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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] [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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2
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Hasan M, He Z, Jia M, Leung ACF, Natarajan K, Xu W, Yap S, Zhou F, Chen S, Su H, Zhu K, Su H. Dynamic expedition of leading mutations in SARS-CoV-2 spike glycoproteins. Comput Struct Biotechnol J 2024; 23:2407-2417. [PMID: 38882678 PMCID: PMC11176665 DOI: 10.1016/j.csbj.2024.05.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 05/21/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
The continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which caused the recent pandemic, has generated countless new variants with varying fitness. Mutations of the spike glycoprotein play a particularly vital role in shaping its evolutionary trajectory, as they have the capability to alter its infectivity and antigenicity. We present a time-resolved statistical method, Dynamic Expedition of Leading Mutations (deLemus), to analyze the evolutionary dynamics of the SARS-CoV-2 spike glycoprotein. The proposed L -index of the deLemus method is effective in quantifying the mutation strength of each amino acid site and outlining evolutionarily significant sites, allowing the comprehensive characterization of the evolutionary mutation pattern of the spike glycoprotein.
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Affiliation(s)
- Muhammad Hasan
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhouyi He
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Mengqi Jia
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Alvin C F Leung
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | | | - Wentao Xu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shanqi Yap
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Feng Zhou
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shihong Chen
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Hailei Su
- Bengbu Hospital of Traditional Chinese Medicine, 4339 Huai-shang Road, Anhui 233080, China
| | - Kaicheng Zhu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Haibin Su
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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3
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Hao Z, Hu S, Huang J, Hu J, Zhang Z, Li H, Yan W. Confounding amplifies the effect of environmental factors on COVID-19. Infect Dis Model 2024; 9:1163-1174. [PMID: 39035783 PMCID: PMC11260012 DOI: 10.1016/j.idm.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/26/2024] [Accepted: 06/16/2024] [Indexed: 07/23/2024] Open
Abstract
The global COVID-19 pandemic has severely impacted human health and socioeconomic development, posing an enormous public health challenge. Extensive research has been conducted into the relationship between environmental factors and the transmission of COVID-19. However, numerous factors influence the development of pandemic outbreaks, and the presence of confounding effects on the mechanism of action complicates the assessment of the role of environmental factors in the spread of COVID-19. Direct estimation of the role of environmental factors without removing the confounding effects will be biased. To overcome this critical problem, we developed a Double Machine Learning (DML) causal model to estimate the debiased causal effects of the influencing factors in the COVID-19 outbreaks in Chinese cities. Comparative experiments revealed that the traditional multiple linear regression model overestimated the impact of environmental factors. Environmental factors are not the dominant cause of widespread outbreaks in China in 2022. In addition, by further analyzing the causal effects of environmental factors, it was verified that there is significant heterogeneity in the role of environmental factors. The causal effect of environmental factors on COVID-19 changes with the regional environment. It is therefore recommended that when exploring the mechanisms by which environmental factors influence the spread of epidemics, confounding factors must be handled carefully in order to obtain clean quantitative results. This study offers a more precise representation of the impact of environmental factors on the spread of the COVID-19 pandemic, as well as a framework for more accurately quantifying the factors influencing the outbreak.
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Affiliation(s)
- Zihan Hao
- College of Atmospheric Sciences, Lanzhou University, Lanzhoum, 730000, China
| | - Shujuan Hu
- College of Atmospheric Sciences, Lanzhou University, Lanzhoum, 730000, China
| | - Jianping Huang
- Collaborative Innovation Center for Western Ecological Safety, College of Atmospheric Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jiaxuan Hu
- College of Atmospheric Sciences, Lanzhou University, Lanzhoum, 730000, China
| | - Zhen Zhang
- College of Atmospheric Sciences, Lanzhou University, Lanzhoum, 730000, China
| | - Han Li
- Collaborative Innovation Center for Western Ecological Safety, College of Atmospheric Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Wei Yan
- Collaborative Innovation Center for Western Ecological Safety, College of Atmospheric Sciences, Lanzhou University, Lanzhou, 730000, China
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4
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González-Parra G, Mahmud MS, Kadelka C. Learning from the COVID-19 pandemic: A systematic review of mathematical vaccine prioritization models. Infect Dis Model 2024; 9:1057-1080. [PMID: 38988830 PMCID: PMC11233876 DOI: 10.1016/j.idm.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/26/2024] [Accepted: 05/10/2024] [Indexed: 07/12/2024] Open
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 González-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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5
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Santoni D. An entropy-based study on the mutational landscape of SARS-CoV-2 in USA: Comparing different variants and revealing co-mutational behavior of proteins. Gene 2024; 922:148556. [PMID: 38754568 DOI: 10.1016/j.gene.2024.148556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/18/2024]
Abstract
COVID-19 emergency has pushed the international scientific community to use every resource to combat the spread of the virus, to understand its biology and predict its possible evolution in terms of new variants. Since the first SARS-CoV-2 virus nucleotide and amino acid sequences were made available, information theory was used to study how viral information content was changing over time and then trace the evolution of its mutational landscape. In this work we analyzed SARS-CoV-2 sequences collected mainly in the USA in a period from March 2020 until December 2022 and computed mutation profiles of viral proteins over time through an entropy-based approach using Shannon Entropy and Hellinger distance. This representation allows an at-a-glance view of the mutational landscape of viral proteins over time and can provide new insights on the evolution of the virus from different points of view. Non-structural proteins typically showed flat mutation profiles, characterized by a very low Average mutation Entropy, while accessory and structural proteins showed mostly non uniform and high mutation profiles, often coupled with the predominance of variants. Interestingly NSP2 protein, whose function is currently still debated, falls in the same branch of NSP14 and NSP10 in the phylogenetic tree of mutations constructed through correlations of mutation profiles, suggesting a co-evolution of those proteins and a possible functional link with each other. To the best of our knowledge this is the first study based on a massive amount of data (n = 107,939,973) that analyzes from an entropy point of view the mutational landscape of SARS-CoV-2 over time and depicts a mutational temporal profile of each protein of the virus.
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Affiliation(s)
- Daniele Santoni
- Institute for System Analysis and Computer Science "Antonio Ruberti", National Research Council of Italy, Via dei Taurini 19, Rome 00185, Italy.
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6
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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; 9:676-686. [PMID: 38572798 DOI: 10.1177/23969873241241885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [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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7
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Jena D, Ghosh A, Jha A, Prasad P, Raghav SK. Impact of vaccination on SARS-CoV-2 evolution and immune escape variants. Vaccine 2024; 42:126153. [PMID: 39060204 DOI: 10.1016/j.vaccine.2024.07.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 06/18/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024]
Abstract
Vaccines and host genetic factors can influence the SARS-CoV-2 evolution and emergence of new variants. Even vaccinated cases get affected as virus continues to evolve, raising concerns about vaccine efficacy and the emergence of immune escape variants. Here, we have analyzed 2295 whole-genome sequences of SARS-CoV-2 collected from vaccinated and unvaccinated cases to evaluate the impact of vaccines on virus diversity within hosts. Our comparative analysis revealed a significant higher incidence of intra-host single nucleotides variants (iSNVs) in vaccinated cases compared to unvaccinated ones (p value<0.0001). Furthermore, we have found that specific mutational processes, including APOBEC (C > T) mediated and ADAR1 (A > G) mediated mutations, were found more prevalent in vaccinated cases. Vaccinated cases exhibited higher accumulation of nonsynonymous mutation than unvaccinated cases. Fixed iSNVs were predominantly located in the ORF1ab and spike genes, several key omicron defining immune escape variants S477N, Q493R, Q498R, Y505H, L452R, and N501Y were identified in the RBD domain of spike gene in vaccinated cases. Our findings suggest that vaccine plays an important role in the evolution of the virus genome. The virus genome acquires random mutations due to error-prone replication of the virus, host modification through APOBEC and ADAR1 mediated editing mechanism, and oxidative stress. These mutations become fixed in the viral population due to the selective pressure imposed by vaccination.
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Affiliation(s)
- Deepak Jena
- DBT - Institute of Life Sciences, Bhubaneswar, India.
| | - Arup Ghosh
- DBT - Institute of Life Sciences, Bhubaneswar, India
| | - Atimukta Jha
- DBT - Institute of Life Sciences, Bhubaneswar, India
| | - Punit Prasad
- DBT - Institute of Life Sciences, Bhubaneswar, India
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8
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Velma GR, Shen Z, Holberg C, Fu J, Soleymani F, Cooper L, Ramos OL, Indukuri D, Musku SR, Rychetsky P, Slilaty S, Li Z, Ratia K, Rong L, Schenten D, Xiong R, J Thatcher GR. Non-Covalent Inhibitors of SARS-CoV-2 Papain-Like Protease (PLpro): In Vitro and In Vivo Antiviral Activity. J Med Chem 2024; 67:13681-13702. [PMID: 39102360 DOI: 10.1021/acs.jmedchem.4c00378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
The SARS-CoV-2 papain-like protease (PLpro), essential for viral processing and immune response disruption, is a promising target for treating acute infection of SARS-CoV-2. To date, there have been no reports of PLpro inhibitors with both submicromolar potency and animal model efficacy. To address the challenge of PLpro's featureless active site, a noncovalent inhibitor library with over 50 new analogs was developed, targeting the PLpro active site by modulating the BL2-loop and engaging the BL2-groove. Notably, compounds 42 and 10 exhibited strong antiviral effects and were further analyzed pharmacokinetically. 10, in particular, showed a significant lung accumulation, up to 12.9-fold greater than plasma exposure, and was effective in a mouse model of SARS-CoV-2 infection, as well as against several SARS-CoV-2 variants. These findings highlight the potential of 10 as an in vivo chemical probe for studying PLpro inhibition in SARS-CoV-2 infection.
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Affiliation(s)
- Ganga Reddy Velma
- Department of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Zhengnan Shen
- Department of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Cameron Holberg
- Department of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Jiqiang Fu
- Department of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Farinaz Soleymani
- Department of Chemistry & Biochemistry, Colleges of Science and Medicine, University of Arizona, Tucson 85721, Arizona, United States
| | - Laura Cooper
- Department of Microbiology, College of Medicine, University of Illinois at Chicago (UIC), Chicago 60612, Illinois, United States
| | - Omar Lozano Ramos
- Department of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Divakar Indukuri
- Department of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Soumya Reddy Musku
- Department of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Pavel Rychetsky
- Department of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Steve Slilaty
- Sunshine Biopharma Inc, 333 Las Olas Way, CU4 Suite 433, Fort Lauderdale 33301, Florida, United States
| | - Zuomei Li
- Sunshine Biopharma Inc, 333 Las Olas Way, CU4 Suite 433, Fort Lauderdale 33301, Florida, United States
| | - Kiira Ratia
- Research Resources Center, University of Illinois at Chicago (UIC), Chicago 60612, Illinois, United States
| | - Lijun Rong
- Department of Microbiology, College of Medicine, University of Illinois at Chicago (UIC), Chicago 60612, Illinois, United States
| | - Dominik Schenten
- Department of Immunology, College of Medicine, University of Arizona, Tucson 85721, Arizona, United States
| | - Rui Xiong
- Department of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Gregory R J Thatcher
- Department of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
- Department of Chemistry & Biochemistry, Colleges of Science and Medicine, University of Arizona, Tucson 85721, Arizona, United States
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9
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Khurana MP, Curran-Sebastian J, Scheidwasser N, Morgenstern C, Rasmussen M, Fonager J, Stegger M, Tang MHE, Juul JL, Escobar-Herrera LA, Møller FT, Albertsen M, Kraemer MUG, du Plessis L, Jokelainen P, Lehmann S, Krause TG, Ullum H, Duchêne DA, Mortensen LH, Bhatt S. High-resolution epidemiological landscape from ~290,000 SARS-CoV-2 genomes from Denmark. Nat Commun 2024; 15:7123. [PMID: 39164246 DOI: 10.1038/s41467-024-51371-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 08/01/2024] [Indexed: 08/22/2024] Open
Abstract
Vast amounts of pathogen genomic, demographic and spatial data are transforming our understanding of SARS-CoV-2 emergence and spread. We examined the drivers of molecular evolution and spread of 291,791 SARS-CoV-2 genomes from Denmark in 2021. With a sequencing rate consistently exceeding 60%, and up to 80% of PCR-positive samples between March and November, the viral genome set is broadly whole-epidemic representative. We identify a consistent rise in viral diversity over time, with notable spikes upon the importation of novel variants (e.g., Delta and Omicron). By linking genomic data with rich individual-level demographic data from national registers, we find that individuals aged < 15 and > 75 years had a lower contribution to molecular change (i.e., branch lengths) compared to other age groups, but similar molecular evolutionary rates, suggesting a lower likelihood of introducing novel variants. Similarly, we find greater molecular change among vaccinated individuals, suggestive of immune evasion. We also observe evidence of transmission in rural areas to follow predictable diffusion processes. Conversely, urban areas are expectedly more complex due to their high mobility, emphasising the role of population structure in driving virus spread. Our analyses highlight the added value of integrating genomic data with detailed demographic and spatial information, particularly in the absence of structured infection surveys.
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Affiliation(s)
- Mark P Khurana
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark.
| | - Jacob Curran-Sebastian
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Neil Scheidwasser
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Christian Morgenstern
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London, London, UK
| | - Morten Rasmussen
- Virus Research and Development Laboratory, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Virus Research and Development Laboratory, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Antimicrobial Resistance and Infectious Diseases Laboratory, Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Man-Hung Eric Tang
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Jonas L Juul
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | | | - Mads Albertsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Louis du Plessis
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Pikka Jokelainen
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Sune Lehmann
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tyra G Krause
- Epidemiological Infectious Disease Preparedness, Statens Serum Institut Copenhagen, Copenhagen, Denmark
| | | | - David A Duchêne
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Laust H Mortensen
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
- Statistics Denmark, Copenhagen, Denmark
| | - Samir Bhatt
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London, London, UK
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10
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Bolaji AJ, Duggan AT. In silico analyses identify sequence contamination thresholds for Nanopore-generated SARS-CoV-2 sequences. PLoS Comput Biol 2024; 20:e1011539. [PMID: 39159257 DOI: 10.1371/journal.pcbi.1011539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 07/14/2024] [Indexed: 08/21/2024] Open
Abstract
The SARS-CoV-2 pandemic has brought molecular biology and genomic sequencing into the public consciousness and lexicon. With an emphasis on rapid turnaround, genomic data informed both diagnostic and surveillance decisions for the current pandemic at a previously unheard-of scale. The surge in the submission of genomic data to publicly available databases proved essential as comparing different genome sequences offers a wealth of knowledge, including phylogenetic links, modes of transmission, rates of evolution, and the impact of mutations on infection and disease severity. However, the scale of the pandemic has meant that sequencing runs are rarely repeated due to limited sample material and/or the availability of sequencing resources, resulting in the upload of some imperfect runs to public repositories. As a result, it is crucial to investigate the data obtained from these imperfect runs to determine whether the results are reliable prior to depositing them in a public database. Numerous studies have identified a variety of sources of contamination in public next-generation sequencing (NGS) data as the number of NGS studies increases along with the diversity of sequencing technologies and procedures. For this study, we conducted an in silico experiment with known SARS-CoV-2 sequences produced from Oxford Nanopore Technologies sequencing to investigate the effect of contamination on lineage calls and single nucleotide variants (SNVs). A contamination threshold below which runs are expected to generate accurate lineage calls and maintain genome-relatedness and integrity was identified. Together, these findings provide a benchmark below which imperfect runs may be considered robust for reporting results to both stakeholders and public repositories and reduce the need for repeat or wasted runs.
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Affiliation(s)
- Ayooluwa J Bolaji
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Canada
- Cadham Provincial Laboratory, Winnipeg, Canada
| | - Ana T Duggan
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Canada
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11
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Kendall M, Ferretti L, Wymant C, Tsallis D, Petrie J, Di Francia A, Di Lauro F, Abeler-Dörner L, Manley H, Panovska-Griffiths J, Ledda A, Didelot X, Fraser C. Drivers of epidemic dynamics in real time from daily digital COVID-19 measurements. Science 2024; 385:eadm8103. [PMID: 38991048 DOI: 10.1126/science.adm8103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 06/19/2024] [Indexed: 07/13/2024]
Abstract
Understanding the drivers of respiratory pathogen spread is challenging, particularly in a timely manner during an ongoing epidemic. In this work, we present insights that we obtained using daily data from the National Health Service COVID-19 app for England and Wales and that we shared with health authorities in almost real time. Our indicator of the reproduction number R(t) was available days earlier than other estimates, with an innovative capability to decompose R(t) into contact rates and probabilities of infection. When Omicron arrived, the main epidemic driver switched from contacts to transmissibility. We separated contacts and transmissions by day of exposure and setting and found pronounced variability over days of the week and during Christmas holidays and events. For example, during the Euro football tournament in 2021, days with England matches showed sharp spikes in exposures and transmissibility. Digital contact-tracing technologies can help control epidemics not only by directly preventing transmissions but also by enabling rapid analysis at scale and with unprecedented resolution.
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Affiliation(s)
- Michelle Kendall
- Department of Statistics, University of Warwick, Coventry CV4 7AL, UK
| | - Luca Ferretti
- Pandemic Sciences Institute, Nuffield Department for Medicine, University of Oxford, Old Road Campus, Oxford OX3 7DQ, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford OX3 7LF, UK
| | - Chris Wymant
- Pandemic Sciences Institute, Nuffield Department for Medicine, University of Oxford, Old Road Campus, Oxford OX3 7DQ, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford OX3 7LF, UK
| | - Daphne Tsallis
- Zühlke Engineering Ltd., 80 Great Eastern Street, London EC2A 3JL, UK
| | - James Petrie
- Pandemic Sciences Institute, Nuffield Department for Medicine, University of Oxford, Old Road Campus, Oxford OX3 7DQ, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford OX3 7LF, UK
| | - Andrea Di Francia
- UK Health Security Agency, Nobel House, 17 Smith Square, London SW1P 3JR, UK
| | - Francesco Di Lauro
- Pandemic Sciences Institute, Nuffield Department for Medicine, University of Oxford, Old Road Campus, Oxford OX3 7DQ, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford OX3 7LF, UK
| | - Lucie Abeler-Dörner
- Pandemic Sciences Institute, Nuffield Department for Medicine, University of Oxford, Old Road Campus, Oxford OX3 7DQ, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford OX3 7LF, UK
| | - Harrison Manley
- UK Health Security Agency, Nobel House, 17 Smith Square, London SW1P 3JR, UK
| | - Jasmina Panovska-Griffiths
- Pandemic Sciences Institute, Nuffield Department for Medicine, University of Oxford, Old Road Campus, Oxford OX3 7DQ, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford OX3 7LF, UK
- UK Health Security Agency, Nobel House, 17 Smith Square, London SW1P 3JR, UK
| | - Alice Ledda
- UK Health Security Agency, Nobel House, 17 Smith Square, London SW1P 3JR, UK
| | - Xavier Didelot
- Department of Statistics, University of Warwick, Coventry CV4 7AL, UK
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Christophe Fraser
- Pandemic Sciences Institute, Nuffield Department for Medicine, University of Oxford, Old Road Campus, Oxford OX3 7DQ, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford OX3 7LF, UK
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12
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Ip JD, Chu WM, Chan WM, Chu AWH, Leung RCY, Peng Q, Tam AR, Chan BPC, Cai JP, Yuen KY, Kok KH, Shi Y, Hung IFN, To KKW. The significance of recurrent de novo amino acid substitutions that emerged during chronic SARS-CoV-2 infection: an observational study. EBioMedicine 2024; 107:105273. [PMID: 39146693 DOI: 10.1016/j.ebiom.2024.105273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 07/24/2024] [Accepted: 07/27/2024] [Indexed: 08/17/2024] Open
Abstract
BACKGROUND De novo amino acid substitutions (DNS) frequently emerge among immunocompromised patients with chronic SARS-CoV-2 infection. While previous studies have reported these DNS, their significance has not been systematically studied. METHODS We performed a review of DNS that emerged during chronic SARS-CoV-2 infection. We searched PubMed until June 2023 using the keywords "(SARS-CoV-2 or COVID-19) and (mutation or sequencing) and ((prolonged infection) or (chronic infection) or (long term))". We included patients with chronic SARS-CoV-2 infection who had SARS-CoV-2 sequencing performed for at least 3 time points over at least 60 days. We also included 4 additional SARS-CoV-2 patients with chronic infection of our hospital not reported previously. We determined recurrent DNS that has appeared in multiple patients and determined the significance of these mutations among epidemiologically-significant variants. FINDINGS A total of 34 cases were analyzed, including 30 that were published previously and 4 from our hospital. Twenty two DNS appeared in ≥3 patients, with 14 (64%) belonging to lineage-defining mutations (LDMs) of epidemiologically-significant variants and 10 (45%) emerging among chronically-infected patients before the appearance of the corresponding variant. Notably, nsp9-T35I substitution (Orf1a T4175I) emerged in all three patients with BA.2.2 infection in 2022 before the appearance of Variants of Interest that carry nsp9-T35I as LDM (EG.5 and BA.2.86/JN.1). Structural analysis suggests that nsp9-T35I substitution may affect nsp9-nsp12 interaction, which could be critical for the function of the replication and transcription complex. INTERPRETATION DNS that emerges recurrently in different chronically-infected patients may be used as a marker for potential epidemiologically-significant variants. FUNDING Theme-Based Research Scheme [T11/709/21-N] of the Research Grants Council (See acknowledgements for full list).
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Affiliation(s)
- 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
| | - Wing-Ming Chu
- Division of Infectious Diseases, Department of Medicine, Queen Mary Hospital, 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
| | - 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
| | - Rhoda Cheuk-Ying Leung
- 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
| | - Qi Peng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Anthony Raymond Tam
- Division of Infectious Diseases, Department of Medicine, Queen Mary Hospital, 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
| | - Jian-Piao Cai
- 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
| | - 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, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Kin-Hang Kok
- 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
| | - Yi Shi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ivan Fan-Ngai Hung
- Division of Infectious Diseases, Department of Medicine, Queen Mary Hospital, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China; Infectious Diseases Division, 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
| | - 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, 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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13
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Benlarbi M, Ding S, Bélanger É, Tauzin A, Poujol R, Medjahed H, El Ferri O, Bo Y, Bourassa C, Hussin J, Fafard J, Pazgier M, Levade I, Abrams C, Côté M, Finzi A. Temperature-dependent Spike-ACE2 interaction of Omicron subvariants is associated with viral transmission. mBio 2024; 15:e0090724. [PMID: 38953636 PMCID: PMC11323525 DOI: 10.1128/mbio.00907-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/27/2024] [Indexed: 07/04/2024] Open
Abstract
The continued evolution of severe acute respiratory syndrome 2 (SARS-CoV-2) requires persistent monitoring of its subvariants. Omicron subvariants are responsible for the vast majority of SARS-CoV-2 infections worldwide, with XBB and BA.2.86 sublineages representing more than 90% of circulating strains as of January 2024. To better understand parameters involved in viral transmission, we characterized the functional properties of Spike glycoproteins from BA.2.75, CH.1.1, DV.7.1, BA.4/5, BQ.1.1, XBB, XBB.1, XBB.1.16, XBB.1.5, FD.1.1, EG.5.1, HK.3, BA.2.86 and JN.1. We tested their capacity to evade plasma-mediated recognition and neutralization, binding to angiotensin-converting enzyme 2 (ACE2), their susceptibility to cold inactivation, Spike processing, as well as the impact of temperature on Spike-ACE2 interaction. We found that compared to the early wild-type (D614G) strain, most Omicron subvariants' Spike glycoproteins evolved to escape recognition and neutralization by plasma from individuals who received a fifth dose of bivalent (BA.1 or BA.4/5) mRNA vaccine and improve ACE2 binding, particularly at low temperatures. Moreover, BA.2.86 had the best affinity for ACE2 at all temperatures tested. We found that Omicron subvariants' Spike processing is associated with their susceptibility to cold inactivation. Intriguingly, we found that Spike-ACE2 binding at low temperature was significantly associated with growth rates of Omicron subvariants in humans. Overall, we report that Spikes from newly emerged Omicron subvariants are relatively more stable and resistant to plasma-mediated neutralization, present improved affinity for ACE2 which is associated, particularly at low temperatures, with their growth rates.IMPORTANCEThe persistent evolution of SARS-CoV-2 gave rise to a wide range of variants harboring new mutations in their Spike glycoproteins. Several factors have been associated with viral transmission and fitness such as plasma-neutralization escape and ACE2 interaction. To better understand whether additional factors could be of importance in SARS-CoV-2 variants' transmission, we characterize the functional properties of Spike glycoproteins from several Omicron subvariants. We found that the Spike glycoprotein of Omicron subvariants presents an improved escape from plasma-mediated recognition and neutralization, Spike processing, and ACE2 binding which was further improved at low temperature. Intriguingly, Spike-ACE2 interaction at low temperature is strongly associated with viral growth rate, as such, low temperatures could represent another parameter affecting viral transmission.
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Affiliation(s)
- Mehdi Benlarbi
- Centre de Recherche du CHUM, Montréal, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Shilei Ding
- Centre de Recherche du CHUM, Montréal, Québec, Canada
| | - Étienne Bélanger
- Centre de Recherche du CHUM, Montréal, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Alexandra Tauzin
- Centre de Recherche du CHUM, Montréal, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Raphaël Poujol
- Montreal Heart Institute, Research Center, Montreal, Quebec, Canada
| | | | - Omar El Ferri
- Department of Biochemistry, Microbiology and Immunology, Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
| | - Yuxia Bo
- Department of Biochemistry, Microbiology and Immunology, Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Julie Hussin
- Montreal Heart Institute, Research Center, Montreal, Quebec, Canada
- Département de Médecine, Université de Montréal, Montréal, Québec, Canada
- Mila—Quebec AI institute, Montreal, Quebec, Canada
| | - Judith Fafard
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine of Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Inès Levade
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Cameron Abrams
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Marceline Côté
- Department of Biochemistry, Microbiology and Immunology, Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montréal, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
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14
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Yang Y, Luo YD, Zhang CB, Xiang Y, Bai XY, Zhang D, Fu ZY, Hao RB, Liu XL. Progress in Research on Inhibitors Targeting SARS-CoV-2 Main Protease (M pro). ACS OMEGA 2024; 9:34196-34219. [PMID: 39157135 PMCID: PMC11325518 DOI: 10.1021/acsomega.4c03023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 07/12/2024] [Accepted: 07/19/2024] [Indexed: 08/20/2024]
Abstract
Since 2019, the novel coronavirus (SARS-CoV-2) has caused significant morbidity and millions of deaths worldwide. The Coronavirus Disease 2019 (COVID-19), caused by SARS-CoV-2 and its variants, has further highlighted the urgent need for the development of effective therapeutic agents. Currently, the highly conserved and broad-spectrum nature of main proteases (Mpro) renders them of great importance in the field of inhibitor study. In this study, we categorize inhibitors targeting Mpro into three major groups: mimetic, nonmimetic, and natural inhibitors. We then present the research progress of these inhibitors in detail, including their mechanism of action, antiviral activity, pharmacokinetic properties, animal experiments, and clinical studies. This review aims to provide valuable insights and potential avenues for the development of more effective antiviral drugs against SARS-CoV-2.
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Affiliation(s)
- Yue Yang
- School
of Medicine, Yan’an University, Yan’an 716000, China
| | - Yi-Dan Luo
- School
of Medicine, Yan’an University, Yan’an 716000, China
| | - Chen-Bo Zhang
- School
of Medicine, Yan’an University, Yan’an 716000, China
| | - Yang Xiang
- School
of Medicine, Yan’an University, Yan’an 716000, China
- College
of Physical Education, Yan’an University, Yan’an 716000, China
| | - Xin-Yue Bai
- School
of Medicine, Yan’an University, Yan’an 716000, China
| | - Die Zhang
- School
of Medicine, Yan’an University, Yan’an 716000, China
| | - Zhao-Ying Fu
- School
of Medicine, Yan’an University, Yan’an 716000, China
| | - Ruo-Bing Hao
- School
of Medicine, Yan’an University, Yan’an 716000, China
| | - Xiao-Long Liu
- School
of Medicine, Yan’an University, Yan’an 716000, China
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15
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Banho CA, de Carvalho Marques B, Sacchetto L, Lima AKS, Parra MCP, Lima ARJ, Ribeiro G, Martins AJ, Barros CRDS, Elias MC, Sampaio SC, Slavov SN, Rodrigues ES, Santos EV, Covas DT, Kashima S, Brassaloti RA, Petry B, Clemente LG, Coutinho LL, Assato PA, da Silva da Costa FA, Grotto RMT, Poleti MD, Lesbon JCC, Mattos EC, Fukumasu H, Giovanetti M, Alcantara LCJ, Souza-Neto JA, Rahal P, Araújo JP, Spilki FR, Althouse BM, Vasilakis N, Nogueira ML. Dynamic clade transitions and the influence of vaccination on the spatiotemporal circulation of SARS-CoV-2 variants. NPJ Vaccines 2024; 9:145. [PMID: 39127725 DOI: 10.1038/s41541-024-00933-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 07/17/2024] [Indexed: 08/12/2024] Open
Abstract
Since 2021, the emergence of variants of concern (VOC) has led Brazil to experience record numbers of in COVID-19 cases and deaths. The expanded spread of the SARS-CoV-2 combined with a low vaccination rate has contributed to the emergence of new mutations that may enhance viral fitness, leading to the persistence of the disease. Due to limitations in the real-time genomic monitoring of new variants in some Brazilian states, we aimed to investigate whether genomic surveillance, coupled with epidemiological data and SARS-CoV-2 variants spatiotemporal spread in a smaller region, can reflect the pandemic progression at a national level. Our findings revealed three SARS-CoV-2 variant replacements from 2021 to early 2022, corresponding to the introduction and increase in the frequency of Gamma, Delta, and Omicron variants, as indicated by peaks of the Effective Reproductive Number (Reff). These distinct clade replacements triggered two waves of COVID-19 cases, influenced by the increasing vaccine uptake over time. Our results indicated that the effectiveness of vaccination in preventing new cases during the Delta and Omicron circulations was six and eleven times higher, respectively, than during the period when Gamma was predominant, and it was highly efficient in reducing the number of deaths. Furthermore, we demonstrated that genomic monitoring at a local level can reflect the national trends in the spread and evolution of SARS-CoV-2.
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Affiliation(s)
- Cecília Artico Banho
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Beatriz de Carvalho Marques
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Lívia Sacchetto
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Ana Karoline Sepedro Lima
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Maisa Carla Pereira Parra
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Alex Ranieri Jeronimo Lima
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | - Gabriela Ribeiro
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | - Antonio Jorge Martins
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | | | - Maria Carolina Elias
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | - Sandra Coccuzzo Sampaio
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | - Svetoslav Nanev Slavov
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Evandra Strazza Rodrigues
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Elaine Vieira Santos
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Dimas Tadeu Covas
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Simone Kashima
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | | | - Bruna Petry
- University of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil
| | - Luan Gaspar Clemente
- University of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil
| | - Luiz Lehmann Coutinho
- University of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil
| | - Patricia Akemi Assato
- São Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil
| | - Felipe Allan da Silva da Costa
- São Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil
| | - Rejane Maria Tommasini Grotto
- São Paulo State University (UNESP), School of Agricultural Sciences, Botucatu, Brazil
- Molecular Biology Laboratory, Applied Biotechnology Laboratory, Clinical Hospital of the Botucatu Medical School, Botucatu, Brazil
| | - Mirele Daiana Poleti
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Jessika Cristina Chagas Lesbon
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Elisangela Chicaroni Mattos
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Heidge Fukumasu
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Marta Giovanetti
- Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro, Brazil
- Climate Amplified Diseases And Epidemics (CLIMADE), Rio de Janeiro, Brazil
- Sciences and Technologies for Sustainable Development and One Health, Universita Campus Bio-Medico di Roma, Selcetta, Italy
| | - Luiz Carlos Junior Alcantara
- Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro, Brazil
- Climate Amplified Diseases And Epidemics (CLIMADE), Rio de Janeiro, Brazil
| | - Jayme A Souza-Neto
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas StateUniversity, Manhattan, KS, USA
| | - Paula Rahal
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista (Unesp), São José do Rio Preto, Brazil
| | - João Pessoa Araújo
- Instituto de Biotecnologia, Universidade Estadual Paulista (Unesp), Botucatu, Brazil
| | - Fernando Rosado Spilki
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Novo Hamburgo, Brazil
| | - Benjamin M Althouse
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
- Information School, University of Washington, Seattle, WA, USA
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
- Center for Vector-Borne and Zoonotic Diseases, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil.
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA.
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16
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Quek AML, Wang S, Teng O, Shunmuganathan B, Er BGC, Mahmud NFB, Ng IXQ, Gupta R, Tan ISL, Tan NY, Qian X, Purushotorman K, Teoh HL, Ng KWP, Goh Y, Soon DTL, Tay SH, Teng GG, Ma M, Chandran NS, Hartono JL, MacAry PA, Seet RCS. Hybrid immunity augments cross-variant protection against COVID-19 among immunocompromised individuals. J Infect 2024:106238. [PMID: 39121971 DOI: 10.1016/j.jinf.2024.106238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 07/24/2024] [Accepted: 07/30/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND Immunity to SARS-CoV-2 vaccination and infection differs considerably among individuals. We investigate the critical pathways that influence vaccine-induced cross-variant serological immunity among individuals at high-risk of COVID-19 complications. METHODS Neutralizing antibodies to the wild-type SARS-CoV-2 virus and its variants (Beta, Gamma, Delta and Omicron) were analyzed in patients with autoimmune diseases, chronic comorbidities (multimorbidity), and healthy controls. Antibody levels were assessed at baseline and at different intervals up to 12-months following primary and booster vaccination with either BNT162b2 or mRNA-1273. Immunity induced by vaccination with and without infection (hybrid immunity) was compared with that of unvaccinated individuals with recent SARS-CoV-2 infection. Plasma cytokines were analyzed to investigate variations in antibody production following vaccination. RESULTS Patients with autoimmune diseases (n=137) produced lesser antibodies to the wild-type SARS-CoV-2 virus and its variants compared with those in the multimorbidity (n=153) and healthy groups (n=229); antibody levels were significantly lower in patients with neuromyelitis optica and those on prednisolone, mycophenolate or rituximab treatment. Multivariate logistic regression analysis identified neuromyelitis optica (odds ratio 8.20, 95% CI 1.68-39.9) and mycophenolate (13.69, 3.78-49.5) as significant predictors of a poorer antibody response to vaccination (i.e, neutralizing antibody <40%). Infected participants exhibited antibody levels that were 28.7% higher (95% CI 24.7-32.7) compared to non-infected participants six months after receiving a booster vaccination. Individuals infected during the Delta outbreak generated cross-protective neutralizing antibodies against the Omicron variant in quantities comparable to those observed after infection with the Omicron variant itself. In contrast, unvaccinated individuals recently infected with the wild-type (n=2390) consistently displayed lower levels of neutralizing antibodies against both the wild-type virus and other variants. Pathway analyses suggested an inverse relationship between baseline T cell subsets and antibody production following vaccination. CONCLUSION Hybrid immunity confers a robust protection against COVID-19 among immunocompromised individuals.
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Affiliation(s)
- Amy May Lin Quek
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Division of Neurology, Department of Medicine, National University Hospital, Singapore
| | - Suqing Wang
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ooiean Teng
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Bhuvaneshwari Shunmuganathan
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Bernadette Guek Cheng Er
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Division of Neurology, Department of Medicine, National University Hospital, Singapore
| | - Nor Fa'izah Binte Mahmud
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Division of Neurology, Department of Medicine, National University Hospital, Singapore
| | - Isabel Xue Qi Ng
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Rashi Gupta
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Isabelle Siang Ling Tan
- Cambridge-NUS Cell Phenotyping Center, Center for Life Sciences, National University of Singapore
| | - Nikki Yj Tan
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xinlei Qian
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Kiren Purushotorman
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Hock Luen Teoh
- Division of Neurology, Department of Medicine, National University Hospital, Singapore
| | - Kay Wei Ping Ng
- Division of Neurology, Department of Medicine, National University Hospital, Singapore
| | - Yihui Goh
- Division of Neurology, Department of Medicine, National University Hospital, Singapore
| | - Derek Tuck Loong Soon
- Division of Neurology, Department of Medicine, National University Hospital, Singapore
| | - Sen Hee Tay
- Division of Rheumatology, Department of Medicine, National University Hospital, Singapore
| | - Gim Gee Teng
- Division of Rheumatology, Department of Medicine, National University Hospital, Singapore
| | - Margaret Ma
- Division of Rheumatology, Department of Medicine, National University Hospital, Singapore
| | - Nisha Suyien Chandran
- Division of Dermatology, Department of Medicine, National University Hospital, Singapore
| | - Juanda Leo Hartono
- Division of Gastroenterology and Hepatology, Department of Medicine, National University Hospital, Singapore
| | - Paul A MacAry
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; Cambridge-NUS Cell Phenotyping Center, Center for Life Sciences, National University of Singapore
| | - Raymond Chee Seong Seet
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Division of Neurology, Department of Medicine, National University Hospital, Singapore; Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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17
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Wang Y, Ma Q, Li M, Mai Q, Ma L, Zhang H, Zhong H, Mai K, Cheng N, Feng P, Guan P, Wu S, Zhang L, Dai J, Zhang B, Pan W, Yang Z. A decavalent composite mRNA vaccine against both influenza and COVID-19. mBio 2024:e0066824. [PMID: 39105586 DOI: 10.1128/mbio.00668-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 07/02/2024] [Indexed: 08/07/2024] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has had a persistent and significant impact on global public health for 4 years. Recently, there has been a resurgence of seasonal influenza transmission worldwide. The co-circulation of SARS-CoV-2 and seasonal influenza viruses results in a dual burden on communities. Additionally, the pandemic potential of zoonotic influenza viruses, such as avian Influenza A/H5N1 and A/H7N9, remains a concern. Therefore, a combined vaccine against all these respiratory diseases is in urgent need. mRNA vaccines, with their superior efficacy, speed in development, flexibility, and cost-effectiveness, offer a promising solution for such infectious diseases and potential future pandemics. In this study, we present FLUCOV-10, a novel 10-valent mRNA vaccine created from our proven platform. This vaccine encodes hemagglutinin (HA) proteins from four seasonal influenza viruses and two avian influenza viruses with pandemic potential, as well as spike proteins from four SARS-CoV-2 variants. A two-dose immunization with the FLUCOV-10 elicited robust immune responses in mice, producing IgG antibodies, neutralizing antibodies, and antigen-specific cellular immune responses against all the vaccine-matched viruses of influenza and SARS-CoV-2. Remarkably, the FLUCOV-10 immunization provided complete protection in mouse models against both homologous and heterologous strains of influenza and SARS-CoV-2. These results highlight the potential of FLUCOV-10 as an effective vaccine candidate for the prevention of influenza and COVID-19.IMPORTANCEAmidst the ongoing and emerging respiratory viral threats, particularly the concurrent and sequential spread of SARS-CoV-2 and influenza, our research introduces FLUCOV-10. This novel mRNA-based combination vaccine, designed to counteract both influenza and COVID-19, by incorporating genes for surface glycoproteins from various influenza viruses and SARS-CoV-2 variants. This combination vaccine was highly effective in preclinical trials, generating strong immune responses and ensuring protection against both matching and heterologous strains of influenza viruses and SARS-CoV-2. FLUCOV-10 represents a significant step forward in our ability to address respiratory viral threats, showcasing potential as a singular, adaptable vaccine solution for global health challenges.
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Affiliation(s)
- Yang Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangzhou National Laboratory, Guangzhou, China
| | - Qinhai Ma
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Man Li
- Argorna Pharmaceuticals Co., Ltd., Guangzhou, China
| | - Qianyi Mai
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lin Ma
- Guangzhou RiboBio Co., Ltd, Guangzhou, China
| | - Hong Zhang
- Argorna Pharmaceuticals Co., Ltd., Guangzhou, China
| | | | - Kailin Mai
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Nan Cheng
- Guangzhou RiboBio Co., Ltd, Guangzhou, China
| | - Pei Feng
- Respiratory Disease AI Laboratory on Epidemic and Medical Big Data Instrument Applications, Faculty of Innovation Engineering, Macau University of Science and Technology, Macau SAR, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau SAR, China
| | - Peikun Guan
- Guangzhou National Laboratory, Guangzhou, China
| | - Shengzhen Wu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lu Zhang
- Technology Centre, Guangzhou Customs, Guangzhou, China
| | - Jun Dai
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangzhou National Laboratory, Guangzhou, China
- Technology Centre, Guangzhou Customs, Guangzhou, China
| | - Biliang Zhang
- Argorna Pharmaceuticals Co., Ltd., Guangzhou, China
- State Key Laboratory of Respiratory Disease, Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Weiqi Pan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Respiratory Disease AI Laboratory on Epidemic and Medical Big Data Instrument Applications, Faculty of Innovation Engineering, Macau University of Science and Technology, Macau SAR, China
| | - Zifeng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangzhou National Laboratory, Guangzhou, China
- Respiratory Disease AI Laboratory on Epidemic and Medical Big Data Instrument Applications, Faculty of Innovation Engineering, Macau University of Science and Technology, Macau SAR, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau SAR, China
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Cagliani R, Forni D, Mozzi A, Fuchs R, Tussia-Cohen D, Arrigoni F, Pozzoli U, De Gioia L, Hagai T, Sironi M. Evolution of Virus-like Features and Intrinsically Disordered Regions in Retrotransposon-derived Mammalian Genes. Mol Biol Evol 2024; 41:msae154. [PMID: 39101471 PMCID: PMC11299033 DOI: 10.1093/molbev/msae154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 08/06/2024] Open
Abstract
Several mammalian genes have originated from the domestication of retrotransposons, selfish mobile elements related to retroviruses. Some of the proteins encoded by these genes have maintained virus-like features; including self-processing, capsid structure formation, and the generation of different isoforms through -1 programmed ribosomal frameshifting. Using quantitative approaches in molecular evolution and biophysical analyses, we studied 28 retrotransposon-derived genes, with a focus on the evolution of virus-like features. By analyzing the rate of synonymous substitutions, we show that the -1 programmed ribosomal frameshifting mechanism in three of these genes (PEG10, PNMA3, and PNMA5) is conserved across mammals and originates alternative proteins. These genes were targets of positive selection in primates, and one of the positively selected sites affects a B-cell epitope on the spike domain of the PNMA5 capsid, a finding reminiscent of observations in infectious viruses. More generally, we found that retrotransposon-derived proteins vary in their intrinsically disordered region content and this is directly associated with their evolutionary rates. Most positively selected sites in these proteins are located in intrinsically disordered regions and some of them impact protein posttranslational modifications, such as autocleavage and phosphorylation. Detailed analyses of the biophysical properties of intrinsically disordered regions showed that positive selection preferentially targeted regions with lower conformational entropy. Furthermore, positive selection introduces variation in binary sequence patterns across orthologues, as well as in chain compaction. Our results shed light on the evolutionary trajectories of a unique class of mammalian genes and suggest a novel approach to study how intrinsically disordered region biophysical characteristics are affected by evolution.
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Affiliation(s)
- Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Computational Biology Unit, Bosisio Parini 23842, Italy
| | - Diego Forni
- Scientific Institute IRCCS E. MEDEA, Computational Biology Unit, Bosisio Parini 23842, Italy
| | - Alessandra Mozzi
- Scientific Institute IRCCS E. MEDEA, Computational Biology Unit, Bosisio Parini 23842, Italy
| | - Rotem Fuchs
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Dafna Tussia-Cohen
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Federica Arrigoni
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan 20126, Italy
| | - Uberto Pozzoli
- Scientific Institute IRCCS E. MEDEA, Computational Biology Unit, Bosisio Parini 23842, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan 20126, Italy
| | - Tzachi Hagai
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Computational Biology Unit, Bosisio Parini 23842, Italy
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19
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Fozard JA, Thomson EC, Illingworth CJR. Epidemiological inference at the threshold of data availability: an influenza A(H1N2)v spillover event in the United Kingdom. J R Soc Interface 2024; 21:20240168. [PMID: 39109454 PMCID: PMC11304334 DOI: 10.1098/rsif.2024.0168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/20/2024] [Accepted: 07/12/2024] [Indexed: 08/10/2024] Open
Abstract
Viruses that infect animals regularly spill over into the human population, but individual events may lead to anything from a single case to a novel pandemic. Rapidly gaining an understanding of a spillover event is critical to calibrating a public health response. We here propose a novel method, using likelihood-free rejection sampling, to evaluate the properties of an outbreak of swine-origin influenza A(H1N2)v in the United Kingdom, detected in November 2023. From the limited data available, we generate historical estimates of the probability that the outbreak had died out in the days following the detection of the first case. Our method suggests that the outbreak could have been said to be over with 95% certainty between 19 and 29 days after the first case was detected, depending upon the probability of a case being detected. We further estimate the number of undetected cases conditional upon the outbreak still being live, the epidemiological parameter R 0, and the date on which the spillover event itself occurred. Our method requires minimal data to be effective. While our calculations were performed after the event, the real-time application of our method has potential value for public health responses to cases of emerging viral infection.
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Affiliation(s)
- John A. Fozard
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Emma C. Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK
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20
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ElSawy KM. Competitive Interaction of the SGFRKMAF Peptide with 3CLpro Dimerization Intermediates: A Brownian Dynamics Investigation. J Phys Chem B 2024; 128:7313-7321. [PMID: 39028939 DOI: 10.1021/acs.jpcb.4c01938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2024]
Abstract
The SGFRKMAF peptide is known to inhibit the dimerization of 3CLpro monomers, which is essential for SARS-CoV-2 replication. The mechanism behind this, however, is largely unknown. In this work, we used Brownian dynamics simulations to compare and contrast 3CLpro monomer-monomer interactions and 3CLpro monomer-SGFRKMAF peptide interactions. We found that formation of the 3CLpro wild-type dimer could potentially involve formation of three intermediates that are primarily stabilized by G11-G124, S1-S301, and T118-G278 interactions. Analysis of 3CLpro monomer interaction with the SGFRKMAF peptide, however, revealed the presence of eight basins of interactions where the peptide assumes the highest local densities at the 3CLPro monomer surface. The second highest-density basin was found to coincide with the interface region of the wild-type 3CLpro dimer, thereby directly blocking the 3CLpro dimer-dimer interactions. The other basins, however, were found to lie far from the interface region. Notably, we found that only 6% of the BD trajectories end up directly into the basin at the interface region and ∼39% of the trajectories end up into those basins lying away from the interface region, indicating a greater role for peptide binding at sites away from the dimer interface region. Importantly, the locations of the basins lying away from the interface were found to coincide with the 3CLpro residues involved in stabilization of the 3CLpro monomer-monomer intermediates. Given that the rate constant of the peptide reaching the monomer surface was found to be almost an order of magnitude higher than the rate constant of monomer-monomer association, the SGFRKMAF peptide has the potential to inhibit dimerization of 3CLpro monomers not only through blocking the interface region but also through blocking the formation of the intermediates involved in the dimerization process. This could potentially open new avenues for 3CLpro dimerization inhibitors that transcend traditional X-ray-based discovery approaches.
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Affiliation(s)
- Karim M ElSawy
- Department of Chemistry, College of Science, Qassim University, Buraydah 52571, Saudi Arabia
- York Cross-disciplinary Centre for Systems Analysis (YCCSA), University of York, York YO10 5GE, United Kingdom
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21
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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; 52:1425-1437. [PMID: 38436913 PMCID: PMC11289231 DOI: 10.1007/s15010-024-02201-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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22
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Pontiroli AE, Zanoni I, Tanzi E, Tagliabue E, La Sala L. Effect of influenza vaccination on SARS-CoV-2 infection: Relationship between SARS-CoV-2 infection rates and effects of influenza vaccination. J Med Virol 2024; 96:e29868. [PMID: 39165082 DOI: 10.1002/jmv.29868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/24/2024] [Accepted: 08/08/2024] [Indexed: 08/22/2024]
Affiliation(s)
- Antonio E Pontiroli
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milan, Italy
| | - Ivan Zanoni
- Division of Immunology and Division of Gastroenterology, Harvard Medical School, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Elisabetta Tanzi
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milan, Italy
| | - Elena Tagliabue
- Laboratory of Cardiovascular and Dysmetabolic Disease, and Value-Based Healthcare Unit, IRCCS MultiMedica, Milan, Italy
| | - Lucia La Sala
- Laboratory of Cardiovascular and Dysmetabolic Disease, and Value-Based Healthcare Unit, IRCCS MultiMedica, Milan, Italy
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Milan, Italy
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23
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Gong X, Peng L, Wang F, Liu J, Tang Y, Peng Y, Niu S, Yin J, Guo L, Lu H, Liu Y, Yang Y. Repeated Omicron infection dampens immune imprinting from previous vaccination and induces broad neutralizing antibodies against Omicron sub-variants. J Infect 2024; 89:106208. [PMID: 38908522 DOI: 10.1016/j.jinf.2024.106208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 06/15/2024] [Indexed: 06/24/2024]
Abstract
OBJECTIVE Similar with influenza virus, antigenic drift is highly relevant to SARS-CoV-2 evolution, and immune imprinting has been found to limit the performance of updated vaccines based on the emerging variants of SARS-CoV-2. We aimed to investigate whether repeated exposure to Omicron variant could reduce the immune imprinting from previous vaccination. METHODS A total of 194 participants with different status of vaccination (unvaccinated, regular vaccination and booster vaccination) confirmed for first infection and re-infection with BA.5, BF.7 and XBB variants were enrolled, and the neutralizing profiles against wild type (WT) SARS-CoV-2 and Omicron sub-variants were analyzed. RESULTS Neutralizing potency against the corresponding infected variant is significantly hampered along with the doses of vaccination during first infection. However, for the participants with first infection of BA.5/BF.7 variants and re-infection of XBB variant, immune imprinting was obviously alleviated, indicated as significantly increased ratio of the corresponding infected variant/WT ID50 titers and higher percentage of samples with high neutralizing activities (ID50 > 500) against BA.5, BF.7 and XBB variants. Moreover, repeated Omicron infection could induce strong neutralizing potency with broad neutralizing profiles against a series of other Omicron sub-variants, both in the vaccine naive and vaccine experienced individuals. CONCLUSIONS Our results demonstrate that repeated Omicron infection dampens immune imprinting from vaccination with WT SARS-CoV-2 and induces broad neutralizing profiles against Omicron sub-variants.
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Affiliation(s)
- Xiaohua Gong
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China; Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China
| | - Ling Peng
- Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China
| | - Fuxiang Wang
- Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China
| | - Jiexiang Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China; Shenzhen Clinical School of Medicine, Guangzhou University of Chinese Medicine, China
| | - Yimin Tang
- Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China
| | - Yun Peng
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China; Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China
| | - Shiyu Niu
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China; Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China
| | - Juzhen Yin
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China; Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China
| | - Liping Guo
- Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China
| | - Hongzhou Lu
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China; Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China.
| | - Yingxia Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China; Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China.
| | - Yang Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China; Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China.
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24
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Beaudoin-Bussières G, Finzi A. Deciphering Fc-effector functions against SARS-CoV-2. Trends Microbiol 2024; 32:756-768. [PMID: 38365562 DOI: 10.1016/j.tim.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 02/18/2024]
Abstract
Major efforts were deployed to study the antibody response against SARS-CoV-2. Antibodies neutralizing SARS-CoV-2 have been extensively studied in the context of infections, vaccinations, and breakthrough infections. Antibodies, however, are pleiotropic proteins that have many functions in addition to neutralization. These include Fc-effector functions such as antibody-dependent cellular cytotoxicity (ADCC) and antibody-dependent cellular phagocytosis (ADCP). Although important to combat viral infections, these Fc-effector functions were less studied in the context of SARS-CoV-2 compared with binding and neutralization. This is partly due to the difficulty in developing reliable assays to measure Fc-effector functions compared to antibody binding and neutralization. Multiple assays have now been developed and can be used to measure different Fc-effector functions. Here, we review these assays and what is known regarding anti-SARS-CoV-2 Fc-effector functions. Overall, this review summarizes and updates our current state of knowledge regarding anti-SARS-CoV-2 Fc-effector functions.
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Affiliation(s)
- Guillaume Beaudoin-Bussières
- Centre de recherche du CHUM, Montréal, Québec H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Québec H2X 0A9, Canada
| | - Andrés Finzi
- Centre de recherche du CHUM, Montréal, Québec H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Québec H2X 0A9, Canada.
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25
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Hills RA, Tan TK, Cohen AA, Keeffe JR, Keeble AH, Gnanapragasam PNP, Storm KN, Rorick AV, West AP, Hill ML, Liu S, Gilbert-Jaramillo J, Afzal M, Napier A, Admans G, James WS, Bjorkman PJ, Townsend AR, Howarth MR. Proactive vaccination using multiviral Quartet Nanocages to elicit broad anti-coronavirus responses. NATURE NANOTECHNOLOGY 2024; 19:1216-1223. [PMID: 38710880 PMCID: PMC11329374 DOI: 10.1038/s41565-024-01655-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 03/15/2024] [Indexed: 05/08/2024]
Abstract
Defending against future pandemics requires vaccine platforms that protect across a range of related pathogens. Nanoscale patterning can be used to address this issue. Here, we produce quartets of linked receptor-binding domains (RBDs) from a panel of SARS-like betacoronaviruses, coupled to a computationally designed nanocage through SpyTag/SpyCatcher links. These Quartet Nanocages, possessing a branched morphology, induce a high level of neutralizing antibodies against several different coronaviruses, including against viruses not represented in the vaccine. Equivalent antibody responses are raised to RBDs close to the nanocage or at the tips of the nanoparticle's branches. In animals primed with SARS-CoV-2 Spike, boost immunizations with Quartet Nanocages increase the strength and breadth of an otherwise narrow immune response. A Quartet Nanocage including the Omicron XBB.1.5 'Kraken' RBD induced antibodies with binding to a broad range of sarbecoviruses, as well as neutralizing activity against this variant of concern. Quartet nanocages are a nanomedicine approach with potential to confer heterotypic protection against emergent zoonotic pathogens and facilitate proactive pandemic protection.
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Affiliation(s)
- Rory A Hills
- Department of Biochemistry, University of Oxford, Oxford, UK
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Tiong Kit Tan
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Alexander A Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Anthony H Keeble
- Department of Biochemistry, University of Oxford, Oxford, UK
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | | | - Kaya N Storm
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Annie V Rorick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Michelle L Hill
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Sai Liu
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Javier Gilbert-Jaramillo
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Madeeha Afzal
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Amy Napier
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Gabrielle Admans
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - William S James
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Alain R Townsend
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK.
- Centre for Translational Immunology, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK.
| | - Mark R Howarth
- Department of Biochemistry, University of Oxford, Oxford, UK.
- Department of Pharmacology, University of Cambridge, Cambridge, UK.
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26
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Schön J, Barut GT, Trüeb BS, Halwe NJ, Berenguer Veiga I, Kratzel A, Ulrich L, Kelly JN, Brügger M, Wylezich C, Taddeo A, Aguiar Moreira E, Túrós D, Grau-Roma L, Ahrens AK, Schlottau K, Britzke T, Breithaupt A, Corleis B, Kochmann J, Oliveira Esteves BI, Almeida L, Thomann L, Devisme C, Stalder H, Steiner S, Ochsenbein S, Schmied K, Labroussaa F, Jores J, V'kovski P, Cmiljanovic V, Alves MP, Benarafa C, Ebert N, Hoffmann D, Beer M, Thiel V. A safe, effective and adaptable live-attenuated SARS-CoV-2 vaccine to reduce disease and transmission using one-to-stop genome modifications. Nat Microbiol 2024; 9:2099-2112. [PMID: 38997518 PMCID: PMC11306094 DOI: 10.1038/s41564-024-01755-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 06/10/2024] [Indexed: 07/14/2024]
Abstract
Approved vaccines are effective against severe COVID-19, but broader immunity is needed against new variants and transmission. Therefore, we developed genome-modified live-attenuated vaccines (LAV) by recoding the SARS-CoV-2 genome, including 'one-to-stop' (OTS) codons, disabling Nsp1 translational repression and removing ORF6, 7ab and 8 to boost host immune responses, as well as the spike polybasic cleavage site to optimize the safety profile. The resulting OTS-modified SARS-CoV-2 LAVs, designated as OTS-206 and OTS-228, are genetically stable and can be intranasally administered, while being adjustable and sustainable regarding the level of attenuation. OTS-228 exhibits an optimal safety profile in preclinical animal models, with no side effects or detectable transmission. A single-dose vaccination induces a sterilizing immunity in vivo against homologous WT SARS-CoV-2 challenge infection and a broad protection against Omicron BA.2, BA.5 and XBB.1.5, with reduced transmission. Finally, this promising LAV approach could be applicable to other emerging viruses.
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Affiliation(s)
- Jacob Schön
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - G Tuba Barut
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Bettina Salome Trüeb
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nico Joel Halwe
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Inês Berenguer Veiga
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Lorenz Ulrich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Jenna N Kelly
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- European Virus Bioinformatics Center, Jena, Germany
| | - Melanie Brügger
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Adriano Taddeo
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Etori Aguiar Moreira
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Demeter Túrós
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Llorenç Grau-Roma
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Ann Kathrin Ahrens
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Kore Schlottau
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Tobias Britzke
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Angele Breithaupt
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Björn Corleis
- Institute of Immunology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Jana Kochmann
- Institute of Immunology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Blandina I Oliveira Esteves
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Lea Almeida
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Lisa Thomann
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Christelle Devisme
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Hanspeter Stalder
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Silvio Steiner
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Sarah Ochsenbein
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Kimberly Schmied
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Fabien Labroussaa
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- Institute of Veterinary Bacteriology, Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jörg Jores
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- Institute of Veterinary Bacteriology, Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | | | - Marco P Alves
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Charaf Benarafa
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Nadine Ebert
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Donata Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany.
- European Virus Bioinformatics Center, Jena, Germany.
| | - Volker Thiel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.
- European Virus Bioinformatics Center, Jena, Germany.
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27
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Choi ANX, Siriphanitchakorn T, Choy MM, Ooi JSG, Manuel M, Tan HC, Lin LZ, Yap X, Gubler DJ, Ooi EE. A prM mutation that attenuates dengue virus replication in human cells enhances midgut infection in mosquitoes. Sci Transl Med 2024; 16:eadk4769. [PMID: 39083584 DOI: 10.1126/scitranslmed.adk4769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 07/10/2024] [Indexed: 08/02/2024]
Abstract
Dengue viruses (DENVs), like all viruses, evolve to perpetuate transmission of their species in their hosts. However, how DENV genetics influences dengue disease outbreaks remains poorly understood. Here, we examined isolates of the South Pacific dengue virus type 2 (DENV-2) that emerged in the 1970s and caused major dengue outbreaks in islands in this region until it reached Tonga, where only a few mild cases were reported. Phylogenetically, the DENV-2 strain isolated in Tonga segregated into a clade different from those clades infecting populations in other South Pacific islands. We found that this epidemiological observation could be explained by a single histidine-to-arginine substitution in position 86 of the premembrane (prM) protein of the Tonga DENV-2 strain. This mutation attenuated viral protein translation in mammalian cells but not in midgut cells of the mosquito vector Aedes aegypti. In mammalian cells, the prM mutation resulted in reduced translation of the viral genome and subsequent reduced virus replication. In contrast, in mosquito midgut cells, the prM mutation conferred a selective infection advantage, possibly because of the positively charged arginine residue introduced by the mutation. These findings provide molecular insights into the year-long silent transmission of attenuated DENV-2 in Tonga during the 1970s dengue outbreak in the South Pacific.
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Affiliation(s)
- Allyson N X Choi
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Tanamas Siriphanitchakorn
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Milly M Choy
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Justin S G Ooi
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Menchie Manuel
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Hwee Cheng Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Lowell Z Lin
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Xin Yap
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Duane J Gubler
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Eng Eong Ooi
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
- Viral Research and Experimental Medicine Centre, SingHealth Duke-NUS Academic Medical Centre, Singapore 169857, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549, Singapore
- Department of Clinical Research, Singapore General Hospital, Singapore 169608, Singapore
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28
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Tachibana K, Nakamura Y, Do TL, Kihara T, Kawada H, Yamamoto N, Ando K. Mutations in the SARS-CoV-2 spike proteins affected the ACE2-binding affinity during the development of Omicron pandemic variants. Biochem Biophys Res Commun 2024; 719:150120. [PMID: 38759524 DOI: 10.1016/j.bbrc.2024.150120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 05/19/2024]
Abstract
Mutations in SARS-CoV-2 caused multiple waves of pandemics. To identify the function of such mutations, we investigated the binding affinity of the S protein with its receptor, ACE2. Omicron BA.1 showed significantly lower binding affinity with human ACE2 than prototype SARS-CoV-2 and Alpha strain, indicating that pre-Omicron to Omicron transition was not mediated by increasing the ACE2-binding affinity. Meanwhile, the later Omicron variants, BA.5 and XBB.1.5, showed significantly higher ACE2-binding affinity, suggesting that the increased ACE2-binding could be involved in the variant transition within Omicron strains. Furthermore, Alpha and Omicron variants, but not prototype SARS-CoV-2, bound mouse ACE2, which lead to a hypothesis that early Omicron strains evolved from Alpha strain by acquiring multiple mutations in mice.
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Affiliation(s)
- Kouichi Tachibana
- Tokai University School of Medicine, Department of Internal Medicine, Division of Hematology and Oncology, 143 Shimokasuya, Isehara, Kanagawa, Japan.
| | - Yoshihiko Nakamura
- Tokai University School of Medicine, Center for Regenerative Medicine, 143 Shimokasuya, Isehara, Kanagawa, Japan
| | - Thi Ly Do
- The University of Kitakyusyu, Department of Life and Environment Engineering, 1-1 Hibikino, Wakamatu, Kitakyusyu, Fukuoka, Japan
| | - Takanori Kihara
- The University of Kitakyusyu, Department of Life and Environment Engineering, 1-1 Hibikino, Wakamatu, Kitakyusyu, Fukuoka, Japan
| | - Hiroshi Kawada
- Tokai University School of Medicine, Department of Internal Medicine, Division of Hematology and Oncology, 143 Shimokasuya, Isehara, Kanagawa, Japan
| | - Norio Yamamoto
- Tokai University School of Medicine, Department of Microbiology, 143 Shimokasuya, Isehara, Kanagawa, Japan
| | - Kiyoshi Ando
- Tokai University School of Medicine, Department of Internal Medicine, Division of Hematology and Oncology, 143 Shimokasuya, Isehara, Kanagawa, Japan
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29
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Goldberg AR, Langwig KE, Brown KL, Marano JM, Rai P, King KM, Sharp AK, Ceci A, Kailing CD, Kailing MJ, Briggs R, Urbano MG, Roby C, Brown AM, Weger-Lucarelli J, Finkielstein CV, Hoyt JR. Widespread exposure to SARS-CoV-2 in wildlife communities. Nat Commun 2024; 15:6210. [PMID: 39075057 PMCID: PMC11286844 DOI: 10.1038/s41467-024-49891-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 06/20/2024] [Indexed: 07/31/2024] Open
Abstract
Pervasive SARS-CoV-2 infections in humans have led to multiple transmission events to animals. While SARS-CoV-2 has a potential broad wildlife host range, most documented infections have been in captive animals and a single wildlife species, the white-tailed deer. The full extent of SARS-CoV-2 exposure among wildlife communities and the factors that influence wildlife transmission risk remain unknown. We sampled 23 species of wildlife for SARS-CoV-2 and examined the effects of urbanization and human use on seropositivity. Here, we document positive detections of SARS-CoV-2 RNA in six species, including the deer mouse, Virginia opossum, raccoon, groundhog, Eastern cottontail, and Eastern red bat between May 2022-September 2023 across Virginia and Washington, D.C., USA. In addition, we found that sites with high human activity had three times higher seroprevalence than low human-use areas. We obtained SARS-CoV-2 genomic sequences from nine individuals of six species which were assigned to seven Pango lineages of the Omicron variant. The close match to variants circulating in humans at the time suggests at least seven recent human-to-animal transmission events. Our data support that exposure to SARS-CoV-2 has been widespread in wildlife communities and suggests that areas with high human activity may serve as points of contact for cross-species transmission.
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Affiliation(s)
- Amanda R Goldberg
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Kate E Langwig
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Katherine L Brown
- Virginia Tech Carilion School of Medicine, Virginia Tech, Roanoke, VA, USA
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, USA
- Molecular Diagnostics Laboratory, Fralin Biomedical Research Institute, Virginia Tech, Roanoke, VA, USA
| | - Jeffrey M Marano
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Blacksburg, VA, USA
- Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Roanoke, VA, USA
| | - Pallavi Rai
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Blacksburg, VA, USA
| | - Kelsie M King
- Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, USA
| | - Amanda K Sharp
- Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, USA
| | - Alessandro Ceci
- Molecular Diagnostics Laboratory, Fralin Biomedical Research Institute, Virginia Tech, Roanoke, VA, USA
| | | | - Macy J Kailing
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Russell Briggs
- Molecular Diagnostics Laboratory, Fralin Biomedical Research Institute, Virginia Tech, Roanoke, VA, USA
| | - Matthew G Urbano
- Molecular Diagnostics Laboratory, Fralin Biomedical Research Institute, Virginia Tech, Roanoke, VA, USA
| | - Clinton Roby
- Molecular Diagnostics Laboratory, Fralin Biomedical Research Institute, Virginia Tech, Roanoke, VA, USA
| | - Anne M Brown
- Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, USA
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
- Data Services, University Libraries, Virginia Tech, Blacksburg, VA, USA
- Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA, USA
- Academy of Integrated Science, Virginia Tech, Blacksburg, VA, USA
| | - James Weger-Lucarelli
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, USA
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Blacksburg, VA, USA
| | - Carla V Finkielstein
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.
- Virginia Tech Carilion School of Medicine, Virginia Tech, Roanoke, VA, USA.
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, USA.
- Molecular Diagnostics Laboratory, Fralin Biomedical Research Institute, Virginia Tech, Roanoke, VA, USA.
- Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA, USA.
- Academy of Integrated Science, Virginia Tech, Blacksburg, VA, USA.
| | - Joseph R Hoyt
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.
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30
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Sun K, Bhiman JN, Tempia S, Kleynhans J, Madzorera VS, Mkhize Q, Kaldine H, McMorrow ML, Wolter N, Moyes J, Carrim M, Martinson NA, Kahn K, Lebina L, du Toit JD, Mkhencele T, von Gottberg A, Viboud C, Moore PL, Cohen C. SARS-CoV-2 correlates of protection from infection against variants of concern. Nat Med 2024:10.1038/s41591-024-03131-2. [PMID: 39060660 DOI: 10.1038/s41591-024-03131-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 06/11/2024] [Indexed: 07/28/2024]
Abstract
Serum neutralizing antibodies (nAbs) induced by vaccination have been linked to protection against symptomatic and severe coronavirus disease 2019. However, much less is known about the efficacy of nAbs in preventing the acquisition of infection, especially in the context of natural immunity and against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immune-escape variants. Here we conducted mediation analysis to assess serum nAbs induced by prior SARS-CoV-2 infections as potential correlates of protection against Delta and Omicron infections, in rural and urban household cohorts in South Africa. We find that, in the Delta wave, D614G nAbs mediate 37% (95% confidence interval: 34-40%) of the total protection against infection conferred by prior exposure to SARS-CoV-2, and that protection decreases with waning immunity. In contrast, Omicron BA.1 nAbs mediate 11% (95% confidence interval: 9-12%) of the total protection against Omicron BA.1 or BA.2 infections, due to Omicron's neutralization escape. These findings underscore that correlates of protection mediated through nAbs are variant specific, and that boosting of nAbs against circulating variants might restore or confer immune protection lost due to nAb waning and/or immune escape. However, the majority of immune protection against SARS-CoV-2 conferred by natural infection cannot be fully explained by serum nAbs alone. Measuring these and other immune markers including T cell responses, both in the serum and in other compartments such as the nasal mucosa, may be required to comprehensively understand and predict immune protection against SARS-CoV-2.
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Affiliation(s)
- Kaiyuan Sun
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA.
| | - Jinal N Bhiman
- SAMRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jackie Kleynhans
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Vimbai Sharon Madzorera
- SAMRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Qiniso Mkhize
- SAMRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Haajira Kaldine
- SAMRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Meredith L McMorrow
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
- COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jocelyn Moyes
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Maimuna Carrim
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Neil A Martinson
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Johns Hopkins University Center for TB Research, Baltimore, MD, USA
| | - Kathleen Kahn
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Limakatso Lebina
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Jacques D du Toit
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Thulisa Mkhencele
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cécile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Penny L Moore
- SAMRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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31
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Chung YS, Lam CY, Tan PH, Tsang HF, Wong SCC. Comprehensive Review of COVID-19: Epidemiology, Pathogenesis, Advancement in Diagnostic and Detection Techniques, and Post-Pandemic Treatment Strategies. Int J Mol Sci 2024; 25:8155. [PMID: 39125722 PMCID: PMC11312261 DOI: 10.3390/ijms25158155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
At present, COVID-19 remains a public health concern due to the ongoing evolution of SARS-CoV-2 and its prevalence in particular countries. This paper provides an updated overview of the epidemiology and pathogenesis of COVID-19, with a focus on the emergence of SARS-CoV-2 variants and the phenomenon known as 'long COVID'. Meanwhile, diagnostic and detection advances will be mentioned. Though many inventions have been made to combat the COVID-19 pandemic, some outstanding ones include multiplex RT-PCR, which can be used for accurate diagnosis of SARS-CoV-2 infection. ELISA-based antigen tests also appear to be potential diagnostic tools to be available in the future. This paper also discusses current treatments, vaccination strategies, as well as emerging cell-based therapies for SARS-CoV-2 infection. The ongoing evolution of SARS-CoV-2 underscores the necessity for us to continuously update scientific understanding and treatments for it.
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Affiliation(s)
| | | | | | | | - Sze-Chuen Cesar Wong
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China; (Y.-S.C.); (C.-Y.L.); (P.-H.T.); (H.-F.T.)
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32
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Kulin D, Shah A, Fairlie T, Wong RK, Fang X, Ghoshal UC, Kashyap PC, Mulak A, Lee YY, Talley NJ, Koloski N, Jones MP, Holtmann GJ. The COVID-19 pandemic as a modifier of DGBI symptom severity: A systematic review and meta-analysis. Neurogastroenterol Motil 2024:e14878. [PMID: 39056447 DOI: 10.1111/nmo.14878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/24/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024]
Abstract
BACKGROUND This SRMA reviewed and assessed the changes in the severity of disorders of gut-brain interaction (DGBI) symptoms during the COVID-19 pandemic, and evaluated factors associated with symptom severity changes. METHODS Electronic databases were searched until February 2024, for articles reporting on changes in symptom severity in DGBI patients during the COVID-19 pandemic. The proportion of DGBI patients who reported a change in their symptom severity were pooled using a random-effects model, and subgroup analyses were conducted to assess the effect of socio-cultural modifiers on symptom severity in DGBI. KEY RESULTS Twelve studies including 3610 DGBI patients found that 31.4% (95% CI, 15.9-52.5) of DGBI patients experienced symptom deterioration, while 24.3% (95% CI, 10.2-47.5) experienced improvement. Countries with high gross domestic product (GDP) had a 43.5% (95% CI, 16.3-75.2) likelihood of symptom deterioration, compared to 9.2% (95% CI, 1.4-42.2) in lower GDP countries. Similarly, countries with low COVID fatality rates had a 60.1% (95% CI, 19.7-90.3) likelihood of symptom deterioration, compared to 18.3% (95% CI, 7.8-36.9) in higher fatality rate countries. Countries with lenient COVID policies had a 58.4% (95% CI, 14.1-92.3) likelihood of symptom deterioration, compared to 19% (95% CI, 8.2-38.1) in countries with stricter policies. Patients in high vaccine hesitancy countries had a 51.4% (95% CI, 19.5-82.2) likelihood of symptom deterioration, compared to 10.6% (95% CI, 2.7-33.4) in low vaccine hesitancy countries. CONCLUSIONS & INFERENCES This meta-analysis reveals that a significantly higher proportion of DGBI patients experienced deterioration of symptoms during the COVID-19 pandemic. Various sociocultural, economic and environmental factors potentially modify the effects of the COVID-19 pandemic on DGBI.
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Affiliation(s)
- Dmitrii Kulin
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
- Department of Gastroenterology & Hepatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Ayesha Shah
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
- Department of Gastroenterology & Hepatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Thomas Fairlie
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
- Department of Gastroenterology & Hepatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Reuben K Wong
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xiucai Fang
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Uday C Ghoshal
- Institute of Gastrosciences and Liver Transplantation, Apollo Multispeciality Hospitals, Kolkata, India
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Agata Mulak
- Department of Gastroenterology and Hepatology, Wroclaw Medical University, Wroclaw, Poland
| | - Yeong Yeh Lee
- School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu, Malaysia
- GI Function & Motility Unit, Hospital Universiti Sains Malaysia, Kota Bharu, Malaysia
| | - Nicholas J Talley
- School of Medicine and Public Health, and Hunter Medical Research Institute, The University of Newcastle, Newcastle, New South Wales, Australia
| | - Natasha Koloski
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
- Department of Gastroenterology & Hepatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Michael P Jones
- Macquarie University, School of Psychological Sciences, Sydney, New South Wales, Australia
| | - Gerald J Holtmann
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
- Department of Gastroenterology & Hepatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
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33
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Papaneophytou C. Breaking the Chain: Protease Inhibitors as Game Changers in Respiratory Viruses Management. Int J Mol Sci 2024; 25:8105. [PMID: 39125676 PMCID: PMC11311956 DOI: 10.3390/ijms25158105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/14/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
Respiratory viral infections (VRTIs) rank among the leading causes of global morbidity and mortality, affecting millions of individuals each year across all age groups. These infections are caused by various pathogens, including rhinoviruses (RVs), adenoviruses (AdVs), and coronaviruses (CoVs), which are particularly prevalent during colder seasons. Although many VRTIs are self-limiting, their frequent recurrence and potential for severe health complications highlight the critical need for effective therapeutic strategies. Viral proteases are crucial for the maturation and replication of viruses, making them promising therapeutic targets. This review explores the pivotal role of viral proteases in the lifecycle of respiratory viruses and the development of protease inhibitors as a strategic response to these infections. Recent advances in antiviral therapy have highlighted the effectiveness of protease inhibitors in curtailing the spread and severity of viral diseases, especially during the ongoing COVID-19 pandemic. It also assesses the current efforts aimed at identifying and developing inhibitors targeting key proteases from major respiratory viruses, including human RVs, AdVs, and (severe acute respiratory syndrome coronavirus-2) SARS-CoV-2. Despite the recent identification of SARS-CoV-2, within the last five years, the scientific community has devoted considerable time and resources to investigate existing drugs and develop new inhibitors targeting the virus's main protease. However, research efforts in identifying inhibitors of the proteases of RVs and AdVs are limited. Therefore, herein, it is proposed to utilize this knowledge to develop new inhibitors for the proteases of other viruses affecting the respiratory tract or to develop dual inhibitors. Finally, by detailing the mechanisms of action and therapeutic potentials of these inhibitors, this review aims to demonstrate their significant role in transforming the management of respiratory viral diseases and to offer insights into future research directions.
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Affiliation(s)
- Christos Papaneophytou
- Department of Life Sciences, School of Life and Health Sciences, University of Nicosia, Nicosia 2417, Cyprus
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34
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Shang J, Li H, Liu X, Sun S, Huan S, Xiong B. Single-particle rotational sensing for analyzing the neutralization activity of antiviral antibodies. Talanta 2024; 279:126606. [PMID: 39089080 DOI: 10.1016/j.talanta.2024.126606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 07/13/2024] [Accepted: 07/22/2024] [Indexed: 08/03/2024]
Abstract
Due to the pathogen-specific targeting, neutralization capabilities, and enduring efficacy, neutralizing antibodies (NAs) have received widespread attentions as a critical immunotherapeutic strategy against infectious viruses. However, because of the high variability and complexity of pathogens, rapid determination of neutralization activity of antiviral antibodies remains a challenge. Here, we report a new method, named as out-of-plane polarization imaging based single-particle rotational sensing, for rapid analysis of neutralization activity of antiviral antibody against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Using the spike protein functionalized gold nanorods (AuNRs) and angiotensin-converting enzyme 2 (ACE2) coated gold nanoparticles (AuNPs) as the rotational sensors and chaperone probes, we demonstrated the single-particle rotational sensing strategy for the measurement of rotational diffusion coefficient of the chaperone-bound rotational sensors caused by the specific spike protein-ACE2 interactions. This enables us to measure the neutralizing activity of neutralizing antibody from the analysis of dose-dependent changes in rotational diffusion coefficient (Dr) of the rotational sensors upon the treatment of SARS-CoV-2 antibody. With this technique, we achieved the quantitative determination of neutralization activity of a commercially available SARS-CoV-2 antibody (IC50, 294.1 ng/mL) with satisfying accuracy and anti-interference ability. This simple and robust method holds the potential for rapid and accurate evaluation of neutralization activity against different pathogenic viruses.
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Affiliation(s)
- Jinhui Shang
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Huiwen Li
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Xixuan Liu
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Shijie Sun
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Shuangyan Huan
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Bin Xiong
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
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35
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Bonetti Franceschi V, Volz E. Phylogenetic signatures reveal multilevel selection and fitness costs in SARS-CoV-2. Wellcome Open Res 2024; 9:85. [PMID: 39132669 PMCID: PMC11316176 DOI: 10.12688/wellcomeopenres.20704.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2024] [Indexed: 08/13/2024] Open
Abstract
Background Large-scale sequencing of SARS-CoV-2 has enabled the study of viral evolution during the COVID-19 pandemic. Some viral mutations may be advantageous to viral replication within hosts but detrimental to transmission, thus carrying a transient fitness advantage. By affecting the number of descendants, persistence times and growth rates of associated clades, these mutations generate localised imbalance in phylogenies. Quantifying these features in closely-related clades with and without recurring mutations can elucidate the tradeoffs between within-host replication and between-host transmission. Methods We implemented a novel phylogenetic clustering algorithm ( mlscluster, https://github.com/mrc-ide/mlscluster) to systematically explore time-scaled phylogenies for mutations under transient/multilevel selection. We applied this method to a SARS-CoV-2 time-calibrated phylogeny with >1.2 million sequences from England, and characterised these recurrent mutations that may influence transmission fitness across PANGO-lineages and genomic regions using Poisson regressions and summary statistics. Results We found no major differences across two epidemic stages (before and after Omicron), PANGO-lineages, and genomic regions. However, spike, nucleocapsid, and ORF3a were proportionally more enriched for transmission fitness polymorphisms (TFP)-homoplasies than other proteins. We provide a catalog of SARS-CoV-2 sites under multilevel selection, which can guide experimental investigations within and beyond the spike protein. Conclusions This study provides empirical evidence for the existence of important tradeoffs between within-host replication and between-host transmission shaping the fitness landscape of SARS-CoV-2. This method may be used as a fast and scalable means to shortlist large sequence databases for sites under putative multilevel selection which may warrant subsequent confirmatory analyses and experimental confirmation.
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Affiliation(s)
- Vinicius Bonetti Franceschi
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, England, W2 1PG, UK
| | - Erik Volz
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, England, W2 1PG, UK
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36
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Wu Y, Lai SK, En-Zuo Chan C, Tan BH, Sugrue RJ. Evidence that the SARS-CoV-2 S protein undergoes a conformational change at the Golgi complex that leads to the formation of virus neutralising antibody binding epitopes in the S1 protein subunit. Virology 2024; 598:110187. [PMID: 39094503 DOI: 10.1016/j.virol.2024.110187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 07/11/2024] [Accepted: 07/20/2024] [Indexed: 08/04/2024]
Abstract
Recombinant SARS-CoV-2 S protein expression was examined in Vero cells by imaging using the human monoclonal antibody panel (PD4, PD5, sc23, and sc29). The PD4 and sc29 antibodies recognised conformational specific epitopes in the S2 protein subunit at the Endoplasmic reticulum and Golgi complex. While PD5 and sc23 detected conformationally specific epitopes in the S1 protein subunit at the Golgi complex, only PD5 recognised the receptor binding domain (RBD). A comparison of the staining patterns of PD5 with non-conformationally specific antibodies that recognises the S1 subunit and RBD suggested the PD5 recognised a conformational structure within the S1 protein subunit. Our data suggests the antibody binding epitopes recognised by the human monoclonal antibodies formed at different locations in the secretory pathway during S protein transport, but a conformational change in the S1 protein subunit at the Golgi complex formed antibody binding epitopes that are recognised by virus neutralising antibodies.
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Affiliation(s)
- Yanjun Wu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Soak Kuan Lai
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Conrad En-Zuo Chan
- Infectious Disease Research Laboratory, National Centre for Infectious Diseases, 16 Jalan Tan Tock Seng, Singapore, 308442
| | - Boon Huan Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Richard J Sugrue
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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Euzen V, Xhaard A, Berreira-Ibraim S, Deville L, Quentin A, De Lima Prata PH, Gournay V, Prot M, Rahou Y, Barbet M, Mercier-Delarue S, Peffault De La Tour R, Simon-Loriere E, Legoff J. Zanamivir and baloxavir combination to cure persistent influenza and coronavirus infections after hematopoietic stem cell transplant. Int J Antimicrob Agents 2024; 64:107281. [PMID: 39047913 DOI: 10.1016/j.ijantimicag.2024.107281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 06/14/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
OBJECTIVES Immunocompromised patients may experience prolonged shedding of influenza virus potentially leading to severe infections. Alternatives to monotherapy with neuraminidase inhibitors should be evaluated to entirely suppress viral replication and prevent drug-resistant mutations. METHODS We investigated the clinical and virological evolution in a case of persistent influenza A and human coronavirus OC43 (HCoV-OC43) coinfection in a hematopoietic stem cell transplant recipient after different therapeutic strategies. RESULTS Successive oseltamivir and zanamivir monotherapies failed to control both infections, with positive results persisting for over 110 days each. This led to the emergence of highly resistant oseltamivir strains due to neuraminidase mutations (E119V and R292K) followed by a deletion (del245-248), while maintaining sensitivity to zanamivir. The intra-host viral diversity data showed that the treatments impacted viral diversity of influenza virus, but not of HCoV-OC43. Considering the patient's underlying condition and the impact of prolonged viral shedding on pulmonary function, eradicating the influenza virus was necessary. A 10-day regimen combining zanamivir and baloxavir-marboxil effectively controlled influenza virus replication and was associated with the clearance of HCoV-OC43, finally resulting in comprehensive respiratory recovery. CONCLUSION These observations underscore the importance of further investigating combination treatments as the primary approach to achieve influenza eradication in immunocompromised patients.
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Affiliation(s)
- Victor Euzen
- Virology Department, AP-HP, Hôpital Saint Louis, Paris, France
| | - Aliénor Xhaard
- Hematology Transplantation, AP-HP, Hôpital Saint Louis, Paris, France
| | | | | | | | | | - Viviane Gournay
- Hematology Transplantation, AP-HP, Hôpital Saint Louis, Paris, France
| | - Matthieu Prot
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, Paris, France
| | - Yannis Rahou
- Institut Pasteur, National Reference Center for Respiratory Viruses, Paris, France
| | - Marion Barbet
- Institut Pasteur, National Reference Center for Respiratory Viruses, Paris, France
| | | | | | - Etienne Simon-Loriere
- Institut Pasteur, National Reference Center for Respiratory Viruses, Paris, France; Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, Paris, France
| | - Jérôme Legoff
- Virology Department, AP-HP, Hôpital Saint Louis, Paris, France; Université Paris Cité, Inserm U976, Insight team, Paris, France.
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Pinto A, Caltagirone M, Battista M, Gazzoli GC, Patti C, Pennese E, De Lorenzo S, Pavone V, Merli M, Chiarenza A, Gorgone AG, Piazza F, Puccini B, Noto A, Arcaini L, De Filippi R, Zinzani PL, Ferreri AJM, Ladetto M, Ferrari S, Gritti G. Exposure to obinutuzumab does not affect outcomes of SARS-CoV-2 infection in vaccinated patients with newly diagnosed advanced-stage follicular lymphoma. Br J Haematol 2024. [PMID: 39039666 DOI: 10.1111/bjh.19661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 07/11/2024] [Indexed: 07/24/2024]
Abstract
URBAN is a multicentric, ambispective study evaluating the effectiveness and safety of obinutuzumab-based immuno-chemotherapy and maintenance in patients with untreated advanced follicular lymphoma (FL). The study began before the COVID-19 emergency declaration in Italy. It is currently ongoing for follow-up, and the enrolment timeline encompassed different stages of the pandemic, various vaccination roll-out phases and prevalence of SARS-CoV-2 variants. Outcomes of interest of the present sub-analysis included SARS-CoV-2 infection rates and COVID-19-related hospitalizations/deaths. At data cut-off, 86 (28.8%) and 213 patients (71.2%) were treated before and during/after the COVID-19 outbreak respectively; 294 (98.3%) completed the induction, 31 (10.4%) completed maintenance and 170 (56.9%) were still on maintenance. Overall, 245 patients (81.9%) received at least one SARS-CoV-2 vaccine dose: 13.5%, 31.4% and 55.1% received one, two and three doses respectively. We observed a substantial decrease in COVID-19-related mortality rates in pre- versus post-vaccination phases, along with a reduction in COVID-19-related outcomes due to the shift from alpha/delta to omicron variant predominance. No differences emerged between patients given maintenance or not, although the schedule was modified in 65% of cases. To our knowledge, URBAN represents the largest dataset of COVID-19-related outcomes in FL patients extensively exposed to obinutuzumab. ClinicalTrials.gov identifier: NCT04034056.
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Affiliation(s)
- A Pinto
- Ematologia Oncologica, Istituto Nazionale Tumori, Fondazione 'G. Pascale', IRCCS, Naples, Italy
| | | | - M Battista
- Clinical Operations, Roche S.p.A., Monza, Italy
| | - G C Gazzoli
- International Patient Safety, Roche S.p.A., Monza, Italy
| | - C Patti
- Ospedali Riuniti Villa Sofia - Cervello, Palermo, Italy
| | - E Pennese
- Unità Operativa Complessa Ematologia Presidio Ospedaliero Pescara, Pescara, Italy
| | - S De Lorenzo
- U.O.C. "Ematologia e TMO" AORN "S. G. Moscati", Avellino, Italy
| | - V Pavone
- Unità Operativa Complessa di Ematologia e Trapianto di Cellule Staminali Emopoietiche, Azienda Ospedaliera Cardinale Panico, Tricase, Italy
| | - M Merli
- Hematology, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - A Chiarenza
- U.O.C. Ematologia Con TMO, Azienda Ospedaliero Universitaria Policlinico "G. Rodolico - San Marco", Catania, Italy
| | - A G Gorgone
- UOC Ematologia ARNAS Garibaldi, Catania, Italy
| | - F Piazza
- UOC Ematologia, Azienda Ospedaliero-Universitaria di Padova, University of Padova, Padova, Italy
| | - B Puccini
- Ematologia, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - A Noto
- Hematology, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - L Arcaini
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Division of Hematology, Fondazione IRCCS Policlinico San Matteo di Pavia, University of Pavia, Pavia, Italy
| | - R De Filippi
- Dipartimento di Medicina Clinica e Chirurgia, Scuola di Medicina, Università Federico II, Naples, Italy
| | - P L Zinzani
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli", Bologna, Italy
- Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, Bologna, Italy
| | - A J M Ferreri
- Lymphoma Unit, IRCCS San Raffaele Scientific Institute and University Vita-Salute San Raffaele, Milan, Italy
| | - M Ladetto
- Dipartimento di Medicina Traslazionale, Università del Piemonte Orientale SCDU Ematologia, AOU SS Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - S Ferrari
- UOC Ematologia Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - G Gritti
- UOC Ematologia Ospedale Papa Giovanni XXIII, Bergamo, Italy
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Mehta SK, Pradhan RB. Phytochemicals in antiviral drug development against human respiratory viruses. Drug Discov Today 2024; 29:104107. [PMID: 39032810 DOI: 10.1016/j.drudis.2024.104107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 05/30/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
This review explores the potential antiviral properties of various plant-based compounds, including polyphenols, phytochemicals, and terpenoids. It emphasizes the diverse functionalities of compounds such as epigallocatechin-3-gallate (EGCG), quercetin, griffithsin (GRFT,) resveratrol, linalool, and carvacrol in the context of respiratory virus infections, including SARS-CoV-2. Emphasizing their effectiveness in modulating immune responses, disrupting viral envelopes, and influencing cellular signaling pathways, the review underlines the imperative for thorough research to establish safety and efficacy. Additionally, the review underscores the necessity of well-designed clinical trials to evaluate the efficacy and safety of these compounds as potential antiviral agents. This approach would establish a robust framework for future drug development efforts focused on bolstering host defense mechanisms against human respiratory viral infections.
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Affiliation(s)
- Surya Kant Mehta
- Laboratory of Algal Biology, Department of Botany, School of Life Sciences, Mizoram University, Aizawl, PIN 796004, Mizoram, India.
| | - Ran Bahadur Pradhan
- Laboratory of Algal Biology, Department of Botany, School of Life Sciences, Mizoram University, Aizawl, PIN 796004, Mizoram, India
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Feys S, Carvalho A, Clancy CJ, Gangneux JP, Hoenigl M, Lagrou K, Rijnders BJA, Seldeslachts L, Vanderbeke L, van de Veerdonk FL, Verweij PE, Wauters J. Influenza-associated and COVID-19-associated pulmonary aspergillosis in critically ill patients. THE LANCET. RESPIRATORY MEDICINE 2024:S2213-2600(24)00151-6. [PMID: 39025089 DOI: 10.1016/s2213-2600(24)00151-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 07/20/2024]
Abstract
Influenza-associated pulmonary aspergillosis (IAPA) and COVID-19-associated pulmonary aspergillosis (CAPA) are increasingly recognised as important complications in patients requiring intensive care for severe viral pneumonia. The diagnosis can typically be made in 10-20% of patients with severe influenza or COVID-19, but only when appropriate diagnostic tools are used. Bronchoalveolar lavage sampling for culture, galactomannan testing, and PCR forms the cornerstone of diagnosis, whereas visual examination of the tracheobronchial tract during bronchoscopy is required to detect invasive Aspergillus tracheobronchitis. Azoles are the first-choice antifungal drugs, with liposomal amphotericin B as an alternative in settings where azole resistance is prevalent. Despite antifungal therapy, IAPA and CAPA are associated with poor outcomes, with fatality rates often exceeding 50%. In this Review, we discuss the mechanistic and clinical aspects of IAPA and CAPA. Moreover, we identify crucial knowledge gaps and formulate directions for future research.
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Affiliation(s)
- Simon Feys
- Medical Intensive Care Unit, University Hospitals Leuven, Leuven, Belgium; Department of Internal Medicine, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven, Belgium.
| | - Agostinho Carvalho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's Associate Laboratory, Braga/ Guimarães, Portugal
| | - Cornelius J Clancy
- Division of Infectious Diseases, University of Pittsburgh, PA, USA; VA Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - Jean-Pierre Gangneux
- Université de Rennes, CHU Rennes, INSERM, EHESP, IRSET, UMR_S 1085, Rennes, France; Centre Hospitalier Universitaire de Rennes, Laboratoire de Parasitologie-Mycologie, ECMM Excellence Center in Medical Mycology, French National Reference Center on Mycoses and Antifungals (CNRMA-LA AspC), Rennes, France
| | - Martin Hoenigl
- Division of Infectious Diseases, ECMM Excellence Center in Medical Mycology, Department of Internal Medicine, Medical University of Graz, Graz, Austria; Translational Medical Mycology Research Group, Medical University of Graz, Graz, Austria; Bio TechMed-Graz, Graz, Austria
| | - Katrien Lagrou
- Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven, Belgium; Department of Laboratory Medicine and National Reference Center for Mycosis, University Hospitals Leuven, Leuven, Belgium
| | - Bart J A Rijnders
- Department of Internal Medicine, Section of Infectious Diseases and Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | | | - Lore Vanderbeke
- Department of Internal Medicine, University Hospitals Leuven, Leuven, Belgium
| | | | - Paul E Verweij
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands; Center of Expertise for Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, Netherlands
| | - Joost Wauters
- Medical Intensive Care Unit, University Hospitals Leuven, Leuven, Belgium; Department of Internal Medicine, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven, Belgium
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de Sousa NF, Duarte GD, Moraes CB, Barbosa CG, Martin HJ, Muratov NN, do Nascimento YM, Scotti L, de Freitas-Júnior LHG, Filho JMB, Scotti MT. In Silico and In Vitro Studies of Terpenes from the Fabaceae Family Using the Phenotypic Screening Model against the SARS-CoV-2 Virus. Pharmaceutics 2024; 16:912. [PMID: 39065609 PMCID: PMC11279753 DOI: 10.3390/pharmaceutics16070912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/02/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
In 2019, the emergence of the seventh known coronavirus to cause severe illness in humans triggered a global effort towards the development of new drugs and vaccines for the SARS-CoV-2 virus. These efforts are still ongoing in 2024, including the present work where we conducted a ligand-based virtual screening of terpenes with potential anti-SARS-CoV-2 activity. We constructed a Quantitative Structure-Activity Relationship (QSAR) model from compounds with known activity against SARS-CoV-2 with a model accuracy of 0.71. We utilized this model to predict the activity of a series of 217 terpenes isolated from the Fabaceae family. Four compounds, predominantly triterpenoids from the lupane series, were subjected to an in vitro phenotypic screening in Vero CCL-81 cells to assess their inhibitory activity against SARS-CoV-2. The compounds which showed high rates of SARS-CoV-2 inhibition along with substantial cell viability underwent molecular docking at the SARS-CoV-2 main protease, papain-like protease, spike protein and RNA-dependent RNA polymerase. Overall, virtual screening through our QSAR model successfully identified compounds with the highest probability of activity, as validated using the in vitro study. This confirms the potential of the identified triterpenoids as promising candidates for anti-SARS-CoV-2 therapeutics.
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Affiliation(s)
- Natália Ferreira de Sousa
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, Brazil; (N.F.d.S.); (Y.M.d.N.); (L.S.); (J.M.B.F.)
| | - Gabrielly Diniz Duarte
- Postgraduate Program in Development and Innovation of Drugs and Medicines, Federal University of Paraíba, João Pessoa 58051-900, Brazil;
| | - Carolina Borsoi Moraes
- Institute of Biomedical Sciences, University of São Paulo (ICB-USP), São Paulo 05508-000, Brazil; (C.B.M.); (C.G.B.); (L.H.G.d.F.-J.)
| | - Cecília Gomes Barbosa
- Institute of Biomedical Sciences, University of São Paulo (ICB-USP), São Paulo 05508-000, Brazil; (C.B.M.); (C.G.B.); (L.H.G.d.F.-J.)
| | - Holli-Joi Martin
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA;
| | - Nail N. Muratov
- Department of Chemical Technology, Odessa National Polytechnic University, 65000 Odessa, Ukraine;
- A. V. Bogatsky Physical-Chemical Institute of NASU, 65047 Odessa, Ukraine
| | - Yuri Mangueira do Nascimento
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, Brazil; (N.F.d.S.); (Y.M.d.N.); (L.S.); (J.M.B.F.)
| | - Luciana Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, Brazil; (N.F.d.S.); (Y.M.d.N.); (L.S.); (J.M.B.F.)
| | | | - José Maria Barbosa Filho
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, Brazil; (N.F.d.S.); (Y.M.d.N.); (L.S.); (J.M.B.F.)
| | - Marcus Tullius Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, Brazil; (N.F.d.S.); (Y.M.d.N.); (L.S.); (J.M.B.F.)
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Daigle L, Khalid H, Gagnon CA, Arsenault J, Bienzle D, Bisson SK, Blais MC, Denis-Robichaud J, Forest C, Grenier St-Sauveur V, Koszegi M, MacNicol J, Nantel-Fortier N, Nury C, Prystajecky N, Fraser E, Carabin H, Aenishaenslin C. High prevalence of SARS-CoV-2 antibodies and low prevalence of SARS-CoV-2 RNA in cats recently exposed to human cases. BMC Vet Res 2024; 20:304. [PMID: 38982461 PMCID: PMC11232172 DOI: 10.1186/s12917-024-04150-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/19/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND The primary objective of this cross-sectional study, conducted in Québec and Bristish Columbia (Canada) between February 2021 and January 2022, was to measure the prevalence of viral RNA in oronasal and rectal swabs and serum antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) amongst cats living in households with at least one confirmed human case. Secondary objectives included a description of potential risk factors for the presence of SARS-CoV-2 antibodies and an estimation of the association between the presence of viral RNA in swabs as well as SARS-CoV-2 antibodies and clinical signs. Oronasal and rectal swabs and sera were collected from 55 cats from 40 households at most 15 days after a human case confirmation, and at up to two follow-up visits. A RT-qPCR assay and an ELISA were used to detect SARS-CoV-2 RNA in swabs and serum SARS-CoV-2 IgG antibodies, respectively. Prevalence and 95% Bayesian credibility intervals (BCI) were calculated, and associations were evaluated using prevalence ratio and 95% BCI obtained from Bayesian mixed log-binomial models. RESULTS Nine (0.16; 95% BCI = 0.08-0.28) and 38 (0.69; 95% BCI = 0.56-0.80) cats had at least one positive RT-qPCR and at least one positive serological test result, respectively. No risk factor was associated with the prevalence of SARS-CoV-2 serum antibodies. The prevalence of clinical signs suggestive of COVID-19 in cats, mainly sneezing, was 2.12 (95% BCI = 1.03-3.98) times higher amongst cats with detectable viral RNA compared to those without. CONCLUSIONS We showed that cats develop antibodies to SARS-CoV-2 when exposed to recent human cases, but detection of viral RNA on swabs is rare, even when sampling occurs soon after confirmation of a human case. Moreover, cats with detectable levels of virus showed clinical signs more often than cats without signs, which can be useful for the management of such cases.
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Affiliation(s)
- Laurence Daigle
- Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Qc, Canada.
- Groupe de recherche en épidémiologie des zoonoses et santé publique (GREZOSP), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Qc, Canada.
- Centre de recherche en santé publique de l'Université de Montréal et du CIUSSS du Centre-Sud-de-l'Île-de-Montréal, Montréal, Qc, Canada.
| | - Hattaw Khalid
- BC Centre for Disease Control, Vancouver, BC, Canada
- School of Population and Public Health, UBC Centre for Disease Control, University of British Columbia, Vancouver, BC, Canada
| | - Carl A Gagnon
- Swine and Poultry Infectious Diseases Research Center - FRQ, Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Qc, Canada
- Molecular Diagnostic Laboratory (MDL), Centre de Diagnostic Vétérinaire de l'Université de Montréal (CDVUM), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Qc, Canada
| | - Julie Arsenault
- Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Qc, Canada
- Groupe de recherche en épidémiologie des zoonoses et santé publique (GREZOSP), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Qc, Canada
| | - Dorothee Bienzle
- Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Sarah-Kim Bisson
- Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Qc, Canada
| | - Marie-Claude Blais
- Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Qc, Canada
| | - José Denis-Robichaud
- Groupe de recherche en épidémiologie des zoonoses et santé publique (GREZOSP), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Qc, Canada
- Independent Researcher, Amqui, QC, Canada
| | - Caroline Forest
- Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Qc, Canada
| | - Valérie Grenier St-Sauveur
- Molecular Diagnostic Laboratory (MDL), Centre de Diagnostic Vétérinaire de l'Université de Montréal (CDVUM), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Qc, Canada
| | - Marika Koszegi
- Molecular Diagnostic Laboratory (MDL), Centre de Diagnostic Vétérinaire de l'Université de Montréal (CDVUM), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Qc, Canada
| | - Jennifer MacNicol
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
| | - Nicolas Nantel-Fortier
- Molecular Diagnostic Laboratory (MDL), Centre de Diagnostic Vétérinaire de l'Université de Montréal (CDVUM), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Qc, Canada
| | - Charlotte Nury
- Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Qc, Canada
| | - Natalie Prystajecky
- BC Centre for Disease Control, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Erin Fraser
- BC Centre for Disease Control, Vancouver, BC, Canada
- School of Population and Public Health, UBC Centre for Disease Control, University of British Columbia, Vancouver, BC, Canada
| | - Hélène Carabin
- Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Qc, Canada
- Groupe de recherche en épidémiologie des zoonoses et santé publique (GREZOSP), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Qc, Canada
- Centre de recherche en santé publique de l'Université de Montréal et du CIUSSS du Centre-Sud-de-l'Île-de-Montréal, Montréal, Qc, Canada
| | - Cécile Aenishaenslin
- Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Qc, Canada
- Groupe de recherche en épidémiologie des zoonoses et santé publique (GREZOSP), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Qc, Canada
- Centre de recherche en santé publique de l'Université de Montréal et du CIUSSS du Centre-Sud-de-l'Île-de-Montréal, Montréal, Qc, Canada
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Nowakowska A, Lee SM, Kim M, Chun J, Kim S, Kim BC, In HJ, Lee E, Lee C, Lee H, Jang Y, Cho H, Kim J, Lee J, Lee HJ, Lee YK, Park JS, Kim YB. Timing of maternal vaccination against COVID-19 for effective protection of neonates: cohort study. Front Immunol 2024; 15:1359209. [PMID: 39040104 PMCID: PMC11260787 DOI: 10.3389/fimmu.2024.1359209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 06/18/2024] [Indexed: 07/24/2024] Open
Abstract
Introduction Although the safety and effectiveness of COVID-19 vaccination during pregnancy have been proven, there is still little data explaining neonatal outcomes of maternal pre-pregnancy vaccination. Methods Here, we investigated the impact of vaccination and SARS-CoV-2 infection on maternal-neonate immune response in a cohort study involving 141 pregnant individuals, and defined the importance of maternal COVID-19 vaccination timing for its effectiveness. Results and discussion Our data indicate that vertically transferred maternal hybrid immunity provides significantly better antiviral protection for a neonate than either maternal post-infection or post-vaccination immunity alone. Higher neutralization potency among mothers immunized before pregnancy and their newborns highlights the promising role of pre-pregnancy vaccination in neonatal protection. A comparison of neutralizing antibody titers calculated for each dyad suggests that infection and pre-/during-pregnancy vaccination all support transplacental transfer, providing the offspring with strong passive immunity against SARS-CoV-2. Analysis of neutralizing antibody levels in maternal sera collected during pregnancy and later during delivery shows that immunization may exert a positive effect on maternal protection.
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Affiliation(s)
- Aleksandra Nowakowska
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Seung Mi Lee
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Minjee Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Jungmin Chun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Sehyun Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
- KR Biotech Co., Ltd, Seoul, Republic of Korea
| | - Byung Chul Kim
- Korea Disease Control and Prevention Agency, National Institute of Health, National Institute of Infectious Diseases, Center for Vaccine Research, Division of Vaccine Development Coordination, Cheongju, Republic of Korea
| | - Hyun Ju In
- Korea Disease Control and Prevention Agency, National Institute of Health, National Institute of Infectious Diseases, Center for Vaccine Research, Division of Vaccine Development Coordination, Cheongju, Republic of Korea
| | - Eunji Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Chanyeong Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Hyeondong Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Yuyeon Jang
- Department of Bio-industrial Technologies, Konkuk University, Seoul, Republic of Korea
| | - Hansam Cho
- KR Biotech Co., Ltd, Seoul, Republic of Korea
| | - Jinha Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Jeesun Lee
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hee-Jung Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Yoo-Kyoung Lee
- Korea Disease Control and Prevention Agency, National Institute of Health, National Institute of Infectious Diseases, Center for Vaccine Research, Division of Vaccine Development Coordination, Cheongju, Republic of Korea
| | - Joong Shin Park
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Young Bong Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
- KR Biotech Co., Ltd, Seoul, Republic of Korea
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44
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Lytton SD, Ghosh AK. SARS-CoV-2 Variants and COVID-19 in Bangladesh-Lessons Learned. Viruses 2024; 16:1077. [PMID: 39066238 PMCID: PMC11281597 DOI: 10.3390/v16071077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/27/2024] [Accepted: 07/01/2024] [Indexed: 07/28/2024] Open
Abstract
The coronavirus infectious disease-2019 (COVID-19) in Bangladesh is a paradigm for how one of the most densely populated countries in the world, with 1270 people per square kilometer, managed to cope with the COVID-19 pandemic under extraordinary circumstances. This review highlights the SARS-CoV-2 variants in Bangladesh and the timeline of their detection in the context of the global experience with the management of vaccination and natural SARS-CoV-2 infection. The motivation to overcome the COVID-19 vaccine dilemma and track Bangladeshi SARS-CoV-2 sub-variants underscores the potential for a low-income country to excel in international medical science, despite having stressed health care services and limited availability of resources for SARS-CoV-2 testing and gene sequencing.
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Affiliation(s)
| | - Asish Kumar Ghosh
- Department of Virology, Dhaka Medical College Hospital, Dhaka 1000, Bangladesh;
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Shouman S, El-Kholy N, Hussien AE, El-Derby AM, Magdy S, Abou-Shanab AM, Elmehrath AO, Abdelwaly A, Helal M, El-Badri N. SARS-CoV-2-associated lymphopenia: possible mechanisms and the role of CD147. Cell Commun Signal 2024; 22:349. [PMID: 38965547 PMCID: PMC11223399 DOI: 10.1186/s12964-024-01718-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 06/15/2024] [Indexed: 07/06/2024] Open
Abstract
T lymphocytes play a primary role in the adaptive antiviral immunity. Both lymphocytosis and lymphopenia were found to be associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). While lymphocytosis indicates an active anti-viral response, lymphopenia is a sign of poor prognosis. T-cells, in essence, rarely express ACE2 receptors, making the cause of cell depletion enigmatic. Moreover, emerging strains posed an immunological challenge, potentially alarming for the next pandemic. Herein, we review how possible indirect and direct key mechanisms could contribute to SARS-CoV-2-associated-lymphopenia. The fundamental mechanism is the inflammatory cytokine storm elicited by viral infection, which alters the host cell metabolism into a more acidic state. This "hyperlactic acidemia" together with the cytokine storm suppresses T-cell proliferation and triggers intrinsic/extrinsic apoptosis. SARS-CoV-2 infection also results in a shift from steady-state hematopoiesis to stress hematopoiesis. Even with low ACE2 expression, the presence of cholesterol-rich lipid rafts on activated T-cells may enhance viral entry and syncytia formation. Finally, direct viral infection of lymphocytes may indicate the participation of other receptors or auxiliary proteins on T-cells, that can work alone or in concert with other mechanisms. Therefore, we address the role of CD147-a novel route-for SARS-CoV-2 and its new variants. CD147 is not only expressed on T-cells, but it also interacts with other co-partners to orchestrate various biological processes. Given these features, CD147 is an appealing candidate for viral pathogenicity. Understanding the molecular and cellular mechanisms behind SARS-CoV-2-associated-lymphopenia will aid in the discovery of potential therapeutic targets to improve the resilience of our immune system against this rapidly evolving virus.
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Affiliation(s)
- Shaimaa Shouman
- Center of Excellence for Stem Cells and Regenerative Medicine, Zewail City of Science and Technology, Giza, 12587, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, 12587, Egypt
| | - Nada El-Kholy
- Department of Drug Discovery, H. Lee Moffit Cancer Center& Research Institute, Tampa, FL, 33612, USA
- Cancer Chemical Biology Ph.D. Program, University of South Florida, Tampa, FL, 33620, USA
| | - Alaa E Hussien
- Center of Excellence for Stem Cells and Regenerative Medicine, Zewail City of Science and Technology, Giza, 12587, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, 12587, Egypt
| | - Azza M El-Derby
- Center of Excellence for Stem Cells and Regenerative Medicine, Zewail City of Science and Technology, Giza, 12587, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, 12587, Egypt
| | - Shireen Magdy
- Center of Excellence for Stem Cells and Regenerative Medicine, Zewail City of Science and Technology, Giza, 12587, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, 12587, Egypt
| | - Ahmed M Abou-Shanab
- Center of Excellence for Stem Cells and Regenerative Medicine, Zewail City of Science and Technology, Giza, 12587, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, 12587, Egypt
| | | | - Ahmad Abdelwaly
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, 12587, Egypt
- Institute for Computational Molecular Science, Department of Chemistry, Temple University, Philadelphia, PA, 19122, USA
| | - Mohamed Helal
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, 12587, Egypt
- Medicinal Chemistry Department, Faculty of Pharmacy, Suez Canal University, Ismailia, 41522, Egypt
| | - Nagwa El-Badri
- Center of Excellence for Stem Cells and Regenerative Medicine, Zewail City of Science and Technology, Giza, 12587, Egypt.
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, 12587, Egypt.
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46
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Zagórska A, Czopek A, Fryc M, Jończyk J. Inhibitors of SARS-CoV-2 Main Protease (Mpro) as Anti-Coronavirus Agents. Biomolecules 2024; 14:797. [PMID: 39062511 PMCID: PMC11275247 DOI: 10.3390/biom14070797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
The main protease (Mpro) of SARS-CoV-2 is an essential enzyme that plays a critical part in the virus's life cycle, making it a significant target for developing antiviral drugs. The inhibition of SARS-CoV-2 Mpro has emerged as a promising approach for developing therapeutic agents to treat COVID-19. This review explores the structure of the Mpro protein and analyzes the progress made in understanding protein-ligand interactions of Mpro inhibitors. It focuses on binding kinetics, origin, and the chemical structure of these inhibitors. The review provides an in-depth analysis of recent clinical trials involving covalent and non-covalent inhibitors and emerging dual inhibitors targeting SARS-CoV-2 Mpro. By integrating findings from the literature and ongoing clinical trials, this review captures the current state of research into Mpro inhibitors, offering a comprehensive understanding of challenges and directions in their future development as anti-coronavirus agents. This information provides new insights and inspiration for medicinal chemists, paving the way for developing more effective Mpro inhibitors as novel COVID-19 therapies.
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Affiliation(s)
- Agnieszka Zagórska
- Department of Medicinal Chemistry, Jagiellonian University Medical College, Medyczna 9, 30-688 Kraków, Poland; (A.C.); (M.F.); (J.J.)
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Murdocca M, Romeo I, Citro G, Latini A, Centofanti F, Bugatti A, Caccuri F, Caruso A, Ortuso F, Alcaro S, Sangiuolo F, Novelli G. A Dynamic and Effective Peptide-Based Strategy for Promptly Addressing Emerging SARS-CoV-2 Variants of Concern. Pharmaceuticals (Basel) 2024; 17:891. [PMID: 39065742 PMCID: PMC11279616 DOI: 10.3390/ph17070891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/25/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
Genomic surveillance based on sequencing the entire genetic code of SARS-CoV-2 involves monitoring and studying genetic changes and variations in disease-causing organisms such as viruses and bacteria. By tracing the virus, it is possible to prevent epidemic spread in the community, ensuring a 'precision public health' strategy. A peptide-based design was applied to provide an efficacious strategy that is able to counteract any emerging viral variant of concern dynamically and promptly to affect the outcomes of a pandemic at an early stage while waiting for the production of the anti-variant-specific vaccine, which require longer times. The inhibition of the interaction between the receptor-binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and one of the cellular receptors (DPP4) that its receptors routinely bind to infect human cells is an intriguing therapeutic approach to prevent the virus from entering human cells. Among the other modalities developed for this purpose, peptides surely offer unique advantages, including ease of synthesis, serum stability, low immunogenicity and toxicity, and small production and distribution chain costs. Here, we obtained a potent new inhibitor based on the rearrangement of a previously identified peptide that has been rationally designed on a cell dipeptidyl peptidase 4 (DPP4) sequence, a ubiquitous membrane protein known to bind the RBD-SPIKE domain of the virus. This novel peptide (named DPP4-derived), conceived as an endogenous "drug", is capable of targeting the latest tested variants with a high affinity, reducing the VSV* DG-Fluc pseudovirus Omicron's infection capacity by up to 14%, as revealed by in vitro testing in human Calu-3 cells. Surface plasmon resonance (SPR) confirmed the binding affinity of the new DPP4-derived peptide with Omicron variant RBD.
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Affiliation(s)
- Michela Murdocca
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (M.M.); (G.C.); (A.L.); (F.C.); (G.N.)
| | - Isabella Romeo
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (I.R.); (F.O.); (S.A.)
- Net4Science Srl Academic Spin-Off, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Gennaro Citro
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (M.M.); (G.C.); (A.L.); (F.C.); (G.N.)
| | - Andrea Latini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (M.M.); (G.C.); (A.L.); (F.C.); (G.N.)
| | - Federica Centofanti
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (M.M.); (G.C.); (A.L.); (F.C.); (G.N.)
| | - Antonella Bugatti
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (A.B.); (F.C.); (A.C.)
| | - Francesca Caccuri
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (A.B.); (F.C.); (A.C.)
| | - Arnaldo Caruso
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (A.B.); (F.C.); (A.C.)
| | - Francesco Ortuso
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (I.R.); (F.O.); (S.A.)
- Net4Science Srl Academic Spin-Off, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (I.R.); (F.O.); (S.A.)
- Net4Science Srl Academic Spin-Off, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Federica Sangiuolo
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (M.M.); (G.C.); (A.L.); (F.C.); (G.N.)
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (M.M.); (G.C.); (A.L.); (F.C.); (G.N.)
- IRCCS Neuromed Mediterranean Neurological Institute, 86077 Pozzilli, Italy
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV 89557, USA
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48
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Jang G, Kim J, Lee Y, Son C, Ko KT, Lee H. Analysis of the impact of COVID-19 variants and vaccination on the time-varying reproduction number: statistical methods. Front Public Health 2024; 12:1353441. [PMID: 39022412 PMCID: PMC11253806 DOI: 10.3389/fpubh.2024.1353441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 06/07/2024] [Indexed: 07/20/2024] Open
Abstract
Introduction The COVID-19 pandemic has profoundly impacted global health systems, requiring the monitoring of infection waves and strategies to control transmission. Estimating the time-varying reproduction number is crucial for understanding the epidemic and guiding interventions. Methods Probability distributions of serial interval are estimated for Pre-Delta and Delta periods. We conducted a comparative analysis of time-varying reproduction numbers, taking into account population immunity and variant differences. We incorporated the regional heterogeneity and age distribution of the population, as well as the evolving variants and vaccination rates over time. COVID-19 transmission dynamics were analyzed with variants and vaccination. Results The reproduction number is computed with and without considering variant-based immunity. In addition, values of reproduction number significantly differed by variants, emphasizing immunity's importance. Enhanced vaccination efforts and stringent control measures were effective in reducing the transmission of the Delta variant. Conversely, Pre-Delta variant appeared less influenced by immunity levels, due to lower vaccination rates. Furthermore, during the Pre-Delta period, there was a significant difference between the region-specific and the non-region-specific reproduction numbers, with particularly distinct pattern differences observed in Gangwon, Gyeongbuk, and Jeju in Korea. Discussion This research elucidates the dynamics of COVID-19 transmission concerning the dominance of the Delta variant, the efficacy of vaccinations, and the influence of immunity levels. It highlights the necessity for targeted interventions and extensive vaccination coverage. This study makes a significant contribution to the understanding of disease transmission mechanisms and informs public health strategies.
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Affiliation(s)
- Geunsoo Jang
- Nonlinear Dynamics and Mathematical Application Center, Kyungpook National University, Daegu, Republic of Korea
| | - Jihyeon Kim
- Department of Statistics, Kyungpook National University, Daegu, Republic of Korea
| | - Yeonsu Lee
- Department of Statistics, Kyungpook National University, Daegu, Republic of Korea
| | - Changdae Son
- Department of Statistics, Kyungpook National University, Daegu, Republic of Korea
| | - Kyeong Tae Ko
- Department of Statistics, Kyungpook National University, Daegu, Republic of Korea
| | - Hyojung Lee
- Department of Statistics, Kyungpook National University, Daegu, Republic of Korea
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49
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Singer B, Di Nardo A, Hein J, Ferretti L. Comparing Phylogeographies to Reveal Incompatible Geographical Histories within Genomes. Mol Biol Evol 2024; 41:msae126. [PMID: 38922185 PMCID: PMC11251493 DOI: 10.1093/molbev/msae126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
Modern phylogeography aims at reconstructing the geographic movement of organisms based on their genomic sequences and spatial information. Phylogeographic approaches are often applied to pathogen sequences and therefore tend to neglect the possibility of recombination, which decouples the evolutionary and geographic histories of different parts of the genome. Genomic regions of recombining or reassorting pathogens often originate and evolve at different times and locations, which characterize their unique spatial histories. Measuring the extent of these differences requires new methods to compare geographic information on phylogenetic trees reconstructed from different parts of the genome. Here we develop for the first time a set of measures of phylogeographic incompatibility, aimed at detecting differences between geographical histories in terms of distances between phylogeographies. We study the effect of varying demography and recombination on phylogeographic incompatibilities using coalescent simulations. We further apply these measures to the evolutionary history of human and livestock pathogens, either reassorting or recombining, such as the Victoria and Yamagata lineages of influenza B and the O/Ind-2001 foot-and-mouth disease virus strain. Our results reveal diverse geographical paths of migration that characterize the origins and evolutionary histories of different viral genes and genomic segments. These incompatibility measures can be applied to any phylogeography, and more generally to any phylogeny where each tip has been assigned either a continuous or discrete "trait" independent of the sequence. We illustrate this flexibility with an analysis of the interplay between the phylogeography and phylolinguistics of Uralic-speaking human populations, hinting at patrilinear language transmission.
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Affiliation(s)
- Benjamin Singer
- Department of Medicine, Stanford University, Stanford, CA, USA
| | | | - Jotun Hein
- Department of Statistics, University of Oxford, Oxford, UK
| | - Luca Ferretti
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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50
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Zhang Y, Chamblee M, Xu J, Qu P, Shamseldin MM, Yoo SJ, Misny J, Thongpan I, Kc M, Hall JM, Gupta YA, Evans JP, Lu M, Ye C, Hsu CC, Liang X, Martinez-Sobrido L, Yount JS, Boyaka PN, Liu SL, Dubey P, Peeples ME, Li J. Three SARS-CoV-2 spike protein variants delivered intranasally by measles and mumps vaccines are broadly protective. Nat Commun 2024; 15:5589. [PMID: 38961063 PMCID: PMC11222507 DOI: 10.1038/s41467-024-49443-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 05/29/2024] [Indexed: 07/05/2024] Open
Abstract
As the new SARS-CoV-2 Omicron variants and subvariants emerge, there is an urgency to develop intranasal, broadly protective vaccines. Here, we developed highly efficacious, intranasal trivalent SARS-CoV-2 vaccine candidates (TVC) based on three components of the MMR vaccine: measles virus (MeV), mumps virus (MuV) Jeryl Lynn (JL1) strain, and MuV JL2 strain. Specifically, MeV, MuV-JL1, and MuV-JL2 vaccine strains, each expressing prefusion spike (preS-6P) from a different variant of concern (VoC), were combined to generate TVCs. Intranasal immunization of IFNAR1-/- mice and female hamsters with TVCs generated high levels of S-specific serum IgG antibodies, broad neutralizing antibodies, and mucosal IgA antibodies as well as tissue-resident memory T cells in the lungs. The immunized female hamsters were protected from challenge with SARS-CoV-2 original WA1, B.1.617.2, and B.1.1.529 strains. The preexisting MeV and MuV immunity does not significantly interfere with the efficacy of TVC. Thus, the trivalent platform is a promising next-generation SARS-CoV-2 vaccine candidate.
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Affiliation(s)
- Yuexiu Zhang
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - Michelle Chamblee
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - Jiayu Xu
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - Panke Qu
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - Mohamed M Shamseldin
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, USA
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Department of Microbiology and Immunology, Faculty of Pharmacy, Helwan University, Ain Helwan, Helwan, Egypt
| | - Sung J Yoo
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - Jack Misny
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Ilada Thongpan
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Mahesh Kc
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Jesse M Hall
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Yash A Gupta
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - John P Evans
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - Mijia Lu
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - Chengjin Ye
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Cheng Chih Hsu
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - Xueya Liang
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | | | - Jacob S Yount
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, USA
- Infectious Disease Institute, The Ohio State University, Columbus, OH, USA
| | - Prosper N Boyaka
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
- Infectious Disease Institute, The Ohio State University, Columbus, OH, USA
| | - Shan-Lu Liu
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, USA
- Infectious Disease Institute, The Ohio State University, Columbus, OH, USA
- Center for Retrovirus Research, The Ohio State University, Columbus, OH, USA
| | - Purnima Dubey
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, USA
- Infectious Disease Institute, The Ohio State University, Columbus, OH, USA
| | - Mark E Peeples
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
- Infectious Disease Institute, The Ohio State University, Columbus, OH, USA
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Jianrong Li
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA.
- Infectious Disease Institute, The Ohio State University, Columbus, OH, USA.
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