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Viral evolution

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https://www.readbyqxmd.com/read/28548881/constraints-drivers-and-implications-of-influenza-a-virus-reassortment
#1
Anice C Lowen
Influenza A viruses are constantly changing. This change accounts for seasonal epidemics, infrequent pandemics, and zoonotic outbreaks. A major mechanism underlying the genetic diversification of influenza A virus is reassortment of intact gene segments between coinfecting viruses. This exchange is possible because of the segmented nature of the viral genome. Here, I first consider the constraints and drivers acting on influenza A virus reassortment, including the likelihood of coinfection at the host and cellular levels, mixing and assembly of heterologous gene segments within coinfected cells, and the fitness associated with reassortant genotypes...
May 26, 2017: Annual Review of Virology
https://www.readbyqxmd.com/read/28545432/the-impact-of-migratory-flyways-on-the-spread-of-avian-influenza-virus-in-north-america
#2
Mathieu Fourment, Aaron E Darling, Edward C Holmes
BACKGROUND: Wild birds are the major reservoir hosts for influenza A viruses (AIVs) and have been implicated in the emergence of pandemic events in livestock and human populations. Understanding how AIVs spread within and across continents is therefore critical to the development of successful strategies to manage and reduce the impact of influenza outbreaks. In North America many bird species undergo seasonal migratory movements along a North-South axis, thereby providing opportunities for viruses to spread over long distances...
May 25, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28542550/a-spatio-temporal-assessment-of-simian-human-immunodeficiency-virus-shiv-evolution-reveals-a-highly-dynamic-process-within-the-host
#3
Alison F Feder, Christopher Kline, Patricia Polacino, Mackenzie Cottrell, Angela D M Kashuba, Brandon F Keele, Shiu-Lok Hu, Dmitri A Petrov, Pleuni S Pennings, Zandrea Ambrose
The process by which drug-resistant HIV-1 arises and spreads spatially within an infected individual is poorly understood. Studies have found variable results relating how HIV-1 in the blood differs from virus sampled in tissues, offering conflicting findings about whether HIV-1 throughout the body is homogeneously distributed. However, most of these studies sample only two compartments and few have data from multiple time points. To directly measure how drug resistance spreads within a host and to assess how spatial structure impacts its emergence, we examined serial sequences from four macaques infected with RT-SHIVmne027, a simian immunodeficiency virus encoding HIV-1 reverse transcriptase (RT), and treated with RT inhibitors...
May 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28539654/quasispecies-composition-and-evolution-of-a-typical-zika-virus-clinical-isolate-from-suriname
#4
Sander van Boheemen, Ali Tas, S Yahya Anvar, Rebecca van Grootveld, Irina C Albulescu, Martijn P Bauer, Mariet C Feltkamp, Peter J Bredenbeek, Martijn J van Hemert
The arthropod-borne Zika virus (ZIKV) is currently causing a major international public health threat in the Americas. This study describes the isolation of ZIKV from the plasma of a 29-year-old female traveler that developed typical symptoms, like rash, fever and headache upon return from Suriname. The complete genome sequence including the 5' and 3' untranslated regions was determined and phylogenetic analysis showed the isolate clustering within the Asian lineage, close to other viruses that have recently been isolated in the Americas...
May 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28538739/multiplex-pcr-method-for-minion-and-illumina-sequencing-of-zika-and-other-virus-genomes-directly-from-clinical-samples
#5
Joshua Quick, Nathan D Grubaugh, Steven T Pullan, Ingra M Claro, Andrew D Smith, Karthik Gangavarapu, Glenn Oliveira, Refugio Robles-Sikisaka, Thomas F Rogers, Nathan A Beutler, Dennis R Burton, Lia Laura Lewis-Ximenez, Jaqueline Goes de Jesus, Marta Giovanetti, Sarah C Hill, Allison Black, Trevor Bedford, Miles W Carroll, Marcio Nunes, Luiz Carlos Alcantara, Ester C Sabino, Sally A Baylis, Nuno R Faria, Matthew Loose, Jared T Simpson, Oliver G Pybus, Kristian G Andersen, Nicholas J Loman
Genome sequencing has become a powerful tool for studying emerging infectious diseases; however, genome sequencing directly from clinical samples (i.e., without isolation and culture) remains challenging for viruses such as Zika, for which metagenomic sequencing methods may generate insufficient numbers of viral reads. Here we present a protocol for generating coding-sequence-complete genomes, comprising an online primer design tool, a novel multiplex PCR enrichment protocol, optimized library preparation methods for the portable MinION sequencer (Oxford Nanopore Technologies) and the Illumina range of instruments, and a bioinformatics pipeline for generating consensus sequences...
June 2017: Nature Protocols
https://www.readbyqxmd.com/read/28538734/zika-virus-evolution-and-spread-in-the-americas
#6
Hayden C Metsky, Christian B Matranga, Shirlee Wohl, Stephen F Schaffner, Catherine A Freije, Sarah M Winnicki, Kendra West, James Qu, Mary Lynn Baniecki, Adrianne Gladden-Young, Aaron E Lin, Christopher H Tomkins-Tinch, Simon H Ye, Daniel J Park, Cynthia Y Luo, Kayla G Barnes, Rickey R Shah, Bridget Chak, Giselle Barbosa-Lima, Edson Delatorre, Yasmine R Vieira, Lauren M Paul, Amanda L Tan, Carolyn M Barcellona, Mario C Porcelli, Chalmers Vasquez, Andrew C Cannons, Marshall R Cone, Kelly N Hogan, Edgar W Kopp, Joshua J Anzinger, Kimberly F Garcia, Leda A Parham, Rosa M Gélvez Ramírez, Maria C Miranda Montoya, Diana P Rojas, Catherine M Brown, Scott Hennigan, Brandon Sabina, Sarah Scotland, Karthik Gangavarapu, Nathan D Grubaugh, Glenn Oliveira, Refugio Robles-Sikisaka, Andrew Rambaut, Lee Gehrke, Sandra Smole, M Elizabeth Halloran, Luis Villar, Salim Mattar, Ivette Lorenzana, Jose Cerbino-Neto, Clarissa Valim, Wim Degrave, Patricia T Bozza, Andreas Gnirke, Kristian G Andersen, Sharon Isern, Scott F Michael, Fernando A Bozza, Thiago M L Souza, Irene Bosch, Nathan L Yozwiak, Bronwyn L MacInnis, Pardis C Sabeti
Although the recent Zika virus (ZIKV) epidemic in the Americas and its link to birth defects have attracted a great deal of attention, much remains unknown about ZIKV disease epidemiology and ZIKV evolution, in part owing to a lack of genomic data. Here we address this gap in knowledge by using multiple sequencing approaches to generate 110 ZIKV genomes from clinical and mosquito samples from 10 countries and territories, greatly expanding the observed viral genetic diversity from this outbreak. We analysed the timing and patterns of introductions into distinct geographic regions; our phylogenetic evidence suggests rapid expansion of the outbreak in Brazil and multiple introductions of outbreak strains into Puerto Rico, Honduras, Colombia, other Caribbean islands, and the continental United States...
May 24, 2017: Nature
https://www.readbyqxmd.com/read/28538703/metagenomic-approaches-to-assess-bacteriophages-in-various-environmental-niches
#7
REVIEW
Stephen Hayes, Jennifer Mahony, Arjen Nauta, Douwe van Sinderen
Bacteriophages are ubiquitous and numerous parasites of bacteria and play a critical evolutionary role in virtually every ecosystem, yet our understanding of the extent of the diversity and role of phages remains inadequate for many ecological niches, particularly in cases in which the host is unculturable. During the past 15 years, the emergence of the field of viral metagenomics has drastically enhanced our ability to analyse the so-called viral 'dark matter' of the biosphere. Here, we review the evolution of viral metagenomic methodologies, as well as providing an overview of some of the most significant applications and findings in this field of research...
May 24, 2017: Viruses
https://www.readbyqxmd.com/read/28533973/plastomes-of-the-green-algae-hydrodictyon-reticulatum-and-pediastrum-duplex-sphaeropleales-chlorophyceae
#8
Hilary A McManus, Daniel J Sanchez, Kenneth G Karol
BACKGROUND: Comparative studies of chloroplast genomes (plastomes) across the Chlorophyceae are revealing dynamic patterns of size variation, gene content, and genome rearrangements. Phylogenomic analyses are improving resolution of relationships, and uncovering novel lineages as new plastomes continue to be characterized. To gain further insight into the evolution of the chlorophyte plastome and increase the number of representative plastomes for the Sphaeropleales, this study presents two fully sequenced plastomes from the green algal family Hydrodictyaceae (Sphaeropleales, Chlorophyceae), one from Hydrodictyon reticulatum and the other from Pediastrum duplex...
2017: PeerJ
https://www.readbyqxmd.com/read/28532787/evolution-of-avian-encephalomyelitis-virus-during-embryo-adaptation
#9
Rüdiger Hauck, C Gabriel Sentíes-Cué, Ying Wang, Colin Kern, H L Shivaprasad, Huaijun Zhou, Rodrigo A Gallardo
Wild-type avian encephalomyelitis virus (AEV) causes neurological signs in young chicks but no disease in pullets after oral or intracutaneous infection. However, if the virus gets embryo-adapted by serial passaging in chicken embryos, it will cause AE after intracutaneous infection in chickens of all ages. Recently, several cases of AE in layer pullets occurring shortly after intracutaneous vaccination were described. The present investigation was initiated to determine if vaccines that had inadvertently been embryo-adapted were responsible for these outbreaks...
May 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28532011/molecularly-imprinted-polymer-for-human-viral-pathogen-detection
#10
REVIEW
Aijaz Ahmad Malik, Chanin Nantasenamat, Theeraphon Piacham
Molecular imprinting has become an attractive synthetic approach for the fabrication of novel functional polymers with pre-designed molecular target selectivity. Such molecularly imprinted polymers (MIPs) have been applied in wide range of areas such as chemical and biological sensors, solid phase extraction and drug assays owing to their inherent robustness, reusability and reproducibility. Furthermore, MIPs can also be used as tools for studies concerning antibody/receptor binding site mimicry as well as being used as antibody substitutes for biomedical applications...
August 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28531277/genome-wide-discovery-of-viral-micrornas-based-on-phylogenetic-analysis-and-structural-evolution-of-various-human-papillomavirus-subtypes
#11
Shun-Long Weng, Kai-Yao Huang, Julia Tzu-Ya Weng, Fang-Yu Hung, Tzu-Hao Chang, Tzong-Yi Lee
In mammals, microRNAs (miRNAs) play key roles in controlling posttranscriptional regulation through binding to the mRNAs of target genes. Recently, it was discovered that viral miRNAs may be involved in human cancers and diseases. It is likely that viral miRNAs help viruses enter the latent phase of their life cycle and become undetected by the host's immune system, while increasing the host's risk for cancer development. Cervical cancer is typically related to the infection of human papillomavirus (HPV) through sexual transmission...
May 20, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28530650/multi-virion-infectious-units-arise-from-free-viral-particles-in-an-enveloped-virus
#12
José M Cuevas, María Durán-Moreno, Rafael Sanjuán
Many animal viruses are enveloped in a lipid bilayer taken up from cellular membranes. Because viral surface proteins bind to these membranes to initiate infection, we hypothesized that free virions may also be capable of interacting with the envelopes of other virions extracellularly. Here, we demonstrate this hypothesis in the vesicular stomatitis virus (VSV), a prototypic negative-strand RNA virus composed of an internal ribonucleocapsid, a matrix protein and an external envelope(1). Using microscopy, dynamic light scattering, differential centrifugation and flow cytometry, we show that free viral particles can spontaneously aggregate into multi-virion infectious units...
May 22, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28529975/phylogenetic-analyses-suggest-that-factors-other-than-the-capsid-protein-play-a-role-in-the-epidemic-potential-of-gii-2-norovirus
#13
Kentaro Tohma, Cara J Lepore, Lauren A Ford-Siltz, Gabriel I Parra
Norovirus is the leading cause of acute gastroenteritis worldwide. For over two decades, a single genotype (GII.4) has been responsible for most norovirus-associated cases. However, during the winter of 2014 to 2015, the GII.4 strains were displaced by a rarely detected genotype (GII.17) in several countries of the Asian continent. Moreover, during the winter of 2016 to 2017, the GII.2 strain reemerged as predominant in different countries worldwide. This reemerging GII.2 strain is a recombinant virus that presents a GII...
May 2017: MSphere
https://www.readbyqxmd.com/read/28529718/recent-advances-in-understanding-hiv-evolution
#14
REVIEW
Sophie M Andrews, Sarah Rowland-Jones
The human immunodeficiency virus (HIV) evolves rapidly owing to the combined activity of error-prone reverse transcriptase, recombination, and short generation times, leading to extensive viral diversity both within and between hosts. This diversity is a major contributing factor in the failure of the immune system to eradicate the virus and has important implications for the development of suitable drugs and vaccines to combat infection. This review will discuss the recent technological advances that have shed light on HIV evolution and will summarise emerging concepts in this field...
2017: F1000Research
https://www.readbyqxmd.com/read/28525571/one-year-genome-evolution-of-lausannevirus-in-allopatric-versus-sympatric-conditions
#15
Linda Mueller, Claire Bertelli, Trestan Pillonel, Nicolas Salamin, Gilbert Greub
Amoeba-resisting microorganisms (ARMs) raised a great interest during the last decade. Among them, some large DNA viruses present huge genomes up to 2.5 Mb long, exceeding the size of small bacterial genomes. The rate of genome evolution in terms of mutation, deletion and gene acquisition in these genomes is yet unknown. Given the suspected high plasticity of viral genomes, the microevolution of the 346 kb genome of Lausannevirus, a member of Megavirales, was studied. Hence, Lausannevirus was co-cultured within the amoeba Acanthamoeba castellanii over one year...
May 19, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28523923/genetic-characterization-of-canine-parvovirus-from-dogs-in-pakistan
#16
M Z Shabbir, M U Sohail, U N Chaudhary, W Yaqub, I Rashid, M H Saleem, M Munir
Canine parvoviruses (CPV) exist as antigenic variants with varying frequencies and genetic variabilities across the globe. Given the endemicity and high prevalence in Pakistan, we characterized the CPVs originating from dogs-population to elucidate viral diversity and evolution. Fecal samples from clinically diseased pups (n = 17) of different breeds and age (2-6 months) were processed for hemagglutination assay (HA), and later for partial amplification of VP2 gene sequence and amino acid analysis. A total of 11 samples (64...
2017: Acta Virologica
https://www.readbyqxmd.com/read/28521747/insights-into-the-ancestral-organisation-of-the-mammalian-mhc-class-ii-region-from-the-genome-of-the-pteropid-bat-pteropus-alecto
#17
Justin H J Ng, Mary Tachedjian, Lin-Fa Wang, Michelle L Baker
BACKGROUND: Bats are an extremely successful group of mammals and possess a variety of unique characteristics, including their ability to co-exist with a diverse range of pathogens. The major histocompatibility complex (MHC) is the most gene dense and polymorphic region of the genome and MHC class II (MHC-II) molecules play a vital role in the presentation of antigens derived from extracellular pathogens and activation of the adaptive immune response. Characterisation of the MHC-II region of bats is crucial for understanding the evolution of the MHC and of the role of pathogens in shaping the immune system...
May 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28520969/cell-mediated-immunity-to-target-the-persistent-human-immunodeficiency-virus-reservoir
#18
James L Riley, Luis J Montaner
Effective clearance of virally infected cells requires the sequential activity of innate and adaptive immunity effectors. In human immunodeficiency virus (HIV) infection, naturally induced cell-mediated immune responses rarely eradicate infection. However, optimized immune responses could potentially be leveraged in HIV cure efforts if epitope escape and lack of sustained effector memory responses were to be addressed. Here we review leading HIV cure strategies that harness cell-mediated control against HIV in stably suppressed antiretroviral-treated subjects...
March 15, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28517033/high-throughput-sequencing-of-transposable-element-insertions-suggests-adaptive-evolution-of-the-invasive-asian-tiger-mosquito-towards-temperate-environments
#19
Clément Goubert, Hélène Henri, Guillaume Minard, Claire Valiente Moro, Patrick Mavingui, Cristina Vieira, Matthieu Boulesteix
Invasive species represent unique opportunities to evaluate the role of local adaptation during colonization of new environments. Among these species, the Asian tiger mosquito, Aedes albopictus, is a threatening vector of several human viral diseases, including dengue and chikungunya, and raises concerns about the Zika fever. Its broad presence in both temperate and tropical environments has been considered the reflection of great "ecological plasticity". However, no study has been conducted to assess the role of adaptive evolution in the ecological success of Ae...
May 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28515302/transposon-mutagenesis-of-the-zika-virus-genome-highlights-regions-essential-for-rna-replication-and-restricted-for-immune-evasion
#20
Benjamin O Fulton, David Sachs, Megan C Schwarz, Peter Palese, Matthew J Evans
The molecular constraints affecting Zika virus (ZIKV) evolution are not well understood. To investigate ZIKV genetic flexibility, we used transposon mutagenesis to add 15-nucleotide insertions throughout the MR766 ZIKV genome and subsequently deep sequenced the viable mutants. Few ZIKV insertion mutants replicated, which likely reflects a high degree of functional constraints on the genome. The NS1 gene exhibited distinct mutational tolerances at different stages of the screen. This result may define regions of the NS1 protein that are required for the different stages of the viral life cycle...
May 17, 2017: Journal of Virology
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