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Viral evolution

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https://www.readbyqxmd.com/read/28103791/high-virulence-does-not-necessarily-impede-viral-adaptation-to-a-new-host-a-case-study-using-a-plant-rna-virus
#1
Anouk Willemsen, Mark P Zwart, Santiago F Elena
BACKGROUND: Theory suggests that high virulence could hinder between-host transmission of microparasites, and that virulence therefore will evolve to lower levels. Alternatively, highly virulent microparasites could also curtail host development, thereby limiting both the host resources available to them and their own within-host effective population size. In this case, high virulence might restrain the mutation supply rate and increase the strength with which genetic drift acts on microparasite populations...
January 19, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28103248/effect-of-the-latent-reservoir-on-the-evolution-of-hiv-at-the-within-and-between-host-levels
#2
Hilje M Doekes, Christophe Fraser, Katrina A Lythgoe
The existence of long-lived reservoirs of latently infected CD4+ T cells is the major barrier to curing HIV, and has been extensively studied in this light. However, the effect of these reservoirs on the evolutionary dynamics of the virus has received little attention. Here, we present a within-host quasispecies model that incorporates a long-lived reservoir, which we then nest into an epidemiological model of HIV dynamics. For biologically plausible parameter values, we find that the presence of a latent reservoir can severely delay evolutionary dynamics within a single host, with longer delays associated with larger relative reservoir sizes and/or homeostatic proliferation of cells within the reservoir...
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28102430/innate-and-intrinsic-antiviral-immunity-in-drosophila
#3
REVIEW
Assel Mussabekova, Laurent Daeffler, Jean-Luc Imler
The fruit fly Drosophila melanogaster has been a valuable model to investigate the genetic mechanisms of innate immunity. Initially focused on the resistance to bacteria and fungi, these studies have been extended to include antiviral immunity over the last decade. Like all living organisms, insects are continually exposed to viruses and have developed efficient defense mechanisms. We review here our current understanding on antiviral host defense in fruit flies. A major antiviral defense in Drosophila is RNA interference, in particular the small interfering (si) RNA pathway...
January 19, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28100306/diverse-novel-astroviruses-identified-in-wild-himalayan-marmots
#4
Yuanyun Ao, Jiemei Yu, Lili Li, Jingyuan Cao, Hongyan Deng, Yunyun Xin, Mengmeng Liu, Lin Lin, Shan Lu, Jianguo Xu, Zhaojun Duan
With advances in viral surveillance and next generation sequencing, highly diverse novel astroviruses (AstVs) and different animal hosts have been discovered in recent years. However, the existence of AstVs in marmots has yet to be shown. Here, we identified for the first time two highly divergent strains of AstVs, (tentatively named Qinghai Himalayana marmot AstV, HHMAstV1 and HHMAstV2), by viral metagenomic analysis in liver tissues isolated from wild Marmota himalayana in China. Overall, 12 of 99 (12.1%) M...
January 18, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28098392/bayesian-nonparametric-clustering-in-phylogenetics-modeling-antigenic-evolution-in-influenza
#5
Gabriela B Cybis, Janet S Sinsheimer, Trevor Bedford, Andrew Rambaut, Philippe Lemey, Marc A Suchard
Influenza is responsible for up to 500,000 deaths every year, and antigenic variability represents much of its epidemiological burden. To visualize antigenic differences across many viral strains, antigenic cartography methods use multidimensional scaling on binding assay data to map influenza antigenicity onto a low-dimensional space. Analysis of such assay data ideally leads to natural clustering of influenza strains of similar antigenicity that correlate with sequence evolution. To understand the dynamics of these antigenic groups, we present a framework that jointly models genetic and antigenic evolution by combining multidimensional scaling of binding assay data, Bayesian phylogenetic machinery and nonparametric clustering methods...
January 18, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/28093338/a-virus-like-particle-vaccination-strategy-expands-its-tolerance-to-h3n2-antigenic-drift-by-enhancing-neutralizing-antibodies-against-hemagglutinin-stalk
#6
Ji-Rong Yang, Chieh-Yu Cheng, Chih-Yuan Chen, Chao-Hua Lin, Chuan-Yi Kuo, Hsiang-Yi Huang, Fu-Ting Wu, Yu-Chih Yang, Chia-Ying Wu, Ming-Tsan Liu, Pei-Wen Hsiao
Seasonal influenza viruses impact public health annually due to their continual evolution. However, the current inactivated seasonal vaccines provide poor protection against antigenically drifted viruses and require periodical reformulation through hit-and-miss predictions about which strains will circulate during the next season. To reduce the impact caused by vaccine mismatch, we investigated the drift-tolerance of virus-like particles (VLP) as an improved vaccine candidate. The cross-protective humoral immunity elicited by the H3N2-VLP vaccine constructed for the 2011-2012 season was examined against viruses isolated from 2010 to 2015 in Taiwan evolving chronologically through clades 1, 4, 5, 3B and 3C, as well as viruses that were circulating globally in 2005, 2007 and 2009...
January 13, 2017: Antiviral Research
https://www.readbyqxmd.com/read/28090077/clinical-and-biological-insights-from-viral-genome-sequencing
#7
Charlotte J Houldcroft, Mathew A Beale, Judith Breuer
Whole-genome sequencing (WGS) of pathogens is becoming increasingly important not only for basic research but also for clinical science and practice. In virology, WGS is important for the development of novel treatments and vaccines, and for increasing the power of molecular epidemiology and evolutionary genomics. In this Opinion article, we suggest that WGS of viruses in a clinical setting will become increasingly important for patient care. We give an overview of different WGS methods that are used in virology and summarize their advantages and disadvantages...
January 16, 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/28088686/immune-history-and-influenza-virus-susceptibility
#8
REVIEW
Sarah Cobey, Scott E Hensley
Antibody responses to influenza viruses are critical for protection, but the ways in which repeated viral exposures shape antibody evolution and effectiveness over time remain controversial. Early observations demonstrated that viral exposure history has a profound effect on the specificity and magnitude of antibody responses to a new viral strain, a phenomenon called 'original antigenic sin.' Although 'sin' might suppress some aspects of the immune response, so far there is little indication that hosts with pre-existing immunity are more susceptible to viral infections compared to naïve hosts...
January 12, 2017: Current Opinion in Virology
https://www.readbyqxmd.com/read/28087772/possible-roles-of-new-mutations-shared-by-asian-and-american-zika-viruses
#9
Shozo Yokoyama, William T Starmer
Originating in Africa, the Zika virus (ZIKV) has spread to Asia, Pacific Islands and now to the Americas and beyond. Since the first isolation in 1947, ZIKV strains have been sampled at various times in the last 69 years, but this history has not been reflected in studying the patterns of mutation accumulation in their genomes. Implementing the viral history, we show that the ZIKV ancestor appeared sometime in 1930-1945 and, at that point, its mutation rate was probably less than 0.2 x 10(-3)/nucleotide site/year and subsequently increased significantly in most of its descendants...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28075409/the-hiv-1-vpr-protein-a-multifaceted-target-for-therapeutic-intervention
#10
REVIEW
María Eugenia González
The human immunodeficiency virus type 1 (HIV-1) Vpr protein is an attractive target for antiretroviral drug development. The conservation both of the structure along virus evolution and the amino acid sequence in viral isolates from patients underlines the importance of Vpr for the establishment and progression of HIV-1 disease. While its contribution to virus replication in dividing and non-dividing cells and to the pathogenesis of HIV-1 in many different cell types, both extracellular and intracellular forms, have been extensively studied, its precise mechanism of action nevertheless remains enigmatic...
January 10, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28068340/phylogeography-of-rift-valley-fever-virus-in-africa-and-the-arabian-peninsula
#11
Abdallah M Samy, A Townsend Peterson, Matthew Hall
Rift Valley Fever is an acute zoonotic viral disease caused by Rift Valley Fever virus (RVFV) that affects ruminants and humans in Sub-Saharan Africa and the Arabian Peninsula. We used phylogenetic analyses to understand the demographic history of RVFV populations, using sequence data from the three minigenomic segments of the virus. We used phylogeographic approaches to infer RVFV historical movement patterns across its geographic range, and to reconstruct transitions among host species. Results revealed broad circulation of the virus in East Africa, with many lineages originating in Kenya...
January 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28067906/prophage-mediated-defence-against-viral-attack-and-viral-counter-defence
#12
Rebekah M Dedrick, Deborah Jacobs-Sera, Carlos A Guerrero Bustamante, Rebecca A Garlena, Travis N Mavrich, Welkin H Pope, Juan C Cervantes Reyes, Daniel A Russell, Tamarah Adair, Richard Alvey, J Alfred Bonilla, Jerald S Bricker, Bryony R Brown, Deanna Byrnes, Steven G Cresawn, William B Davis, Leon A Dickson, Nicholas P Edgington, Ann M Findley, Urszula Golebiewska, Julianne H Grose, Cory F Hayes, Lee E Hughes, Keith W Hutchison, Sharon Isern, Allison A Johnson, Margaret A Kenna, Karen K Klyczek, Catherine M Mageeney, Scott F Michael, Sally D Molloy, Matthew T Montgomery, James Neitzel, Shallee T Page, Marie C Pizzorno, Marianne K Poxleitner, Claire A Rinehart, Courtney J Robinson, Michael R Rubin, Joseph N Teyim, Edwin Vazquez, Vassie C Ware, Jacqueline Washington, Graham F Hatfull
Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage...
January 9, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28063924/diversity-in-vp3-nsp3-and-nsp4-of-rotavirus-b-detected-from-japanese-cattle
#13
Michiko Hayashi-Miyamoto, Toshiaki Murakami, Fujiko Minami-Fukuda, Shinobu Tsuchiaka, Mai Kishimoto, Kaori Sano, Yuki Naoi, Keigo Asano, Toru Ichimaru, Kei Haga, Tsutomu Omatsu, Yukie Katayama, Mami Oba, Hiroshi Aoki, Junsuke Shirai, Motohiko Ishida, Kazuhiko Katayama, Tetsuya Mizutani, Makoto Nagai
Bovine rotavirus B (RVB) is an etiological agent of diarrhea mostly in adult cattle. Currently, a few sequences of viral protein (VP)1, 2, 4, 6, and 7 and nonstructural protein (NSP)1, 2, and 5 of bovine RVB are available in the DDBJ/EMBL/GenBank databases, and none have been reported for VP3, NSP3, and NSP4. In order to fill this gap in the genetic characterization of bovine RVB strains, we used a metagenomics approach and sequenced and analyzed the complete coding sequences (CDS) of VP3, NSP3, and NSP4 genes, as well as the partial or complete CDS of other genes of RVBs detected from Japanese cattle...
January 4, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28062756/phylogenetic-origin-and-diversification-of-rnai-pathway-genes-in-insects
#14
Daniel Dowling, Thomas Pauli, Alexander Donath, Karen Meusemann, Lars Podsiadlowski, Malte Petersen, Ralph S Peters, Christoph Mayer, Shanlin Liu, Xin Zhou, Bernhard Misof, Oliver Niehuis
RNA interference (RNAi) refers to the set of molecular processes found in eukaryotic organisms in which small RNA molecules mediate the silencing or down-regulation of target genes. In insects, RNAi serves a number of functions, including regulation of endogenous genes, anti-viral defense, and defense against transposable elements. Despite being well studied in model organisms, such as Drosophila, the distribution of core RNAi pathway genes and their evolution in insects is not well understood. Here we present the most comprehensive overview of the distribution and diversity of core RNAi pathway genes across 100 insect species, encompassing all currently recognized insect orders...
January 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28062387/molecular-diversity-recombination-and-population-structure-of-alphasatellites-associated-with-begomovirus-disease-complexes
#15
R Vinoth Kumar, Divya Singh, Achuit K Singh, S Chakraborty
The genus, begomovirus (family Geminiviridae) includes a large number of viruses infecting a wide range of plant species worldwide. The majority of monopartite begomoviruses are associated with satellites (betasatellites) and/or satellite-like molecules (alphasatellites). In spite of the Indo-China region being regarded as the centre of origin of begomoviruses and satellites, a detailed study on the emergence and evolution of alphasatellites in India has not yet conducted. Our present analysis indicated the association of 22 alphasatellites with monopartite and bipartite begomovirus-betasatellite complexes in India...
January 4, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28062191/tracking-hcv-protease-population-diversity-during-transmission-and-susceptibility-of-founder-populations-to-antiviral-therapy
#16
Tanvi Khera, Daniel Todt, Koen Vercauteren, C Patrick McClure, Lieven Verhoye, Ali Farhoudi, Sabin Bhuju, Robert Geffers, Thomas F Baumert, Eike Steinmann, Philip Meuleman, Thomas Pietschmann, Richard J P Brown
Due to the highly restricted species-tropism of Hepatitis C virus (HCV) a limited number of animal models exist for pre-clinical evaluation of vaccines and antiviral compounds. The human-liver chimeric mouse model allows heterologous challenge with clinically relevant strains derived from patients. However, to date, the transmission and longitudinal evolution of founder viral populations in this model have not been characterized in-depth using state-of-the-art sequencing technologies. Focusing on NS3 protease encoding region of the viral genome, mutant spectra in a donor inoculum and individual recipient mice were determined via Illumina sequencing and compared, to determine the effects of transmission on founder viral population complexity...
January 3, 2017: Antiviral Research
https://www.readbyqxmd.com/read/28061906/bilateral-rectus-sheath-haematoma-complicating-dengue-virus-infection-in-a-patient-on-warfarin-for-mechanical-aortic-valve-replacement-a-case-report
#17
Chamith Thushanga Rosa, Mitrakrishnan Rayno Navinan, Sincy Samarawickrama, Himam Hamza, Maheshika Gunarathne, Arulprashanth Arulanantham, Neeha Subba, Udari Samarasiri, Thushara Mathias, Aruna Kulatunga
BACKGROUND: The management of Dengue virus infection can be challenging. Varied presentations and numerous complications intrinsic to dengue by itself increase the complexity of treatment and potential mortality. When burdened with the presence of additional comorbidities and the need to continue compulsory medications, clear stepwise definitive guidance is lacking and patients tend to have more complex complications and outcomes calling to question the clinical decisions that may have been taken...
January 7, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28058113/transmission-bottlenecks-and-rnai-collectively-influence-tick-borne-flavivirus-evolution
#18
Nathan D Grubaugh, Claudia Rückert, Philip M Armstrong, Angela Bransfield, John F Anderson, Gregory D Ebel, Doug E Brackney
Arthropod-borne RNA viruses exist within hosts as heterogeneous populations of viral variants and, as a result, possess great genetic plasticity. Understanding the micro-evolutionary forces shaping these viruses can provide insights into how they emerge, adapt, and persist in new and changing ecological niches. While considerable attention has been directed toward studying the population dynamics of mosquito-borne viruses, little is known about tick-borne virus populations. Therefore, using a mouse and Ixodes scapularis tick transmission model, we examined Powassan virus (POWV; Flaviviridae, Flavivirus) populations in and between both the vertebrate host and arthropod vector...
July 2016: Virus Evolution
https://www.readbyqxmd.com/read/28057901/genetic-diversity-and-phylogenetic-analysis-of-porcine-reproductive-and-respiratory-syndrome-virus-in-southern-china-from-2007-to-2014
#19
Qiwen Wu, Zhili Li, Guanqun Zhang, Jianqiang Niu, Xiduo Zeng, Baoli Sun, Jingyun Ma
Porcine reproductive and respiratory syndrome virus (PRRSV) has a high degree of genetic variation. Here, we characterized the genetic variation and evolutionary relationships among circulating PRRSV strains in Southern China. In this study, we analyzed 29 NSP2 strains and 150 ORF5 strains from clinical samples collected in Southern China during 2007-2014. The alignment results showed that the nucleotide identities of the two genes among these strains were 80.5-99.7% and 80.9-100%, respectively. Phylogenetic analysis based on NSP2 gene showed that high pathogenic PRRSV were still the dominant virus in Southern China from 2013 to 2014...
January 4, 2017: Journal of Veterinary Science
https://www.readbyqxmd.com/read/28057258/nonsegmented-negative-sense-rna-viruses-structural-data-bring-new-insights-into-nucleocapsid-assembly
#20
REVIEW
M Jamin, F Yabukarski
Viruses with a nonsegmented negative-sense RNA genome (NNVs) include important human pathogens as well as life-threatening zoonotic viruses. These viruses share a common RNA replication complex, including the genomic RNA and three proteins, the nucleoprotein (N), the phosphoprotein (P), and the RNA-dependent RNA polymerase (L). During genome replication, the RNA polymerase complex first synthesizes positive-sense antigenomes, which in turn serve as template for the production of negative-sense progeny genomes...
2017: Advances in Virus Research
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