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Blanco-Rodríguez R, Tetteh JNA, Hernández-Vargas E. Assessing the impacts of vaccination and viral evolution in contact networks. Sci Rep 2024; 14:15753. [PMID: 38977773 PMCID: PMC11231155 DOI: 10.1038/s41598-024-66070-5] [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: 04/06/2023] [Accepted: 06/25/2024] [Indexed: 07/10/2024] Open
Abstract
A key lesson learned with COVID-19 is that public health measures were very different from country to country. In this study, we provide an analysis of epidemic dynamics using three well-known stochastic network models-small-world networks (Watts-Strogatz), random networks (Erdös-Rényi), and scale-free networks (Barabási-Albert)-to assess the impact of different viral strains, lockdown strategies, and vaccination campaigns. We highlight the significant role of highly connected nodes in the spread of infections, particularly within Barabási-Albert networks. These networks experienced earlier and higher peaks in infection rates, but ultimately had the lowest total number of infections, indicating their rapid transmission dynamics. We also found that intermittent lockdown strategies, particularly those with 7-day intervals, effectively reduce the total number of infections, serving as viable alternatives to prolonged continuous lockdowns. When simulating vaccination campaigns, we observed a bimodal distribution leading to two distinct outcomes: pandemic contraction and pandemic expansion. For WS and ER networks, rapid mass vaccination campaigns significantly reduced infection rates compared to slower campaigns; however, for BA networks, differences between vaccination strategies were minimal. To account for the evolution of a virus into a more transmissible strain, we modeled vaccination scenarios that varied vaccine efficacy against the wild-type virus and noted a decline in this efficacy over time against a second variant. Our results showed that vaccination coverage above 40% significantly flattened infection peaks for the wild-type virus, while at least 80% coverage was required to similarly reduce peaks for variant 2. Furthermore, the effect of vaccine efficacy on reducing the peak of variant 2 infection was minimal. Although vaccination strategies targeting hub nodes in scale-free networks did not substantially reduce the total number of infections, they were effective in increasing the probability of preventing pandemic outbreaks. These findings underscore the need to consider the network structure for effective pandemic control.
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Affiliation(s)
- Rodolfo Blanco-Rodríguez
- Department of Mathematics and Statistical Science, University of Idaho, Moscow, ID, 83844-1103, USA
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID, 83844-1103, USA
| | | | - Esteban Hernández-Vargas
- Department of Mathematics and Statistical Science, University of Idaho, Moscow, ID, 83844-1103, USA.
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID, 83844-1103, USA.
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2
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Seprianus, Nuraini N, Saputro SW. A computational model of epidemic process with three variants on a synthesized human interaction network. Sci Rep 2024; 14:7470. [PMID: 38553546 DOI: 10.1038/s41598-024-58162-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 03/26/2024] [Indexed: 04/02/2024] Open
Abstract
Virus mutations give rise to new variants that cause multiple waves of pandemics and escalate the infected number of individuals. In this paper, we develop both a simple random network that we define as a synthesized human interaction network and an epidemiological model based on the microscopic process of disease spreading to describe the epidemic process with three variants in a population with some features of social structure. The features of social structure we take into account in the model are the average number of degrees and the frequency of contacts. This paper shows many computational results from several scenarios both in varying network structures and epidemiological parameters that cannot be obtained numerically by using the compartmental model.
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Affiliation(s)
- Seprianus
- Department of Mathematics, Institut Teknologi Bandung, Bandung, Indonesia.
| | - Nuning Nuraini
- Department of Mathematics, Institut Teknologi Bandung, Bandung, Indonesia
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3
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Wu J, Yang H, Yu D, Yang X. Blood-derived product therapies for SARS-CoV-2 infection and long COVID. MedComm (Beijing) 2023; 4:e426. [PMID: 38020714 PMCID: PMC10651828 DOI: 10.1002/mco2.426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/15/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is capable of large-scale transmission and has caused the coronavirus disease 2019 (COVID-19) pandemic. Patients with COVID-19 may experience persistent long-term health issues, known as long COVID. Both acute SARS-CoV-2 infection and long COVID have resulted in persistent negative impacts on global public health. The effective application and development of blood-derived products are important strategies to combat the serious damage caused by COVID-19. Since the emergence of COVID-19, various blood-derived products that target or do not target SARS-CoV-2 have been investigated for therapeutic applications. SARS-CoV-2-targeting blood-derived products, including COVID-19 convalescent plasma, COVID-19 hyperimmune globulin, and recombinant anti-SARS-CoV-2 neutralizing immunoglobulin G, are virus-targeting and can provide immediate control of viral infection in the short term. Non-SARS-CoV-2-targeting blood-derived products, including intravenous immunoglobulin and human serum albumin exhibit anti-inflammatory, immunomodulatory, antioxidant, and anticoagulatory properties. Rational use of these products can be beneficial to patients with SARS-CoV-2 infection or long COVID. With evidence accumulated since the pandemic began, we here summarize the progress of blood-derived product therapies for COVID-19, discuss the effective methods and scenarios regarding these therapies, and provide guidance and suggestions for clinical treatment.
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Affiliation(s)
- Junzheng Wu
- Chengdu Rongsheng Pharmaceuticals Co., Ltd.ChengduChina
| | | | - Ding Yu
- Chengdu Rongsheng Pharmaceuticals Co., Ltd.ChengduChina
- Beijing Tiantan Biological Products Co., Ltd.BeijingChina
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4
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Meijers M, Ruchnewitz D, Eberhardt J, Łuksza M, Lässig M. Population immunity predicts evolutionary trajectories of SARS-CoV-2. Cell 2023; 186:5151-5164.e13. [PMID: 37875109 PMCID: PMC10964984 DOI: 10.1016/j.cell.2023.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 08/26/2023] [Accepted: 09/21/2023] [Indexed: 10/26/2023]
Abstract
The large-scale evolution of the SARS-CoV-2 virus has been marked by rapid turnover of genetic clades. New variants show intrinsic changes, notably increased transmissibility, and antigenic changes that reduce cross-immunity induced by previous infections or vaccinations. How this functional variation shapes global evolution has remained unclear. Here, we establish a predictive fitness model for SARS-CoV-2 that integrates antigenic and intrinsic selection. The model is informed by tracking of time-resolved sequence data, epidemiological records, and cross-neutralization data of viral variants. Our inference shows that immune pressure, including contributions of vaccinations and previous infections, has become the dominant force driving the recent evolution of SARS-CoV-2. The fitness model can serve continued surveillance in two ways. First, it successfully predicts the short-term evolution of circulating strains and flags emerging variants likely to displace the previously predominant variant. Second, it predicts likely antigenic profiles of successful escape variants prior to their emergence.
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Affiliation(s)
- Matthijs Meijers
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937 Köln, Germany
| | - Denis Ruchnewitz
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937 Köln, Germany
| | - Jan Eberhardt
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937 Köln, Germany
| | - Marta Łuksza
- Tisch Cancer Institute, Departments of Oncological Sciences and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Lässig
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937 Köln, Germany.
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5
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Fan R, Geritz SAH. Evolution of pathogens with cross-immunity in response to healthcare interventions. J Theor Biol 2023; 572:111575. [PMID: 37423484 DOI: 10.1016/j.jtbi.2023.111575] [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: 12/22/2022] [Revised: 06/22/2023] [Accepted: 07/03/2023] [Indexed: 07/11/2023]
Abstract
Cross-immunity, as an evolutionary driver, can contribute to pathogen evolution, particularly pathogen diversity. Healthcare interventions aimed at reducing disease severity or transmission are commonly used to control diseases and can also induce pathogen evolution. Understanding pathogen evolution in the context of cross-immunity and healthcare interventions is crucial for infection control. This study starts by modelling cross-immunity, the extent of which is determined by strain traits and host characteristics. Given that all hosts have the same characteristics, full cross-immunity between residents and mutants occurs when mutation step sizes are small enough. Cross-immunity can be partial when the step size is large. The presence of partial cross-immunity reduces pathogen load and shortens the infectious period inside hosts, reducing transmission between hosts and improving host population survival and recovery. This study focuses on how pathogens evolve through small and large mutational steps and how healthcare interventions affect pathogen evolution. Using the theory of adaptive dynamics, we found that when mutational steps are small (only full cross-immunity is present), pathogen diversity cannot occur because it maximises the basic reproduction number. This results in intermediate values for both pathogen growth and clearance rates. However, when large mutational steps are allowed (with full and partial cross-immunity present), pathogens can evolve into multiple strains and induce pathogen diversity. The study also shows that different healthcare interventions can have varying effects on pathogen evolution. Generally, low levels of intervention are more likely to induce strain diversity, while high levels are more likely to result in strain reduction.
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Affiliation(s)
- Ruili Fan
- Department of Mathematics and Statistics, University of Helsinki, FIN-00014, Finland.
| | - Stefan A H Geritz
- Department of Mathematics and Statistics, University of Helsinki, FIN-00014, Finland
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6
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Khan MMUR, Arefin MR, Tanimoto J. Time delay of the appearance of a new strain can affect vaccination behavior and disease dynamics: An evolutionary explanation. Infect Dis Model 2023; 8:656-671. [PMID: 37346475 PMCID: PMC10257886 DOI: 10.1016/j.idm.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/26/2023] [Accepted: 06/05/2023] [Indexed: 06/23/2023] Open
Abstract
The emergence of a novel strain during a pandemic, like the current COVID-19, is a major concern to the healthcare system. The most effective strategy to control this type of pandemic is vaccination. Many previous studies suggest that the existing vaccine may not be fully effective against the new strain. Additionally, the new strain's late arrival has a significant impact on the disease dynamics and vaccine coverage. Focusing on these issues, this study presents a two-strain epidemic model in which the new strain appears with a time delay. We considered two vaccination provisions, namely preinfection and postinfection vaccinations, which are governed by human behavioral dynamics. In such a framework, individuals have the option to commit vaccination before being infected with the first strain. Additionally, people who forgo vaccination and become infected with the first train have the chance to be vaccinated (after recovery) in an attempt to avoid infection from the second strain. However, a second strain can infect vaccinated and unvaccinated individuals. People may have additional opportunities to be vaccinated and to protect themselves from the second strain due to the time delay. Considering the cost of the vaccine, the severity of the new strain, and the vaccine's effectiveness, our results indicated that delaying the second strain decreases the peak size of the infected individuals. Finally, by estimating the social efficiency deficit, we discovered that the social dilemma for receiving immunization decreases with the delay in the arrival of the second strain.
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Affiliation(s)
- Md Mamun-Ur-Rashid Khan
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Kasuga-koen, Kasuga-shi, Fukuoka, 816-8580, Japan
- Department of Mathematics, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Md Rajib Arefin
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Kasuga-koen, Kasuga-shi, Fukuoka, 816-8580, Japan
- Department of Mathematics, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Jun Tanimoto
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Kasuga-koen, Kasuga-shi, Fukuoka, 816-8580, Japan
- Faculty of Engineering Sciences, Kyushu University, Kasuga-koen, Kasuga-shi, Fukuoka, 816-8580, Japan
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7
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Lobinska G, Pilpel Y, Nowak MA. Evolutionary safety of lethal mutagenesis driven by antiviral treatment. PLoS Biol 2023; 21:e3002214. [PMID: 37552682 PMCID: PMC10409280 DOI: 10.1371/journal.pbio.3002214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 06/23/2023] [Indexed: 08/10/2023] Open
Abstract
Nucleoside analogs are a major class of antiviral drugs. Some act by increasing the viral mutation rate causing lethal mutagenesis of the virus. Their mutagenic capacity, however, may lead to an evolutionary safety concern. We define evolutionary safety as a probabilistic assurance that the treatment will not generate an increased number of mutants. We develop a mathematical framework to estimate the total mutant load produced with and without mutagenic treatment. We predict rates of appearance of such virus mutants as a function of the timing of treatment and the immune competence of patients, employing realistic assumptions about the vulnerability of the viral genome and its potential to generate viable mutants. We focus on the case study of Molnupiravir, which is an FDA-approved treatment against Coronavirus Disease-2019 (COVID-19). We estimate that Molnupiravir is narrowly evolutionarily safe, subject to the current estimate of parameters. Evolutionary safety can be improved by restricting treatment with this drug to individuals with a low immunological clearance rate and, in future, by designing treatments that lead to a greater increase in mutation rate. We report a simple mathematical rule to determine the fold increase in mutation rate required to obtain evolutionary safety that is also applicable to other pathogen-treatment combinations.
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Affiliation(s)
- Gabriela Lobinska
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Martin A. Nowak
- Department of Mathematics, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
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8
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Jing S, Milne R, Wang H, Xue L. Vaccine hesitancy promotes emergence of new SARS-CoV-2 variants. J Theor Biol 2023; 570:111522. [PMID: 37210068 DOI: 10.1016/j.jtbi.2023.111522] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/30/2023] [Accepted: 05/03/2023] [Indexed: 05/22/2023]
Abstract
The successive emergence of SARS-CoV-2 mutations has led to an unprecedented increase in COVID-19 incidence worldwide. Currently, vaccination is considered to be the best available solution to control the ongoing COVID-19 pandemic. However, public opposition to vaccination persists in many countries, which can lead to increased COVID-19 caseloads and hence greater opportunities for vaccine-evasive mutant strains to arise. To determine the extent that public opinion regarding vaccination can induce or hamper the emergence of new variants, we develop a model that couples a compartmental disease transmission framework featuring two strains of SARS-CoV-2 with game theoretical dynamics on whether or not to vaccinate. We combine semi-stochastic and deterministic simulations to explore the effect of mutation probability, perceived cost of receiving vaccines, and perceived risks of infection on the emergence and spread of mutant SARS-CoV-2 strains. We find that decreasing the perceived costs of being vaccinated and increasing the perceived risks of infection (that is, decreasing vaccine hesitation) will decrease the possibility of vaccine-resistant mutant strains becoming established by about fourfold for intermediate mutation rates. Conversely, we find increasing vaccine hesitation to cause both higher probability of mutant strains emerging and more wild-type cases after the mutant strain has appeared. We also find that once a new variant has emerged, perceived risk of being infected by the original variant plays a much larger role than perceptions of the new variant in determining future outbreak characteristics. Furthermore, we find that rapid vaccination under non-pharmaceutical interventions is a highly effective strategy for preventing new variant emergence, due to interaction effects between non-pharmaceutical interventions and public support for vaccination. Our findings indicate that policies that combine combating vaccine-related misinformation with non-pharmaceutical interventions (such as reducing social contact) will be the most effective for avoiding the establishment of harmful new variants.
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Affiliation(s)
- Shuanglin Jing
- College of Mathematical Sciences, Harbin Engineering University, Harbin, Heilongjiang, 150001, China
| | - Russell Milne
- Department of Mathematical and Statistical Sciences & Interdisciplinary Lab for Mathematical Ecology and Epidemiology, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Hao Wang
- Department of Mathematical and Statistical Sciences & Interdisciplinary Lab for Mathematical Ecology and Epidemiology, University of Alberta, Edmonton, Alberta T6G 2R3, Canada.
| | - Ling Xue
- College of Mathematical Sciences, Harbin Engineering University, Harbin, Heilongjiang, 150001, China
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9
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Nair MS, Ribeiro RM, Wang M, Bowen AD, Liu L, Guo Y, Chang JY, Wang P, Sheng Z, Sobieszczyk ME, Perelson AS, Huang Y, Ho DD. Changes in serum-neutralizing antibody potency and breadth post-SARS-CoV-2 mRNA vaccine boost. iScience 2023; 26:106345. [PMID: 36925721 PMCID: PMC9987605 DOI: 10.1016/j.isci.2023.106345] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/07/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
A better understanding of the durability and breadth of serum-neutralizing antibody responses against multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants elicited by COVID-19 vaccines is crucial in addressing the current pandemic. In this study, we quantified the decay of serum neutralization antibodies (nAbs) after second and third doses of the original COVID-19 mRNA vaccine. Using an authentic virus-neutralization assay, we found that decay half-lives of WA1- and Delta-nAbs were both ∼60 days after second and third vaccine dose. Unexpectedly, the durability of serum antibodies that neutralize three different Omicron subvariants (BA.1.1, BA.5, BA.2.12.1) was substantially better, with half-lives of ≥6 months. A booster dose of the original COVID-19 vaccine was also found to broaden antibody responses against SARS-CoV and four other sarbecoviruses, in addition to multiple SARS-CoV-2 strains. These findings suggest that repeated vaccinations with the COVID-19 vaccine may confer a degree of protection against future spillover of sarbecoviruses from animal reservoirs.
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Affiliation(s)
- Manoj S. Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Ruy M. Ribeiro
- Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Maple Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Anthony D. Bowen
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Division of Infectious Diseases, Department of Internal Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Yicheng Guo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Jennifer Y. Chang
- Division of Infectious Diseases, Department of Internal Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Magdalena E. Sobieszczyk
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Division of Infectious Diseases, Department of Internal Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Alan S. Perelson
- Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - David D. Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Division of Infectious Diseases, Department of Internal Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
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10
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Khiali S, Rezagholizadeh A, Behzad H, Bannazadeh Baghi H, Entezari-Maleki T. Current evidence of COVID-19 vaccination-related cardiovascular events. Postgrad Med 2023; 135:102-120. [PMID: 36567602 DOI: 10.1080/00325481.2022.2161249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Currently, the world is recovering from the shock of the coronavirus disease 2019 (COVID-19) pandemic; however, this situation is still fragile. Health authorities recommend administering COVID-19 vaccines as the safest and most reliable tool for eliminating COVID-19. Subsequent to the extensive administration of the COVID-19 vaccines, a series of cardiovascular adverse effects have been reported. This comprehensive review aimed to provide an update on the etiology, pathophysiology, clinical features, and management of the cardiovascular adverse events associated with COVID-19 vaccines, including myocarditis, pericarditis, thrombosis with thrombocytopenia syndrome, myocardial infarction, cardiac arrhythmias, hypertension, and stress-induced cardiomyopathy. The benefits of COVID-19 vaccination far outweigh the reported adverse events. It would be clinically important to provide diagnostic scoring systems to differentiate COVID-19-related cardiovascular adverse events from other causes and develop therapeutic approaches for their management. Further evaluation of cardiovascular adverse events of the COVID-19 vaccines is crucial for implementing vaccination programs and developing safer and more reliable vaccines.
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Affiliation(s)
- Sajad Khiali
- Department of Clinical Pharmacy, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Afra Rezagholizadeh
- Department of Clinical Pharmacy, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Behzad
- Department of Clinical Pharmacy, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Bannazadeh Baghi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Taher Entezari-Maleki
- Department of Clinical Pharmacy, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.,Cardiovascular Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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11
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Nie Y, Zhong X, Lin T, Wang W. Pathogen diversity in meta-population networks. CHAOS, SOLITONS, AND FRACTALS 2023; 166:112909. [PMID: 36467017 PMCID: PMC9699689 DOI: 10.1016/j.chaos.2022.112909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/15/2022] [Accepted: 11/13/2022] [Indexed: 06/17/2023]
Abstract
The pathogen diversity means that multiple strains coexist, and widely exist in the biology systems. The new mutation of SARS-CoV-2 leading to worldwide pathogen diversity is a typical example. What are the main factors of inducing the pathogen diversity? Previous studies indicated the pathogen mutation is the most important reason for inducing the pathogen diversity. The traffic network and gene network are crucial in shaping the dynamics of pathogen contagion, while their roles for the pathogen diversity still lacking a theoretical study. To this end, we propose a reaction-diffusion process of pathogens with mutations on meta-population networks, which includes population movement and strain mutation. We extend the Microscopic Markov Chain Approach (MMCA) to describe the model. Traffic networks make pathogen diversity more likely to occur in cities with lower infection densities. The likelihood of pathogen diversity is low in cities with short effective distances in the traffic network. Star-type gene network is more likely to lead to pathogen diversity than lattice-type and chain-type gene networks. When pathogen localization is present, infection is localized to strains that are at the endpoints of the gene network. Both the increased probability of movement and mutation promote pathogen diversity. The results also show that the population tends to move to cities with short effective distances, resulting in the infection density is high.
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Affiliation(s)
- Yanyi Nie
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China
- College of Computer Science, Sichuan University, Chengdu 610065, China
| | - Xiaoni Zhong
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China
| | - Tao Lin
- College of Computer Science, Sichuan University, Chengdu 610065, China
| | - Wei Wang
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China
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12
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Epidemic spreading under mutually independent intra- and inter-host pathogen evolution. Nat Commun 2022; 13:6218. [PMID: 36266285 PMCID: PMC9584276 DOI: 10.1038/s41467-022-34027-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 10/10/2022] [Indexed: 12/24/2022] Open
Abstract
The dynamics of epidemic spreading is often reduced to the single control parameter R0 (reproduction-rate), whose value, above or below unity, determines the state of the contagion. If, however, the pathogen evolves as it spreads, R0 may change over time, potentially leading to a mutation-driven spread, in which an initially sub-pandemic pathogen undergoes a breakthrough mutation. To predict the boundaries of this pandemic phase, we introduce here a modeling framework to couple the inter-host network spreading patterns with the intra-host evolutionary dynamics. We find that even in the extreme case when these two process are driven by mutually independent selection forces, mutations can still fundamentally alter the pandemic phase-diagram. The pandemic transitions, we show, are now shaped, not just by R0, but also by the balance between the epidemic and the evolutionary timescales. If mutations are too slow, the pathogen prevalence decays prior to the appearance of a critical mutation. On the other hand, if mutations are too rapid, the pathogen evolution becomes volatile and, once again, it fails to spread. Between these two extremes, however, we identify a broad range of conditions in which an initially sub-pandemic pathogen can breakthrough to gain widespread prevalence.
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13
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Park J. Regional Disparities in COVID-19 Vaccine Hesitancy: The Moderating
Role of Social Distancing and Vaccine Rollout in the U.S. INTERNATIONAL REGIONAL SCIENCE REVIEW 2022; 46:01600176221132231. [PMCID: PMC9561503 DOI: 10.1177/01600176221132231] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
This study examines the relationship between statewide contexts and individuals’ COVID-19 vaccine hesitancy by using the Household Pulse Survey, a national and near real-time data timely deployed by the U.S. Census Bureau. Controlling for the individual- and state-level variables in addition to temporal effect, this study finds that racial and ethnic minorities and COVID-19-infected people are more hesitant than their counterparts to receive a vaccine. Individuals who reside in a state where more stringent social distancing measures – particularly mask mandate – are implemented and vaccine rollout conditions are better appear to be less hesitant to receive a COVID-19 vaccine. Vulnerable subpopulation groups such as people of color and COVID-19-infected individuals are more hesitant to vaccine uptake even if regional circumstances are equal. These findings suggest that the continuation and extension of vaccine campaigns at the regional as well as individual levels are all important for expediting COVID-19 vaccination and reducing vaccine hesitancy as the world is in the middle of the third year of the pandemic.
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Affiliation(s)
- JungHo Park
- Department of Housing & Interior Design (BK21
Four AgeTech-Service Convergence Major), College of Human Ecology, Kyung Hee University, Seoul, South Korea
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14
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Tong C, Shi W, Siu GKH, Zhang A, Shi Z. Understanding spatiotemporal symptom onset risk of Omicron BA.1, BA.2 and hamster-related Delta AY.127. Front Public Health 2022; 10:978052. [PMID: 36187667 PMCID: PMC9523538 DOI: 10.3389/fpubh.2022.978052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/22/2022] [Indexed: 01/25/2023] Open
Abstract
Purpose Investigation of the community-level symptomatic onset risk regarding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern, is crucial to the pandemic control in the new normal. Methods Investigated in this study is the spatiotemporal symptom onset risk with Omicron BA.1, BA.2, and hamster-related Delta AY.127 by a joint analysis of community-based human mobility, virus genomes, and vaccinations in Hong Kong. Results The spatial spread of Omicron BA.2 was found to be 2.91 times and 2.56 times faster than that of Omicron BA.1 and Delta AY.127. Identified has been an early spatial invasion process in which spatiotemporal symptom onset risk was associated with intercommunity and cross-community human mobility of a dominant source location, especially regarding enhancement of the effects of the increased intrinsic transmissibility of Omicron BA.2. Further explored is the spread of Omicron BA.1, BA.2, and Delta AY.127 under different full and booster vaccination rate levels. An increase in full vaccination rates has primarily contributed to the reduction in areas within lower onset risk. An increase in the booster vaccination rate can promote a reduction in those areas within higher onset risk. Conclusions This study has provided a comprehensive investigation concerning the spatiotemporal symptom onset risk of Omicron BA.1, BA.2, and hamster-related Delta AY.127, and as such can contribute some help to countries and regions regarding the prevention of the emergence of such as these variants, on a strategic basis. Moreover, this study provides scientifically derived findings on the impact of full and booster vaccination campaigns working in the area of the reduction of symptomatic infections.
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Affiliation(s)
- Chengzhuo Tong
- Department of Land Surveying and Geo-Informatics, Otto Poon Charitable Foundation Smart Cities Research Institute, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Wenzhong Shi
- Department of Land Surveying and Geo-Informatics, Otto Poon Charitable Foundation Smart Cities Research Institute, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China,*Correspondence: Wenzhong Shi
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Anshu Zhang
- Department of Land Surveying and Geo-Informatics, Otto Poon Charitable Foundation Smart Cities Research Institute, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Zhicheng Shi
- Research Institute for Smart Cities, School of Architecture and Urban Planning, Shenzhen University, Shenzhen, China,Zhicheng Shi
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15
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Thoene J, Gavin RF, Towne A, Wattay L, Ferrari MG, Navarrete J, Pal R. In vitro activity of cysteamine against SARS-CoV-2 variants. Mol Genet Metab 2022; 137:192-200. [PMID: 36115282 PMCID: PMC9444157 DOI: 10.1016/j.ymgme.2022.08.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 01/09/2023]
Abstract
Global COVID-19 pandemic is caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Continuous emergence of new variants and their rapid spread are jeopardizing vaccine countermeasures to a significant extent. While currently available vaccines are effective at preventing illness associated with SARS-CoV-2 infection, these have been shown to be less effective at preventing breakthrough infection and transmission from a vaccinated individual to others. Here we demonstrate broad antiviral activity of cysteamine HCl in vitro against major emergent infectious variants of SARS-CoV-2 in a highly permissible Vero cell line. Cysteamine HCl inhibited infection of wild type, alpha, beta, gamma, delta, lambda, and omicron variants effectively. Cysteamine is a very well-tolerated US FDA-approved drug used chronically as a topical ophthalmic solution to treat ocular cystinosis in patients who receive it hourly or QID lifelong at concentrations 6 times higher than that required to inhibit SARS CoV-2 in tissue culture. Application of cysteamine as a topical nasal treatment can potentially1) mitigate existing infection 2) prevent infection in exposed individuals, and 3) limit the contagion in vulnerable populations.
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Affiliation(s)
- Jess Thoene
- Division of Pediatric Genetics, University of Michigan, United States of America.
| | | | - Aaron Towne
- Mechanical Engineering, College of Engineering, University of Michigan, United States of America
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16
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Describing a landscape we are yet discovering. ASTA ADVANCES IN STATISTICAL ANALYSIS 2022; 106:399-402. [PMID: 35698579 PMCID: PMC9178930 DOI: 10.1007/s10182-022-00449-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 11/02/2022]
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17
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COVID-19 Vaccine Mandates for Healthcare Professionals in the United States. Vaccines (Basel) 2022; 10:vaccines10091425. [PMID: 36146503 PMCID: PMC9504674 DOI: 10.3390/vaccines10091425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/25/2022] [Accepted: 08/25/2022] [Indexed: 12/03/2022] Open
Abstract
Healthcare workers (HCWs) need to be vaccinated against COVID-19 because they care for vulnerable patients. Hesitation to receiving the COVID-19 vaccine stems from the argument of bodily autonomy, novel mRNA vaccine technology, and conspiracy theories. However, vaccinations may prevent thousands of hospitalizations and deaths. HCWs have previously complied with other required vaccinations to care for children, elderly, and immunocompromised patients. Yet, COVID-19 vaccination mandates in the healthcare setting have been faced with resistance and subsequent staffing shortages. As HCWs display their hesitation to the vaccine, the community loses trust in its efficacy and safety. Speculation on pharmaceutical profiteering has also contributed to vaccine mistrust. As the pandemic continues, the healthcare field must decide on a course of action: adhere to vaccination mandates and cope with decreased staffing, repeal vaccination mandates to recover staff, rely on personal protective equipment (PPE) alone for protection, or do nothing and expect survival through herd immunity. To date, the United States has chosen to mandate COVID-19 vaccinations for any healthcare worker employed by Medicare and/or Medicaid-accepting facilities, allowing allergy and religious exemptions. This COVID-19 vaccination mandate for HCWs ethically protects the vulnerable people who HCWs vow to care for.
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18
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Piroddi C. Non-pharmaceutical Interventions and Social Distancing as Intersubjective Care and Collective Protection. Asian Bioeth Rev 2022; 14:379-395. [PMID: 35990569 PMCID: PMC9375195 DOI: 10.1007/s41649-022-00212-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 11/15/2022] Open
Abstract
The paper discusses non-pharmaceutical interventions (NPIs) as a collective form of protection that, in terms of health justice, benefits groups at risk, allowing them to engage in social life and activities during health crises. More specifically, the paper asserts that NPIs that realize social distancing are justifiable insofar as they are constitutive of a type of social protection that allows everyone, especially social disadvantaged agents, to access the public health sphere and other fundamental social spheres, such as the family and civil society.
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19
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Li Q, Wang Y, Sun Q, Knopf J, Herrmann M, Lin L, Jiang J, Shao C, Li P, He X, Hua F, Niu Z, Ma C, Zhu Y, Ippolito G, Piacentini M, Estaquier J, Melino S, Weiss FD, Andreano E, Latz E, Schultze JL, Rappuoli R, Mantovani A, Mak TW, Melino G, Shi Y. Immune response in COVID-19: what is next? Cell Death Differ 2022; 29:1107-1122. [PMID: 35581387 PMCID: PMC9110941 DOI: 10.1038/s41418-022-01015-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 04/16/2022] [Accepted: 04/26/2022] [Indexed: 12/18/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) has been a global pandemic for more than 2 years and it still impacts our daily lifestyle and quality in unprecedented ways. A better understanding of immunity and its regulation in response to SARS-CoV-2 infection is urgently needed. Based on the current literature, we review here the various virus mutations and the evolving disease manifestations along with the alterations of immune responses with specific focuses on the innate immune response, neutrophil extracellular traps, humoral immunity, and cellular immunity. Different types of vaccines were compared and analyzed based on their unique properties to elicit specific immunity. Various therapeutic strategies such as antibody, anti-viral medications and inflammation control were discussed. We predict that with the available and continuously emerging new technologies, more powerful vaccines and administration schedules, more effective medications and better public health measures, the COVID-19 pandemic will be under control in the near future. ![]()
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Affiliation(s)
- Qing Li
- The Third Affiliated Hospital of Soochow University/The First People's Hospital of Changzhou, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine of Soochow University, Medical College, Suzhou, China
| | - Ying Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences/Shanghai Jiao Tong University School of Medicine, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qiang Sun
- Beijing Institute of Biotechnology, Research Unit of Cell Death Mechanism, Chinese Academy of Medical Sciences, 2021RU008, 20 Dongda Street, 100071, Beijing, China
| | - Jasmin Knopf
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany.,Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Martin Herrmann
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany.,Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Liangyu Lin
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences/Shanghai Jiao Tong University School of Medicine, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jingting Jiang
- The Third Affiliated Hospital of Soochow University/The First People's Hospital of Changzhou, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine of Soochow University, Medical College, Suzhou, China
| | - Changshun Shao
- The Third Affiliated Hospital of Soochow University/The First People's Hospital of Changzhou, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine of Soochow University, Medical College, Suzhou, China
| | - Peishan Li
- The Third Affiliated Hospital of Soochow University/The First People's Hospital of Changzhou, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine of Soochow University, Medical College, Suzhou, China
| | - Xiaozhou He
- The Third Affiliated Hospital of Soochow University/The First People's Hospital of Changzhou, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine of Soochow University, Medical College, Suzhou, China
| | - Fei Hua
- The Third Affiliated Hospital of Soochow University/The First People's Hospital of Changzhou, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine of Soochow University, Medical College, Suzhou, China
| | - Zubiao Niu
- Beijing Institute of Biotechnology, Research Unit of Cell Death Mechanism, Chinese Academy of Medical Sciences, 2021RU008, 20 Dongda Street, 100071, Beijing, China
| | - Chaobing Ma
- Beijing Institute of Biotechnology, Research Unit of Cell Death Mechanism, Chinese Academy of Medical Sciences, 2021RU008, 20 Dongda Street, 100071, Beijing, China
| | - Yichao Zhu
- Beijing Institute of Biotechnology, Research Unit of Cell Death Mechanism, Chinese Academy of Medical Sciences, 2021RU008, 20 Dongda Street, 100071, Beijing, China
| | | | - Mauro Piacentini
- Department of Biology, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Jerome Estaquier
- INSERM-U1124, Université Paris, Paris, France.,CHU de Québec - Université Laval Research Center, Québec City, QC, Canada
| | - Sonia Melino
- Department of Biology, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Felix Daniel Weiss
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, 53127, Bonn, Germany
| | - Emanuele Andreano
- Research and Development Center, GlaxoSmithKline (GSK), Siena, Italy
| | - Eicke Latz
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, 53127, Bonn, Germany.,Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Joachim L Schultze
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Genomics & Immunoregulation, LIMES-Institute, University of Bonn, Bonn, Germany
| | - Rino Rappuoli
- Research and Development Center, GlaxoSmithKline (GSK), Siena, Italy
| | - Alberto Mantovani
- Department of Biomedical Sciences, Humanitas University, via Rita Levi Montalcini 4, Pieve Emanuele, 20072, Milan, Italy.,IRCCS Humanitas Clinical Research Hospital, via Manzoni 56, Rozzano, 20089, Milan, Italy.,William Harvey Research Institute, Queen Mary University, London, UK
| | - Tak Wah Mak
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Toronto, ON, M5G 2M9, Canada.,Department of Pathology, University of Hong Kong, Hong Kong, Pok Fu Lam, 999077, Hong Kong
| | - Gerry Melino
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany. .,Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy.
| | - Yufang Shi
- The Third Affiliated Hospital of Soochow University/The First People's Hospital of Changzhou, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine of Soochow University, Medical College, Suzhou, China. .,CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences/Shanghai Jiao Tong University School of Medicine, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. .,Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy.
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20
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Bordon Y. Social distancing plus rapid vaccination prevents emergence of SARS-CoV-2 variants. Nat Rev Immunol 2022; 22:208. [PMID: 35288705 PMCID: PMC8919904 DOI: 10.1038/s41577-022-00710-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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