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within-host evolution

Elsa Rousseau, Benoît Moury, Ludovic Mailleret, Rachid Senoussi, Alain Palloix, Vincent Simon, Sophie Valière, Frédéric Grognard, Frédéric Fabre
By combining high-throughput sequencing (HTS) with experimental evolution, we can observe the within-host dynamics of pathogen variants of biomedical or ecological interest. We studied the evolutionary dynamics of five variants of Potato virus Y (PVY) in 15 doubled-haploid lines of pepper. All plants were inoculated with the same mixture of virus variants and, variant frequencies were determined by HTS in eight plants of each pepper line, at each of six sampling dates. We developed a method for estimating the intensities of selection and genetic drift in a multi-allelic Wright-Fisher model, applicable whether these forces are strong or weak, and in the absence of neutral markers...
November 20, 2017: PLoS Pathogens
Tom Hill, Robert L Unckless
Viruses coevolve with their hosts to overcome host resistance and gain the upper hand in the evolutionary arms race. Drosophila innubila nudivirus (DiNV) is a double stranded DNA virus, closely related to Oryctes rhinoceros nudivirus (OrNV) and Kallithea virus. DiNV is the first DNA virus found to naturally infect Drosophila and therefore has the potential to be developed as a model for DNA virus immune defense and host/virus coevolution within its well-studied host system. Here we sequence and annotate the genome of DiNV and identify signatures of adaptation, revealing clues for genes involved in host-parasite coevolution...
November 16, 2017: Infection, Genetics and Evolution
Yong Zhang, Li-Jun Ma
Fusarium oxysporum is a large species complex of both plant and human pathogens that attack a diverse array of species in a host-specific manner. Comparative genomic studies have revealed that the host-specific pathogenicity of the F. oxysporum species complex (FOSC) was determined by distinct sets of supernumerary (SP) chromosomes. In contrast to common vertical transfer, where genetic materials are transmitted via cell division, SP chromosomes can be transmitted horizontally between phylogenetic lineages, explaining the polyphyletic nature of the host-specific pathogenicity of the FOSC...
2017: Advances in Genetics
Jūlija Pečerska, James Wood, Mark M Tanaka, Tanja Stadler
This chapter reviews the use of mathematical and computational models to facilitate understanding of the epidemiology and evolution of Mycobacterium tuberculosis. First, we introduce general epidemiological models, and describe their use with respect to epidemiological dynamics of a single strain and of multiple strains of M. tuberculosis. In particular, we discuss multi-strain models that include drug sensitivity and drug resistance. Second, we describe models for the evolution of M. tuberculosis within and between hosts, and how the resulting diversity of strains can be assessed by considering the evolutionary relationships among different strains...
2017: Advances in Experimental Medicine and Biology
Daniela Brites, Sebastien Gagneux
The Mycobacterium tuberculosis Complex (MTBC) consists of a clonal group of several mycobacterial lineages pathogenic to a range of different mammalian hosts. In this chapter, we discuss the origins and the evolutionary forces shaping the genomic diversity of the human-adapted MTBC. Advances in whole-genome sequencing have brought invaluable insights into the macro-evolution of the MTBC, and the biogeographical distribution of the different MTBC lineages, the phylogenetic relationships between these lineages...
2017: Advances in Experimental Medicine and Biology
H Miao, J Lorenzana, G Seibold, Y Y Peng, A Amorese, F Yakhou-Harris, K Kummer, N B Brookes, R M Konik, V Thampy, G D Gu, G Ghiringhelli, L Braicovich, M P M Dean
Although all superconducting cuprates display charge-ordering tendencies, their low-temperature properties are distinct, impeding efforts to understand the phenomena within a single conceptual framework. While some systems exhibit stripes of charge and spin, with a locked periodicity, others host charge density waves (CDWs) without any obviously related spin order. Here we use resonant inelastic X-ray scattering to follow the evolution of charge correlations in the canonical stripe-ordered cuprate La1.875Ba0...
November 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
Mara Villa, Michael Lässig
Reassortment, which is the exchange of genome sequence between viruses co-infecting a host cell, plays an important role in the evolution of segmented viruses. In the human influenza virus, reassortment happens most frequently between co-existing variants within the same lineage. This process breaks genetic linkage and fitness correlations between viral genome segments, but the resulting net effect on viral fitness has remained unclear. In this paper, we determine rate and average selective effect of reassortment processes in the human influenza lineage A/H3N2...
November 2017: PLoS Pathogens
Mang Shi, Yong-Zhen Zhang, Edward C Holmes
Metagenomics is transforming the study of virus evolution, allowing the full assemblage of virus genomes within a host sample to be determined rapidly and cheaply. The genomic analysis of complete transcriptomes, so-called meta-transcriptomics, is providing a particularly rich source of data on the global diversity of RNA viruses and their evolutionary history. Herein we review some of the insights that meta-transcriptomics has provided on the fundamental patterns and processes of virus evolution, with a focus on the recent discovery of a multitude of novel invertebrate viruses...
October 27, 2017: Virus Research
John T McCrone, Adam S Lauring
Ultimately, viral evolution is a consequence of mutations that arise within and spread between infected hosts. The transmission bottleneck determines how much of the viral diversity generated in one host passes to another during transmission. It therefore plays a vital role in linking within-host processes to larger evolutionary trends. Although many studies suggest that transmission severely restricts the amount of genetic diversity that passes between individuals, there are important exceptions to this rule...
November 3, 2017: Current Opinion in Virology
Shelbi L Russell, Colleen M Cavanaugh
Even the simplest microbial-eukaryotic mutualisms are comprised of entire populations of symbionts at the level of the host individual. Early work suggested that these intrahost populations maintain low genetic diversity as a result of transmission bottlenecks or to avoid competition between symbiont genotypes. However, the amount of genetic diversity among symbionts within a single host remains largely unexplored. To address this, we investigated the chemosynthetic symbiosis between the bivalve Solemya velum and its intracellular bacterial symbionts, which exhibits evidence of both vertical and horizontal transmission...
November 1, 2017: Molecular Biology and Evolution
Luis Andrés Gimeno-Feliu, Amaia Calderón-Larrañaga, Esperanza Díaz, Clara Laguna-Berna, Beatriz Poblador-Plou, Carlos Coscollar, Alexandra Prados-Torres
Aim: Multimorbidity is a growing phenomenon in primary care, and knowledge of the influence of social determinants on its evolution is vital. The aim of this study was to understand the relationship between multimorbidity and immigration, taking into account length of residence in the host country and area of origin of the immigrant population. Methods: Cross-sectional retrospective study of all adult patients registered within the public health service of Aragon, Spain (N = 1092279; 144238 were foreign-born), based on data from the EpiChron Cohort...
November 16, 2017: Family Practice
Ian S Barton, Clay Fuqua, Thomas G Platt
Many important pathogens maintain significant populations in highly disparate disease and non-disease environments. The consequences of this environmental heterogeneity in shaping the ecological and evolutionary dynamics of these facultative pathogens are incompletely understood. Agrobacterium tumefaciens, the causative agent for crown gall disease of plants has proven a productive model for many aspects of interactions between pathogens and their hosts and with other microbes. In this review, we highlight how this past work provides valuable context for the use of this system to examine how heterogeneity and transitions between disease and non-disease environments influence the ecology and evolution of facultative pathogens...
November 3, 2017: Environmental Microbiology
Jackie Lighten, Alexander S T Papadopulos, Ryan S Mohammed, Ben J Ward, Ian G Paterson, Lyndsey Baillie, Ian R Bradbury, Andrew P Hendry, Paul Bentzen, Cock van Oosterhout
Red Queen host-parasite co-evolution can drive adaptations of immune genes by positive selection that erodes genetic variation (Red Queen arms race) or results in a balanced polymorphism (Red Queen dynamics) and long-term preservation of genetic variation (trans-species polymorphism). These two Red Queen processes are opposite extremes of the co-evolutionary spectrum. Here we show that both Red Queen processes can operate simultaneously by analysing the major histocompatibility complex (MHC) in guppies (Poecilia reticulata and P...
November 3, 2017: Nature Communications
Samuel J Bloomfield, Anne C Midwinter, Patrick J Biggs, Nigel P French, Jonathan C Marshall, David T S Hayman, Philip E Carter, Craig Thornley, Rudyard Yap, Jackie Benschop
Background: Campylobacteriosis is inflammation of the gastrointestinal tract as a result of Campylobacter infection. Most campylobacteriosis cases are acute and self-limiting, with Campylobacter excretion ceasing a few weeks after symptoms cease. We identified a patient who had tested faecally-positive for Campylobacter jejuni (ST45), intermittently for ten years. Methods: Sixteen Campylobacter isolates were collected from the patient from 2006-2016. The isolates' genomes were sequenced to determine their relatedness, and their antimicrobial susceptibility patterns and motility were measured to determine the effects of antibiotic therapy and long-term excretion on the Campylobacter...
November 1, 2017: Journal of Infectious Diseases
Inês Fontes, Hanna Hartikainen, Chris Williams, Beth Okamura
BACKGROUND: Persistent covert infections of the myxozoan, Tetracapsuloides bryosalmonae, in primary invertebrate hosts (the freshwater bryozoan, Fredericella sultana) have been proposed to represent a reservoir for proliferative kidney disease in secondary fish hosts. However, we have limited understanding of how covert infections persist and vary in bryozoan populations over time and space and how they may impact these populations. In addition, previous studies have likely underestimated covert infection prevalence...
November 2, 2017: Parasites & Vectors
Eric R Weiss, Susanna L Lamers, Jennifer L Henderson, Alexandre Melnikov, Mohan Somasundaran, Manuel Garber, Liisa Selin, Chad Nusbaum, Katherine Luzuriaga
Over 90% of the world's population is persistently infected with Epstein-Barr virus. While EBV does not cause disease in most individuals, it is the common cause of acute infectious mononucleosis (AIM), has been associated with several cancers and autoimmune diseases, highlighting a need for a preventive vaccine. At present, very few primary, circulating EBV genomes have been sequenced directly from infected individuals. While low levels of diversity and viral evolution rates have been predicted for dsDNA viruses, recent studies have demonstrated appreciable diversity in common dsDNA pathogens (e...
November 1, 2017: Journal of Virology
Jie-Yin Chen, Chun Liu, Yue-Jing Gui, Kai-Wei Si, Dan-Dan Zhang, Jie Wang, Dylan P G Short, Jin-Qun Huang, Nan-Yang Li, Yong Liang, Wen-Qi Zhang, Lin Yang, Xue-Feng Ma, Ting-Gang Li, Lei Zhou, Bao-Li Wang, Yu-Ming Bao, Krishna V Subbarao, Geng-Yun Zhang, Xiao-Feng Dai
Verticillium dahliae isolates are most virulent on the host from which they were originally isolated. Mechanisms underlying these dominant host adaptations are currently unknown. We sequenced the genome of V. dahliae Vd991, which is highly virulent on its original host, cotton, and performed comparisons with the reference genomes of JR2 (from tomato) and VdLs.17 (from lettuce). Pathogenicity-related factor prediction, orthology and multigene family classification, transcriptome analyses, phylogenetic analyses, and pathogenicity experiments were performed...
October 30, 2017: New Phytologist
Yan-Hong Du, Yuan-Jun Zhao, Fa-Hui Tang
We analyzed the secondary structure of the small subunit (SSU) rRNA genes of Mobilida (Ciliophora, Peritrichia) and found that the secondary structures of some regions within the SSU-rRNA gene are distinct between the families Trichodinidae and Urceolariidae. Therefore, some of these important regions including H10, H11, H17, H47, H29, H30, H37, E10-1, H45-H46, and V4 (E23-4, E23-7) could be used as the barcodes for classification of these two families. In contrast, V4 (E23-1, E23-2) belongs to a hypervariable region and is not a good barcode at the genus level because of its great inter-specific variation...
October 26, 2017: Current Microbiology
Riccardo Baroncelli, Pedro Talhinhas, Flora Pensec, Serenella A Sukno, Gaetan Le Floch, Michael R Thon
Colletotrichum spp. infect a wide diversity of hosts, causing plant diseases on many economically important crops worldwide. The genus contains approximately 189 species organized into at least 11 major phylogenetic lineages, also known as species complexes. The Colletotrichum acutatum species complex is a diverse yet relatively closely related group of plant pathogenic fungi within this genus. Within the species complex we find a wide diversity of important traits such as host range and host preference, mode of reproduction and differences in the strategy used to infect their hosts...
2017: Frontiers in Microbiology
Jemma L Geoghegan, Edward C Holmes
The study of virus disease emergence, whether it can be predicted and how it might be prevented, has become a major research topic in biomedicine. Here we show that efforts to predict disease emergence commonly conflate fundamentally different evolutionary and epidemiological time scales, and are likely to fail because of the enormous number of unsampled viruses that could conceivably emerge in humans. Although we know much about the patterns and processes of virus evolution on evolutionary time scales as depicted in family-scale phylogenetic trees, these data have little predictive power to reveal the short-term microevolutionary processes that underpin cross-species transmission and emergence...
October 2017: Open Biology
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