Journal of The Royal Society Interface最新文献

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A systematic evaluation of the language-of-viral-escape model using multiple machine learning frameworks. 使用多个机器学习框架对病毒逃逸语言模型进行系统评估。
IF 3.7 2区 综合性期刊
Journal of The Royal Society Interface Pub Date : 2025-04-01 Epub Date: 2025-04-30 DOI: 10.1098/rsif.2024.0598
Brent E Allman, Luiz Vieira, Daniel J Diaz, Claus O Wilke
{"title":"A systematic evaluation of the language-of-viral-escape model using multiple machine learning frameworks.","authors":"Brent E Allman, Luiz Vieira, Daniel J Diaz, Claus O Wilke","doi":"10.1098/rsif.2024.0598","DOIUrl":"https://doi.org/10.1098/rsif.2024.0598","url":null,"abstract":"<p><p>Predicting the evolutionary patterns of emerging and endemic viruses is key for mitigating their spread. In particular, it is critical to rapidly identify mutations with the potential for immune escape or increased disease burden. Knowing which circulating mutations pose a concern can inform treatment or mitigation strategies such as alternative vaccines or targeted social distancing. In 2021, Hie B, Zhong ED, Berger B, Bryson B. 2021 Learning the language of viral evolution and escape. <i>Science</i> <b>371</b>, 284-288. (doi:10.1126/science.abd7331) proposed that variants of concern can be identified using two quantities extracted from protein language models, grammaticality and semantic change. These quantities are defined by analogy to concepts from natural language processing. Grammaticality is intended to be a measure of whether a variant viral protein is viable, and semantic change is intended to be a measure of potential for immune escape. Here, we systematically test this hypothesis, taking advantage of several high-throughput datasets that have become available, and also comparing this model with several more recently published machine learning models. We find that grammaticality can be a measure of protein viability, though methods that are trained explicitly to predict mutational effects appear to be more effective. By contrast, we do not find compelling evidence that semantic change is a useful tool for identifying immune escape mutations.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 225","pages":"20240598"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12040448/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144027190","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Resolving the kinetics of an ensemble of muscle myosin motors via a temperature-dependent fitting procedure. 通过温度相关拟合程序解决肌球蛋白马达整体动力学问题。
IF 3.7 2区 综合性期刊
Journal of The Royal Society Interface Pub Date : 2025-04-01 Epub Date: 2025-04-30 DOI: 10.1098/rsif.2025.0040
Valentina Buonfiglio, Niccolò Zagli, Irene Pertici, Vincenzo Lombardi, Pasquale Bianco, Duccio Fanelli
{"title":"Resolving the kinetics of an ensemble of muscle myosin motors via a temperature-dependent fitting procedure.","authors":"Valentina Buonfiglio, Niccolò Zagli, Irene Pertici, Vincenzo Lombardi, Pasquale Bianco, Duccio Fanelli","doi":"10.1098/rsif.2025.0040","DOIUrl":"https://doi.org/10.1098/rsif.2025.0040","url":null,"abstract":"<p><p>A data fitting procedure is devised and thoroughly tested to provide self-consistent estimates of the relevant mechanokinetic parameters involved in a plausible scheme underpinning the output of an ensemble of myosin II molecular motors mimicking the contraction of skeletal muscle. The method builds on a stochastic model accounting for the force exerted by the motor ensemble operated both in the low and high force-generating regimes corresponding to different temperature ranges. The proposed interpretative framework is successfully challenged against simulated data, meant to mimic the experimental output of a one-dimensional synthetic nanomachine powered by pure muscle myosin isoforms.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 225","pages":"20250040"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12041895/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143999516","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Something to sink your teeth into: the mechanics of tooth indentation in frugivorous fishes. 让你的牙齿沉入其中:食果鱼类牙齿压痕的机制。
IF 3.7 2区 综合性期刊
Journal of The Royal Society Interface Pub Date : 2025-04-01 Epub Date: 2025-04-16 DOI: 10.1098/rsif.2024.0725
Jack Rosen, Karly Cohen, Cassandra M Donatelli, Adam Summers, Stephanie Crofts, Matthew Kolmann
{"title":"Something to sink your teeth into: the mechanics of tooth indentation in frugivorous fishes.","authors":"Jack Rosen, Karly Cohen, Cassandra M Donatelli, Adam Summers, Stephanie Crofts, Matthew Kolmann","doi":"10.1098/rsif.2024.0725","DOIUrl":"https://doi.org/10.1098/rsif.2024.0725","url":null,"abstract":"<p><p>Frugivorous vertebrates engage in a mutualism with fruiting plants: the former receive a nutrient subsidy, and the latter benefit by having their seeds dispersed far from parent plants. Vertebrate frugivores like primates and bats have particular morphologies suited for gripping fruit and then pulverizing fruit soft tissues; however, variation among frugivores and fruits has made the identification of common frugivore phenotypes difficult. Here, we evaluated the performance of frugivorous fish (pacu and piranha; Serrasalmidae) dentitions when puncturing fruits and seeds and compared specialist frugivorous species to facultative frugivorous and non-herbivorous relatives. We also explored how fruit characteristics affect puncture performance and how the indentation of fruit differs mechanically from harder foods like nuts. Based on expectations from studies on frugivorous bats and primates, we expected that frugivore dentitions would exhibit low force and then high work when engaging fruit tissues. Aligning with our expectation, the specialized frugivorous pacu, <i>Colossoma</i>, had dental performance that matched this low force, high work prediction. We also document how frugivory in omnivorous piranhas may be driven more by seed predation than a focus on softer fruit tissues like pulp. Overall, this study demonstrates remarkable similarity in the form and function of frugivore dentitions across vertebrates.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 225","pages":"20240725"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12001085/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144016535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Hormesis and hydra effects revealed by intraspecific overcompensation models and dose-response curves. 种内过度补偿模型和剂量-反应曲线揭示的激效效应和水螅效应。
IF 3.7 2区 综合性期刊
Journal of The Royal Society Interface Pub Date : 2025-04-01 Epub Date: 2025-04-30 DOI: 10.1098/rsif.2025.0169
Sanyi Tang, Xin Feng, Dingding Yan, Juhua Liang, Lili Liu, Yanni Xiao, Biao Tang, Robert Alexander Cheke
{"title":"Hormesis and hydra effects revealed by intraspecific overcompensation models and dose-response curves.","authors":"Sanyi Tang, Xin Feng, Dingding Yan, Juhua Liang, Lili Liu, Yanni Xiao, Biao Tang, Robert Alexander Cheke","doi":"10.1098/rsif.2025.0169","DOIUrl":"https://doi.org/10.1098/rsif.2025.0169","url":null,"abstract":"<p><p>Overcompensation, defined as recovery beyond a baseline state, arises from both hormetic and hydra effects, illustrating adaptive responses to stress. The overcompensation framework of a re-evaluated fishery resource management model was examined through nonlinear growth patterns based on logistic or Ricker models, emphasizing population size over carrying capacity. This complete overcompensation model's threshold conditions reveal an interplay between hydra and hormetic effects. Also, when dividing a population into distinct subgroups, such as susceptible and infected classes in disease transmission, the population size can be modelled as a function of the basic reproduction number ([Formula: see text]). A threshold condition of [Formula: see text] allows examination of how disease infectivity triggers hydra or hormetic effects and, also, development of a partial overcompensation model that elucidates the internal mechanisms of overcompensation. Analysis of data from 24 groups of U-shaped or inverted U-shaped dose-response curves validated the dose-response curves. The simplified modelling approach developed revealed the mechanisms underlying hydra and hormetic effects, highlighting the importance of strong growth or regenerative capabilities, overcompensatory responses (strong nonlinearity), mild external stimuli (weak stressors) and the baseline population size. Our new analytical techniques for overcompensation modelling can be adapted to many fields, including tumour treatment and toxicology.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 225","pages":"20250169"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12041897/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144029658","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Indirect reciprocity in the public goods game with collective reputations. 具有集体声誉的公共物品博弈中的间接互惠。
IF 3.7 2区 综合性期刊
Journal of The Royal Society Interface Pub Date : 2025-04-01 Epub Date: 2025-04-02 DOI: 10.1098/rsif.2024.0827
Ming Wei, Xin Wang, Longzhao Liu, Hongwei Zheng, Yishen Jiang, Yajing Hao, Zhiming Zheng, Feng Fu, Shaoting Tang
{"title":"Indirect reciprocity in the public goods game with collective reputations.","authors":"Ming Wei, Xin Wang, Longzhao Liu, Hongwei Zheng, Yishen Jiang, Yajing Hao, Zhiming Zheng, Feng Fu, Shaoting Tang","doi":"10.1098/rsif.2024.0827","DOIUrl":"10.1098/rsif.2024.0827","url":null,"abstract":"<p><p>Indirect reciprocity unveils how social cooperation is founded upon moral systems. Within the frame of dyadic games based on individual reputations, the 'leading-eight' strategies distinguish themselves in promoting and sustaining cooperation. However, in real-world societies, there are widespread interactions at the group level, where individuals need to make a singular action choice when facing multiple individuals with different reputations. Here, through introducing the assessment of collective reputations, we develop a framework that embeds group-level reputation structure into public goods games to study the evolution of group-level indirect reciprocity. We show that changing the criteria of group assessment destabilizes the reputation dynamics of leading-eight strategies. In a particular range of social assessment criteria, all leading-eight strategies can break the social dilemma in public goods games and sustain cooperation. Specifically, there exists an optimal, moderately set assessment criterion that is most conducive to promoting cooperation. Moreover, in the evolution of assessment criteria, the preference of the leading-eight strategies for social strictness is inversely correlated with the payoff level. Our work reveals the impact of social strictness on prosocial behaviour, highlighting the importance of group-level interactions in the analysis of evolutionary games and complex social dynamics.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 225","pages":"20240827"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764426","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Do early warning signals of tipping points lead to better decisions? 临界点的早期预警信号是否会带来更好的决策?
IF 3.7 2区 综合性期刊
Journal of The Royal Society Interface Pub Date : 2025-04-01 Epub Date: 2025-04-09 DOI: 10.1098/rsif.2024.0864
Florian Diekert, Daniel Heyen, Frikk Nesje, Soheil Shayegh
{"title":"Do early warning signals of tipping points lead to better decisions?","authors":"Florian Diekert, Daniel Heyen, Frikk Nesje, Soheil Shayegh","doi":"10.1098/rsif.2024.0864","DOIUrl":"10.1098/rsif.2024.0864","url":null,"abstract":"<p><p>Abrupt changes in some complex socio-ecological systems can be anticipated by observing their behaviour under increasing stress before they cross a tipping point. Despite notable progress in identifying statistical indicators that can provide early warning signals (EWS) of tipping points, they have yet to find direct application in management. Here, we develop a theoretical model of an early warning system (EWSys) that integrates EWS information into a simple decision-making process. This model consists of a tipping indicator, whose value increases as the system approaches the tipping point, and a trigger value, beyond which a binary EWS is sent. We demonstrate that although EWSys can help balance the risk of tipping by providing information to update the belief about the location of the tipping point, it may also result in more risky behaviour in the case that no EWS is received. This leads to a tension between better information about the location of the tipping point and increased risk of crossing it. Our framework complements the emergence of resilience indicators of complex human-natural systems by providing a better understanding of how, when and why they can be used to improve decision making.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 225","pages":"20240864"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11978447/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Optimizing energetics of lateral undulatory locomotion: unveiling morphological adaptations in different environments. 优化横向波动运动的能量学:揭示不同环境下的形态适应。
IF 3.7 2区 综合性期刊
Journal of The Royal Society Interface Pub Date : 2025-04-01 Epub Date: 2025-04-23 DOI: 10.1098/rsif.2024.0440
Basit Yaqoob, Maurizio Porfiri, Nicola M Pugno
{"title":"Optimizing energetics of lateral undulatory locomotion: unveiling morphological adaptations in different environments.","authors":"Basit Yaqoob, Maurizio Porfiri, Nicola M Pugno","doi":"10.1098/rsif.2024.0440","DOIUrl":"https://doi.org/10.1098/rsif.2024.0440","url":null,"abstract":"<p><p>Ongoing efforts seek to unravel theories that can make simple, quantitative and reasonably accurate predictions of the morphological adaptive changes that arise with the size variation. Yet, relatively scant attention has been directed towards lateral undulatory locomotion. In the current study, we explore: (i) the constraints imposed by the variation of length and mass in viscous and dry friction environments on the cost of transport (COT) of lateral undulatory locomotion and (ii) the role of the body, environment and input oscillations in such an intricate interplay. In a dry friction environment, minimum COT correlates with stiffer and longer bodies, higher frictional anisotropy and angular amplitudes greater than approximately 10<sup>o</sup>. Conversely, a viscous environment favours flexible long bodies, higher frictional anisotropy and angular amplitudes lower than approximately 30<sup>o</sup>. In both environments, optimizing mass and maintaining low angular frequencies minimizes COT. Our conclusions are applicable only in the low-Reynolds-number regime, and it is essential to consider the interdependence of parameters when applying the generalized results. Our findings highlight musculoskeletal and biomechanical adaptations that animals may use to mitigate the consequences of size variation and to meet the energetic demands of lateral undulatory locomotion. These insights enhance foundational biomechanics knowledge while offering practical applications in robotics and ecology.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 225","pages":"20240440"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12014235/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144006228","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Designing biological network motif-based controllers by reverse engineering Hill function-type models from linear models. 从线性模型逆向工程希尔函数模型设计基于生物网络基元的控制器。
IF 3.7 2区 综合性期刊
Journal of The Royal Society Interface Pub Date : 2025-04-01 Epub Date: 2025-04-23 DOI: 10.1098/rsif.2024.0811
Matthew Spurgeon, Tea Clark, Thales Rossi Spartalis, Alexander Darlington, Xun Tang, Mathias Foo
{"title":"Designing biological network motif-based controllers by reverse engineering Hill function-type models from linear models.","authors":"Matthew Spurgeon, Tea Clark, Thales Rossi Spartalis, Alexander Darlington, Xun Tang, Mathias Foo","doi":"10.1098/rsif.2024.0811","DOIUrl":"https://doi.org/10.1098/rsif.2024.0811","url":null,"abstract":"<p><p>Perfect adaptation, the ability to regulate and maintain gene expression to its desired value despite disturbances, is important in the development of organisms. Building biological controllers to endow engineered biological systems with such perfect adaptation capability is a key goal in synthetic biology. Model-guided exploration of such synthetic circuits has been effective in designing such systems. However, theoretical analysis to guarantee controller properties with nonlinear models, such as Hill functions, remains challenging, while use of linear models fails to capture the inherent nonlinear dynamics of gene expression systems. Here, we propose a reverse engineering approach to infer the kinetic parameters for nonlinear Hill function-type models from analysis of linear models and apply our method to design controllers, which achieve perfect adaptation. Focusing on three biological network motif-based controllers, we demonstrate via simulation the efficacy of the proposed approach in combining linear system theories with nonlinear modelling, to design multiple gene circuits that could deliver perfect adaptation. Given the ubiquitous use of Hill functions in describing the dynamics of biological regulatory networks, we anticipate the proposed reverse engineering approach to benefit a wide range of systems and synthetic biology applications.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 225","pages":"20240811"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12014233/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144008702","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Reconstructing illusory camouflage patterns on moth wings using computer vision. 利用计算机视觉重建飞蛾翅膀上的虚幻伪装图案。
IF 3.7 2区 综合性期刊
Journal of The Royal Society Interface Pub Date : 2025-04-01 Epub Date: 2025-04-30 DOI: 10.1098/rsif.2024.0757
Laurent Valentin Jospin, James Wang Porter, Farid Boussaid, Mohammed Bennamoun, Jennifer L Kelley
{"title":"Reconstructing illusory camouflage patterns on moth wings using computer vision.","authors":"Laurent Valentin Jospin, James Wang Porter, Farid Boussaid, Mohammed Bennamoun, Jennifer L Kelley","doi":"10.1098/rsif.2024.0757","DOIUrl":"https://doi.org/10.1098/rsif.2024.0757","url":null,"abstract":"<p><p>Monocular depth cues, such as shading, are fundamental for resolving three-dimensional information, such as an object's shape. Animal colour patterns may potentially exploit this mechanism of depth perception, generating false illusions for functions such as camouflage. Reconstructing the potential percept produced by false depth cues is challenging, especially for non-human, animal viewers. Here, we provide a novel step towards solving this problem, taking advantage of state-of-the-art computer vision algorithms typically used for three-dimensional scene reconstruction. We used two approaches for single-image monocular depth estimation: intrinsic image decomposition and deep learning. We first examined how these models performed using images of natural three-dimensional surfaces that moth wing patterns may mimic. We then applied these models to the wing patterns of six species of moth (Lepidoptera) with varying amounts of potential depth information. For one species, we then performed a multi-view reconstruction of the wing pattern to reveal the true (flat) wing shape. Intrinsic image decomposition, which is based on Retinex theory, was sensitive to both real depth cues and high contrast patterns, while the deep-learning models only responded to moths with strong pictorial depth cues. Both approaches reveal how the interpretation of visual cues depends not only on the information available, but also on experience with the natural world.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 225","pages":"20240757"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12042220/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144028812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Eco-evolutionary dynamics of pathogen immune-escape: deriving a population-level phylodynamic curve. 病原体免疫逃逸的生态进化动力学:推导种群水平的系统动力学曲线。
IF 3.7 2区 综合性期刊
Journal of The Royal Society Interface Pub Date : 2025-04-01 Epub Date: 2025-04-02 DOI: 10.1098/rsif.2024.0675
Bjarke Frost Nielsen, Chadi M Saad-Roy, C Jessica E Metcalf, Cécile Viboud, Bryan T Grenfell
{"title":"Eco-evolutionary dynamics of pathogen immune-escape: deriving a population-level phylodynamic curve.","authors":"Bjarke Frost Nielsen, Chadi M Saad-Roy, C Jessica E Metcalf, Cécile Viboud, Bryan T Grenfell","doi":"10.1098/rsif.2024.0675","DOIUrl":"10.1098/rsif.2024.0675","url":null,"abstract":"<p><p>The phylodynamic curve (Grenfell <i>et al</i>. 2004 <i>Science</i> <b>303</b>, 327-332 (doi:10.1126/science.1090727)) conceptualizes how immunity shapes the rate of viral adaptation in a non-monotonic fashion, through its opposing effects on viral abundance and the strength of selection. However, concrete and quantitative model realizations of this influential concept are rare. Here, we present an analytic, stochastic framework in which a population-scale phylodynamic curve emerges dynamically, allowing us to address questions regarding the risk and timing of the emergence of viral immune escape variants. We explore how pathogen- and population-specific parameters such as strength of immunity, transmissibility, seasonality and antigenic constraints affect the emergence risk. For pathogens exhibiting pronounced seasonality, we find that the timing of likely immune-escape variant emergence depends on the level of case importation between regions. Motivated by the COVID-19 pandemic, we probe the likely effects of non-pharmaceutical interventions (NPIs), and the lifting thereof, on the risk of viral escape variant emergence. Looking ahead, the framework has the potential to become a useful tool for probing how natural immunity, as well as choices in vaccine design and distribution and the implementation of NPIs, affect the evolution of common viral pathogens.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 225","pages":"20240675"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11963905/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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