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Within host evolution

J van Beek, M de Graaf, S L Smits, C M E Schapendonk, G M G M Verjans, H Vennema, A A van der Eijk, M V T Phan, M L Cotten, M P G Koopmans
Background: The genus Norovirus comprises large genetic diversity and new GII.4 variants emerge every 2-3 years. It is unknown in which host these new variants originate. Here we study whether prolonged shedders within the immunocompromised population could be a reservoir for newly emerging strains. Methods: Faecal samples (n=65) from immunocompromised patients (n=16) were retrospectively selected. Isolated viral RNA was enriched by hybridization with a custom norovirus whole-genome RNA bait set and deep sequenced on the Illumina MiSeq platform...
September 27, 2017: Journal of Infectious Diseases
Bram Vrancken, Marc A Suchard, Philippe Lemey
Analyses of virus evolution in known transmission chains have the potential to elucidate the impact of transmission dynamics on the viral evolutionary rate and its difference within and between hosts. Lin et al. (2015, Journal of Virology, 89/7: 3512-22) recently investigated the evolutionary history of hepatitis B virus in a transmission chain and postulated that the 'colonization-adaptation-transmission' model can explain the differential impact of transmission on synonymous and non-synonymous substitution rates...
July 2017: Virus Evolution
Nieves Rodríguez-Cousiño, Pilar Gómez, Rosa Esteban
Yeasts within the Saccharomyces sensu stricto cluster can produce different killer toxins. Each toxin is encoded by a medium size (1.5-2.4 Kb) M dsRNA virus, maintained by a larger helper virus generally called L-A (4.6 Kb). Different types of L-A are found associated to specific Ms: L-A in K1 strains and L-A-2 in K2 strains. Here, we extend the analysis of L-A helper viruses to yeasts other than S. cerevisiae, namely S. paradoxus, S. uvarum and S. kudriavzevii. Our sequencing data from nine new L-A variants confirm the specific association of each toxin-producing M and its helper virus, suggesting co-evolution...
October 11, 2017: Toxins
Nicholas M Fountain-Jones, Meggan E Craft, W Chris Funk, Chris Kozakiewicz, Daryl Trumbo, Erin E Boydston, Lisa M Lyren, Kevin Crooks, Justin S Lee, Sue VandeWoude, Scott Carver
Urban expansion has widespread impacts on wildlife species globally, including the transmission and emergence of infectious diseases. However, there is almost no information about how urban landscapes shape transmission dynamics in wildlife. Using an innovative phylodynamic approach combining host and pathogen molecular data with landscape characteristics and host traits, we untangle the complex factors that drive transmission networks of Feline Immunodeficiency Virus (FIV) in bobcats (Lynx rufus). We found that the urban landscape played a significant role in shaping FIV transmission...
October 7, 2017: Molecular Ecology
Richard Moxon, Edo Kussell
Microbial pathogens and viruses can often maintain sufficient population diversity to evade a wide range of host immune responses. However, when populations experience bottlenecks, as occurs frequently during initiation of new infections, pathogens require specialized mechanisms to regenerate diversity. We address the evolution of such mechanisms, known as stochastic phenotype switches, which are prevalent in pathogenic bacteria. We analyze a model of pathogen diversification in a changing host environment that accounts for selective bottlenecks, wherein different phenotypes have distinct transmission probabilities between hosts...
October 5, 2017: Evolution; International Journal of Organic Evolution
Xue-Yan Zheng, Min Qiu, Wei-Jie Guan, Jin-Ming Li, Shao-Wei Chen, Ming-Ji Cheng, Shu-Ting Huo, Zhong Chen, Yi Wu, Li-Na Jiang, Qing Chen
Accumulating studies have shown that bats could harbor various important pathogenic viruses that could be transmitted to humans and other animals. Extensive metagenomic studies of different organs/tissues from bats have revealed a large number of novel or divergent viruses. To elucidate viral diversity and epidemiological and phylogenetic characteristics, six pooled fecal samples from bats were generated (based on bat species and geographic regions characteristic for virome analysis). These contained 500 fecal samples from six bat species, collected in four geographic regions...
October 5, 2017: Archives of Virology
Bo Zhang, Yanhua Zhai, Yang Liu, Zemao Gu
Two species of Myxobolus Bütschli, 1882 were found in yellow catfish Tachysurus fulvidraco (Richardson). A species of Myxobolus infecting the gills was morphologically identified as Myxobolus voremkhai (Akhmerov, 1960) and it was characterised here with additional morphological and molecular data. The other species of Myxobolus infecting the host's skin did not conform to any known myxosporean species. It is characterised by the presence of round, black or milky white plasmodia with black spots. Myxospores are pyriform in frontal view and lemon-shaped in lateral view, measuring 12...
September 27, 2017: Folia Parasitologica
Marie Cariou, Laurent Duret, Sylvain Charlat
The spread of maternally inherited microorganisms, such as Wolbachia bacteria, can induce indirect selective sweeps on host mitochondria, to which they are linked within the cytoplasm. The resulting reduction in effective population size might lead to smaller mitochondrial diversity and reduced efficiency of natural selection. While documented in several host species, it is currently unclear if such a scenario is common enough to globally impact the diversity and evolution of mitochondria in Wolbachia-infected lineages...
October 4, 2017: Journal of Evolutionary Biology
Jens Frickel, Loukas Theodosiou, Lutz Becks
Ecosystems are complex food webs in which multiple species interact and ecological and evolutionary processes continuously shape populations and communities. Previous studies on eco-evolutionary dynamics have shown that the presence of intraspecific diversity affects community structure and function, and that eco-evolutionary feedback dynamics can be an important driver for its maintenance. Within communities, feedbacks are, however, often indirect, and they can feed back over many generations. Here, we studied eco-evolutionary feedbacks in evolving communities over many generations and compared two-species systems (virus-host and prey-predator) with a more complex three-species system (virus-host-predator)...
October 2, 2017: Proceedings of the National Academy of Sciences of the United States of America
Nargesalsadat Dorratoltaj, Ryan Nikin-Beers, Stanca M Ciupe, Stephen G Eubank, Kaja M Abbas
OBJECTIVE: The objective of this study is to conduct a systematic review of multi-scale HIV immunoepidemiological models to improve our understanding of the synergistic impact between the HIV viral-immune dynamics at the individual level and HIV transmission dynamics at the population level. BACKGROUND: While within-host and between-host models of HIV dynamics have been well studied at a single scale, connecting the immunological and epidemiological scales through multi-scale models is an emerging method to infer the synergistic dynamics of HIV at the individual and population levels...
2017: PeerJ
Charissa de Bekker, Robin A Ohm, Harry C Evans, Andreas Brachmann, David P Hughes
Much can be gained from revealing the mechanisms fungal entomopathogens employ. Especially intriguing are fungal parasites that manipulate insect behavior because, presumably, they secrete a wealth of bioactive compounds. To gain more insight into their strategies, we compared the genomes of five ant-infecting Ophiocordyceps species from three species complexes. These species were collected across three continents, from five different ant species in which they induce different levels of manipulation. A considerable number of (small) secreted and pathogenicity-related proteins were only found in these ant-manipulating Ophiocordyceps species, and not in other ascomycetes...
October 2, 2017: Scientific Reports
Sanford D Eigenbrode, Nilsa Bosque-Pérez, Thomas S Davis
The transmission of insect-borne plant pathogens, including viruses, bacteria, phytoplasmas, and fungi depends upon the abundance and behavior of their vectors. These pathogens should therefore be selected to influence their vectors to enhance their transmission, either indirectly, through the infected host plant, or directly, after acquisition of the pathogen by the vector. Accumulating evidence provides partial support for the occurrence of vector manipulation by plant pathogens, especially for plant viruses, for which a theoretical framework can explain patterns in the specific effects on vector behavior and performance depending on their modes of transmission...
October 2, 2017: Annual Review of Entomology
Ignacio M Durante, Pablo E La Spina, Santiago J Carmona, Fernán Agüero, Carlos A Buscaglia
BACKGROUND: The Trypanosoma cruzi genome bears a huge family of genes and pseudogenes coding for Mucin-Associated Surface Proteins (MASPs). MASP molecules display a 'mosaic' structure, with highly conserved flanking regions and a strikingly variable central and mature domain made up of different combinations of a large repertoire of short sequence motifs. MASP molecules are highly expressed in mammal-dwelling stages of T. cruzi and may be involved in parasite-host interactions and/or in diverting the immune response...
September 2017: PLoS Neglected Tropical Diseases
Timothy P Driscoll, Victoria I Verhoeve, Mark L Guillotte, Stephanie S Lehman, Sherri A Rennoll, Magda Beier-Sexton, M Sayeedur Rahman, Abdu F Azad, Joseph J Gillespie
Reductive genome evolution has purged many metabolic pathways from obligate intracellular Rickettsia (Alphaproteobacteria; Rickettsiaceae). While some aspects of host-dependent rickettsial metabolism have been characterized, the array of host-acquired metabolites and their cognate transporters remains unknown. This dearth of information has thwarted efforts to obtain an axenic Rickettsia culture, a major impediment to conventional genetic approaches. Using phylogenomics and computational pathway analysis, we reconstructed the Rickettsia metabolic and transport network, identifying 51 host-acquired metabolites (only 21 previously characterized) needed to compensate for degraded biosynthesis pathways...
September 26, 2017: MBio
Catriona P Harkins, Kerry A Pettigrew, Katarina Oravcová, June Gardner, R M Ross Hearn, Debbie Rice, Alison E Mather, Julian Parkhill, Sara J Brown, Charlotte M Proby, Matthew T G Holden
Staphylococcus aureus is an opportunistic pathogen and variable component of the human microbiota. In atopic eczema (AE) a characteristic of the disease is colonization by S. aureus, with exacerbations associated with an increased bacterial burden of the organism. Despite this, the origins and genetic diversity of S. aureus colonizing individual patients during AE disease flares is poorly understood. To examine the micro-evolution of S. aureus colonization we have deep-sequenced S. aureus populations from nine children with moderate to severe AE, and 18 non-atopic children asymptomatically carrying S...
September 23, 2017: Journal of Investigative Dermatology
J Michael Conlon, Laure Guilhaudis, Jérôme Leprince, Laurent Coquet, Maria Luisa Mangoni, Samir Attoub, Thierry Jouenne, Jay D King
The Mexican burrowing toad Rhinophrynus dorsalis is the sole extant representative of the Rhinophrynidae. United in the superfamily Pipoidea, the Rhinophrynidae is considered to be the sister-group to the extant Pipidae which comprises Hymenochirus, Pipa, Pseudhymenochirus and Xenopus. Cationic, α-helical host-defense peptides of the type found in Hymenochirus, Pseudhymenochirus, and Xenopus species (hymenochirins, pseudhymenochirins, magainins, and peptides related to PGLa, XPF, and CPF) were not detected in norepinephrine-stimulated skin secretions of R...
September 23, 2017: Peptides
Mario López-Pérez, Jose M Haro-Moreno, Rafael Gonzalez-Serrano, Marcos Parras-Moltó, Francisco Rodriguez-Valera
Marine viruses play a critical role not only in the global geochemical cycles but also in the biology and evolution of their hosts. Despite their importance, viral diversity remains underexplored mostly due to sampling and cultivation challenges. Direct sequencing approaches such as viromics has provided new insights into the marine viral world. As a complementary approach, we analysed 24 microbial metagenomes (>0.2 μm size range) obtained from six sites in the Mediterranean Sea that vary by depth, season and filter used to retrieve the fraction...
September 2017: PLoS Genetics
Nariman Shahhosseini, Renke Lühken, Hanna Jöst, Stephanie Jansen, Jessica Börstler, Toni Rieger, Andreas Krüger, Anges Yadouleton, Renata de Mendonça Campos, Claudio Cesar Cirne-Santos, Davis Fernandes Ferreira, Rolf Garms, Norbert Becker, Egbert Tannich, Daniel Cadar, Jonas Schmidt-Chanasit
Thanks to recent advances in random amplification technologies, metagenomic surveillance expanded the number of novel, often unclassified viruses within the family Rhabdoviridae. Using a vector-enabled metagenomic (VEM) tool, we identified a novel rhabdovirus in Aedes cantans mosquitoes collected from Germany provisionally named Ohlsdorf virus (OHSDV). The OHSDV genome encodes the canonical rhabdovirus structural proteins (N, P, M, G and L) with alternative ORF in the P gene. Sequence analysis indicated that OHSDV exhibits a similar genome organization and characteristics compared to other mosquito-associated rhabdoviruses (Riverside virus, Tongilchon virus and North Creek virus)...
September 21, 2017: Infection, Genetics and Evolution
Esa-Pekka Kumpula, Isa Pires, Devaki Lasiwa, Henni Piirainen, Ulrich Bergmann, Juha Vahokoski, Inari Kursula
Filamentous actin is critical for apicomplexan motility and host cell invasion. Yet, parasite actin filaments are short and unstable. Their kinetic characterization has been hampered by the lack of robust quantitative methods. Using a modified labeling method, we carried out thorough biochemical characterization of malaria parasite actin. In contrast to the isodesmic polymerization mechanism suggested for Toxoplasma gondii actin, Plasmodium falciparum actin I polymerizes via the classical nucleation-elongation pathway, with kinetics similar to canonical actins...
September 22, 2017: Scientific Reports
Carlos A Loncoman, Carol A Hartley, Mauricio J C Coppo, Paola K Vaz, Andrés Diaz-Méndez, Glenn F Browning, Maricarmen García, Stephen Spatz, Joanne M Devlin
Recombination is a feature of many alphaherpesviruses that infect people and animals. Infectious laryngotracheitis virus (ILTV - Gallid alphaherpesvirus 1), causes respiratory disease in chickens, resulting in significant production losses in poultry industries worldwide. Natural (field) ILTV recombination is widespread, particularly recombination between attenuated ILTV vaccine strains to create virulent viruses. These virulent recombinants have had a major impact on animal health. Recently, the development of a single nucleotide polymorphism (SNP) genotyping assay for ILTV has helped to understand ILTV recombination under laboratory settings...
September 22, 2017: Applied and Environmental Microbiology
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