Article
Multidisciplinary Sciences
Andaine Seguin-Orlando, Caroline Costedoat, Clio Der Sarkissian, Stefan Tzortzis, Celia Kamel, Norbert Telmon, Love Dalen, Catherine Theves, Michel Signoli, Ludovic Orlando
Summary: The study found that the 17th-century plague epidemic in Italy may have originated from the Alps region, and showed that the spatial distribution of the epidemic in Europe was more heterogeneous, suggesting that the trajectory of the epidemic in Italy was more likely influenced by environmental or social factors.
Article
Biology
Olivier Thomine, Samuel Alizon, Corentin Boennec, Marc Barthelemy, Mircea Sofonea
Summary: Simulating realistic individual movements with detailed geographical resolution can help optimize public health policies, as shown by the Epidemap framework capturing the daily activities of over 60 million people in a country. The tool reveals previously overlooked effects in disease spread, such as multiple peaks in cases and the impact of local density on epidemic timing. Furthermore, it shows that the importance of super-spreading events varies significantly over time.
Article
Microbiology
Anna Pikula, Anna Lisowska
Summary: This report presents the genetic and pathotypic characterization of a natural reassortant of infectious bursal disease virus emerging in Latvia. The reassortant strain has lower virulence but causes severe damage to lymphoid organs, potentially leading to impaired immune response.
Article
Mathematics, Applied
Mengyue Wang, Jiabiao Yi, Wen Jiang
Summary: This study is the first attempt to investigate the effects of non-pharmaceutical interventions (NPIs) and the physical condition of the public on the virulence evolution of SARS-CoV-2 and the trend of COVID-19 epidemics using an adaptive dynamics framework. The study shows that enhancing NPIs and the physical condition of the public can decrease the prevalence of COVID-19 and reduce the virulence of SARS-CoV-2. Controlling the contact and infection rates is key in controlling the scale and harm of the epidemic.
MATHEMATICAL METHODS IN THE APPLIED SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Sarah P. Otto, Troy Day, Julien Arino, Caroline Colijn, Jonathan Dushoff, Michael Li, Samir Mechai, Gary Van Domselaar, Jianhong Wu, David J. D. Earn, Nicholas H. Ogden
Summary: After a year into the COVID-19 pandemic, attention has shifted to the emergence and spread of variants of concern (VOCs) of SARS-CoV-2. These variants have shown detrimental effects on virus transmission and severity, prompting global efforts to understand their impact on disease control and public health interventions. Efforts are being made to explore the evolutionary processes involved in the emergence of new variants and to minimize their impact on the ongoing pandemic.
Article
Immunology
Sanda Ravlic, Ana Hecimovic, Tihana Kurtovic, Jelena Ivancic Jelecki, Dubravko Forcic, Anamarija Slovic, Ivan Christian Kurolt, Zeljka Macak Safranko, Tatjana Muslin, Dina Rnjak, Ozren Jaksic, Ena Soric, Gorana Dzepina, Oktavija Dakovic Rode, Kristina Kujavec Sljivac, Tomislav Vuk, Irena Jukic, Alemka Markotic, Beata Halassy
Summary: During the COVID-19 epidemic, efforts have been made to investigate SARS-CoV-2-specific antibodies as potential therapeutics. A method of establishing antibody characterisation has been proposed, showing a positive correlation between neutralising antibodies and disease severity, with a gradual decline in convalescents.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Business
Yiwei Wang, Ke Wang, Quan-Jing Wang
Summary: The research reveals a negative impact of epidemics on atmospheric quality, possibly due to retaliatory emissions from companies and poor government oversight post-epidemics. Furthermore, a higher level of economic development is associated with a stronger cointegration between epidemics and atmospheric quality.
EMERGING MARKETS FINANCE AND TRADE
(2021)
Article
Biology
Montserrat Vila, Alison M. Dunn, Franz Essl, Elena Gomez-Diaz, Philip E. Hulme, Jonathan M. Jeschke, Martin A. Nunez, Richard S. Ostfeld, Anibal Pauchard, Anthony Ricciardi, Belinda Gallardo
Summary: Invasion biology focuses on the impact of species introduced through human activities on ecosystems and human health, and draws parallels between invasive species and human disease spread. By understanding the interaction between invasive species and infectious diseases, we can improve prediction, prevention, and management strategies for both. Cross-disciplinary collaboration between invasion biology and epidemiology is essential for effective surveillance and control of invasive species and disease outbreaks.
Article
Biochemistry & Molecular Biology
Henry Goehlich, Olivia Roth, Michael Sieber, Cynthia M. Chibani, Anja Poehlein, Jelena Rajkov, Heiko Liesegang, Carolin C. Wendling
Summary: Infections by filamentous phages can influence bacterial fitness, with the production of viral particles being energetically costly. Bacteria can evolve resistance if the costs outweigh the benefits, shortening phage epidemics. The impact of abiotic conditions on host resistance evolution is still unknown.
Article
Immunology
Andrea Brizzi, Megan O'Driscoll, Ilaria Dorigatti
Summary: This study aims to improve the estimation method of infectious disease transmission capacity by correcting incomplete observations and underreporting of initial generations of infections, providing more accurate estimation results. Through the application of simulated data and real-world data, the method shows good performance in improving estimation accuracy.
CLINICAL INFECTIOUS DISEASES
(2022)
Review
Microbiology
Tom Fieldman
Summary: Current methods for combatting infectious diseases primarily focus on prevention, vaccination, and the use of small molecules to slow down or kill pathogens. However, the evolution of pathogens is often not taken into consideration. Natural selection favors different levels of virulence in different circumstances, and many evolutionary determinants of virulence have been identified. This article provides an overview of virulence and analyzes modifiable evolutionary determinants such as vaccinations, antibiotics, and transmission dynamics. The importance and limitations of adopting an evolutionary approach to reduce pathogen virulence are also discussed.
CRITICAL REVIEWS IN MICROBIOLOGY
(2023)
Article
Engineering, Civil
Mumtaz Karatas, Levent Eriskin, Elif Bozkaya
Summary: Explored transportation and location-related decision problems during the COVID-19 pandemic and applied Operations Research tools to solve them.
IEEE TRANSACTIONS ON INTELLIGENT TRANSPORTATION SYSTEMS
(2022)
Review
Ecology
A. Marm Kilpatrick
Summary: The COVID-19 pandemic has advanced our understanding of the ecology and evolution of infectious diseases, with insights into viral evolution, the impact of vaccination and host immunity, and the variable transmission and severity of the disease. The pandemic highlighted the dynamic nature of human social behavior and the broad range of hosts affected by the SARS-CoV-2 virus.
ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS
(2023)
Article
Biology
David A. Kennedy
Summary: A common assumption in the evolution of virulence theory is that pathogens transmit better when they exploit their host more heavily. However, the cost of mortality imposed on the host is often too small to constrain the increase in host exploitation. Detection costs, where hosts alter their behavior when infection is detectable, may be a stronger constraint on pathogen evolution. Empirical data shows that detection costs are frequently high in human and animal populations. The choice between mortality and detection costs can significantly impact evolutionary predictions.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Infectious Diseases
Ignacio Garcia-Bocanegra, Leonor Camacho-Sillero, Javier Caballero-Gomez, Montserrat Aguero, Felix Gomez-Guillamon, Juan Manuel Ruiz-Casas, Jose Manuel Diaz-Cao, Elena Garcia, Maria Jose Ruano, Rafael de la Haza
Summary: A novel hare MYXV (ha-MYXV) epidemic was identified in Iberian hares in Spain, with outbreaks detected in most regions where the species is present. The virus was found to have been circulating since June 2018, with fluctuations in outbreak numbers over specific time periods. High susceptibility of Iberian hares to ha-MYXV infection and significant consequences on their health status were observed, highlighting the need for further research on the impact of this emerging virus on wild lagomorph populations and ecosystems.
TRANSBOUNDARY AND EMERGING DISEASES
(2021)
Article
Biotechnology & Applied Microbiology
Nguyen Thi Bich Van, On Thuong Vi, Nguyen Thi Phuong Yen, Nguyen Thi Nhung, Nguyen Van Cuong, Bach Tuan Kiet, Nguyen Van Hoang, Vo Be Hien, Guy Thwaites, James Campell, Marc Choisy, Juan Carrique-Mas
Summary: The study found that increases in minimum inhibitory concentration (MIC) of antibiotics generally correlates with increased tolerance to essential oils (EOs), except for cinnamon EO which showed the opposite. Cinnamon EO exhibited strong antibacterial effects against multi-drug resistant pathogens, suggesting potential for therapeutic use in combating bacterial poultry pathogens.
JOURNAL OF APPLIED MICROBIOLOGY
(2022)
Article
Microbiology
Anna-Ursula Happel, Brian R. Kullin, Hoyam Gamieldien, Heather B. Jaspan, Arvind Varsani, Darren Martin, Jo-Ann S. Passmore, Remy Froissart
Summary: The presence of prophages in Lactobacillaceae strains used for optimizing vaginal microbiota could impact their safety and efficacy. Through genomic analysis and in vitro experiments, it was found that prophages are prevalent in Lactobacillaceae genomes and pose a potential risk that needs to be characterized further.
Article
Ecology
Sebastien Lion, Sylvain Gandon
Summary: In this study, the authors present a theoretical framework to understand and predict the long-term evolution of life-history traits under periodic environmental fluctuations. They investigate the influence of these fluctuations on selection in populations structured in distinct classes. The analysis reveals the time-varying selection gradients and their impact on the competitive ability of specific life-history mutations. Using this framework, the authors analyze the evolution of key life-history traits in pathogens and demonstrate how periodic fluctuations in the environment can affect the evolution of virulence, transmission, and host preference. These findings provide new and testable predictions on pathogen evolution and highlight the importance of considering time-varying environmental fluctuations in evolutionary studies.
Article
Ecology
David McLeod, Sylvain Gandon
Summary: This study investigates the joint evolution mechanism of pathogen adaptation to vaccine-induced immune response and pathogen virulence, with a focus on the protective effects of vaccines. The research reveals that vaccines that block infection, reduce transmission, and/or increase clearance generate positive epistasis between vaccine-escape and virulence alleles, while vaccines that reduce mortality generate negative epistasis. High rates of recombination can also affect these predictions.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Jeffrey Lazarus, Diana Romero, Christopher J. Kopka, Salim Abdool Karim, Laith J. Abu-Raddad, Gisele Almeida, Ricardo Baptista-Leite, Joshua A. Barocas, Mauricio L. Barreto, Yaneer Bar-Yam, Quique Bassat, Carolina Batista, Morgan Bazilian, Shu-Ti Chiou, Carlos del Rio, Gregory J. Dore, George F. Gao, Lawrence O. Gostin, Margaret Hellard, Jose L. Jimenez, Gagandeep Kang, Nancy Lee, Mojca Maticic, Martin McKee, Sabin Nsanzimana, Miquel Oliu-Barton, Bary Pradelski, Oksana Pyzik, Kenneth Rabin, Sunil Raina, Sabina Faiz Rashid, Magdalena Rathe, Rocio Saenz, Sudhvir Singh, Malene Trock-Hempler, Sonia Villapol, Peiling Yap, Agnes Binagwaho, Adeeba Kamarulzaman, Ayman El-Mohandes
Summary: Despite scientific and medical advances, political, socioeconomic, and behavioral factors continue to undermine the response to the COVID-19 pandemic. A Delphi study involving a diverse panel of experts from 112 countries and territories developed a set of recommendations across various domains to address this global threat to public health.
Article
Biochemistry & Molecular Biology
Troy Day, David A. Kennedy, Andrew F. Read, Sylvain Gandon
Summary: This Essay summarizes the current research on pathogen evolution in the context of immune priming and discusses the future evolution of SARS-CoV-2.
Article
Ecology
Gonche Danesh, Emma Saulnier, Olivier Gascuel, Marc Choisy, Samuel Alizon
Summary: Stochastic population dynamics simulations play a crucial role in ecological and epidemiological studies as they can generate time series and genealogies that capture the relatedness between individuals. However, current software packages for simulating phylogenetic trees often have simplified population dynamics models and are not suitable for simulating a large number of trees. To address these limitations, this study introduces TiPS, an R package that can generate trajectories and phylogenetic trees associated with a compartmental model. TiPS uses different simulation algorithms and a backwards-in-time approach to simulate trajectories and trees, respectively. It combines the flexibility of R for model definition and the speed of C++ for simulations execution. Benchmarking analyses show that TiPS is faster than existing packages and it is particularly useful for population genetics and phylodynamics studies that require a large number of phylogenies for population dynamics analysis.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Article
Genetics & Heredity
Jasmine Gamblin, Sylvain Gandon, Francois Blanquart, Amaury Lambert
Summary: This study theoretically investigates the effects of population bottlenecks on the accessibility of evolutionary paths and the rate of evolution. In the case of large population sizes and small mutation rates, bottlenecks act as a deterministic control of evolutionary paths by influencing the supply and loss of mutants. Additionally, demographic parameters can be tuned to force each possible evolutionary scenario to occur.
Article
Infectious Diseases
Hannah E. Brindle, Leonardo S. Bastos, Robert Christley, Lucie Contamin, Le Hai Dang, Dang Duc Anh, Neil French, Michael Griffiths, Behzad Nadjm, H. Rogier van Doorn, Pham Quang Thai, Tran Nhu Duong, Marc Choisy
Summary: The incidence of AES in Vietnam varies by region and season, with the highest incidence during the summer in the northern provinces. The cause of AES remains unknown in many cases. This study aims to understand the spatio-temporal distribution of, and risk factors for AES in Vietnam to help hypothesise the aetiology.
BMC INFECTIOUS DISEASES
(2023)
Article
Immunology
C. Louise Thwaites, Tran Tan Thanh, Nguyen Thi Han Ny, Lam Anh Nguyet, Nguyen Thi Duy Nhat, Cao Thu Thuy, Nguyen Thi Le Thanh, Nguyen Thanh Dung, James Campbell, Pham Quang Thai, Le Van Tan, Marc Choisy, Maciej F. Boni
Summary: Vietnam has high vaccination coverage for tetanus in infants and young children, but older children and men show reduced immunity to tetanus.
Article
Mathematical & Computational Biology
Ramses Djidjou-Demasse, Mircea T. Sofonea, Marc Choisy, Samuel Alizon
Summary: Antimicrobial efficacy is traditionally described by MIC, but bacterial resistance is a continuous trait. This study introduces a model of within-host evolution of resistance, tracking the dynamics of bacterial population density and resistance level. The findings show that resistance level can be explained by the reproduction number R0.
MATHEMATICAL MODELLING OF NATURAL PHENOMENA
(2023)
Article
Infectious Diseases
Hoang Thi An Ha, Phuong Thi Lan Nguyen, Tran Thi Mai Hung, Le Anh Tuan, Bui Thanh Thuy, Tran Hoang My Lien, Pham Duy Thai, Nguyen Ha Thanh, Vu Thi Ngoc Bich, Tran Hai Anh, Ngo Thi Hong Hanh, Nguyen Thi Minh, Duy Pham Thanh, Si-Nguyen T. Mai, Hao Chung The, Nguyen Vu Trung, Nguyen Hoai Thu, Tran Nhu Duong, Dang Duc Anh, Pham Thi Ngoc, Anne-Laure Banuls, Marc Choisy, H. Rogier van Doorn, Masato Suzuki, Tran Huy Hoang
Summary: This study investigates the prevalence of optrA positive E. faecalis (OPEfs) in 6 reservoirs in farms in Ha Nam province, Vietnam, and its associated factors, as well as explores the genetic relationship of OPEfs isolates. The highest prevalence of OPEfs was found in flies (46.8%), followed by chickens (37.3%), dogs (33.3%), humans (18.7%), wastewater (16.4%), and pigs (11.3%). The presence of OPEfs was associated with the total feeding area and total livestock unit of the farm in chickens, flies, and wastewater. Moreover, 86% of OPEfs strains were resistant to the last resort antibiotic linezolid.
Article
Multidisciplinary Sciences
Van Hai Khong, Philippe Carmona, Sylvain Gandon
Summary: Seasonality can have unpredictable effects on the persistence of vector-borne diseases, as it varies across different stages of the pathogen's life cycle. This study uses a general disease model to analyze the impact of periodic fluctuations on the basic reproduction ratio of the pathogen. The analysis reveals that seasonal variations in vector density or biting rate can either increase or decrease pathogen persistence, depending on the covariance between key compartments of the epidemiological model.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2023)
Article
Infectious Diseases
Nguyen Thi Nhung, Nguyen Thi Phuong Yen, Nguyen Thi Thuy Dung, Nguyen Thi Minh Nhan, Doan Hoang Phu, Bach Tuan Kiet, Guy Thwaites, Ronald B. Geskus, Stephen Baker, Juan Carrique-Mas, Marc Choisy
Summary: This study investigated the relationship between phenotypic antimicrobial resistance (AMR) and antimicrobial use (AMU), as well as potential inter-species transmission, in Escherichia coli isolates from humans and chickens in households in the Mekong Delta of Vietnam. The study found that AMU was significantly higher in chickens compared to humans, and isolates from chickens showed a higher prevalence of multidrug resistance. The study also demonstrated the co-influence of AMU and potential transmission on observed AMR patterns. Restricting unnecessary AMU and limiting interspecies contact are important for reducing the burden of AMR.
JAC-ANTIMICROBIAL RESISTANCE
(2022)
Article
Health Care Sciences & Services
Timothy M. Walker, Marc Choisy, Martin Dedicoat, Philip G. Drennan, David Wyllie, Fan Yang-Turner, Derrick W. Crook, Esther R. Robinson, A. Sarah Walker, E. Grace Smith, Timothy E. A. Peto
Summary: This study utilized over 10 years of whole-genome sequencing (WGS) data of Mycobacterium tuberculosis in Birmingham to investigate epidemiological trends and risk factors for transmission. The research found that there was seasonal variation in diagnoses, specifically among clustered cases. Risk factors for future clustered cases included UK birth, infectious forms of tuberculosis, and infection with lineage 3 or 4. There was also significant heterogeneity in transmission patterns between postcode districts.
LANCET REGIONAL HEALTH-EUROPE
(2022)
