA 16, Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005 Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 Rue Saint-Pierre, 13005 Marseille, France
| | - Christian Devaux
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Department of Biological Sciences, Centre National de la Recherche Scientifique (CNRS)-SNC5039, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005 Marseille, France.
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9
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Yadav AJ, Kumar S, Maurya S, Bhagat K, Padhi AK. Interface design of SARS-CoV-2 symmetrical nsp7 dimer and machine learning-guided nsp7 sequence prediction reveals physicochemical properties and hotspots for nsp7 stability, adaptation, and therapeutic design. Phys Chem Chem Phys 2024. [PMID: 38686454 DOI: 10.1039/d4cp01014k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The COVID-19 pandemic, driven by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), necessitates a profound understanding of the virus and its lifecycle. As an RNA virus with high mutation rates, SARS-CoV-2 exhibits genetic variability leading to the emergence of variants with potential implications. Among its key proteins, the RNA-dependent RNA polymerase (RdRp) is pivotal for viral replication. Notably, RdRp forms dimers via non-structural protein (nsp) subunits, particularly nsp7, crucial for efficient viral RNA copying. Similar to the main protease (Mpro) of SARS-CoV-2, there is a possibility that the nsp7 might also undergo mutational selection events to generate more stable and adaptable versions of nsp7 dimer during virus evolution. However, efforts to obtain such cohesive and comprehensive information are lacking. To address this, we performed this study focused on deciphering the molecular intricacies of nsp7 dimerization using a multifaceted approach. Leveraging computational protein design (CPD), machine learning (ML), AlphaFold v2.0-based structural analysis, and several related computational approaches, we aimed to identify critical residues and mutations influencing nsp7 dimer stability and adaptation. Our methodology involved identifying potential hotspot residues within the dimeric nsp7 interface using an interface-based CPD approach. Through Rosetta-based symmetrical protein design, we designed and modulated nsp7 dimerization, considering selected interface residues. Analysis of physicochemical features revealed acceptable structural changes and several structural and residue-specific insights emphasizing the intricate nature of such protein-protein complexes. Our ML models, particularly the random forest regressor (RFR), accurately predicted binding affinities and ML-guided sequence predictions corroborated CPD findings, elucidating potential nsp7 mutations and their impact on binding affinity. Validation against clinical sequencing data demonstrated the predictive accuracy of our approach. Moreover, AlphaFold v2.0 structural analyses validated optimal dimeric configurations of affinity-enhancing designs, affirming methodological precision. Affinity-enhancing designs exhibited favourable energetics and higher binding affinity as compared to their counterparts. The obtained physicochemical properties, molecular interactions, and sequence predictions advance our understanding of SARS-CoV-2 evolution and inform potential avenues for therapeutic intervention against COVID-19.
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Affiliation(s)
- Amar Jeet Yadav
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India.
| | - Shivank Kumar
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India.
| | - Shweata Maurya
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India.
| | - Khushboo Bhagat
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India.
| | - Aditya K Padhi
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India.
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10
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Suwanchaikasem P, Rattanapisit K, Strasser R, Phoolcharoen W. Quality control in SARS-CoV-2 RBD-Fc vaccine production using LC-MS to confirm strain selection and detect contaminations from other strains. Sci Rep 2024; 14:9629. [PMID: 38671013 PMCID: PMC11053075 DOI: 10.1038/s41598-024-59860-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Coronavirus disease of 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an ongoing outbreak, disrupting human life worldwide. Vaccine development was prioritized to obtain a biological substance for combating the viral pathogen and lessening disease severity. In vaccine production, biological origin and relevant materials must be carefully examined for potential contaminants in conformity with good manufacturing practice. Due to fast mutation, several SARS-CoV-2 variants and sublineages have been identified. Currently, most of COVID-19 vaccines are developed based on the protein sequence of the Wuhan wild type strain. New vaccines specific for emerging SARS-CoV-2 strains are continuously needed to tackle the incessant evolution of the virus. Therefore, in vaccine development and production, a reliable method to identify the nature of subunit vaccines is required to avoid cross-contamination. In this study, liquid chromatography-mass spectrometry using quadrupole-time of flight along with tryptic digestion was developed for distinguishing protein materials derived from different SARS-CoV-2 strains. After analyzing the recombinantly produced receptor-binding domain (RBD) of the SARS-CoV-2 spike protein, nine characteristic peptides were identified with acceptable limits of detection. They can be used together to distinguish 14 SARS-CoV-2 strains, except Kappa and Epsilon. Plant-produced RBD-Fc protein derived from Omicron strains can be easily distinguished from the others with 4-5 unique peptides. Eventually, a peptide key was developed based on the nine peptides, offering a prompt and precise flowchart to facilitate SARS-CoV-2 strain identification in COVID-19 vaccine manufacturing.
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Affiliation(s)
| | | | - Richard Strasser
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, 1180, Vienna, Austria
| | - Waranyoo Phoolcharoen
- Center of Excellence in Plant-Produced Pharmaceuticals, Chulalongkorn University, Bangkok, 10330, Thailand.
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand.
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11
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Bukhari SNH, Elshiekh E, Abbas M. Physicochemical properties-based hybrid machine learning technique for the prediction of SARS-CoV-2 T-cell epitopes as vaccine targets. PeerJ Comput Sci 2024; 10:e1980. [PMID: 38686005 PMCID: PMC11057572 DOI: 10.7717/peerj-cs.1980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/15/2024] [Indexed: 05/02/2024]
Abstract
Majority of the existing SARS-CoV-2 vaccines work by presenting the whole pathogen in the attenuated form to immune system to invoke an immune response. On the other hand, the concept of a peptide based vaccine (PBV) is based on the identification and chemical synthesis of only immunodominant peptides known as T-cell epitopes (TCEs) to induce a specific immune response against a particular pathogen. However PBVs have received less attention despite holding huge untapped potential for boosting vaccine safety and immunogenicity. To identify these TCEs for designing PBV, wet-lab experiments are difficult, expensive, and time-consuming. Machine learning (ML) techniques can accurately predict TCEs, saving time and cost for speedy vaccine development. This work proposes novel hybrid ML techniques based on the physicochemical properties of peptides to predict SARS-CoV-2 TCEs. The proposed hybrid ML technique was evaluated using various ML model evaluation metrics and demonstrated promising results. The hybrid technique of decision tree classifier with chi-squared feature weighting technique and forward search optimal feature searching algorithm has been identified as the best model with an accuracy of 98.19%. Furthermore, K-fold cross-validation (KFCV) was performed to ensure that the model is reliable and the results indicate that the hybrid random forest model performs consistently well in terms of accuracy with respect to other hybrid approaches. The predicted TCEs are highly likely to serve as promising vaccine targets, subject to evaluations both in-vivo and in-vitro. This development could potentially save countless lives globally, prevent future epidemic-scale outbreaks, and reduce the risk of mutation escape.
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Affiliation(s)
- Syed Nisar Hussain Bukhari
- National Institute of Electronics and Information Technology (NIELIT), Srinagar, Jammu and Kashmir, India
| | - E. Elshiekh
- Department of Radiological Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Mohamed Abbas
- Electrical Engineering Department, College of Engineering, King Khalid University, Abha, Saudi Arabia
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12
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Ameratunga R, Jordan A, Lehnert K, Leung E, Mears ER, Snell R, Steele R, Woon ST. SARS-CoV-2 evolution has increased resistance to monoclonal antibodies and first-generation COVID-19 vaccines: Is there a future therapeutic role for soluble ACE2 receptors for COVID-19? Antiviral Res 2024:105894. [PMID: 38677595 DOI: 10.1016/j.antiviral.2024.105894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 04/29/2024]
Abstract
COVID-19 has caused calamitous health, economic and societal consequences. Although several COVID-19 vaccines have received full authorization for use, global deployment has faced political, financial and logistical challenges. The efficacy of first-generation COVID-19 vaccines is waning and breakthrough infections are allowing ongoing transmission and evolution of SARS-CoV-2. Furthermore, COVID-19 vaccine efficacy relies on a functional immune system. Despite receiving three primary doses and three or more heterologous boosters, some immunocompromised patients may not be adequately protected by COVID-19 vaccines and remain vulnerable to severe disease. The evolution of new SARS-CoV-2 variants has also resulted in the rapid obsolescence of monoclonal antibodies. Convalescent plasma from COVID-19 survivors has produced inconsistent results. New drugs such as Paxlovid (nirmatrelvir/ritonavir) are beyond the reach of low- and middle-income countries. With widespread use of Paxlovid, it is likely nirmatrelvir-resistant clades of SARS-CoV-2 will emerge in the future. There is thus an urgent need for new effective anti-SARS-CoV-2 treatments. The in vitro efficacy of soluble ACE2 against multiple SARS-CoV-2 variants including omicron (B.1.1.529), was recently described using a competitive ELISA assay as a surrogate marker for virus neutralization. This indicates soluble wild-type ACE2 receptors are likely to be resistant to viral evolution. Nasal and inhaled treatment with soluble ACE2 receptors has abrogated severe disease in animal models of COVID-19. There is an urgent need for clinical trials of this new class of antiviral therapeutics, which could complement vaccines and Paxlovid.
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Affiliation(s)
- Rohan Ameratunga
- Department of Clinical Immunology, Auckland Hospital, Park Rd, Grafton 1010, Auckland New Zealand; Department of Virology and Immunology, Auckland Hospital, Park Rd, Grafton 1010, Auckland, New Zealand; Department of Molecular Medicine and Pathology, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland.
| | - Anthony Jordan
- Department of Clinical Immunology, Auckland Hospital, Park Rd, Grafton 1010, Auckland New Zealand
| | - Klaus Lehnert
- School of Biological Sciences, Center for Brain Research, University of Auckland, Auckland, New Zealand
| | - Euphemia Leung
- Cancer Research, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland
| | - Emily R Mears
- School of Biological Sciences, Center for Brain Research, University of Auckland, Auckland, New Zealand
| | - Russell Snell
- School of Biological Sciences, Center for Brain Research, University of Auckland, Auckland, New Zealand
| | - Richard Steele
- Department of Virology and Immunology, Auckland Hospital, Park Rd, Grafton 1010, Auckland, New Zealand
| | - See-Tarn Woon
- Department of Virology and Immunology, Auckland Hospital, Park Rd, Grafton 1010, Auckland, New Zealand; Department of Molecular Medicine and Pathology, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland
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13
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Visser LG. Identifying efficacious SARS-CoV-2 antivirals in a changing immune landscape. Lancet Infect Dis 2024:S1473-3099(24)00254-8. [PMID: 38677299 DOI: 10.1016/s1473-3099(24)00254-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 04/29/2024]
Affiliation(s)
- Leo G Visser
- Leiden University Center for Infectious Diseases, Leiden University Medical Center, 2333 ZA Leiden, Netherlands.
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14
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Apostolopoulos V, Feehan J, Chavda VP. How do we change our approach to COVID with the changing face of disease? Expert Rev Anti Infect Ther 2024. [PMID: 38642067 DOI: 10.1080/14787210.2024.2345881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
INTRODUCTION The emergence of SARS-CoV-2 triggered a global health emergency, causing > 7 million deaths thus far. Limited early knowledge spurred swift research, treatment, and vaccine developments. Implementation of public health measures such as, lockdowns and social distancing, disrupted economies and strained healthcare. Viral mutations highlighted the need for flexible strategies and strong public health infrastructure, with global collaboration crucial for pandemic control. AREAS COVERED (i) Revisiting diagnostic strategies, (ii) adapting to the evolving challenge of the virus, (iii) vaccines against new variants, (iv) vaccine hesitancy in the light of the evolving disease, (v) treatment strategies, (vi) hospital preparedness for changing clinical needs, (vii) global cooperation and data sharing, (viii) economic implications, and (ix) education and awareness- keeping communities informed. EXPERT OPINION The COVID-19 crisis forced unprecedented adaptation, emphasizing public health readiness, global unity, and scientific advancement. Key lessons highlight the importance of adaptability and resilience against uncertainties. As the pandemic evolves into a 'new normal,' ongoing vigilance, improved understanding, and available vaccines and treatments equip us for future challenges. Priorities now include proactive pandemic strategies, early warnings, supported healthcare, public education, and addressing societal disparities for better health resilience and sustainability.
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Affiliation(s)
- Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Australia
- Australian Institute for Musculoskeletal Science (AIMSS), Immunology Program, St Albans, Australia
| | - Jack Feehan
- Institute for Health and Sport, Victoria University, Australia
- Australian Institute for Musculoskeletal Science (AIMSS), Immunology Program, St Albans, Australia
| | - Vivek P Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L.M. College of Pharmacy, Ahmedabad, Gujarat, India
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15
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McGough L, Cobey S. A speed limit on serial strain replacement from original antigenic sin. bioRxiv 2024:2024.01.04.574172. [PMID: 38260288 PMCID: PMC10802292 DOI: 10.1101/2024.01.04.574172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Many pathogens evolve to escape immunity, yet it remains difficult to predict whether immune pressure will lead to diversification, serial replacement of one variant by another, or more complex patterns. Pathogen strain dynamics are mediated by cross-protective immunity, whereby exposure to one strain partially protects against infection by antigenically diverged strains. There is growing evidence that this protection is influenced by early exposures, a phenomenon referred to as original antigenic sin (OAS) or imprinting. In this paper, we derive new constraints on the emergence of the pattern of successive strain replacements demonstrated by influenza, SARS-CoV-2, seasonal coronaviruses, and other pathogens. We find that OAS implies that the limited diversity found with successive strain replacement can only be maintained if R 0 is less than a threshold set by the characteristic antigenic distances for cross-protection and for the creation of new immune memory. This bound implies a "speed limit" on the evolution of new strains and a minimum variance of the distribution of infecting strains in antigenic space at any time. To carry out this analysis, we develop a theoretical model of pathogen evolution in antigenic space that implements OAS by decoupling the antigenic distances required for protection from infection and strain-specific memory creation. Our results demonstrate that OAS can play an integral role in the emergence of strain structure from host immune dynamics, preventing highly transmissible pathogens from maintaining serial strain replacement without diversification.
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Affiliation(s)
- Lauren McGough
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
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16
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Padilla S, Ledesma C, García-Abellán J, García JA, Fernández-González M, de la Rica A, Galiana A, Gutiérrez F, Masiá M. Long COVID across SARS-CoV-2 variants, lineages, and sublineages. iScience 2024; 27:109536. [PMID: 38585665 PMCID: PMC10995878 DOI: 10.1016/j.isci.2024.109536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/09/2024] [Accepted: 03/17/2024] [Indexed: 04/09/2024] Open
Abstract
This prospective study aimed to determine the prevalence of long COVID in patients hospitalized for SARS-CoV-2 infection from March 2020 to July 2022 and assess the impact of different viral lineages. A total of 2,524 patients were followed up for 12 months, with persistent symptoms reported in 35.2% at one month, decreasing thereafter. Omicron variant patients initially showed higher symptom intensity, but this trend diminished over time. Certain viral lineages, notably Delta lineages AY.126 and AY.43, and Omicron sublineages BA.1.17, BA.2.56, and BA.5.1, consistently correlated with more severe symptoms. Overall, long COVID prevalence and severity were similar across SARS-CoV-2 variants. Specific lineages may influence post-COVID sequelae persistence and severity.
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Affiliation(s)
- Sergio Padilla
- Infectious Diseases Unit, Hospital General Universitario de Elche, Alicante, Spain
- Universidad Miguel Hernández de Elche, San Juan de Alicante, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Christian Ledesma
- Infectious Diseases Unit, Hospital General Universitario de Elche, Alicante, Spain
| | - Javier García-Abellán
- Infectious Diseases Unit, Hospital General Universitario de Elche, Alicante, Spain
- Universidad Miguel Hernández de Elche, San Juan de Alicante, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - José Alberto García
- Infectious Diseases Unit, Hospital General Universitario de Elche, Alicante, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Fernández-González
- Infectious Diseases Unit, Hospital General Universitario de Elche, Alicante, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Alba de la Rica
- Microbiology Service, Hospital General Universitario de Elche, Alicante, Spain
| | - Antonio Galiana
- Microbiology Service, Hospital General Universitario de Elche, Alicante, Spain
| | - Félix Gutiérrez
- Infectious Diseases Unit, Hospital General Universitario de Elche, Alicante, Spain
- Universidad Miguel Hernández de Elche, San Juan de Alicante, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Mar Masiá
- Infectious Diseases Unit, Hospital General Universitario de Elche, Alicante, Spain
- Universidad Miguel Hernández de Elche, San Juan de Alicante, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
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17
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Wu F, Jiang Y, Yang H, Ma L. Development of Detection Antibody Targeting the Linear Epitope in SARS-CoV-2 Nucleocapsid Protein with Ultra-High Sensitivity. Int J Mol Sci 2024; 25:4436. [PMID: 38674021 PMCID: PMC11050370 DOI: 10.3390/ijms25084436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/04/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 highlighted the importance of reliable detection methods for disease control and surveillance. Optimizing detection antibodies by rational screening antigens would improve the sensitivity and specificity of antibody-based detection methods such as colloidal gold immunochromatography. In this study, we screened three peptide antigens with conserved sequences in the N protein of SARS-CoV-2 using bioinformatical and structural biological analyses. Antibodies that specifically recognize these peptides were prepared. The epitope of the peptide that had the highest binding affinity with its antibody was located on the surface of the N protein, which was favorable for antibody binding. Using the optimal antibody that can recognize this epitope, we developed colloidal gold immunochromatography, which can detect the N protein at 10 pg/mL. Importantly, this antibody could effectively recognize both the natural peptide antigen and mutated peptide antigen in the N protein, showing the feasibility of being applied in the large-scale population testing of SARS-CoV-2. Our study provides a platform with reference significance for the rational screening of detection antibodies with high sensitivity, specificity, and reliability for SARS-CoV-2 and other pathogens.
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Affiliation(s)
- Feng Wu
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (F.W.); (H.Y.)
- Shenzhen Institute of Drug Control, Shenzhen 518057, China
| | - Yike Jiang
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China;
| | - Hongtian Yang
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (F.W.); (H.Y.)
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China;
| | - Lan Ma
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (F.W.); (H.Y.)
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China;
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
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Calderón LCL, Cabanne GS, Marcos A, Novo SG, Torres C, Perez AM, Pybus OG, König GA. Phylodynamic analysis of foot-and-mouth disease virus evolution in Mar Chiquita, Argentina. Arch Virol 2024; 169:101. [PMID: 38630189 DOI: 10.1007/s00705-024-06028-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/16/2024] [Indexed: 04/19/2024]
Abstract
Foot-and-mouth disease is a highly contagious disease affecting cloven-hoofed animals, resulting in considerable economic losses. Its causal agent is foot-and-mouth disease virus (FMDV), a picornavirus. Due to its error-prone replication and rapid evolution, the transmission and evolutionary dynamics of FMDV can be studied using genomic epidemiological approaches. To analyze FMDV evolution and identify possible transmission routes in an Argentinean region, field samples that tested positive for FMDV by PCR were obtained from 21 farms located in the Mar Chiquita district. Whole FMDV genome sequences were obtained by PCR amplification in seven fragments and sequencing using the Sanger technique. The genome sequences obtained from these samples were then analyzed using phylogenetic, phylogeographic, and evolutionary approaches. Three local transmission clusters were detected among the sampled viruses. The dataset was analyzed using Bayesian phylodynamic methods with appropriate coalescent and relaxed molecular clock models. The estimated mean viral evolutionary rate was 1.17 × 10- 2 substitutions/site/year. No significant differences in the rate of viral evolution were observed between farms with vaccinated animals and those with unvaccinated animals. The most recent common ancestor of the sampled sequences was dated to approximately one month before the first reported case in the outbreak. Virus transmission started in the south of the district and later dispersed to the west, and finally arrived in the east. Different transmission routes among the studied herds, such as non-replicating vectors and close contact contagion (i.e., aerosols), may be responsible for viral spread.
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Affiliation(s)
| | - Gustavo S Cabanne
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"-CONICET, Buenos Aires, Argentina
| | - Andrea Marcos
- Coordinación general de Epidemiología y Análisis de Riesgo, SENASA, Buenos Aires, Argentina
| | - Sabrina Galdo Novo
- DGLYCT - Dirección de Laboratorio Animal, SENASA, Buenos Aires, Argentina
| | - Carolina Torres
- Instituto de Investigaciones en Bacteriología y Virología Molecular FFyB, UBA, Buenos Aires, Argentina
| | - Andrés M Perez
- Department of Veterinary Population Medicine, UMN, St Paul, USA
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, United Kingdom
| | - Guido A König
- Instituto de Agrobiotecnología y Biología Molecular, INTA-CONICET, Buenos Aires, Argentina.
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19
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Reis AC, Pinto D, Monteiro S, Santos R, Martins JV, Sousa A, Páscoa R, Lourinho R, Cunha MV. Systematic SARS-CoV-2 S-gene sequencing in wastewater samples enables early lineage detection and uncovers rare mutations in Portugal. Sci Total Environ 2024; 921:170961. [PMID: 38367735 DOI: 10.1016/j.scitotenv.2024.170961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/23/2023] [Accepted: 02/11/2024] [Indexed: 02/19/2024]
Abstract
As the COVID-19 pandemic reached its peak, many countries implemented genomic surveillance systems to track the evolution and transmission of SARS-CoV-2. Transition from the pandemic to the endemic phase prioritized alternative testing strategies to maintain effective epidemic surveillance at the population level, with less intensive sequencing efforts. One such promising approach was Wastewater-Based Surveillance (WBS), which offers non-invasive, cost-effective means for analysing virus trends at the sewershed level. From 2020 onwards, wastewater has been recognized as an instrumental source of information for public health, with national and international authorities exploring options to implement national wastewater surveillance systems and increasingly relying on WBS as early warning of potential pathogen outbreaks. In Portugal, several pioneer projects joined the academia, water utilities and Public Administration around WBS. To validate WBS as an effective genomic surveillance strategy, it is crucial to collect long term performance data. In this work, we present one year of systematic SARS-CoV-2 wastewater surveillance in Portugal, representing 35 % of the mainland population. We employed two complementary methods for lineage determination - allelic discrimination by RT-PCR and S-gene sequencing. This combination allowed us to monitor variant evolution in near-real-time and identify low-frequency mutations. Over the course of this year-long study, spanning from May 2022 to April 2023, we successfully tracked the dominant Omicron sub-lineages, their progression and evolution, which aligned with concurrent clinical surveillance data. Our results underscore the effectiveness of WBS as a tracking system for virus variants, with the ability to unveil mutations undetected via massive sequencing of clinical samples from Portugal, demonstrating the ability of WBS to uncover new mutations and detect rare genetic variants. Our findings emphasize that knowledge of the genetic diversity of SARS-CoV-2 at the population level can be extended far beyond via the combination of routine clinical genomic surveillance with wastewater sequencing and genotyping.
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Affiliation(s)
- Ana C Reis
- Centre for Ecology, Evolution and Environmental Changes (cE3c), CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Daniela Pinto
- Centre for Ecology, Evolution and Environmental Changes (cE3c), CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Sílvia Monteiro
- Laboratório de Análises, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal; CERIS - Civil Engineering Research and Innovation for Sustainability, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal; DECN - Department of Nuclear Sciences and Engineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Ricardo Santos
- Laboratório de Análises, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal; CERIS - Civil Engineering Research and Innovation for Sustainability, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal; DECN - Department of Nuclear Sciences and Engineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | | | | | | | | | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.
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20
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Shi Y, Ma Y, Zheng Z, Qin Y, Du Z, Liu J. Development and validation of a predicting nomogram for in-hospital mortality of COVID-19 Omicron variant: A cohort study of 1324 cases in Beijing Anzhen Hospital. Heliyon 2024; 10:e28627. [PMID: 38590893 PMCID: PMC11000003 DOI: 10.1016/j.heliyon.2024.e28627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/14/2024] [Accepted: 03/21/2024] [Indexed: 04/10/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19) is continuously posing high global public health concerns due to its high morbidity and mortality. This study aimed to construct a convenient risk model for predicting in-hospital mortality of COVID-19 Omicron variant. A total of 1324 hospitalized patients with Omicron variant were enrolled from Beijing Anzhen Hospital. During hospitalization, the Omicron variant mortality rate was found to be 24.4%. Using the datasets of clinical demographics and laboratory tests, three machine learning algorithms, including best subset selection, stepwise selection, and least absolute shrinkage and selection operator regression analyses were employed to identify the potential predictors of in-hospital mortality. The results found that a panel of twenty-four clinical variables (including age, hyperlipemia, stroke, tumor, and several cardiovascular markers) identified by stepwise selection model exhibited significant performances in predicting the in-hospital mortality of COVID-19. The resultant nomogram showed good discrimination, highlighted by the areas under the curve values of 0.88 for 10 days, 0.81 for 20 days, and 0.82 for 30 days, respectively. Furthermore, decision curve analysis showed a significant reliability and precision for the established stepwise selection model. Collectively, this study developed an accurate and convenience risk model for predicting the in-hospital mortality of COVID-19 Omicron.
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Affiliation(s)
- Yuchen Shi
- Center for Coronary Artery Disease(CCAD), Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing, China
| | - Ying Ma
- The State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Ze Zheng
- Center for Coronary Artery Disease(CCAD), Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing, China
| | - Yanwen Qin
- Center for Coronary Artery Disease(CCAD), Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing, China
| | - Zhiyong Du
- Center for Coronary Artery Disease(CCAD), Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing, China
| | - Jinghua Liu
- Center for Coronary Artery Disease(CCAD), Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing, China
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21
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Sarkar A, Ghosh TA, Bandyopadhyay B, Maiti S, Panja AS. Prediction of Prospective Mutational Landscape of SARS-CoV-2 Spike ssRNA and Evolutionary Basis of Its Host Interaction. Mol Biotechnol 2024:10.1007/s12033-024-01146-1. [PMID: 38619800 DOI: 10.1007/s12033-024-01146-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/14/2024] [Indexed: 04/16/2024]
Abstract
Booster doses are crucial against severe COVID-19, as rapid virus mutations and variant emergence prolong the pandemic crisis. The virus's quick evolution, short generation-time, and adaptive changes impact virulence and evolvability, helping predictions about variant of concerns' (VOCs') landscapes. Here, in this study, we used a new computational algorithm, to predict the mutational pattern in SARS-CoV-2 ssRNA, proteomics, structural identification, mutation stability, and functional correlation, as well as immune escape mechanisms. Interestingly, the sequence diversity of SARS Coronavirus-2 has demonstrated a predominance of G- > A and C- > U substitutions. The best validation statistics are explored here in seven homologous models of the expected mutant SARS-CoV-2 spike ssRNA and employed for hACE2 and IgG interactions. The interactome profile of SARS-CoV-2 spike with hACE2 and IgG revealed a strong correlation between phylogeny and divergence time. The systematic adaptation of SARS-CoV-2 spike ssRNA influences infectivity and immune escape. Data suggest higher propensity of Adenine rich sequence promotes MHC system avoidance, preferred by A-rich codons. Phylogenetic data revealed the evolution of SARS-CoV-2 lineages' epidemiology. Our findings may unveil processes governing the genesis of immune-resistant variants, prompting a critical reassessment of the coronavirus mutation rate and exploration of hypotheses beyond mechanical aspects.
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Affiliation(s)
- Aniket Sarkar
- Post Graduate Department of Biotechnology, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Trijit Arka Ghosh
- Department of Computer Application, Burdwan Institute of Management and Computer Science, The University of Burdwan, Dewandighi, Burdwan, West Bengal, 713102, India
| | - Bidyut Bandyopadhyay
- Post Graduate Department of Biotechnology, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Smarajit Maiti
- Department of Medical Laboratory Technology, Haldia Institute of Health Sciences, ICARE Complex, Haldia, West Bengal, 721657, India
| | - Anindya Sundar Panja
- Post Graduate Department of Biotechnology, Molecular Informatics Laboratory, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, West Bengal, 721102, India.
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22
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Jagst M, Pottkämper L, Gömer A, Pitarokoili K, Steinmann E. Neuroinvasion and neurotropism of severe acute respiratory syndrome coronavirus 2 infection. Curr Opin Microbiol 2024; 79:102474. [PMID: 38615394 DOI: 10.1016/j.mib.2024.102474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/16/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019, contributes to neurological pathologies in nearly 30% of patients, extending beyond respiratory symptoms. These manifestations encompass disorders of both the peripheral and central nervous systems, causing among others cerebrovascular issues and psychiatric manifestations during the acute and/or post-acute infection phases. Despite ongoing research, uncertainties persist about the precise mechanism the virus uses to infiltrate the central nervous system and the involved entry portals. This review discusses the potential entry routes, including hematogenous and anterograde transport. Furthermore, we explore variations in neurotropism, neurovirulence, and neurological manifestations among pandemic-associated variants of concern. In conclusion, SARS-CoV-2 can infect numerous cells within the peripheral and central nervous system, provoke inflammatory responses, and induce neuropathological changes.
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Affiliation(s)
- Michelle Jagst
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany; Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Lilli Pottkämper
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - André Gömer
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Kalliopi Pitarokoili
- Department of Neurology, St. Josef Hospital, Ruhr University Bochum, Bochum, Germany
| | - Eike Steinmann
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany; German Centre for Infection Research (DZIF), External Partner Site, Bochum, Germany.
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23
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Baek K, Kim D, Kim J, Kang BM, Park H, Park S, Shin HE, Lee MH, Maharjan S, Kim M, Kim S, Park MS, Lee Y, Kwon HJ. Analysis of SARS-CoV-2 omicron mutations that emerged during long-term replication in a lung cancer xenograft mouse model. Virus Genes 2024:10.1007/s11262-024-02067-6. [PMID: 38587722 DOI: 10.1007/s11262-024-02067-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/12/2024] [Indexed: 04/09/2024]
Abstract
SARS-CoV-2 Omicron has the largest number of mutations among all the known SARS-CoV-2 variants. The presence of these mutations might explain why Omicron is more infectious and vaccines have lower efficacy to Omicron than other variants, despite lower virulence of Omicron. We recently established a long-term in vivo replication model by infecting Calu-3 xenograft tumors in immunodeficient mice with parental SARS-CoV-2 and found that various mutations occurred majorly in the spike protein during extended replication. To investigate whether there are differences in the spectrum and frequency of mutations between parental SARS-CoV-2 and Omicron, we here applied this model to Omicron. At 30 days after infection, we found that the virus was present at high titers in the tumor tissues and had developed several rare sporadic mutations, mainly in ORF1ab with additional minor spike protein mutations. Many of the mutant isolates had higher replicative activity in Calu-3 cells compared with the original SARS-CoV-2 Omicron virus, suggesting that the novel mutations contributed to increased viral replication. Serial propagation of SARS-CoV-2 Omicron in cultured Calu-3 cells resulted in several rare sporadic mutations in various viral proteins with no mutations in the spike protein. Therefore, the genome of SARS-CoV-2 Omicron seems largely stable compared with that of the parental SARS-CoV-2 during extended replication in Calu-3 cells and xenograft model. The sporadic mutations and modified growth properties observed in Omicron might explain the emergence of Omicron sublineages. However, we cannot exclude the possibility of some differences in natural infection.
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Affiliation(s)
- Kyeongbin Baek
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea
| | - Dongbum Kim
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea
| | - Jinsoo Kim
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea
| | - Bo Min Kang
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea
| | - Heedo Park
- Department of Microbiology, Institute for Viral Diseases, Vaccine Innovation Center, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Sangkyu Park
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Ha-Eun Shin
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Myeong-Heon Lee
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Sony Maharjan
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea
| | - Minyoung Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea
| | - Suyeon Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, Vaccine Innovation Center, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Younghee Lee
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Hyung-Joo Kwon
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea.
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea.
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24
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Lina A, Keith H, Jenny H, Mariana M, Gregorio T, Laure WV, Paolo T. Facing SARS-CoV-2 emergence on the animal health perspective: The role of the World Organisation for Animal Health in preparedness and official reporting of disease occurrence. Zoonoses Public Health 2024. [PMID: 38584342 DOI: 10.1111/zph.13133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 03/17/2024] [Accepted: 03/19/2024] [Indexed: 04/09/2024]
Abstract
AIMS Current data suggest that SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) emerged from an animal source. However, to date, there is insufficient scientific evidence to identify the source of SARS-CoV-2 or to explain the original route of transmission to humans. A wide range of mammalian species have been shown to be susceptible to the virus through experimental infection, and in natural environments when in contact with infected humans. The main objective of this work was to provide a summary of the official data shared by countries on SARS-CoV-2 in animals with the World Organisation for Animal Health (WOAH), to highlight the role of WOAH as an international organization in coordinating scientific information actions and to discuss the implications and impact of these activities. METHODS AND RESULTS Between January 2020 and December 2022, 36 countries in Europe, the Americas, Asia and Africa officially reported SARS-CoV-2 identification in 26 animal species. Affected countries were generally responsive in confirming the pathogen (median of 5 days after onset) and reporting to WOAH (median of 7 days after confirmation). CONCLUSIONS During the pandemic, WOAH, supported by its network of experts, played a crucial role in collecting, analysing and disseminating veterinary scientific information, acting as the reference organization on these issues, thus avoiding misinformation and disinformation. Future perspectives to avoid new emerging threats are discussed.
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Affiliation(s)
- Awada Lina
- World Organisation for Animal Health (WOAH), Paris, France
| | - Hamilton Keith
- World Organisation for Animal Health (WOAH), Paris, France
| | | | | | | | | | - Tizzani Paolo
- World Organisation for Animal Health (WOAH), Paris, France
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25
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Scutelnic A, van de Munckhof A, Miraclin AT, Aaron S, Hameed S, Wasay M, Grosu O, Krzywicka K, Sánchez van Kammen M, Lindgren E, Moreira T, Acampora R, Negro A, Karapanayiotides T, Yaghi S, Revert A, Cuadrado Godia E, Garcia-Madrona S, La Spina P, Grillo F, Giammello F, Nguyen TN, Abdalkader M, Buture A, Sofia Cotelli M, Raposo N, Tsivgoulis G, Candelaresi P, Ciacciarelli A, Mbroh J, Batenkova T, Scoppettuolo P, Zedde M, Pascarella R, Antonenko K, Kristoffersen ES, Kremer Hovinga JA, Jood K, Aguiar de Sousa D, Poli S, Tatlisumak T, Putaala J, Coutinho JM, Ferro JM, Arnold M, Heldner MR. Characteristics and outcomes of cerebral venous thrombosis associated with COVID-19. Eur Stroke J 2024:23969873241241885. [PMID: 38572798 DOI: 10.1177/23969873241241885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Abstract
INTRODUCTION Previous reports and meta-analyses derived from small case series reported a mortality rate of up to 40% in patients with coronavirus disease 2019 associated cerebral venous thrombosis (COVID-CVT). We assessed the clinical characteristics and outcomes in an international cohort of patients with COVID-CVT. PATIENTS AND METHODS This was a registry study of consecutive COVID-CVT patients diagnosed between March 2020 and March 2023. Data collected by the International Cerebral Venous Thrombosis Consortium from patients with CVT diagnosed between 2017 and 2018 served as a comparison. Outcome analyses were adjusted for age and sex. RESULTS We included 70 patients with COVID-CVT from 23 hospitals in 15 countries and 206 controls from 14 hospitals in 13 countries. The proportion of women was smaller in the COVID-CVT group (50% vs 68%, p < 0.01). A higher proportion of COVID-CVT patients presented with altered mental state (44% vs 25%, p < 0.01), the median thrombus load was higher in COVID-CVT patients (3 [IQR 2-4] vs 2 [1-3], p < 0.01) and the length of hospital stay was longer compared to controls (11 days [IQR 7-20] vs 8 [4-15], p = 0.02). In-hospital mortality did not differ (5/67 [7%, 95% CI 3-16] vs 7/206 [3%, 2-7], aOR 2.6 [95% CI 0.7-9]), nor did the frequency of functional independence after 6 months (modified Rankin Scale 0-2; 45/58 [78%, 95% CI 65-86] vs 161/185 [87%, 81-91], aOR 0.5 [95% CI 0.2-1.02]). CONCLUSION In contrast to previous studies, the in-hospital mortality rate and functional outcomes during follow-up did not differ between COVID-CVT patients and the pre-COVID-19 controls.
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Affiliation(s)
- Adrian Scutelnic
- Department of Neurology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Anita van de Munckhof
- Department of Neurology, Amsterdam UMC, location University of Amsterdam, Amsterdam, The Netherlands
| | - Angel T Miraclin
- Department of Neurosciences, Christian Medical College Hospital, Vellore, Tamil Nadu, India
| | - Sanjith Aaron
- Department of Neurosciences, Christian Medical College Hospital, Vellore, Tamil Nadu, India
| | | | | | - Oxana Grosu
- Institute of Neurology and Neurosurgery "Diomid Gherman," Chisinau, Republic of Moldova
| | - Katarzyna Krzywicka
- Department of Neurology, Amsterdam UMC, location University of Amsterdam, Amsterdam, The Netherlands
| | - Mayte Sánchez van Kammen
- Department of Neurology, Amsterdam UMC, location University of Amsterdam, Amsterdam, The Netherlands
| | - Erik Lindgren
- Department of Neurology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Sweden
| | - Tiago Moreira
- Department of Neurology, Karolinska University Hospital, Stockholm, Sweden
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Roberto Acampora
- Department of Neurology and Stroke Unit, Ospedale del Mare Hospital, Naples, Italy
| | - Alberto Negro
- Department of Neurology and Stroke Unit, Ospedale del Mare Hospital, Naples, Italy
| | - Theodoros Karapanayiotides
- 2nd Department of Neurology, Aristotle University of Thessaloniki, School of Medicine, AHEPA University Hospital, Greece
| | - Shadi Yaghi
- Department of Neurology, Brown University, Providence, RI, USA
| | - Anna Revert
- Hospital del Mar, Faculty of Medicine and Life Sciences, Pompeu Fabra University Barcelona, Spain
| | - Elisa Cuadrado Godia
- Hospital del Mar, Faculty of Medicine and Life Sciences, Pompeu Fabra University Barcelona, Spain
| | | | - Paolino La Spina
- Translational Molecular Medicine and Surgery 36th Cycle, Department of BIOMORF, Stroke Unit, Department of Clinical and Experimental Medicine, University Hospital G. Martino, Messina, Italy
| | - Francesco Grillo
- Translational Molecular Medicine and Surgery 36th Cycle, Department of BIOMORF, Stroke Unit, Department of Clinical and Experimental Medicine, University Hospital G. Martino, Messina, Italy
| | - Fabrizio Giammello
- Translational Molecular Medicine and Surgery 36th Cycle, Department of BIOMORF, Stroke Unit, Department of Clinical and Experimental Medicine, University Hospital G. Martino, Messina, Italy
| | - Thanh N Nguyen
- Neurology, Boston Medical Center, MA, USA
- Radiology, Boston Medical Center, MA, USA
| | | | - Alina Buture
- Mater Misericordiae University Hospital, Dublin, Ireland
| | | | - Nicolas Raposo
- Department of Neurology, University Hospital of Toulouse, Toulouse, France
| | - Georgios Tsivgoulis
- Second Department of Neurology, National & Kapodistrian University of Athens, School of Medicine, "Attikon University Hospital", Athens, Greece
| | | | - Antonio Ciacciarelli
- Neurology Division, Santa Maria Goretti Hospital, Latina, Italy
- Department of Translation and Precision Medicine, Sapienza University of Rome, Italy
| | - Joshua Mbroh
- Department of Neurology & Stroke, University Hospital Tuebingen, Eberhard-Karls University, Tuebingen, Germany
| | | | - Pasquale Scoppettuolo
- Neurology Department, Cliniques Universitaires Saint Luc, Université Catholique de Louvain (UCL), Brussels, Belgium
| | - Marialuisa Zedde
- Neurology Unit, Stroke Unit, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Rosario Pascarella
- Neuroradiology Unit, Azienda Unità Sanitaria-IRCCS di Reggio Emilia, Italy
| | - Kateryna Antonenko
- Department of Neurology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | | | - Johanna A Kremer Hovinga
- Department of Hematology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Katarina Jood
- Department of Neurology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Sweden
| | - Diana Aguiar de Sousa
- Lisbon Central University Hospital and Faculdade de Medicina da Universidade de Lisboa, Portugal
| | - Sven Poli
- Department of Neurology & Stroke, University Hospital Tuebingen, Eberhard-Karls University, Tuebingen, Germany
- Hertie Institute for Clinical Brain Research, Eberhard-Karls University, Tuebingen, Germany
| | - Turgut Tatlisumak
- Department of Neurology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Sweden
| | - Jukka Putaala
- Neurology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Jonathan M Coutinho
- Department of Neurology, Amsterdam UMC, location University of Amsterdam, Amsterdam, The Netherlands
| | - José M Ferro
- Centro de Estudos Egas Moniz, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Marcel Arnold
- Department of Neurology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Mirjam R Heldner
- Department of Neurology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
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Bykonia EN, Kleymenov DA, Gushchin VA, Siniavin AE, Mazunina EP, Kozlova SR, Zolotar AN, Usachev EV, Kuznetsova NA, Shidlovskaya EV, Pochtovyi AA, Kustova DD, Ivanov IA, Dmitriev SE, Ivanov RA, Logunov DY, Gintsburg AL. Major Role of S-Glycoprotein in Providing Immunogenicity and Protective Immunity in mRNA Lipid Nanoparticle Vaccines Based on SARS-CoV-2 Structural Proteins. Vaccines (Basel) 2024; 12:379. [PMID: 38675761 PMCID: PMC11053793 DOI: 10.3390/vaccines12040379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/21/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
SARS-CoV-2 variants have evolved over time in recent years, demonstrating immune evasion of vaccine-induced neutralizing antibodies directed against the original S protein. Updated S-targeted vaccines provide a high level of protection against circulating variants of SARS-CoV-2, but this protection declines over time due to ongoing virus evolution. To achieve a broader protection, novel vaccine candidates involving additional antigens with low mutation rates are currently needed. Based on our recently studied mRNA lipid nanoparticle (mRNA-LNP) platform, we have generated mRNA-LNP encoding SARS-CoV-2 structural proteins M, N, S from different virus variants and studied their immunogenicity separately or in combination in vivo. As a result, all mRNA-LNP vaccine compositions encoding the S and N proteins induced excellent titers of RBD- and N-specific binding antibodies. The T cell responses were mainly specific CD4+ T cell lymphocytes producing IL-2 and TNF-alpha. mRNA-LNP encoding the M protein did not show a high immunogenicity. High neutralizing activity was detected in the sera of mice vaccinated with mRNA-LNP encoding S protein (alone or in combinations) against closely related strains, but was undetectable or significantly lower against an evolutionarily distant variant. Our data showed that the addition of mRNAs encoding S and M antigens to mRNA-N in the vaccine composition enhanced the immunogenicity of mRNA-N and induced a more robust immune response to the N protein. Based on our results, we suggested that the S protein plays a key role in enhancing the immune response to the N protein when they are both encoded in the mRNA-LNP vaccine.
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Affiliation(s)
- Evgeniia N. Bykonia
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
| | - Denis A. Kleymenov
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
| | - Vladimir A. Gushchin
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
- Department of Virology, Lomonosov Moscow State University, Moscow 119234, Russia
- Department of Medical Genetics, Federal State Autonomous Educational Institution of Higher Education I M Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow 119991, Russia
| | - Andrei E. Siniavin
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Elena P. Mazunina
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
| | - Sofia R. Kozlova
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
| | - Anastasia N. Zolotar
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
| | - Evgeny V. Usachev
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
| | - Nadezhda A. Kuznetsova
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
| | - Elena V. Shidlovskaya
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
| | - Andrei A. Pochtovyi
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
- Department of Virology, Lomonosov Moscow State University, Moscow 119234, Russia
- Department of Medical Genetics, Federal State Autonomous Educational Institution of Higher Education I M Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow 119991, Russia
| | - Daria D. Kustova
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
- Department of Virology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Igor A. Ivanov
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Sergey E. Dmitriev
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Roman A. Ivanov
- Translational Medicine Research Center, Sirius University of Science and Technology, Sochi 354340, Russia;
| | - Denis Y. Logunov
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
| | - Alexander L. Gintsburg
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
- Infectiology Department, I. M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
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Surie D, Yuengling KA, DeCuir J, Zhu Y, Lauring AS, Gaglani M, Ghamande S, Peltan ID, Brown SM, Ginde AA, Martinez A, Mohr NM, Gibbs KW, Hager DN, Ali H, Prekker ME, Gong MN, Mohamed A, Johnson NJ, Srinivasan V, Steingrub JS, Leis AM, Khan A, Hough CL, Bender WS, Duggal A, Bendall EE, Wilson JG, Qadir N, Chang SY, Mallow C, Kwon JH, Exline MC, Shapiro NI, Columbus C, Vaughn IA, Ramesh M, Mosier JM, Safdar B, Casey JD, Talbot HK, Rice TW, Halasa N, Chappell JD, Grijalva CG, Baughman A, Womack KN, Swan SA, Johnson CA, Lwin CT, Lewis NM, Ellington S, McMorrow ML, Martin ET, Self WH. Severity of Respiratory Syncytial Virus vs COVID-19 and Influenza Among Hospitalized US Adults. JAMA Netw Open 2024; 7:e244954. [PMID: 38573635 DOI: 10.1001/jamanetworkopen.2024.4954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Abstract
Importance On June 21, 2023, the Centers for Disease Control and Prevention recommended the first respiratory syncytial virus (RSV) vaccines for adults aged 60 years and older using shared clinical decision-making. Understanding the severity of RSV disease in adults can help guide this clinical decision-making. Objective To describe disease severity among adults hospitalized with RSV and compare it with the severity of COVID-19 and influenza disease by vaccination status. Design, Setting, and Participants In this cohort study, adults aged 18 years and older admitted to the hospital with acute respiratory illness and laboratory-confirmed RSV, SARS-CoV-2, or influenza infection were prospectively enrolled from 25 hospitals in 20 US states from February 1, 2022, to May 31, 2023. Clinical data during each patient's hospitalization were collected using standardized forms. Data were analyzed from August to October 2023. Exposures RSV, SARS-CoV-2, or influenza infection. Main Outcomes and Measures Using multivariable logistic regression, severity of RSV disease was compared with COVID-19 and influenza severity, by COVID-19 and influenza vaccination status, for a range of clinical outcomes, including the composite of invasive mechanical ventilation (IMV) and in-hospital death. Results Of 7998 adults (median [IQR] age, 67 [54-78] years; 4047 [50.6%] female) included, 484 (6.1%) were hospitalized with RSV, 6422 (80.3%) were hospitalized with COVID-19, and 1092 (13.7%) were hospitalized with influenza. Among patients with RSV, 58 (12.0%) experienced IMV or death, compared with 201 of 1422 unvaccinated patients with COVID-19 (14.1%) and 458 of 5000 vaccinated patients with COVID-19 (9.2%), as well as 72 of 699 unvaccinated patients with influenza (10.3%) and 20 of 393 vaccinated patients with influenza (5.1%). In adjusted analyses, the odds of IMV or in-hospital death were not significantly different among patients hospitalized with RSV and unvaccinated patients hospitalized with COVID-19 (adjusted odds ratio [aOR], 0.82; 95% CI, 0.59-1.13; P = .22) or influenza (aOR, 1.20; 95% CI, 0.82-1.76; P = .35); however, the odds of IMV or death were significantly higher among patients hospitalized with RSV compared with vaccinated patients hospitalized with COVID-19 (aOR, 1.38; 95% CI, 1.02-1.86; P = .03) or influenza disease (aOR, 2.81; 95% CI, 1.62-4.86; P < .001). Conclusions and Relevance Among adults hospitalized in this US cohort during the 16 months before the first RSV vaccine recommendations, RSV disease was less common but similar in severity compared with COVID-19 or influenza disease among unvaccinated patients and more severe than COVID-19 or influenza disease among vaccinated patients for the most serious outcomes of IMV or death.
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Affiliation(s)
- Diya Surie
- Coronavirus and Other Respiratory Viruses Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Katharine A Yuengling
- Coronavirus and Other Respiratory Viruses Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jennifer DeCuir
- Coronavirus and Other Respiratory Viruses Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Yuwei Zhu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Adam S Lauring
- Department of Internal Medicine, University of Michigan, Ann Arbor
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor
| | - Manjusha Gaglani
- Baylor Scott & White Health, Temple, Texas
- Texas A&M University College of Medicine, Temple
- Baylor College of Medicine, Temple, Texas
| | - Shekhar Ghamande
- Baylor Scott & White Health, Temple, Texas
- Texas A&M University College of Medicine, Temple
- Baylor College of Medicine, Temple, Texas
| | - Ithan D Peltan
- Department of Medicine, Intermountain Medical Center, Murray, Utah and University of Utah, Salt Lake City
| | - Samuel M Brown
- Department of Medicine, Intermountain Medical Center, Murray, Utah and University of Utah, Salt Lake City
| | - Adit A Ginde
- Department of Emergency Medicine, University of Colorado School of Medicine, Aurora
| | - Amanda Martinez
- Department of Emergency Medicine, University of Colorado School of Medicine, Aurora
| | | | - Kevin W Gibbs
- Department of Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - David N Hager
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Harith Ali
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Matthew E Prekker
- Department of Emergency Medicine, Hennepin County Medical Center, Minneapolis, Minnesota
| | - Michelle N Gong
- Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York
| | - Amira Mohamed
- Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York
| | - Nicholas J Johnson
- Department of Emergency Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle
| | | | - Jay S Steingrub
- Department of Medicine, Baystate Medical Center, Springfield, Massachusetts
| | - Aleda M Leis
- School of Public Health, University of Michigan, Ann Arbor
| | - Akram Khan
- Department of Medicine, Oregon Health and Sciences University, Portland
| | - Catherine L Hough
- Department of Medicine, Oregon Health and Sciences University, Portland
| | | | - Abhijit Duggal
- Department of Medicine, Cleveland Clinic, Cleveland, Ohio
| | - Emily E Bendall
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor
| | - Jennifer G Wilson
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, California
| | - Nida Qadir
- Department of Medicine, University of California, Los Angeles
| | - Steven Y Chang
- Department of Medicine, University of California, Los Angeles
| | | | - Jennie H Kwon
- Department of Medicine, Washington University in St Louis, St Louis, Missouri
| | | | - Nathan I Shapiro
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Cristie Columbus
- Baylor Scott &White Health, Dallas, Texas
- Texas A&M University College of Medicine, Dallas
| | - Ivana A Vaughn
- Department of Public Health Sciences, Henry Ford Health, Detroit, Michigan
| | - Mayur Ramesh
- Division of Infectious Diseases, Henry Ford Health, Detroit, Michigan
| | - Jarrod M Mosier
- Department of Emergency Medicine, University of Arizona, Tucson
| | - Basmah Safdar
- Yale University School of Medicine, New Haven, Connecticut
| | - Jonathan D Casey
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - H Keipp Talbot
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Todd W Rice
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Natasha Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - James D Chappell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Carlos G Grijalva
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Adrienne Baughman
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Kelsey N Womack
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sydney A Swan
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Cassandra A Johnson
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Cara T Lwin
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Nathaniel M Lewis
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Sascha Ellington
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Meredith L McMorrow
- Coronavirus and Other Respiratory Viruses Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Emily T Martin
- School of Public Health, University of Michigan, Ann Arbor
| | - Wesley H Self
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee
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Qiu Y, Mo C, Chen L, Ye W, Chen G, Zhu T. Alterations in microbiota of patients with COVID-19: implications for therapeutic interventions. MedComm (Beijing) 2024; 5:e513. [PMID: 38495122 PMCID: PMC10943180 DOI: 10.1002/mco2.513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 03/19/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) recently caused a global pandemic, resulting in more than 702 million people being infected and over 6.9 million deaths. Patients with coronavirus disease (COVID-19) may suffer from diarrhea, sleep disorders, depression, and even cognitive impairment, which is associated with long COVID during recovery. However, there remains no consensus on effective treatment methods. Studies have found that patients with COVID-19 have alterations in microbiota and their metabolites, particularly in the gut, which may be involved in the regulation of immune responses. Consumption of probiotics may alleviate the discomfort caused by inflammation and oxidative stress. However, the pathophysiological process underlying the alleviation of COVID-19-related symptoms and complications by targeting the microbiota remains unclear. In the current study, we summarize the latest research and evidence on the COVID-19 pandemic, together with symptoms of SARS-CoV-2 and vaccine use, with a focus on the relationship between microbiota alterations and COVID-19-related symptoms and vaccine use. This work provides evidence that probiotic-based interventions may improve COVID-19 symptoms by regulating gut microbiota and systemic immunity. Probiotics may also be used as adjuvants to improve vaccine efficacy.
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Affiliation(s)
- Yong Qiu
- Department of AnesthesiologyNational Clinical Research Center for Geriatrics and The Research Units of West China (2018RU012)West China HospitalSichuan UniversityChengduChina
- Laboratory of Anesthesia and Critical Care MedicineNational‐Local Joint Engineering Research Center of Translational Medicine of AnesthesiologyWest China HospitalSichuan UniversityChengduChina
| | - Chunheng Mo
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOEState Key Laboratory of BiotherapyWest China Second University HospitalSichuan UniversityChengduChina
| | - Lu Chen
- Department of AnesthesiologyNational Clinical Research Center for Geriatrics and The Research Units of West China (2018RU012)West China HospitalSichuan UniversityChengduChina
- Laboratory of Anesthesia and Critical Care MedicineNational‐Local Joint Engineering Research Center of Translational Medicine of AnesthesiologyWest China HospitalSichuan UniversityChengduChina
| | - Wanlin Ye
- Department of AnesthesiologyNational Clinical Research Center for Geriatrics and The Research Units of West China (2018RU012)West China HospitalSichuan UniversityChengduChina
- Laboratory of Anesthesia and Critical Care MedicineNational‐Local Joint Engineering Research Center of Translational Medicine of AnesthesiologyWest China HospitalSichuan UniversityChengduChina
| | - Guo Chen
- Department of AnesthesiologyNational Clinical Research Center for Geriatrics and The Research Units of West China (2018RU012)West China HospitalSichuan UniversityChengduChina
- Laboratory of Anesthesia and Critical Care MedicineNational‐Local Joint Engineering Research Center of Translational Medicine of AnesthesiologyWest China HospitalSichuan UniversityChengduChina
| | - Tao Zhu
- Department of AnesthesiologyNational Clinical Research Center for Geriatrics and The Research Units of West China (2018RU012)West China HospitalSichuan UniversityChengduChina
- Laboratory of Anesthesia and Critical Care MedicineNational‐Local Joint Engineering Research Center of Translational Medicine of AnesthesiologyWest China HospitalSichuan UniversityChengduChina
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Satapathy P, Kumar P, Gupta JK, Rabaan AA, Al Kaabi NA, Mohanty D, Naveen P, Khatib MN, Gaidhane S, Zahiruddin QS, Neyazi A. The emergence and implications of SARS-CoV-2 omicron subvariant BA.2.86 on global health. Int J Surg 2024; 110:2498-2501. [PMID: 38215252 PMCID: PMC11020040 DOI: 10.1097/js9.0000000000001070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/24/2023] [Indexed: 01/14/2024]
Abstract
The SARS-CoV-2 subvariant BA.2.86 'Pirola', first identified in Denmark in August 2023, has manifested with a significantly mutated spike protein profile, suggesting a heightened ability to evade vaccine-induced and infection-induced antibodies. This article outlines the epidemiological spread, immune response implications, and global responses to BA.2.86. Preliminary observations indicate community transmissions of the subvariant, even among those previously infected or vaccinated. Notably, the BA.2.86 infection has shown a potential to amplify antibody responses. The variant's emergence has evoked memories of the Omicron variant's rise in late 2021, though global immunity levels might modulate the impact of BA.2.86 impact differently. Continuous genomic surveillance, coupled with integrated diagnostic and epidemiological strategies, proves crucial in early detection and management. The emergence of BA.2.86 reaffirms the unpredictable nature of the COVID-19 pandemic, emphasizing the need for ongoing research, adaptability, and global collaboration.
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Affiliation(s)
- Prakasini Satapathy
- Center for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu
- School of Pharmacy, Graphic Era Hill University
- School of Applied and Life Sciences, Uttaranchal University, Dehradun, Uttarakhand
| | - Pawan Kumar
- Global Center for Evidence Synthesis, Chandigarh
- EvidenceSynthesis Lab, Kolkata, West Bengal
| | - Jeetendra K. Gupta
- Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh
| | - Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran
- College of Medicine, Alfaisal University, Riyadh
- Department of Public Health and Nutrition, The University of Haripur, Haripur, Pakistan
| | - Nawal A. Al Kaabi
- College of Medicine and Health Science, Khalifa University
- Sheikh Khalifa Medical City, Abu Dhabi Health Services Company (SEHA), Abu Dhabi, United Arab Emirates
| | | | | | | | - Shilpa Gaidhane
- One Health Centre (COHERD), Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education, Wardha, Maharashtra, India
| | | | - Ahmad Neyazi
- Afghanistan Center for Epidemiological Studies
- Academic Affairs, Herat Regional Hospital, Herat, Afghanistan
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Ameratunga R, Woon ST, Leung E, Lea E, Chan L, Mehrtens J, Longhurst HJ, Steele R, Lehnert K, Lindsay K. The autoimmune rheumatological presentation of Common Variable Immunodeficiency Disorders with an overview of genetic testing. Semin Arthritis Rheum 2024; 65:152387. [PMID: 38330740 DOI: 10.1016/j.semarthrit.2024.152387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/06/2024] [Accepted: 01/16/2024] [Indexed: 02/10/2024]
Abstract
Primary immunodeficiency Disorders (PIDS) are rare, mostly monogenetic conditions which can present to a number of specialties. Although infections predominate in most PIDs, some individuals can manifest autoimmune or inflammatory sequelae as their initial clinical presentation. Identifying patients with PIDs can be challenging, as some can present later in life. This is often seen in patients with Common Variable Immunodeficiency Disorders (CVID), where symptoms can begin in the sixth or even seventh decades of life. Some patients with PIDs including CVID can initially present to rheumatologists with autoimmune musculoskeletal manifestations. It is imperative for these patients to be identified promptly as immunosuppression could lead to life-threatening opportunistic infections in these immunocompromised individuals. These risks could be mitigated by prior treatment with subcutaneous or intravenous (SCIG/IVIG) immunoglobulin replacement or prophylactic antibiotics. Importantly, many of these disorders have an underlying genetic defect. Individualized treatments may be available for the specific mutation, which may obviate or mitigate the need for hazardous broad-spectrum immunosuppression. Identification of the genetic defect has profound implications not only for the patient but also for affected family members, who may be at risk of symptomatic disease following an environmental trigger such as a viral infection. Finally, there may be clinical clues to the underlying PID, such as recurrent infections, the early presentation of severe or multiple autoimmune disorders, as well as a relevant family history. Early referral to a clinical immunologist will facilitate appropriate diagnostic evaluation and institution of treatment such as SCIG/IVIG immunoglobulin replacement. This review comprises three sections; an overview of PIDs, focusing on CVID, secondly genetic testing of PIDs and finally the clinical presentation of these disorders to rheumatologists.
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Affiliation(s)
- Rohan Ameratunga
- Department of Clinical immunology, Auckland Hospital, Park Rd, Grafton 1010, Auckland, New Zealand; Department of Virology and Immunology, Auckland Hospital, Park Rd, Grafton 1010, Auckland, New Zealand; Department of Molecular Medicine and Pathology, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland, New Zealand.
| | - See-Tarn Woon
- Department of Virology and Immunology, Auckland Hospital, Park Rd, Grafton 1010, Auckland, New Zealand; Department of Molecular Medicine and Pathology, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland, New Zealand
| | - Euphemia Leung
- Maurice Wilkins Centre, School of Biological Sciences, University of Auckland, Symonds St, Auckland, New Zealand; Auckland Cancer Society Research Centre, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Edward Lea
- Department of Clinical immunology, Auckland Hospital, Park Rd, Grafton 1010, Auckland, New Zealand
| | - Lydia Chan
- Department of Clinical immunology, Auckland Hospital, Park Rd, Grafton 1010, Auckland, New Zealand
| | - James Mehrtens
- Department of Clinical immunology, Auckland Hospital, Park Rd, Grafton 1010, Auckland, New Zealand
| | - Hilary J Longhurst
- Department of Clinical immunology, Auckland Hospital, Park Rd, Grafton 1010, Auckland, New Zealand; Department of Virology and Immunology, Auckland Hospital, Park Rd, Grafton 1010, Auckland, New Zealand; Department of Medicine, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland, New Zealand
| | - Richard Steele
- Department of Clinical immunology, Auckland Hospital, Park Rd, Grafton 1010, Auckland, New Zealand; Department of Respiratory Medicine, Wellington Hospital, Wellington, New Zealand
| | - Klaus Lehnert
- Maurice Wilkins Centre, School of Biological Sciences, University of Auckland, Symonds St, Auckland, New Zealand; Applied Translational Genetics, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Karen Lindsay
- Department of Clinical immunology, Auckland Hospital, Park Rd, Grafton 1010, Auckland, New Zealand
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Lee K, Na Y, Kim M, Lee D, Choi J, Kim G, Kim M. Ursodeoxycholic acid may protect from severe acute respiratory syndrome coronavirus 2 Omicron variant by reducing angiotensin-converting enzyme 2. Pharmacol Res Perspect 2024; 12:e1194. [PMID: 38573021 PMCID: PMC10993777 DOI: 10.1002/prp2.1194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/22/2024] [Accepted: 03/09/2024] [Indexed: 04/05/2024] Open
Abstract
The SARS-CoV-2 caused COVID-19 pandemic has posed a global health hazard. While some vaccines have been developed, protection against viral infection is not perfect because of the urgent approval process and the emergence of mutant SARS-CoV-2 variants. Here, we employed UDCA as an FXR antagonist to regulate ACE2 expression, which is one of the key pathways activated by SARS-CoV-2 Delta variant infection. UDCA is a well-known reagent of liver health supplements and the only clinically approved bile acid. In this paper, we investigated the protective efficacy of UDCA on Omicron variation, since it has previously been verified for protection against Delta variant. When co-housing with an Omicron variant-infected hamster group resulted in spontaneous airborne transmission, the UDCA pre-supplied group was protected from weight loss relative to the non-treated group at 4 days post-infection by more than 5%-10%. Furthermore, UDCA-treated groups had a 3-fold decrease in ACE2 expression in nasal cavities, as well as reduced viral expressing genes in the respiratory tract. Here, the data show that the UDCA serves an alternative option for preventive drug, providing SARS-CoV-2 protection against not only Delta but also Omicron variant. Our results of this study will help to propose drug-repositioning of UDCA from liver health supplement to preventive drug of SARS-CoV-2 infection.
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Affiliation(s)
- Kyungmin Lee
- Pharmaceutical Technology CenterDaewoong Pharmaceutical Co., LtdYongin‐siGyeonggi‐doRepublic of Korea
- College of Pharmacy, Pusan National UniversityBusanRepublic of Korea
| | - Yujeong Na
- Pharmaceutical Technology CenterDaewoong Pharmaceutical Co., LtdYongin‐siGyeonggi‐doRepublic of Korea
| | - Minjin Kim
- Drug Discovery CenterDaewoong Pharmaceutical Co., LtdYongin‐siGyeonggi‐doRepublic of Korea
| | - Dongjin Lee
- Pharmaceutical Technology CenterDaewoong Pharmaceutical Co., LtdYongin‐siGyeonggi‐doRepublic of Korea
| | - Jongseo Choi
- Pharmaceutical Technology CenterDaewoong Pharmaceutical Co., LtdYongin‐siGyeonggi‐doRepublic of Korea
| | - Gwanyoung Kim
- Pharmaceutical Technology CenterDaewoong Pharmaceutical Co., LtdYongin‐siGyeonggi‐doRepublic of Korea
| | - Min‐Soo Kim
- College of Pharmacy, Pusan National UniversityBusanRepublic of Korea
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32
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Majumdar R, Taye B, Bjornberg C, Giljork M, Lynch D, Farah F, Abdullah I, Osiecki K, Yousaf I, Luckstein A, Turri W, Sampathkumar P, Moyer AM, Kipp BR, Cattaneo R, Sussman CR, Navaratnarajah CK. From pandemic to endemic: Divergence of COVID-19 positive-tests and hospitalization numbers from SARS-CoV-2 RNA levels in wastewater of Rochester, Minnesota. Heliyon 2024; 10:e27974. [PMID: 38515669 PMCID: PMC10955309 DOI: 10.1016/j.heliyon.2024.e27974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
Traditionally, public health surveillance relied on individual-level data but recently wastewater-based epidemiology (WBE) for the detection of infectious diseases including COVID-19 became a valuable tool in the public health arsenal. Here, we use WBE to follow the course of the COVID-19 pandemic in Rochester, Minnesota (population 121,395 at the 2020 census), from February 2021 to December 2022. We monitored the impact of SARS-CoV-2 infections on public health by comparing three sets of data: quantitative measurements of viral RNA in wastewater as an unbiased reporter of virus level in the community, positive results of viral RNA or antigen tests from nasal swabs reflecting community reporting, and hospitalization data. From February 2021 to August 2022 viral RNA levels in wastewater were closely correlated with the oscillating course of COVID-19 case and hospitalization numbers. However, from September 2022 cases remained low and hospitalization numbers dropped, whereas viral RNA levels in wastewater continued to oscillate. The low reported cases may reflect virulence reduction combined with abated inclination to report, and the divergence of virus levels in wastewater from reported cases may reflect COVID-19 shifting from pandemic to endemic. WBE, which also detects asymptomatic infections, can provide an early warning of impending cases, and offers crucial insights during pandemic waves and in the transition to the endemic phase.
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Affiliation(s)
| | - Biruhalem Taye
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | | | | | | | | | | | - Iris Yousaf
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | | | - Priya Sampathkumar
- Division of Infectious Diseases, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ann M. Moyer
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Benjamin R. Kipp
- Advanced Diagnostics Laboratory, Mayo Clinic, Rochester, MN, USA
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Roberto Cattaneo
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Caroline R. Sussman
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
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Ahmad Wadi AFA, Onomura D, Funamori H, Khatun MM, Okada S, Iizasa H, Yoshiyama H. Effects of Strain Differences, Humidity Changes, and Saliva Contamination on the Inactivation of SARS-CoV-2 by Ion Irradiation. Viruses 2024; 16:520. [PMID: 38675863 PMCID: PMC11055001 DOI: 10.3390/v16040520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
One of the methods to inactivate viruses is to denature viral proteins using released ions. However, there have been no reports detailing the effects of changes in humidity or contamination with body fluids on the inactivation of viruses. This study investigated the effects of humidity changes and saliva contamination on the efficacy of SARS-CoV-2 inactivation with ions using multiple viral strains. Virus solutions with different infectious titers were dropped onto a circular nitrocellulose membrane and irradiated with ions from 10 cm above the membrane. After the irradiation of ions for 60, 90, and 120 min, changes in viral infectious titers were measured. The effect of ions on virus inactivation under different humidity conditions was also examined using virus solutions containing 90% mixtures of saliva collected from 10 people. A decrease in viral infectivity was observed over time for all strains, but ion irradiation further accelerated the decrease in viral infectivity. Ion irradiation can inactivate all viral strains, but at 80% humidity, the effect did not appear until 90 min after irradiation. The presence of saliva protected the virus from drying and maintained infectiousness for a longer period compared with no saliva. In particular, the Omicron strain retained its infectivity titer longer than the other strains. Ion irradiation demonstrated a consistent reduction in the number of infectious viruses when compared to the control across varying levels of humidity and irradiation periods. This underscores the notable effectiveness of irradiation, even when the reduction effect is as modest as 50%, thereby emphasizing its crucial role in mitigating the rapid dissemination of SARS-CoV-2.
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Affiliation(s)
- Afifah Fatimah Azzahra Ahmad Wadi
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo 693-8504, Shimane, Japan; (A.F.A.A.W.); (M.M.K.); (S.O.); (H.I.)
- Faculty of Medicine, University of Muslim Indonesia, Makassar 9023, South Sulawesi, Indonesia
| | - Daichi Onomura
- Division of Virology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan;
| | | | - Mst Mahmuda Khatun
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo 693-8504, Shimane, Japan; (A.F.A.A.W.); (M.M.K.); (S.O.); (H.I.)
| | - Shunpei Okada
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo 693-8504, Shimane, Japan; (A.F.A.A.W.); (M.M.K.); (S.O.); (H.I.)
| | - Hisashi Iizasa
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo 693-8504, Shimane, Japan; (A.F.A.A.W.); (M.M.K.); (S.O.); (H.I.)
| | - Hironori Yoshiyama
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo 693-8504, Shimane, Japan; (A.F.A.A.W.); (M.M.K.); (S.O.); (H.I.)
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Kibria MK, Ali MA, Yaseen M, Khan IA, Bhat MA, Islam MA, Mahumud RA, Mollah MNH. Discovery of Bacterial Key Genes from 16S rRNA-Seq Profiles That Are Associated with the Complications of SARS-CoV-2 Infections and Provide Therapeutic Indications. Pharmaceuticals (Basel) 2024; 17:432. [PMID: 38675393 PMCID: PMC11053588 DOI: 10.3390/ph17040432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
SARS-CoV-2 infections, commonly referred to as COVID-19, remain a critical risk to both human life and global economies. Particularly, COVID-19 patients with weak immunity may suffer from different complications due to the bacterial co-infections/super-infections/secondary infections. Therefore, different variants of alternative antibacterial therapeutic agents are required to inhibit those infection-causing drug-resistant pathogenic bacteria. This study attempted to explore these bacterial pathogens and their inhibitors by using integrated statistical and bioinformatics approaches. By analyzing bacterial 16S rRNA sequence profiles, at first, we detected five bacterial genera and taxa (Bacteroides, Parabacteroides, Prevotella Clostridium, Atopobium, and Peptostreptococcus) based on differentially abundant bacteria between SARS-CoV-2 infection and control samples that are significantly enriched in 23 metabolic pathways. A total of 183 bacterial genes were found in the enriched pathways. Then, the top-ranked 10 bacterial genes (accB, ftsB, glyQ, hldD, lpxC, lptD, mlaA, ppsA, ppc, and tamB) were selected as the pathogenic bacterial key genes (bKGs) by their protein-protein interaction (PPI) network analysis. Then, we detected bKG-guided top-ranked eight drug molecules (Bemcentinib, Ledipasvir, Velpatasvir, Tirilazad, Acetyldigitoxin, Entreatinib, Digitoxin, and Elbasvir) by molecular docking. Finally, the binding stability of the top-ranked three drug molecules (Bemcentinib, Ledipasvir, and Velpatasvir) against three receptors (hldD, mlaA, and lptD) was investigated by computing their binding free energies with molecular dynamic (MD) simulation-based MM-PBSA techniques, respectively, and was found to be stable. Therefore, the findings of this study could be useful resources for developing a proper treatment plan against bacterial co-/super-/secondary-infection in SARS-CoV-2 infections.
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Affiliation(s)
- Md. Kaderi Kibria
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
- Department of Statistics, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh
| | - Md. Ahad Ali
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
- Department of Chemistry, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Muhammad Yaseen
- Institute of Chemical Sciences, University of Swat, Main Campus, Charbagh 19130, Pakistan;
| | - Imran Ahmad Khan
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan;
| | - Mashooq Ahmad Bhat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11421, Saudi Arabia;
| | - Md. Ariful Islam
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
| | - Rashidul Alam Mahumud
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia;
| | - Md. Nurul Haque Mollah
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
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Rizzi M, Avellis V, Messina A, Germano C, Tavella E, Dodaro V, Vitale R, Revelli A, Zola P, Picone S, Paolillo PM, Mondì V, Masturzo B, Manzoni P, Sainaghi PP. Vitamin D Supplementation in Neonatal and Infant MIS-C Following COVID-19 Infection. Int J Mol Sci 2024; 25:3712. [PMID: 38612523 PMCID: PMC11011671 DOI: 10.3390/ijms25073712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
To date, the SARS-CoV-2 pandemic still represents a great clinical challenge worldwide, and effective anti-COVID-19 drugs are limited. For this reason, nutritional supplements have been investigated as adjuvant therapeutic approaches in disease management. Among such supplements, vitamin D has gained great interest, due to its immunomodulatory and anti-inflammatory actions both in adult and pediatric populations. Even if there is conflicting evidence about its prevention and/or mitigation effectiveness in SARS-CoV-2 infection, several studies demonstrated a strict correlation between hypovitaminosis D and disease severity in acute COVID-19 and MIS-C (multisystem inflammatory syndrome in children). This narrative review offers a resume of the state of the art about vitamin D's role in immunity and its clinical use in the context of the current pandemic, specially focusing on pediatric manifestations and MIS-C. It seems biologically reasonable that interventions aimed at normalizing circulating vitamin D levels could be beneficial. To help clinicians in establishing the correct prophylaxis and/or supportive therapy with vitamin D, well-designed and adequately statistically powered clinical trials involving both adult and pediatric populations are needed. Moreover, this review will also discuss the few other nutraceuticals evaluated in this context.
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Affiliation(s)
- Manuela Rizzi
- Department of Health Sciences (DiSS), Università del Piemonte Orientale (UPO), 28100 Novara, Italy
- IRCAD (Interdisciplinary Research Center of Autoimmune Diseases), Università del Piemonte Orientale (UPO), 28100 Novara, Italy
| | - Vincenzo Avellis
- School of Medicine, University of Turin, 10124 Turin, Italy
- Sant’Anna Hospital, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy (B.M.)
| | - Alessandro Messina
- School of Medicine, University of Turin, 10124 Turin, Italy
- Sant’Anna Hospital, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy (B.M.)
| | - Chiara Germano
- Sant’Anna Hospital, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy (B.M.)
- Department of Maternal, Neonatal and Infant Medicine, University Hospital “Degli Infermi”, 13875 Ponderano, Italy
| | - Elena Tavella
- School of Medicine, University of Turin, 10124 Turin, Italy
- Sant’Anna Hospital, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy (B.M.)
| | - Valentina Dodaro
- Sant’Anna Hospital, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy (B.M.)
| | - Raffaele Vitale
- School of Medicine, University of Turin, 10124 Turin, Italy
- Sant’Anna Hospital, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy (B.M.)
| | - Alberto Revelli
- School of Medicine, University of Turin, 10124 Turin, Italy
- Sant’Anna Hospital, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy (B.M.)
| | - Paolo Zola
- School of Medicine, University of Turin, 10124 Turin, Italy
- Sant’Anna Hospital, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy (B.M.)
| | - Simonetta Picone
- Neonatology and Neonatal Intensive Care Unit, Policlinico Casilino, 00169 Rome, Italy
| | - Pier Michele Paolillo
- Neonatology and Neonatal Intensive Care Unit, Policlinico Casilino, 00169 Rome, Italy
| | - Vito Mondì
- Neonatology and Neonatal Intensive Care Unit, Policlinico Casilino, 00169 Rome, Italy
| | - Bianca Masturzo
- Sant’Anna Hospital, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy (B.M.)
- Department of Maternal, Neonatal and Infant Medicine, University Hospital “Degli Infermi”, 13875 Ponderano, Italy
| | - Paolo Manzoni
- Sant’Anna Hospital, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy (B.M.)
- Department of Maternal, Neonatal and Infant Medicine, University Hospital “Degli Infermi”, 13875 Ponderano, Italy
| | - Pier Paolo Sainaghi
- IRCAD (Interdisciplinary Research Center of Autoimmune Diseases), Università del Piemonte Orientale (UPO), 28100 Novara, Italy
- Department of Translational Medicine (DiMeT), Università del Piemonte Orientale (UPO), 28100 Novara, Italy
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Scarpa F, Branda F, Petrosillo N, Ciccozzi M. On the SARS-CoV-2 Variants. Infect Dis Rep 2024; 16:289-297. [PMID: 38667750 PMCID: PMC11050187 DOI: 10.3390/idr16020024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/09/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
The evolutionary dynamics of viruses, particularly exemplified by SARS-CoV-2 during the ongoing COVID-19 pandemic, underscore the intricate interplay between genetics, host adaptation, and viral spread. This paper delves into the genetic evolution of SARS-CoV-2, emphasizing the implications of viral variants on global health. Initially emerging from the Wuhan-Hu-1 lineage, SARS-CoV-2 rapidly diversified into numerous variants, each characterized by distinct mutations in the spike protein and other genomic regions. Notable variants such as B.1.1.7 (α), B.1.351 (β), P.1 (γ), B.1.617.2 (δ), and the Omicron variant have garnered significant attention due to their heightened transmissibility and immune evasion capabilities. In particular, the Omicron variant has presented a myriad of subvariants, raising concerns about its potential impact on public health. Despite the emergence of numerous variants, the vast majority have exhibited limited expansion capabilities and have not posed significant threats akin to early pandemic strains. Continued genomic surveillance is imperative to identify emerging variants of concern promptly. While genetic adaptation is intrinsic to viral evolution, effective public health responses must be grounded in empirical evidence to navigate the evolving landscape of the pandemic with resilience and precision.
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Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy
| | - Francesco Branda
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, 00128 Rome, Italy; (F.B.); (M.C.)
| | - Nicola Petrosillo
- Infection Prevention Control/Infectious Disease Service, Fondazione Policlinico Universitario Campus Bio-Medico, 00127 Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, 00128 Rome, Italy; (F.B.); (M.C.)
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Caobi A, Saeed M. Upping the ante: enhanced expression of interferon-antagonizing ORF6 and ORF9b proteins by SARS-CoV-2 variants of concern. Curr Opin Microbiol 2024; 79:102454. [PMID: 38518551 DOI: 10.1016/j.mib.2024.102454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 03/24/2024]
Abstract
SARS-CoV-2 exhibits a remarkable capability to subvert the host antiviral innate immune system. This adeptness is orchestrated by viral proteins, which initially attempt to obstruct the activation of the antiviral immune program and then act as a fail-safe mechanism to mitigate the downstream effects of the activated immune response. This dual strategy leads to delayed expression and enfeebled action of type-I and -III interferons at the infection site, enabling the virus to replicate extensively in the lungs and subsequently disseminate to other organs. Throughout the course of the COVID-19 pandemic, SARS-CoV-2 has undergone evolution, giving rise to several variants of concern, some with exceedingly higher transmission and virulence. These improved features have been linked, at least in part, to the heightened expression or activity of specific viral proteins involved in circumventing host defense mechanisms. In this review, we aim to provide a concise summary of two SARS-CoV-2 proteins, ORF6 and ORF9b, which provided selective advantage to certain variants, affecting their biology and pathogenesis.
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Affiliation(s)
- Allen Caobi
- Department of Biochemistry and Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
| | - Mohsan Saeed
- Department of Biochemistry and Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA.
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Arevalo-Romero JA, Chingaté-López SM, Camacho BA, Alméciga-Díaz CJ, Ramirez-Segura CA. Next-generation treatments: Immunotherapy and advanced therapies for COVID-19. Heliyon 2024; 10:e26423. [PMID: 38434363 PMCID: PMC10907543 DOI: 10.1016/j.heliyon.2024.e26423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 03/05/2024] Open
Abstract
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in 2019 following prior outbreaks of coronaviruses like SARS and MERS in recent decades, underscoring their high potential of infectivity in humans. Insights from previous outbreaks of SARS and MERS have played a significant role in developing effective strategies to mitigate the global impact of SARS-CoV-2. As of January 7, 2024, there have been 774,075,242 confirmed cases of COVID-19 worldwide. To date, 13.59 billion vaccine doses have been administered, and there have been 7,012,986 documented fatalities (https://www.who.int/) Despite significant progress in addressing the COVID-19 pandemic, the rapid evolution of SARS-CoV-2 challenges human defenses, presenting ongoing global challenges. The emergence of new SARS-CoV-2 lineages, shaped by mutation and recombination processes, has led to successive waves of infections. This scenario reveals the need for next-generation vaccines as a crucial requirement for ensuring ongoing protection against SARS-CoV-2. This demand calls for formulations that trigger a robust adaptive immune response without leading the acute inflammation linked with the infection. Key mutations detected in the Spike protein, a critical target for neutralizing antibodies and vaccine design -specifically within the Receptor Binding Domain region of Omicron variant lineages (B.1.1.529), currently dominant worldwide, have intensified concerns due to their association with immunity evasion from prior vaccinations and infections. As the world deals with this evolving threat, the narrative extends to the realm of emerging variants, each displaying new mutations with implications that remain largely misunderstood. Notably, the JN.1 Omicron lineage is gaining global prevalence, and early findings suggest it stands among the immune-evading variants, a characteristic attributed to its mutation L455S. Moreover, the detrimental consequences of the novel emergence of SARS-CoV-2 lineages bear a particularly critical impact on immunocompromised individuals and older adults. Immunocompromised individuals face challenges such as suboptimal responses to COVID-19 vaccines, rendering them more susceptible to severe disease. Similarly, older adults have an increased risk of severe disease and the presence of comorbid conditions, find themselves at a heightened vulnerability to develop COVID-19 disease. Thus, recognizing these intricate factors is crucial for effectively tailoring public health strategies to protect these vulnerable populations. In this context, this review aims to describe, analyze, and discuss the current progress of the next-generation treatments encompassing immunotherapeutic approaches and advanced therapies emerging as complements that will offer solutions to counter the disadvantages of the existing options. Preliminary outcomes show that these strategies target the virus and address the immunomodulatory responses associated with COVID-19. Furthermore, the capacity to promote tissue repair has been demonstrated, which can be particularly noteworthy for immunocompromised individuals who stand as vulnerable actors in the global landscape of coronavirus infections. The emerging next-generation treatments possess broader potential, offering protection against a wide range of variants and enhancing the ability to counter the impact of the constant evolution of the virus. Furthermore, advanced therapies are projected as potential treatment alternatives for managing Chronic Post-COVID-19 syndromeand addressing its associated long-term complications.
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Affiliation(s)
- Jenny Andrea Arevalo-Romero
- Laboratorio de Investigación en Ingeniería Celular y Molecular, Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud, IDCBIS, 111611, Bogotá, DC, Colombia
- Instituto de Errores Innatos del Metabolismo, Facultad de Ciencias, Pontificia Universidad Javeriana, 110231, Bogotá, D.C., Colombia
| | - Sandra M. Chingaté-López
- Laboratorio de Investigación en Ingeniería Celular y Molecular, Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud, IDCBIS, 111611, Bogotá, DC, Colombia
| | - Bernardo Armando Camacho
- Laboratorio de Investigación en Ingeniería Celular y Molecular, Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud, IDCBIS, 111611, Bogotá, DC, Colombia
| | - Carlos Javier Alméciga-Díaz
- Instituto de Errores Innatos del Metabolismo, Facultad de Ciencias, Pontificia Universidad Javeriana, 110231, Bogotá, D.C., Colombia
| | - Cesar A. Ramirez-Segura
- Laboratorio de Investigación en Ingeniería Celular y Molecular, Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud, IDCBIS, 111611, Bogotá, DC, Colombia
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Priyadarsinee L, Jamir E, Nagamani S, Mahanta HJ, Kumar N, John L, Sarma H, Kumar A, Gaur AS, Sahoo R, Vaikundamani S, Murugan NA, Priyakumar UD, Raghava GPS, Bharatam PV, Parthasarathi R, Subramanian V, Sastry GM, Sastry GN. Molecular Property Diagnostic Suite for COVID-19 (MPDS COVID-19): an open-source disease-specific drug discovery portal. GigaByte 2024; 2024:gigabyte114. [PMID: 38525218 PMCID: PMC10958779 DOI: 10.46471/gigabyte.114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/11/2024] [Indexed: 03/26/2024] Open
Abstract
Molecular Property Diagnostic Suite (MPDS) was conceived and developed as an open-source disease-specific web portal based on Galaxy. MPDSCOVID-19 was developed for COVID-19 as a one-stop solution for drug discovery research. Galaxy platforms enable the creation of customized workflows connecting various modules in the web server. The architecture of MPDSCOVID-19 effectively employs Galaxy v22.04 features, which are ported on CentOS 7.8 and Python 3.7. MPDSCOVID-19 provides significant updates and the addition of several new tools updated after six years. Tools developed by our group in Perl/Python and open-source tools are collated and integrated into MPDSCOVID-19 using XML scripts. Our MPDS suite aims to facilitate transparent and open innovation. This approach significantly helps bring inclusiveness in the community while promoting free access and participation in software development. Availability & Implementation The MPDSCOVID-19 portal can be accessed at https://mpds.neist.res.in:8085/.
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Affiliation(s)
- Lipsa Priyadarsinee
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Esther Jamir
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
| | - Selvaraman Nagamani
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Hridoy Jyoti Mahanta
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Nandan Kumar
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
| | - Lijo John
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
| | - Himakshi Sarma
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
| | - Asheesh Kumar
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
| | - Anamika Singh Gaur
- CSIR-Indian Institute of Toxicology Research, Lucknow, 226001, Uttar Pradesh, India
| | - Rosaleen Sahoo
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - S. Vaikundamani
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
| | - N. Arul Murugan
- Indraprastha Institute of Information Technology, Delhi, 110020, India
| | - U. Deva Priyakumar
- International Institute of Information Technology, Gachibowli, Hyderabad, 500032, India
| | - G. P. S. Raghava
- Indraprastha Institute of Information Technology, Delhi, 110020, India
| | - Prasad V. Bharatam
- National Institute of Pharmaceutical Education and Research, S.A.S. Nagar (Mohali), 160062, India
| | - Ramakrishnan Parthasarathi
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- CSIR-Indian Institute of Toxicology Research, Lucknow, 226001, Uttar Pradesh, India
| | - V. Subramanian
- Department of Chemistry, Indian Institute of Technology, Chennai, 600036, India
| | - G. Madhavi Sastry
- Schrödinger Inc., Octave, Salarpuria Sattva Knowledge City, 1st Floor, Unit 3A, Hyderabad, 500081, India
| | - G. Narahari Sastry
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Indian Institute of Technology (IIT) Hyderabad, Kandi, Sangareddy, Telangana, 502284, India
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Marques AD, Graham-Wooten J, Fitzgerald AS, Sobel Leonard A, Cook EJ, Everett JK, Rodino KG, Moncla LH, Kelly BJ, Collman RG, Bushman FD. SARS-CoV-2 evolution during prolonged infection in immunocompromised patients. mBio 2024; 15:e0011024. [PMID: 38364100 PMCID: PMC10936176 DOI: 10.1128/mbio.00110-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/18/2024] Open
Abstract
Prolonged infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in immunocompromised patients provides an opportunity for viral evolution, potentially leading to the generation of new pathogenic variants. To investigate the pathways of viral evolution, we carried out a study on five patients experiencing prolonged SARS-CoV-2 infection (quantitative polymerase chain reaction-positive for 79-203 days) who were immunocompromised due to treatment for lymphoma or solid organ transplantation. For each timepoint analyzed, we generated at least two independent viral genome sequences to assess the heterogeneity and control for sequencing error. Four of the five patients likely had prolonged infection; the fifth apparently experienced a reinfection. The rates of accumulation of substitutions in the viral genome per day were higher in hospitalized patients with prolonged infection than those estimated for the community background. The spike coding region accumulated a significantly greater number of unique mutations than other viral coding regions, and the mutation density was higher. Two patients were treated with monoclonal antibodies (bebtelovimab and sotrovimab); by the next sampled timepoint, each virus population showed substitutions associated with monoclonal antibody resistance as the dominant forms (spike K444N and spike E340D). All patients received remdesivir, but remdesivir-resistant substitutions were not detected. These data thus help elucidate the trends of emergence, evolution, and selection of mutational variants within long-term infected immunocompromised individuals. IMPORTANCE SARS-CoV-2 is responsible for a global pandemic, driven in part by the emergence of new viral variants. Where do these new variants come from? One model is that long-term viral persistence in infected individuals allows for viral evolution in response to host pressures, resulting in viruses more likely to replicate efficiently in humans. In this study, we characterize replication in several hospitalized and long-term infected individuals, documenting efficient pathways of viral evolution.
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Affiliation(s)
- Andrew D. Marques
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jevon Graham-Wooten
- Division of Pulmonary, Allergy, and Critical Care, Philadelphia, Pennsylvania, USA
| | | | - Ashley Sobel Leonard
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Emma J. Cook
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John K. Everett
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kyle G. Rodino
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Louise H. Moncla
- Department of Pathobiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Brendan J. Kelly
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ronald G. Collman
- Division of Pulmonary, Allergy, and Critical Care, Philadelphia, Pennsylvania, USA
| | - Frederic D. Bushman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Kern AL, Pink I, Bonifacius A, Kaireit T, Speth M, Behrendt L, Klimeš F, Voskrebenzev A, Hohlfeld JM, Hoeper MM, Welte T, Wacker F, Eiz-Vesper B, Vogel-Claussen J. Alveolar membrane and capillary function in COVID-19 convalescents: insights from chest MRI. Eur Radiol 2024:10.1007/s00330-024-10669-9. [PMID: 38460013 DOI: 10.1007/s00330-024-10669-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/22/2024] [Accepted: 02/10/2024] [Indexed: 03/11/2024]
Abstract
OBJECTIVES To investigate potential presence and resolution of longer-term pulmonary diffusion limitation and microvascular perfusion impairment in COVID-19 convalescents. MATERIALS AND METHODS This prospective, longitudinal study was carried out between May 2020 and April 2023. COVID-19 convalescents repeatedly and age/sex-matched healthy controls once underwent MRI including hyperpolarized 129Xe MRI. Blood samples were obtained in COVID-19 convalescents for immunophenotyping. Ratios of 129Xe in red blood cells (RBC), tissue/plasma (TP), and gas phase (GP) as well as lung surface-volume ratio were quantified and correlations with CD4+/CD8+ T cell frequencies were assessed using Pearson's correlation coefficient. Signed-rank tests were used for longitudinal and U tests for group comparisons. RESULTS Thirty-five participants were recruited. Twenty-three COVID-19 convalescents (age 52.1 ± 19.4 years, 13 men) underwent baseline MRI 12.6 ± 4.2 weeks after symptom onset. Fourteen COVID-19 convalescents underwent follow-up MRI and 12 were included for longitudinal comparison (baseline MRI at 11.5 ± 2.7 weeks and follow-up 38.0 ± 5.5 weeks). Twelve matched controls were included for comparison. In COVID-19 convalescents, RBC-TP was increased at follow-up (p = 0.04). Baseline RBC-TP was lower in patients treated on intensive care unit (p = 0.03) and in patients with severe/critical disease (p = 0.006). RBC-TP correlated with CD4+/CD8+ T cell frequencies (R = 0.61/ - 0.60) at baseline. RBC-TP was not significantly different compared to matched controls at follow-up (p = 0.25). CONCLUSION Impaired microvascular pulmonary perfusion and alveolar membrane function persisted 12 weeks after symptom onset and resolved within 38 weeks after COVID-19 symptom onset. CLINICAL RELEVANCE STATEMENT 129Xe MRI shows improvement of microvascular pulmonary perfusion and alveolar membrane function between 11.5 ± 2.7 weeks and 38.0 ± 5.5 weeks after symptom onset in patients after COVID-19, returning to normal in subjects without significant prior disease. KEY POINTS • The study aims to investigate long-term effects of COVID-19 on lung function, in particular gas uptake efficiency, and on the cardiovascular system. • In COVID-19 convalescents, the ratio of 129Xe in red blood cells/tissue plasma increased longitudinally (p = 0.04), but was not different from matched controls at follow-up (p = 0.25). • Microvascular pulmonary perfusion and alveolar membrane function are impaired 11.5 weeks after symptom onset in patients after COVID-19, returning to normal in subjects without significant prior disease at 38.0 weeks.
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Affiliation(s)
- Agilo Luitger Kern
- Institute for Diagnostic and Interventional Radiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
- Medizinische Hochschule Hannover, Carl-Neuberg-Straße 1, Hannover, 30625, Germany.
| | - Isabell Pink
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Department of Respiratory Medicine and Infectious Diseases, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Agnes Bonifacius
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover/Brunswick, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Till Kaireit
- Institute for Diagnostic and Interventional Radiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Milan Speth
- Institute for Diagnostic and Interventional Radiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Lea Behrendt
- Institute for Diagnostic and Interventional Radiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Filip Klimeš
- Institute for Diagnostic and Interventional Radiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Andreas Voskrebenzev
- Institute for Diagnostic and Interventional Radiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Jens M Hohlfeld
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Medizinische Hochschule Hannover, Carl-Neuberg-Straße 1, Hannover, 30625, Germany
- Department of Clinical Airway Research, Fraunhofer Institute for Toxicology and Experimental Medicine, Nikolai-Fuchs-Str. 1, 30625, Hannover, Germany
| | - Marius M Hoeper
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Department of Respiratory Medicine and Infectious Diseases, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Tobias Welte
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Department of Respiratory Medicine and Infectious Diseases, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Frank Wacker
- Institute for Diagnostic and Interventional Radiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Britta Eiz-Vesper
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover/Brunswick, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Jens Vogel-Claussen
- Institute for Diagnostic and Interventional Radiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Carl-Neuberg-Str. 1, 30625, Hannover, Germany
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Lanz-Mendoza H, Gálvez D, Contreras-Garduño J. The plasticity of immune memory in invertebrates. J Exp Biol 2024; 227:jeb246158. [PMID: 38449328 DOI: 10.1242/jeb.246158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Whether specific immune protection after initial pathogen exposure (immune memory) occurs in invertebrates has long been uncertain. The absence of antibodies, B-cells and T-cells, and the short lifespans of invertebrates led to the hypothesis that immune memory does not occur in these organisms. However, research in the past two decades has supported the existence of immune memory in several invertebrate groups, including Ctenophora, Cnidaria, Nematoda, Mollusca and Arthropoda. Interestingly, some studies have demonstrated immune memory that is specific to the parasite strain. Nonetheless, other work does not provide support for immune memory in invertebrates or offers only partial support. Moreover, the expected biphasic immune response, a characteristic of adaptive immune memory in vertebrates, varies within and between invertebrate species. This variation may be attributed to the influence of biotic or abiotic factors, particularly parasites, on the outcome of immune memory. Despite its critical importance for survival, the role of phenotypic plasticity in immune memory has not been systematically examined in the past two decades. Additionally, the features of immune responses occurring in diverse environments have yet to be fully characterized.
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Affiliation(s)
- Humberto Lanz-Mendoza
- Centro de Investigaciones sobre Enfermedades Infecciosas, INSP, 62100 Cuernavaca, Morelos, Mexico
| | - Dumas Gálvez
- Coiba Scientific Station, City of Knowledge, Calle Gustavo Lara, Boulevard 145B, Clayton 0843-01853, Panama
- Programa Centroamericano de Maestría en Entomología, Universidad de Panamá, Estafeta universitaria, Avenida Simón Bolívar, 0824, Panama
- Sistema Nacional de Investigación, Edificio 205, Ciudad del Saber, 0816-02852, Panama
| | - Jorge Contreras-Garduño
- Escuela Nacional de Estudios Superiores, Unidad Morelia, UNAM, 58190 Morelia, Mexico
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
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Gonzalez-Parra G, Mahmud MS, Kadelka C. Learning from the COVID-19 pandemic: a systematic review of mathematical vaccine prioritization models. medRxiv 2024:2024.03.04.24303726. [PMID: 38496570 PMCID: PMC10942533 DOI: 10.1101/2024.03.04.24303726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
As the world becomes ever more connected, the chance of pandemics increases as well. The recent COVID-19 pandemic and the concurrent global mass vaccine roll-out provides an ideal setting to learn from and refine our understanding of infectious disease models for better future preparedness. In this review, we systematically analyze and categorize mathematical models that have been developed to design optimal vaccine prioritization strategies of an initially limited vaccine. As older individuals are disproportionately affected by COVID-19, the focus is on models that take age explicitly into account. The lower mobility and activity level of older individuals gives rise to non-trivial trade-offs. Secondary research questions concern the optimal time interval between vaccine doses and spatial vaccine distribution. This review showcases the effect of various modeling assumptions on model outcomes. A solid understanding of these relationships yields better infectious disease models and thus public health decisions during the next pandemic.
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Affiliation(s)
- Gilberto Gonzalez-Parra
- Instituto de Matemática Multidisciplinar, Universitat Politècnica de València, València, Spain
- Department of Mathematics, New Mexico Tech, 801 Leroy Place, Socorro, 87801, NM, USA
| | - Md Shahriar Mahmud
- Department of Mathematics, Iowa State University, 411 Morrill Rd, Ames, 50011, IA, USA
| | - Claus Kadelka
- Department of Mathematics, Iowa State University, 411 Morrill Rd, Ames, 50011, IA, USA
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White CL, Glover MA, Gandhapudi SK, Richards KA, Sant AJ. Flublok Quadrivalent Vaccine Adjuvanted with R-DOTAP Elicits a Robust and Multifunctional CD4 T Cell Response That Is of Greater Magnitude and Functional Diversity Than Conventional Adjuvant Systems. Vaccines (Basel) 2024; 12:281. [PMID: 38543915 PMCID: PMC10975948 DOI: 10.3390/vaccines12030281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/20/2024] [Accepted: 02/29/2024] [Indexed: 04/01/2024] Open
Abstract
It is clear that new approaches are needed to promote broadly protective immunity to viral pathogens, particularly those that are prone to mutation and escape from antibody-mediated immunity. CD4+ T cells, known to target many viral proteins and highly conserved peptide epitopes, can contribute greatly to protective immunity through multiple mechanisms. Despite this potential, CD4+ T cells are often poorly recruited by current vaccine strategies. Here, we have analyzed a promising new adjuvant (R-DOTAP), as well as conventional adjuvant systems AddaVax with or without an added TLR9 agonist CpG, to promote CD4+ T cell responses to the licensed vaccine Flublok containing H1, H3, and HA-B proteins. Our studies, using a preclinical mouse model of vaccination, revealed that the addition of R-DOTAP to Flublok dramatically enhances the magnitude and functionality of CD4+ T cells specific for HA-derived CD4+ T cell epitopes, far outperforming conventional adjuvant systems based on cytokine EliSpot assays and multiparameter flow cytometry. The elicited CD4+ T cells specific for HA-derived epitopes produce IL-2, IFN-γ, IL-4/5, and granzyme B and have multifunctional potential. Hence, R-DOTAP, which has been verified safe by human studies, can offer exciting opportunities as an immune stimulant for next-generation prophylactic recombinant protein-based vaccines.
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Affiliation(s)
- Chantelle L. White
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA; (C.L.W.); (M.A.G.); (K.A.R.)
| | - Maryah A. Glover
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA; (C.L.W.); (M.A.G.); (K.A.R.)
| | - Siva K. Gandhapudi
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky School of Medicine, Lexington, KY 40508, USA;
| | - Katherine A. Richards
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA; (C.L.W.); (M.A.G.); (K.A.R.)
| | - Andrea J. Sant
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA; (C.L.W.); (M.A.G.); (K.A.R.)
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Chen H, Zhuang Z, Xu N, Feng Y, Fang K, Tan C, Tan Y. Simple, Visual, Point-of-Care SARS-CoV-2 Detection Incorporating Recombinase Polymerase Amplification and Target DNA-Protein Crosslinking Enhanced Chemiluminescence. Biosensors (Basel) 2024; 14:135. [PMID: 38534242 DOI: 10.3390/bios14030135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/14/2023] [Accepted: 12/26/2023] [Indexed: 03/28/2024]
Abstract
The ongoing COVID-19 pandemic, driven by persistent SARS-CoV-2 transmission, threatens human health worldwide, underscoring the urgent need for an efficient, low-cost, rapid SARS-CoV-2 detection method. Herein, we developed a point-of-care SARS-CoV-2 detection method incorporating recombinase polymerase amplification (RPA) and DNA-protein crosslinking chemiluminescence (DPCL) (RPADPCL). RPADPCL involves the crosslinking of biotinylated double-stranded RPA DNA products with horseradish peroxidase (HRP)-labeled streptavidin (SA-HRP). Modified products are captured using SA-labeled magnetic beads, and then analyzed using a chemiluminescence detector and smartphone after the addition of a chemiluminescent substrate. Under optimal conditions, the RPADPCL limit of detection (LOD) was observed to be 6 copies (within the linear detection range of 1-300 copies) for a plasmid containing the SARS-CoV-2 N gene and 15 copies (within the linear range of 10-500 copies) for in vitro transcribed (IVT) SARS-CoV-2 RNA. The proposed method is convenient, specific, visually intuitive, easy to use, and does not require external excitation. The effective RPADPCL detection of SARS-CoV-2 in complex matrix systems was verified by testing simulated clinical samples containing 10% human saliva or a virus transfer medium (VTM) spiked with a plasmid containing a SARS-CoV-2 N gene sequence or SARS-CoV-2 IVT RNA. Consequently, this method has great potential for detecting targets in clinical samples.
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Affiliation(s)
- Hui Chen
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Zhiyuan Zhuang
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Naihan Xu
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- School of Food and Drug, Shenzhen Polytechnic University, Shenzhen 518055, China
| | - Ying Feng
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Kaixin Fang
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Chunyan Tan
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ying Tan
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Department of Chemistry, Tsinghua University, Beijing 100084, China
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Álvarez-Herrera M, Sevilla J, Ruiz-Rodriguez P, Vergara A, Vila J, Cano-Jiménez P, González-Candelas F, Comas I, Coscollá M. VIPERA: Viral Intra-Patient Evolution Reporting and Analysis. Virus Evol 2024; 10:veae018. [PMID: 38510921 PMCID: PMC10953798 DOI: 10.1093/ve/veae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/02/2024] [Accepted: 03/05/2024] [Indexed: 03/22/2024] Open
Abstract
Viral mutations within patients nurture the adaptive potential of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during chronic infections, which are a potential source of variants of concern. However, there is no integrated framework for the evolutionary analysis of intra-patient SARS-CoV-2 serial samples. Herein, we describe Viral Intra-Patient Evolution Reporting and Analysis (VIPERA), a new software that integrates the evaluation of the intra-patient ancestry of SARS-CoV-2 sequences with the analysis of evolutionary trajectories of serial sequences from the same viral infection. We have validated it using positive and negative control datasets and have successfully applied it to a new case, which revealed population dynamics and evidence of adaptive evolution. VIPERA is available under a free software license at https://github.com/PathoGenOmics-Lab/VIPERA.
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Affiliation(s)
- Miguel Álvarez-Herrera
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia—CSIC), FISABIO Joint Research Unit ‘Infection and Public Health’, C/Agustín Escardino, 9, Paterna 46980, Spain
| | - Jordi Sevilla
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia—CSIC), FISABIO Joint Research Unit ‘Infection and Public Health’, C/Agustín Escardino, 9, Paterna 46980, Spain
| | - Paula Ruiz-Rodriguez
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia—CSIC), FISABIO Joint Research Unit ‘Infection and Public Health’, C/Agustín Escardino, 9, Paterna 46980, Spain
| | - Andrea Vergara
- Department of Clinical Microbiology, CDB, Hospital Clínic of Barcelona; University of Barcelona; ISGlobal, C. de Villarroel, 170, Barcelona 08007, Spain
- CIBER of Infectious Diseases (CIBERINFEC), Av. Monforte de Lemos, 3-5, Madrid 28029, Spain
| | - Jordi Vila
- Department of Clinical Microbiology, CDB, Hospital Clínic of Barcelona; University of Barcelona; ISGlobal, C. de Villarroel, 170, Barcelona 08007, Spain
- CIBER of Infectious Diseases (CIBERINFEC), Av. Monforte de Lemos, 3-5, Madrid 28029, Spain
| | - Pablo Cano-Jiménez
- Institute of Biomedicine of Valencia (IBV-CSIC), C/ Jaime Roig, 11, Valencia 46010, Spain
| | - Fernando González-Candelas
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia—CSIC), FISABIO Joint Research Unit ‘Infection and Public Health’, C/Agustín Escardino, 9, Paterna 46980, Spain
- CIBER of Epidemiology and Public Health (CIBERESP), Av. Monforte de Lemos, 3-5, Madrid 28029, Spain
| | - Iñaki Comas
- Institute of Biomedicine of Valencia (IBV-CSIC), C/ Jaime Roig, 11, Valencia 46010, Spain
- CIBER of Epidemiology and Public Health (CIBERESP), Av. Monforte de Lemos, 3-5, Madrid 28029, Spain
| | - Mireia Coscollá
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia—CSIC), FISABIO Joint Research Unit ‘Infection and Public Health’, C/Agustín Escardino, 9, Paterna 46980, Spain
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Song T, Cooper L, Galván Achi J, Wang X, Dwivedy A, Rong L, Wang X. Polyvalent Nanobody Structure Designed for Boosting SARS-CoV-2 Inhibition. J Am Chem Soc 2024; 146:5894-5900. [PMID: 38408177 PMCID: PMC10965196 DOI: 10.1021/jacs.3c11760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Coronavirus transmission and mutations have brought intensive challenges on pandemic control and disease treatment. Developing robust and versatile antiviral drugs for viral neutralization is highly desired. Here, we created a new polyvalent nanobody (Nb) structure that shows the effective inhibition of SARS-CoV-2 infections. Our polyvalent Nb structure, called "PNS", is achieved by first conjugating single-stranded DNA (ssDNA) and the receptor-binding domain (RBD)-targeting Nb with retained binding ability to SARS-CoV-2 spike protein and then coalescing the ssDNA-Nb conjugates around a gold nanoparticle (AuNP) via DNA hybridization with a desired Nb density that offers spatial pattern-matching with that of the Nb binding sites on the trimeric spike. The surface plasmon resonance (SPR) assays show that the PNS binds the SARS-CoV-2 trimeric spike proteins with a ∼1000-fold improvement in affinity than that of monomeric Nbs. Furthermore, our viral entry inhibition assays using the PNS against SARS-CoV-2 WA/2020 and two recent variants of interest (BQ1.1 and XBB) show an over 400-fold enhancement in viral inhibition compared to free Nbs. Our PNS strategy built on a new DNA-protein conjugation chemistry provides a facile approach to developing robust virus inhibitors by using a corresponding virus-targeting Nb with a desired Nb density.
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Affiliation(s)
- Tingjie Song
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Laura Cooper
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Jazmin Galván Achi
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Xiaojing Wang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Abhisek Dwivedy
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Lijun Rong
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Xing Wang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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Chaki SP, Kahl-McDonagh MM, Neuman BW, Zuelke KA. Validating the inactivation of viral pathogens with a focus on SARS-CoV-2 to safely transfer samples from high-containment laboratories. Front Cell Infect Microbiol 2024; 14:1292467. [PMID: 38510962 PMCID: PMC10951993 DOI: 10.3389/fcimb.2024.1292467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/19/2024] [Indexed: 03/22/2024] Open
Abstract
Introduction Pathogen leak from a high-containment laboratory seriously threatens human safety, animal welfare, and environmental security. Transportation of pathogens from a higher (BSL4 or BSL3) to a lower (BSL2) containment laboratory for downstream experimentation requires complete pathogen inactivation. Validation of pathogen inactivation is necessary to ensure safety during transportation. This study established a validation strategy for virus inactivation. Methods SARS-CoV-2 wild type, delta, and omicron variants underwent heat treatment at 95°C for 10 minutes using either a hot water bath or a thermocycler. To validate the inactivation process, heat-treated viruses, and untreated control samples were incubated with A549-hACE2 and Vero E6-TMPRSS2-T2A-ACE2 cells. The cells were monitored for up to 72 hours for any cytopathic effects, visually and under a microscope, and for virus genome replication via RT-qPCR. The quality of post-treated samples was assessed for suitability in downstream molecular testing applications. Results Heat treatment at 95°C for 10 minutes effectively inactivated SARS-CoV-2 variants. The absence of cytopathic effects, coupled with the inability of virus genome replication, validated the efficacy of the inactivation process. Furthermore, the heat-treated samples proved to be qualified for COVID-19 antigen testing, RT-qPCR, and whole-genome sequencing. Discussion By ensuring the safety of sample transportation for downstream experimentation, this validation approach enhances biosecurity measures. Considerations for potential limitations, comparisons with existing inactivation methods, and broader implications of the findings are discussed.
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Affiliation(s)
- Sankar Prasad Chaki
- Global Health Research Complex, Division of Research, Texas A&M University, College Station, TX, United States
| | - Melissa M. Kahl-McDonagh
- Global Health Research Complex, Division of Research, Texas A&M University, College Station, TX, United States
| | - Benjamin W. Neuman
- Global Health Research Complex, Division of Research, Texas A&M University, College Station, TX, United States
- Department of Biological Sciences, Texas A&M University, College Station, TX, United States
- Department of Molecular Pathogenesis and Immunology, Texas A&M University, College Station, TX, United States
| | - Kurt A. Zuelke
- Global Health Research Complex, Division of Research, Texas A&M University, College Station, TX, United States
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Delgado S, Somovilla P, Ferrer-Orta C, Martínez-González B, Vázquez-Monteagudo S, Muñoz-Flores J, Soria ME, García-Crespo C, de Ávila AI, Durán-Pastor A, Gadea I, López-Galíndez C, Moran F, Lorenzo-Redondo R, Verdaguer N, Perales C, Domingo E. Incipient functional SARS-CoV-2 diversification identified through neural network haplotype maps. Proc Natl Acad Sci U S A 2024; 121:e2317851121. [PMID: 38416684 DOI: 10.1073/pnas.2317851121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/08/2024] [Indexed: 03/01/2024] Open
Abstract
Since its introduction in the human population, SARS-CoV-2 has evolved into multiple clades, but the events in its intrahost diversification are not well understood. Here, we compare three-dimensional (3D) self-organized neural haplotype maps (SOMs) of SARS-CoV-2 from thirty individual nasopharyngeal diagnostic samples obtained within a 19-day interval in Madrid (Spain), at the time of transition between clades 19 and 20. SOMs have been trained with the haplotype repertoire present in the mutant spectra of the nsp12- and spike (S)-coding regions. Each SOM consisted of a dominant neuron (displaying the maximum frequency), surrounded by a low-frequency neuron cloud. The sequence of the master (dominant) neuron was either identical to that of the reference Wuhan-Hu-1 genome or differed from it at one nucleotide position. Six different deviant haplotype sequences were identified among the master neurons. Some of the substitutions in the neural clouds affected critical sites of the nsp12-nsp8-nsp7 polymerase complex and resulted in altered kinetics of RNA synthesis in an in vitro primer extension assay. Thus, the analysis has identified mutations that are relevant to modification of viral RNA synthesis, present in the mutant clouds of SARS-CoV-2 quasispecies. These mutations most likely occurred during intrahost diversification in several COVID-19 patients, during an initial stage of the pandemic, and within a brief time period.
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Affiliation(s)
- Soledad Delgado
- Departamento de Sistemas Informáticos, Escuela Técnica Superior de Ingeniería de Sistemas Informáticos, Universidad Politécnica de Madrid, Madrid 28031, Spain
| | - Pilar Somovilla
- Microbes in Health and Welfare Program, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Cristina Ferrer-Orta
- Structural and Molecular Biology Department, Institut de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona 08028, Spain
| | - Brenda Martínez-González
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid 28040, Spain
| | - Sergi Vázquez-Monteagudo
- Structural and Molecular Biology Department, Institut de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona 08028, Spain
| | | | - María Eugenia Soria
- Microbes in Health and Welfare Program, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid 28040, Spain
| | - Carlos García-Crespo
- Microbes in Health and Welfare Program, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
| | - Ana Isabel de Ávila
- Microbes in Health and Welfare Program, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
| | - Antoni Durán-Pastor
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
| | - Ignacio Gadea
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid 28040, Spain
| | - Cecilio López-Galíndez
- Unidad de Virología Molecular, Laboratorio de Referencia e Investigación en retrovirus, Centro Nacional de Microbiología, Instituto de salud Carlos III, Majadahonda 28222, Spain
| | - Federico Moran
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611
| | - Nuria Verdaguer
- Structural and Molecular Biology Department, Institut de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona 08028, Spain
| | - Celia Perales
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid 28040, Spain
| | - Esteban Domingo
- Microbes in Health and Welfare Program, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
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50
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Wratil PR, Le Thi TG, Osterman A, Badell I, Huber M, Zhelyazkova A, Wichert SP, Litwin A, Hörmansdorfer S, Strobl F, Grote V, Jebrini T, Török HP, Hornung V, Choukér A, Koletzko B, Adorjan K, Koletzko S, Keppler OT. Dietary habits, traveling and the living situation potentially influence the susceptibility to SARS-CoV-2 infection: results from healthcare workers participating in the RisCoin Study. Infection 2024:10.1007/s15010-024-02201-4. [PMID: 38436913 DOI: 10.1007/s15010-024-02201-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 01/25/2024] [Indexed: 03/05/2024]
Abstract
PURPOSE To explore occupational and non-occupational risk and protective factors for the coronavirus disease 2019 (COVID-19) in healthcare workers (HCWs). METHODS Serum specimens and questionnaire data were obtained between October 7 and December 16, 2021 from COVID-19-vaccinated HCWs at a quaternary care hospital in Munich, Germany, and were analyzed in the RisCoin Study. RESULTS Of 3,696 participants evaluated, 6.6% have had COVID-19 at least once. Multivariate logistic regression analysis identified working in patient care occupations (7.3% had COVID-19, 95% CI 6.4-8.3, Pr = 0.0002), especially as nurses, to be a potential occupation-related COVID-19 risk factor. Non-occupational factors significantly associated with high rates of the disease were contacts to COVID-19 cases in the community (12.8% had COVID-19, 95% CI 10.3-15.8, Pr < 0.0001), being obese (9.9% had COVID-19, 95% CI 7.1-13.5, Pr = 0.0014), and frequent traveling abroad (9.4% had COVID-19, 95% CI 7.1-12.3, Pr = 0.0088). On the contrary, receiving the basic COVID-19 immunization early during the pandemic (5.9% had COVID-19, 95% CI 5.1-6.8, Pr < 0.0001), regular smoking (3.6% had COVID-19, 95% CI 2.1-6.0, Pr = 0.0088), living with the elderly (3.0% had COVID-19, 95% CI 1.0-8.0, Pr = 0.0475), and frequent consumption of ready-to-eat meals (2.6% had COVID-19, 95% CI 1.1-5.4, Pr = 0.0045) were non-occupational factors potentially protecting study participants against COVID-19. CONCLUSION The newly discovered associations between the living situation, traveling as well as dietary habits and altered COVID-19 risk can potentially help refine containment measures and, furthermore, contribute to new mechanistic insights that may aid the protection of risk groups and vulnerable individuals.
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Affiliation(s)
- Paul R Wratil
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Thu Giang Le Thi
- Department of Pediatrics, Dr. von Hauner Children's Hospital, LMU University Hospital, LMU Munich, Lindwurmstraße 4, 80337, Munich, Germany
| | - Andreas Osterman
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Irina Badell
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Melanie Huber
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Ana Zhelyazkova
- Institut für Notfallmedizin und Medizinmanagement (INM), LMU University Hospital, LMU Munich, Munich, Germany
| | - Sven P Wichert
- Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstraße 7, 80336, Munich, Germany
| | - Anna Litwin
- Department of Pediatrics, Dr. von Hauner Children's Hospital, LMU University Hospital, LMU Munich, Lindwurmstraße 4, 80337, Munich, Germany
| | | | - Frances Strobl
- Department of Pediatrics, Dr. von Hauner Children's Hospital, LMU University Hospital, LMU Munich, Lindwurmstraße 4, 80337, Munich, Germany
| | - Veit Grote
- Department of Pediatrics, Dr. von Hauner Children's Hospital, LMU University Hospital, LMU Munich, Lindwurmstraße 4, 80337, Munich, Germany
| | - Tarek Jebrini
- Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstraße 7, 80336, Munich, Germany
| | - Helga P Török
- Department of Neurology, LMU University Hospital, LMU Munich, Munich, Germany
| | - Veit Hornung
- Gene Center and Department of Biochemistry, LMU Munich, Munich, Germany
| | - Alexander Choukér
- Department of Anesthesiology, Laboratory of Translational Research Stress and Immunity, LMU University Hospital, LMU Munich, Munich, Germany
| | - Berthold Koletzko
- Department of Pediatrics, Dr. von Hauner Children's Hospital, LMU University Hospital, LMU Munich, Lindwurmstraße 4, 80337, Munich, Germany
| | - Kristina Adorjan
- Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstraße 7, 80336, Munich, Germany.
- Institute of Psychiatric Phenomics and Genomics (IPPG), LMU University Hospital, LMU Munich, Munich, Germany.
- Center for International Health (CIH), LMU Munich, Munich, Germany.
- University Hospital of Psychiatry and Psychotherapy, University of Bern, Bern, Switzerland.
| | - Sibylle Koletzko
- Department of Pediatrics, Dr. von Hauner Children's Hospital, LMU University Hospital, LMU Munich, Lindwurmstraße 4, 80337, Munich, Germany.
- Department of Pediatrics, Gastroenterology and Nutrition, School of Medicine Collegium Medicum, University of Warmia and Mazury, Olsztyn, Poland.
| | - Oliver T Keppler
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
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