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Jung SM, Loo SL, Howerton E, Contamin L, Smith CP, Carcelén EC, Yan K, Bents SJ, Levander J, Espino J, Lemaitre JC, Sato K, McKee CD, Hill AL, Chinazzi M, Davis JT, Mu K, Vespignani A, Rosenstrom ET, Rodriguez-Cartes SA, Ivy JS, Mayorga ME, Swann JL, España G, Cavany S, Moore SM, Perkins TA, Chen S, Paul R, Janies D, Thill JC, Srivastava A, Aawar MA, Bi K, Bandekar SR, Bouchnita A, Fox SJ, Meyers LA, Porebski P, Venkatramanan S, Adiga A, Hurt B, Klahn B, Outten J, Chen J, Mortveit H, Wilson A, Hoops S, Bhattacharya P, Machi D, Vullikanti A, Lewis B, Marathe M, Hochheiser H, Runge MC, Shea K, Truelove S, Viboud C, Lessler J. Potential impact of annual vaccination with reformulated COVID-19 vaccines: Lessons from the US COVID-19 scenario modeling hub. PLoS Med 2024; 21:e1004387. [PMID: 38630802 PMCID: PMC11062554 DOI: 10.1371/journal.pmed.1004387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 05/01/2024] [Accepted: 03/27/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Coronavirus Disease 2019 (COVID-19) continues to cause significant hospitalizations and deaths in the United States. Its continued burden and the impact of annually reformulated vaccines remain unclear. Here, we present projections of COVID-19 hospitalizations and deaths in the United States for the next 2 years under 2 plausible assumptions about immune escape (20% per year and 50% per year) and 3 possible CDC recommendations for the use of annually reformulated vaccines (no recommendation, vaccination for those aged 65 years and over, vaccination for all eligible age groups based on FDA approval). METHODS AND FINDINGS The COVID-19 Scenario Modeling Hub solicited projections of COVID-19 hospitalization and deaths between April 15, 2023 and April 15, 2025 under 6 scenarios representing the intersection of considered levels of immune escape and vaccination. Annually reformulated vaccines are assumed to be 65% effective against symptomatic infection with strains circulating on June 15 of each year and to become available on September 1. Age- and state-specific coverage in recommended groups was assumed to match that seen for the first (fall 2021) COVID-19 booster. State and national projections from 8 modeling teams were ensembled to produce projections for each scenario and expected reductions in disease outcomes due to vaccination over the projection period. From April 15, 2023 to April 15, 2025, COVID-19 is projected to cause annual epidemics peaking November to January. In the most pessimistic scenario (high immune escape, no vaccination recommendation), we project 2.1 million (90% projection interval (PI) [1,438,000, 4,270,000]) hospitalizations and 209,000 (90% PI [139,000, 461,000]) deaths, exceeding pre-pandemic mortality of influenza and pneumonia. In high immune escape scenarios, vaccination of those aged 65+ results in 230,000 (95% confidence interval (CI) [104,000, 355,000]) fewer hospitalizations and 33,000 (95% CI [12,000, 54,000]) fewer deaths, while vaccination of all eligible individuals results in 431,000 (95% CI: 264,000-598,000) fewer hospitalizations and 49,000 (95% CI [29,000, 69,000]) fewer deaths. CONCLUSIONS COVID-19 is projected to be a significant public health threat over the coming 2 years. Broad vaccination has the potential to substantially reduce the burden of this disease, saving tens of thousands of lives each year.
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Affiliation(s)
- Sung-mok Jung
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sara L. Loo
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Emily Howerton
- The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Lucie Contamin
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Claire P. Smith
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Erica C. Carcelén
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Katie Yan
- The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Samantha J. Bents
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - John Levander
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jessi Espino
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Joseph C. Lemaitre
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Koji Sato
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Clifton D. McKee
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Alison L. Hill
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Matteo Chinazzi
- Northeastern University, Boston, Massachusetts, United States of America
| | - Jessica T. Davis
- Northeastern University, Boston, Massachusetts, United States of America
| | - Kunpeng Mu
- Northeastern University, Boston, Massachusetts, United States of America
| | | | - Erik T. Rosenstrom
- North Carolina State University, Raleigh, North Carolina, United States of America
| | | | - Julie S. Ivy
- North Carolina State University, Raleigh, North Carolina, United States of America
| | - Maria E. Mayorga
- North Carolina State University, Raleigh, North Carolina, United States of America
| | - Julie L. Swann
- North Carolina State University, Raleigh, North Carolina, United States of America
| | - Guido España
- University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Sean Cavany
- University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Sean M. Moore
- University of Notre Dame, Notre Dame, Indiana, United States of America
| | - T. Alex Perkins
- University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Shi Chen
- University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Rajib Paul
- University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Daniel Janies
- University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Jean-Claude Thill
- University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Ajitesh Srivastava
- University of Southern California, Los Angeles, California, United States of America
| | - Majd Al Aawar
- University of Southern California, Los Angeles, California, United States of America
| | - Kaiming Bi
- University of Texas at Austin, Austin, Texas, United States of America
| | | | - Anass Bouchnita
- University of Texas at El Paso, El Paso, Texas, United States of America
| | - Spencer J. Fox
- University of Georgia, Athens, Georgia, United States of America
| | | | | | | | - Aniruddha Adiga
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Benjamin Hurt
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Brian Klahn
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Joseph Outten
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Jiangzhuo Chen
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Henning Mortveit
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Amanda Wilson
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Stefan Hoops
- University of Virginia, Charlottesville, Virginia, United States of America
| | | | - Dustin Machi
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Anil Vullikanti
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Bryan Lewis
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Madhav Marathe
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Harry Hochheiser
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Michael C. Runge
- U.S. Geological Survey, Laurel, Maryland, United States of America
| | - Katriona Shea
- The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Shaun Truelove
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Cécile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Justin Lessler
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
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2
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Igyártó BZ, Qin Z. The mRNA-LNP vaccines - the good, the bad and the ugly? Front Immunol 2024; 15:1336906. [PMID: 38390323 PMCID: PMC10883065 DOI: 10.3389/fimmu.2024.1336906] [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: 11/11/2023] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
The mRNA-LNP vaccine has received much attention during the COVID-19 pandemic since it served as the basis of the most widely used SARS-CoV-2 vaccines in Western countries. Based on early clinical trial data, these vaccines were deemed safe and effective for all demographics. However, the latest data raise serious concerns about the safety and effectiveness of these vaccines. Here, we review some of the safety and efficacy concerns identified to date. We also discuss the potential mechanism of observed adverse events related to the use of these vaccines and whether they can be mitigated by alterations of this vaccine mechanism approach.
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Affiliation(s)
- Botond Z. Igyártó
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA, United States
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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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Sunagawa J, Park H, Kim KS, Komorizono R, Choi S, Ramirez Torres L, Woo J, Jeong YD, Hart WS, Thompson RN, Aihara K, Iwami S, Yamaguchi R. Isolation may select for earlier and higher peak viral load but shorter duration in SARS-CoV-2 evolution. Nat Commun 2023; 14:7395. [PMID: 37989736 PMCID: PMC10663562 DOI: 10.1038/s41467-023-43043-2] [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: 08/19/2023] [Accepted: 10/30/2023] [Indexed: 11/23/2023] Open
Abstract
During the COVID-19 pandemic, human behavior change as a result of nonpharmaceutical interventions such as isolation may have induced directional selection for viral evolution. By combining previously published empirical clinical data analysis and multi-level mathematical modeling, we find that the SARS-CoV-2 variants selected for as the virus evolved from the pre-Alpha to the Delta variant had earlier and higher peak in viral load dynamics but a shorter duration of infection. Selection for increased transmissibility shapes the viral load dynamics, and the isolation measure is likely to be a driver of these evolutionary transitions. In addition, we show that a decreased incubation period and an increased proportion of asymptomatic infection are also positively selected for as SARS-CoV-2 mutated to adapt to human behavior (i.e., Omicron variants). The quantitative information and predictions we present here can guide future responses in the potential arms race between pandemic interventions and viral evolution.
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Affiliation(s)
- Junya Sunagawa
- Department of Advanced Transdisciplinary Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Hyeongki Park
- interdisciplinary Biology Laboratory (iBLab), Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Kwang Su Kim
- interdisciplinary Biology Laboratory (iBLab), Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
- Department of Scientific Computing, Pukyong National University, Busan, South Korea
- Department of Mathematics, Pusan National University, Busan, South Korea
| | - Ryo Komorizono
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Life and Medical Sciences (LiMe), Kyoto University, Kyoto, Japan
| | - Sooyoun Choi
- interdisciplinary Biology Laboratory (iBLab), Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
- Department of Mathematics, Pusan National University, Busan, South Korea
| | - Lucia Ramirez Torres
- interdisciplinary Biology Laboratory (iBLab), Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Joohyeon Woo
- interdisciplinary Biology Laboratory (iBLab), Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Yong Dam Jeong
- interdisciplinary Biology Laboratory (iBLab), Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
- Department of Mathematics, Pusan National University, Busan, South Korea
| | - William S Hart
- Mathematical Institute, University of Oxford, Oxford, UK
| | - Robin N Thompson
- Mathematical Institute, University of Oxford, Oxford, UK
- Mathematics Institute, University of Warwick, Coventry, UK
- Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, UK
| | - Kazuyuki Aihara
- International Research Center for Neurointelligence, The University of Tokyo Institutes for Advanced Study, The University of Tokyo, Tokyo, Japan
| | - Shingo Iwami
- interdisciplinary Biology Laboratory (iBLab), Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan.
- Institute of Mathematics for Industry, Kyushu University, Fukuoka, Japan.
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.
- Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS), RIKEN, Saitama, Japan.
- NEXT-Ganken Program, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan.
- Science Groove Inc, Fukuoka, Japan.
| | - Ryo Yamaguchi
- Department of Advanced Transdisciplinary Sciences, Hokkaido University, Sapporo, Hokkaido, Japan.
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
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5
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Jung SM, Loo SL, Howerton E, Contamin L, Smith CP, Carcelén EC, Yan K, Bents SJ, Levander J, Espino J, Lemaitre JC, Sato K, McKee CD, Hill AL, Chinazzi M, Davis JT, Mu K, Vespignani A, Rosenstrom ET, Rodriguez-Cartes SA, Ivy JS, Mayorga ME, Swann JL, España G, Cavany S, Moore SM, Perkins A, Chen S, Paul R, Janies D, Thill JC, Srivastava A, Al Aawar M, Bi K, Bandekar SR, Bouchnita A, Fox SJ, Meyers LA, Porebski P, Venkatramanan S, Adiga A, Hurt B, Klahn B, Outten J, Chen J, Mortveit H, Wilson A, Hoops S, Bhattacharya P, Machi D, Vullikanti A, Lewis B, Marathe M, Hochheiser H, Runge MC, Shea K, Truelove S, Viboud C, Lessler J. Potential impact of annual vaccination with reformulated COVID-19 vaccines: lessons from the U.S. COVID-19 Scenario Modeling Hub. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.26.23297581. [PMID: 37961207 PMCID: PMC10635209 DOI: 10.1101/2023.10.26.23297581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Importance COVID-19 continues to cause significant hospitalizations and deaths in the United States. Its continued burden and the impact of annually reformulated vaccines remain unclear. Objective To project COVID-19 hospitalizations and deaths from April 2023-April 2025 under two plausible assumptions about immune escape (20% per year and 50% per year) and three possible CDC recommendations for the use of annually reformulated vaccines (no vaccine recommendation, vaccination for those aged 65+, vaccination for all eligible groups). Design The COVID-19 Scenario Modeling Hub solicited projections of COVID-19 hospitalization and deaths between April 15, 2023-April 15, 2025 under six scenarios representing the intersection of considered levels of immune escape and vaccination. State and national projections from eight modeling teams were ensembled to produce projections for each scenario. Setting The entire United States. Participants None. Exposure Annually reformulated vaccines assumed to be 65% effective against strains circulating on June 15 of each year and to become available on September 1. Age and state specific coverage in recommended groups was assumed to match that seen for the first (fall 2021) COVID-19 booster. Main outcomes and measures Ensemble estimates of weekly and cumulative COVID-19 hospitalizations and deaths. Expected relative and absolute reductions in hospitalizations and deaths due to vaccination over the projection period. Results From April 15, 2023-April 15, 2025, COVID-19 is projected to cause annual epidemics peaking November-January. In the most pessimistic scenario (high immune escape, no vaccination recommendation), we project 2.1 million (90% PI: 1,438,000-4,270,000) hospitalizations and 209,000 (90% PI: 139,000-461,000) deaths, exceeding pre-pandemic mortality of influenza and pneumonia. In high immune escape scenarios, vaccination of those aged 65+ results in 230,000 (95% CI: 104,000-355,000) fewer hospitalizations and 33,000 (95% CI: 12,000-54,000) fewer deaths, while vaccination of all eligible individuals results in 431,000 (95% CI: 264,000-598,000) fewer hospitalizations and 49,000 (95% CI: 29,000-69,000) fewer deaths. Conclusion and Relevance COVID-19 is projected to be a significant public health threat over the coming two years. Broad vaccination has the potential to substantially reduce the burden of this disease.
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Affiliation(s)
- Sung-mok Jung
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Sara L. Loo
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Emily Howerton
- The Pennsylvania State University, State College, Pennsylvania
| | | | - Claire P. Smith
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Erica C. Carcelén
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Katie Yan
- The Pennsylvania State University, State College, Pennsylvania
| | - Samantha J. Bents
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland
| | | | - Jessi Espino
- University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Joseph C. Lemaitre
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Koji Sato
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Clif D. McKee
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Alison L. Hill
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | | | - Kunpeng Mu
- University of Massachusetts Amherst, Amherst, Massachusetts
| | | | | | | | - Julie S. Ivy
- North Carolina State University, Raleigh, North Carolina
| | | | - Julie L. Swann
- North Carolina State University, Raleigh, North Carolina
| | | | - Sean Cavany
- University of Notre Dame, Notre Dame, Indiana
| | | | | | - Shi Chen
- University of North Carolina at Charlotte, Charlotte, North Carolina
| | - Rajib Paul
- University of North Carolina at Charlotte, Charlotte, North Carolina
| | - Daniel Janies
- University of North Carolina at Charlotte, Charlotte, North Carolina
| | - Jean-Claude Thill
- University of North Carolina at Charlotte, Charlotte, North Carolina
| | | | - Majd Al Aawar
- University of Southern California, Los Angeles, California
| | - Kaiming Bi
- University of Texas at Austin, Austin, Texas
| | | | | | | | | | | | | | | | | | - Brian Klahn
- University of Virginia, Charlottesville, Virginia
| | | | | | | | | | - Stefan Hoops
- University of Virginia, Charlottesville, Virginia
| | | | - Dustin Machi
- University of Virginia, Charlottesville, Virginia
| | | | - Bryan Lewis
- University of Virginia, Charlottesville, Virginia
| | | | | | | | - Katriona Shea
- The Pennsylvania State University, State College, Pennsylvania
| | - Shaun Truelove
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Cécile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland
| | - Justin Lessler
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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Miele L, Evans RML, Cunniffe NJ, Torres-Barceló C, Bevacqua D. Evolutionary Epidemiology Consequences of Trait-Dependent Control of Heterogeneous Parasites. Am Nat 2023; 202:E130-E146. [PMID: 37963120 DOI: 10.1086/726062] [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: 11/16/2023]
Abstract
AbstractDisease control can induce both demographic and evolutionary responses in host-parasite systems. Foreseeing the outcome of control therefore requires knowledge of the eco-evolutionary feedback between control and system. Previous work has assumed that control strategies have a homogeneous effect on the parasite population. However, this is not true when control targets those traits that confer to the parasite heterogeneous levels of resistance, which can additionally be related to other key parasite traits through evolutionary trade-offs. In this work, we develop a minimal model coupling epidemiological and evolutionary dynamics to explore possible trait-dependent effects of control strategies. In particular, we consider a parasite expressing continuous levels of a trait-determining resource exploitation and a control treatment that can be either positively or negatively correlated with that trait. We demonstrate the potential of trait-dependent control by considering that the decision maker may want to minimize both the damage caused by the disease and the use of treatment, due to possible environmental or economic costs. We identify efficient strategies showing that the optimal type of treatment depends on the amount applied. Our results pave the way for the study of control strategies based on evolutionary constraints, such as collateral sensitivity and resistance costs, which are receiving increasing attention for both public health and agricultural purposes.
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Chardès V, Mazzolini A, Mora T, Walczak AM. Evolutionary stability of antigenically escaping viruses. Proc Natl Acad Sci U S A 2023; 120:e2307712120. [PMID: 37871216 PMCID: PMC10622963 DOI: 10.1073/pnas.2307712120] [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: 05/08/2023] [Accepted: 08/24/2023] [Indexed: 10/25/2023] Open
Abstract
Antigenic variation is the main immune escape mechanism for RNA viruses like influenza or SARS-CoV-2. While high mutation rates promote antigenic escape, they also induce large mutational loads and reduced fitness. It remains unclear how this cost-benefit trade-off selects the mutation rate of viruses. Using a traveling wave model for the coevolution of viruses and host immune systems in a finite population, we investigate how immunity affects the evolution of the mutation rate and other nonantigenic traits, such as virulence. We first show that the nature of the wave depends on how cross-reactive immune systems are, reconciling previous approaches. The immune-virus system behaves like a Fisher wave at low cross-reactivities, and like a fitness wave at high cross-reactivities. These regimes predict different outcomes for the evolution of nonantigenic traits. At low cross-reactivities, the evolutionarily stable strategy is to maximize the speed of the wave, implying a higher mutation rate and increased virulence. At large cross-reactivities, where our estimates place H3N2 influenza, the stable strategy is to increase the basic reproductive number, keeping the mutation rate to a minimum and virulence low.
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Affiliation(s)
- Victor Chardès
- Laboratoire de Physique de l’École Normale Supérieure, CNRS, Paris Sciences & Lettres University, Sorbonne Université, and Université Paris-Cité, 75005Paris, France
- Center for Computational Biology, Flatiron Institute, New York, NY10010
| | - Andrea Mazzolini
- Laboratoire de Physique de l’École Normale Supérieure, CNRS, Paris Sciences & Lettres University, Sorbonne Université, and Université Paris-Cité, 75005Paris, France
| | - Thierry Mora
- Laboratoire de Physique de l’École Normale Supérieure, CNRS, Paris Sciences & Lettres University, Sorbonne Université, and Université Paris-Cité, 75005Paris, France
| | - Aleksandra M. Walczak
- Laboratoire de Physique de l’École Normale Supérieure, CNRS, Paris Sciences & Lettres University, Sorbonne Université, and Université Paris-Cité, 75005Paris, France
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8
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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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9
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Tamura T, Ito J, Uriu K, Zahradnik J, Kida I, Anraku Y, Nasser H, Shofa M, Oda Y, Lytras S, Nao N, Itakura Y, Deguchi S, Suzuki R, Wang L, Begum MM, Kita S, Yajima H, Sasaki J, Sasaki-Tabata K, Shimizu R, Tsuda M, Kosugi Y, Fujita S, Pan L, Sauter D, Yoshimatsu K, Suzuki S, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Yamamoto Y, Nagamoto T, Schreiber G, Maenaka K, Hashiguchi T, Ikeda T, Fukuhara T, Saito A, Tanaka S, Matsuno K, Takayama K, Sato K. Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants. Nat Commun 2023; 14:2800. [PMID: 37193706 DOI: 10.1038/s41467-023-38435-3] [Citation(s) in RCA: 110] [Impact Index Per Article: 110.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 05/02/2023] [Indexed: 05/18/2023] Open
Abstract
In late 2022, SARS-CoV-2 Omicron subvariants have become highly diversified, and XBB is spreading rapidly around the world. Our phylogenetic analyses suggested that XBB emerged through the recombination of two cocirculating BA.2 lineages, BJ.1 and BM.1.1.1 (a progeny of BA.2.75), during the summer of 2022. XBB.1 is the variant most profoundly resistant to BA.2/5 breakthrough infection sera to date and is more fusogenic than BA.2.75. The recombination breakpoint is located in the receptor-binding domain of spike, and each region of the recombinant spike confers immune evasion and increases fusogenicity. We further provide the structural basis for the interaction between XBB.1 spike and human ACE2. Finally, the intrinsic pathogenicity of XBB.1 in male hamsters is comparable to or even lower than that of BA.2.75. Our multiscale investigation provides evidence suggesting that XBB is the first observed SARS-CoV-2 variant to increase its fitness through recombination rather than substitutions.
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Affiliation(s)
- Tomokazu Tamura
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Keiya Uriu
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jiri Zahradnik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia
| | - Izumi Kida
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yuki Anraku
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Hesham Nasser
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
- Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Maya Shofa
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
| | - Yoshitaka Oda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Spyros Lytras
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Naganori Nao
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Yukari Itakura
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Sayaka Deguchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Japan
| | - Lei Wang
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Mst Monira Begum
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Shunsuke Kita
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Hisano Yajima
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Jiei Sasaki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kaori Sasaki-Tabata
- Department of Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Ryo Shimizu
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Masumi Tsuda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Yusuke Kosugi
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shigeru Fujita
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Lin Pan
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Daniel Sauter
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | | | - Saori Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Japan
| | | | - Mami Nagashima
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Kenji Sadamasu
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | | | | | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Katsumi Maenaka
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Japan
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo, Japan
- Division of Pathogen Structure, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - Shinya Tanaka
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan.
| | - Keita Matsuno
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Japan.
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
- One Health Research Center, Hokkaido University, Sapporo, Japan.
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.
- CREST, Japan Science and Technology Agency, Kawaguchi, Japan.
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
- CREST, Japan Science and Technology Agency, Kawaguchi, Japan.
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan.
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10
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Kun Á, Hubai AG, Král A, Mokos J, Mikulecz BÁ, Radványi Á. Do pathogens always evolve to be less virulent? The virulence–transmission trade-off in light of the COVID-19 pandemic. Biol Futur 2023:10.1007/s42977-023-00159-2. [PMID: 37002448 PMCID: PMC10066022 DOI: 10.1007/s42977-023-00159-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 03/09/2023] [Indexed: 04/03/2023]
Abstract
AbstractThe direction the evolution of virulence takes in connection with any pathogen is a long-standing question. Formerly, it was theorized that pathogens should always evolve to be less virulent. As observations were not in line with this theoretical outcome, new theories emerged, chief among them the transmission–virulence trade-off hypotheses, which predicts an intermediate level of virulence as the endpoint of evolution. At the moment, we are very much interested in the future evolution of COVID-19’s virulence. Here, we show that the disease does not fulfill all the assumptions of the hypothesis. In the case of COVID-19, a higher viral load does not mean a higher risk of death; immunity is not long-lasting; other hosts can act as reservoirs for the virus; and death as a consequence of viral infection does not shorten the infectious period. Consequently, we cannot predict the short- or long-term evolution of the virulence of COVID-19.
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11
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Rubio-Tomás T, Sotiriou A, Tavernarakis N. The interplay between selective types of (macro)autophagy: Mitophagy and xenophagy. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 374:129-157. [PMID: 36858654 DOI: 10.1016/bs.ircmb.2022.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Autophagy is a physiological response, activated by a myriad of endogenous and exogenous cues, including DNA damage, perturbation of proteostasis, depletion of nutrients or oxygen and pathogen infection. Upon sensing those stimuli, cells employ multiple non-selective and selective autophagy pathways to promote fitness and survival. Importantly, there are a variety of selective types of autophagy. In this review we will focus on autophagy of bacteria (xenophagy) and autophagy of mitochondria (mitophagy). We provide a brief introduction to bulk autophagy, as well as xenophagy and mitophagy, highlighting their common molecular factors. We also describe the role of xenophagy and mitophagy in the detection and elimination of pathogens by the immune system and the adaptive mechanisms that some pathogens have developed through evolution to escape the host autophagic response. Finally, we summarize the recent articles (from the last five years) linking bulk autophagy with xenophagy and/or mitophagy in the context on developmental biology, cancer and metabolism.
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Affiliation(s)
- Teresa Rubio-Tomás
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Aggeliki Sotiriou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece; Division of Basic Sciences, School of Medicine, University of Crete, Heraklion, Crete, Greece
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece; Division of Basic Sciences, School of Medicine, University of Crete, Heraklion, Crete, Greece.
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12
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Carabelli AM, Peacock TP, Thorne LG, Harvey WT, Hughes J, Peacock SJ, Barclay WS, de Silva TI, Towers GJ, Robertson DL. SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nat Rev Microbiol 2023; 21:162-177. [PMID: 36653446 PMCID: PMC9847462 DOI: 10.1038/s41579-022-00841-7] [Citation(s) in RCA: 245] [Impact Index Per Article: 245.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2022] [Indexed: 01/19/2023]
Abstract
In late 2020, after circulating for almost a year in the human population, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exhibited a major step change in its adaptation to humans. These highly mutated forms of SARS-CoV-2 had enhanced rates of transmission relative to previous variants and were termed 'variants of concern' (VOCs). Designated Alpha, Beta, Gamma, Delta and Omicron, the VOCs emerged independently from one another, and in turn each rapidly became dominant, regionally or globally, outcompeting previous variants. The success of each VOC relative to the previously dominant variant was enabled by altered intrinsic functional properties of the virus and, to various degrees, changes to virus antigenicity conferring the ability to evade a primed immune response. The increased virus fitness associated with VOCs is the result of a complex interplay of virus biology in the context of changing human immunity due to both vaccination and prior infection. In this Review, we summarize the literature on the relative transmissibility and antigenicity of SARS-CoV-2 variants, the role of mutations at the furin spike cleavage site and of non-spike proteins, the potential importance of recombination to virus success, and SARS-CoV-2 evolution in the context of T cells, innate immunity and population immunity. SARS-CoV-2 shows a complicated relationship among virus antigenicity, transmission and virulence, which has unpredictable implications for the future trajectory and disease burden of COVID-19.
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Affiliation(s)
| | - Thomas P Peacock
- Department of Infectious Disease, St Mary's Medical School, Imperial College London, London, UK
| | - Lucy G Thorne
- Division of Infection and Immunity, University College London, London, UK
| | - William T Harvey
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - Wendy S Barclay
- Department of Infectious Disease, St Mary's Medical School, Imperial College London, London, UK
| | - Thushan I de Silva
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Greg J Towers
- Division of Infection and Immunity, University College London, London, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
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13
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Kumata R, Sasaki A. Antigenic escape is accelerated by the presence of immunocompromised hosts. Proc Biol Sci 2022; 289:20221437. [PMID: 36350217 PMCID: PMC9653221 DOI: 10.1098/rspb.2022.1437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/17/2022] [Indexed: 04/01/2024] Open
Abstract
The repeated emergence of SARS-CoV-2 escape mutants from host immunity has obstructed the containment of the current pandemic and poses a serious threat to humanity. Prolonged infection in immunocompromised patients has received increasing attention as a driver of immune escape, and accumulating evidence suggests that viral genomic diversity and emergence of immune-escape mutants are promoted in immunocompromised patients. However, because immunocompromised patients comprise a small proportion of the host population, whether they have a significant impact on antigenic evolution at the population level is unknown. We consider an evolutionary epidemiological model that combines antigenic evolution and epidemiological dynamics. Applying this model to a heterogeneous host population, we study the impact of immunocompromised hosts on the evolutionary dynamics of pathogen antigenic escape from host immunity. We derived analytical formulae of the speed of antigenic evolution in heterogeneous host populations and found that even a small number of immunocompromised hosts in the population significantly accelerates antigenic evolution. Our results demonstrate that immunocompromised hosts play a key role in viral adaptation at the population level and emphasize the importance of critical care and surveillance of immunocompromised hosts.
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Affiliation(s)
- Ryuichi Kumata
- Department of Evolutionary Studies of Biosystems, The Graduate University of Advanced Studies, SOKENDAI, Hayama, Kanagawa 2400139, Japan
| | - Akira Sasaki
- Department of Evolutionary Studies of Biosystems, The Graduate University of Advanced Studies, SOKENDAI, Hayama, Kanagawa 2400139, Japan
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14
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AbdelMassih A, Sedky A, Shalaby A, Shalaby AF, Yasser A, Mohyeldin A, Amin B, Saleheen B, Osman D, Samuel E, Abdelfatah E, Albustami E, ElGhamry F, Khaled H, Amr H, Gaber H, Makhlouf I, Abdeldayem J, El-Beialy JW, Milad K, El Sharkawi L, Abosenna L, Safi MG, AbdelKareem M, Gaber M, Elkady M, Ihab M, AbdelRaouf N, Khaled R, Shalata R, Mahgoub R, Jamal S, El Hawary SED, ElRashidy S, El Shorbagy S, Gerges T, Kassem Y, Magdy Y, Omar Y, Shokry Y, Kamel A, Hozaien R, El-Husseiny N, El Shershaby M. From HIV to COVID-19, Molecular mechanisms of pathogens' trade-off and persistence in the community, potential targets for new drug development. BULLETIN OF THE NATIONAL RESEARCH CENTRE 2022; 46:194. [PMID: 35818410 PMCID: PMC9258762 DOI: 10.1186/s42269-022-00879-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND On the staggering emergence of the Omicron variant, numerous questions arose about the evolution of virulence and transmissibility in microbes. MAIN BODY OF THE ABSTRACT The trade-off hypothesis has long speculated the exchange of virulence for the sake of superior transmissibility in a wide array of pathogens. While this certainly applies to the case of the Omicron variant, along with influenza virus, various reports have been allocated for an array of pathogens such as human immunodeficiency virus (HIV), malaria, hepatitis B virus (HBV) and tuberculosis (TB). The latter abide to another form of trade-off, the invasion-persistence trade-off. In this study, we aim to explore the molecular mechanisms and mutations of different obligate intracellular pathogens that attenuated their more morbid characters, virulence in acute infections and invasion in chronic infections. SHORT CONCLUSION Recognizing the mutations that attenuate the most morbid characters of pathogens such as virulence or persistence can help in tailoring new therapies for such pathogens. Targeting macrophage tropism of HIV by carbohydrate-binding agents, or targeting the TMPRSS2 receptors to prevent pulmonary infiltrates of COVID-19 is an example of how important is to recognize such genetic mechanisms.
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Affiliation(s)
- Antoine AbdelMassih
- Pediatric Department, Pediatric Cardiology Unit, Faculty of Medicine, Cairo University Children Hospital, Cairo University, Kasr Al Ainy Street, Cairo, 12411 Egypt
| | - Abrar Sedky
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Ahmed Shalaby
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - AlAmira-Fawzia Shalaby
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Alia Yasser
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Aya Mohyeldin
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Basma Amin
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Basma Saleheen
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Dina Osman
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Elaria Samuel
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Emmy Abdelfatah
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Eveen Albustami
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Farida ElGhamry
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Habiba Khaled
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Hana Amr
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Hanya Gaber
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Ismail Makhlouf
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Janna Abdeldayem
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | | | - Karim Milad
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Laila El Sharkawi
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Lina Abosenna
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Madonna G. Safi
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mariam AbdelKareem
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Marwa Gaber
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mirna Elkady
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mohamed Ihab
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Nora AbdelRaouf
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Rawan Khaled
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Reem Shalata
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Rudayna Mahgoub
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Sarah Jamal
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Seif El-Din El Hawary
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Shady ElRashidy
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Sherouk El Shorbagy
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Tony Gerges
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Yara Kassem
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Yasmeen Magdy
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Yasmin Omar
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Yasmine Shokry
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Aya Kamel
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Rafeef Hozaien
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Nadine El-Husseiny
- Faculty of Dentistry, Cairo University, Cairo, Egypt
- Pixagon Graphic Design Agency, Cairo, Egypt
| | - Meryam El Shershaby
- Internship Research Program (Research Accessibility Team), Faculty of Medicine, Cairo University, Cairo, Egypt
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15
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Affiliation(s)
- Veronika Bernhauerová
- Department of Biophysics and Physical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic.
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16
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Lion S, Boots M, Sasaki A. Multi-morph eco-evolutionary dynamics in structured populations. Am Nat 2022; 200:345-372. [DOI: 10.1086/720439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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17
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Antigenic evolution can drive virulence evolution. Nat Ecol Evol 2021; 6:24-25. [PMID: 34949815 DOI: 10.1038/s41559-021-01600-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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