Unifying the epidemiological and evolutionary dynamics of pathogens.
Bryan T. Grenfell,Oliver G. Pybus,Julia R. Gog,James L. N. Wood,Janet M. Daly,J. A. Mumford,Edward C. Holmes +6 more
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TLDR
A phylodynamic framework for the dissection of dynamic forces that determine the diversity of epidemiological and phylogenetic patterns observed in RNA viruses of vertebrates is introduced.Abstract:
A key priority for infectious disease research is to clarify how pathogen genetic variation, modulated by host immunity, transmission bottlenecks, and epidemic dynamics, determines the wide variety of pathogen phylogenies observed at scales that range from individual host to population. We call the melding of immunodynamics, epidemiology, and evolutionary biology required to achieve this synthesis pathogen “phylodynamics.” We introduce a phylodynamic framework for the dissection of dynamic forces that determine the diversity of epidemiological and phylogenetic patterns observed in RNA viruses of vertebrates. A central pillar of this model is the Evolutionary Infectivity Profile, which captures the relationship between immune selection and pathogen transmission.read more
Citations
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Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10
TL;DR: The BEAST software package unifies molecular phylogenetic reconstruction with complex discrete and continuous trait evolution, divergence-time dating, and coalescent demographic models in an efficient statistical inference engine using Markov chain Monte Carlo integration.
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Mapping the Antigenic and Genetic Evolution of Influenza Virus
Derek J. Smith,Derek J. Smith,Alan Lapedes,Jan C. de Jong,Theo M. Bestebroer,Guus F. Rimmelzwaan,Albert D. M. E. Osterhaus,Ron A. M. Fouchier +7 more
TL;DR: The antigenic evolution of influenza A (H3N2) virus was quantified and visualized from its introduction into humans in 1968 to 2003 and offers a route to predicting the relative success of emerging strains.
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Genetic Consequences of Range Expansions
TL;DR: Interestingly, most of these patterns had been previously attributed to distinct selective processes, showing that taking into account the dynamic nature of a species range can lead to a paradigm shift in the authors' perception of evolutionary processes.
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The neuropathogenesis of AIDS
TL;DR: The studies that are being carried out to determine the respective contributions of infection, and monocyte and macrophage activation, to disease progression are discussed.
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The co-evolution of host cationic antimicrobial peptides and microbial resistance
Andreas Peschel,Hans-Georg Sahl +1 more
TL;DR: It is proposed that CAMPs and CAMP-resistance mechanisms have co-evolved, leading to a transient host–pathogen balance that has shaped the existing CAMP repertoire.
References
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Book
Infectious Diseases of Humans: Dynamics and Control
Roy M. Anderson,Robert M. May +1 more
TL;DR: This book discusses the biology of host-microparasite associations, dynamics of acquired immunity heterogeneity within the human community indirectly transmitted helminths, and the ecology and genetics of hosts and parasites.
Journal ArticleDOI
HIV-1 Dynamics in Vivo: Virion Clearance Rate, Infected Cell Life-Span, and Viral Generation Time
TL;DR: A new mathematical model was used to analyze a detailed set of human immunodeficiency virus-type 1 (HIV-1) viral load data collected from five infected individuals after the administration of a potent inhibitor of HIV-1 protease, providing not only a kinetic picture ofAIDS pathogenesis, but also theoretical principles to guide the development of treatment strategies.
Journal ArticleDOI
Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection
Raj Shankarappa,Joseph B. Margolick,Stephen J. Gange,Allen G. Rodrigo,David Upchurch,Homayoon Farzadegan,Phalguni Gupta,Charles R. Rinaldo,Gerald H. Learn,Xi C. He,Xiao Li Huang,James I. Mullins +11 more
TL;DR: In this article, the authors studied the evolution of the C2-V5 region of the HIV-1 env gene and of T-cell subsets in nine men with a moderate or slow rate of disease progression.
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The outcome of acute hepatitis C predicted by the evolution of the viral quasispecies.
Patrizia Farci,Atsushi Shimoda,Alessandra Coiana,Giacomo Diaz,Giovanna Peddis,Jacqueline C. Melpolder,Antonello Strazzera,David Y. Chien,Santiago J. Munoz,Angelo Balestrieri,Robert H. Purcell,Harvey J. Alter +11 more
TL;DR: Sequences within the HCV E1 and E2 envelope genes were analyzed during the acute phase of hepatitis C in 12 patients with different clinical outcomes to indicate that the evolutionary dynamics of theHCV quasispecies during the emergency phase predict whether the infection will resolve or become chronic.