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https://www.readbyqxmd.com/read/28644134/the-conundrum-of-the-epstein-barr-virus-associated-gastric-carcinoma-in-the-americas
#1
REVIEW
Gonzalo Carrasco-Avino, Ismael Riquelme, Oslando Padilla, Miguel Villaseca, Francisco R Aguayo, Alejandro H Corvalan
Epstein-Barr virus-associated gastric carcinoma shows a higher prevalence in the Americas than Asia. We summarize all studies of Epstein Barr virus-associated gastric carcinoma in the Americas, focusing on host characteristics, environmental associations and phylogeographic diversity of Epstein-Barr virus strains. In the Americas, the prevalence of Epstein Barr virus-associated gastric carcinoma is 11.4%, more frequent in males and portray predominantly diffuse-type histology. EBERs, EBNAs, BARTs and LMP are the highest expressed genes; their variations in healthy individuals may explain the phylogeographic diversity of Epstein-Barr virus across the region...
June 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28643581/a-white-paper-on-global-wheat-health-based-on-scenario-development-and-analysis
#2
Serge Savary, Annika Djurle, Jonathan Yuen, Andrea Ficke, Vittorio Rossi, Paul Esker, Jose M Fernandes, Emerson Del Ponte, Jatindra Kumar, Laurence V Madden, Pierce A Paul, Neil McRoberts, Pawan Kumar Singh, Laurent Huber, Claude Pope de Vallavieille, Sébastien Saint-Jean, Laetitia Willocquet
Scenario analysis constitutes a useful approach to synthesize knowledge and derive hypotheses in the case of complex systems which are documented with mainly qualitative or very diverse information. In this article, a framework for scenario analysis is designed and then, applied to global wheat health within a timeframe from today to 2050. Scenario analysis entails the choice of settings, the definition of scenarios of change, and the analysis of outcomes of these scenarios in the chosen settings. Three idealized agrosystems, representing a large fraction of the global diversity of wheat-based agrosystems, are considered, which represent the settings of the analysis...
June 23, 2017: Phytopathology
https://www.readbyqxmd.com/read/28642465/structural-basis-for-biologically-relevant-mechanical-stiffening-of-a-virus-capsid-by-cavity-creating-or-spacefilling-mutations
#3
Pablo Guerra, Alejandro Valbuena, Jordi Querol-Audí, Cristina Silva, Milagros Castellanos, Alicia Rodríguez-Huete, Damià Garriga, Mauricio G Mateu, Nuria Verdaguer
Recent studies reveal that the mechanical properties of virus particles may have been shaped by evolution to facilitate virus survival. Manipulation of the mechanical behavior of virus capsids is leading to a better understanding of viral infection, and to the development of virus-based nanoparticles with improved mechanical properties for nanotechnological applications. In the minute virus of mice (MVM), deleterious mutations around capsid pores involved in infection-related translocation events invariably increased local mechanical stiffness and interfered with pore-associated dynamics...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28640898/competition-between-influenza-a-virus-subtypes-through-heterosubtypic-immunity-modulates-re-infection-and-antibody-dynamics-in-the-mallard-duck
#4
Neus Latorre-Margalef, Justin D Brown, Alinde Fojtik, Rebecca L Poulson, Deborah Carter, Monique Franca, David E Stallknecht
Our overall hypothesis is that host population immunity directed at multiple antigens will influence the prevalence, diversity and evolution of influenza A virus (IAV) in avian populations where the vast subtype diversity is maintained. To investigate how initial infection influences the outcome of later infections with homologous or heterologous IAV subtypes and how viruses interact through host immune responses, we carried out experimental infections in mallard ducks (Anas platyrhynchos). Mallards were pre-challenged with an H3N8 low-pathogenic IAV and were divided into six groups...
June 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28637760/discovery-of-a-highly-divergent-coronavirus-in-the-asian-house-shrew-from-china-illuminates-the-origin-of-the-alphacoronaviruses
#5
Wen Wang, Xian-Dan Lin, Yong Liao, Xiao-Qing Guan, Wen-Ping Guo, Jian-Guang Xing, Edward C Holmes, Yong-Zhen Zhang
Although shrews are one of the largest groups of mammals little is known about their role in the evolution and transmission of viral pathogens including coronaviruses. We captured 266 Asian house shrews (Suncus murinus) in Jiangxi and Zhejiang provinces, China, during 2013-2015. Coronavirus (CoV) RNA was detected in 24 Asian house shrews, with an overall prevalence of 9.02%. Complete viral genome sequences were successfully recovered from the RNA positive samples. The newly discovered shrew CoV fell into four lineages reflecting their geographic origins, indicative of largely allopatric evolution...
June 21, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28637754/functional-evolution-of-influenza-ns1-protein-in-currently-circulating-human-2009-pandemic-h1n1-viruses
#6
Amelia M Clark, Aitor Nogales, Luis Martinez-Sobrido, David J Topham, Marta L DeDiego
In 2009, a novel H1N1 influenza virus emerged in humans, causing a global pandemic. It was previously shown that the NS1 protein from this human 2009 pandemic H1N1 (pH1N1) virus was an effective interferon (IFN) antagonist, but could not inhibit general host gene expression, unlike other NS1 proteins from seasonal human H1N1 and H3N2 viruses. Here, we show that the NS1 protein from currently circulating pH1N1 viruses has evolved to encode 6 amino acid changes (E55K, L90I, I123V, E125D, K131E, and N205S) with respect to the original protein...
June 21, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28637388/progressive-multifocal-leukoencephalopathy-endemic-viruses-and-lethal-brain-disease
#7
Sheila A Haley, Walter J Atwood
In 1971, the first human polyomavirus was isolated from the brain of a patient who died from a rapidly progressing demyelinating disease known as progressive multifocal leukoencephalopathy. The virus was named JC virus after the initials of the patient. In that same year a second human polyomavirus was discovered in the urine of a kidney transplant patient and named BK virus. In the intervening years it became clear that both viruses were widespread in the human population but only rarely caused disease. The past decade has witnessed the discovery of eleven new human polyomaviruses, two of which cause unusual and rare cancers...
June 21, 2017: Annual Review of Virology
https://www.readbyqxmd.com/read/28637337/matrix-completion-with-side-information-and-its-applications-in-predicting-the-antigenicity-of-influenza-viruses
#8
Li Huang, Xianhong Li, Pengfei Guo, Yuhua Yao, Bo Liao, Weiwei Zhang, Fayou Wang, Jiasheng Yang, Yulong Zhao, Hailiang Sun, Pingan He, Jialiang Yang
Motivation: Low-rank matrix completion has been demonstrated to be powerful in predicting antigenic distances among influenza viruses and vaccines from partially revealed hemagglutination inhibition (HI) table. Meanwhile, influenza hemagglutinin (HA) protein sequences are also effective in inferring antigenic distances. Thus, it is natural to integrate HA protein sequence information into low-rank matrix completion model to help infer influenza antigenicity, which is critical to influenza vaccine development...
June 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28634337/evolutionary-and-network-analysis-of-virus-sequences-from-infants-infected-with-an-australian-recombinant-strain-of-human-parechovirus-type-3
#9
Soren Alexandersen, Tiffanie M Nelson, Jason Hodge, Julian Druce
We present the near complete virus genome sequences with phylogenetic and network analyses of potential transmission networks of a total of 18 Australian cases of human parechovirus type 3 (HPeV3) infection in infants in the period from 2012-2015. Overall the results support our previous finding that the Australian outbreak strain/lineage is a result of a major recombination event that took place between March 2012 and November 2013 followed by further virus evolution and possibly recombination. While the nonstructural coding region of unknown provenance appears to evolve significantly both at the nucleotide and amino acid level, the capsid encoding region derived from the Yamagata 2011 lineage of HPeV3 appears to be very stable, particularly at the amino acid level...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28634106/biology-evolution-and-medical-importance-of-polyomaviruses-an-update
#10
REVIEW
Ugo Moens, Andi Krumbholz, Bernhard Ehlers, Roland Zell, Reimar Johne, Sébastien Calvignac-Spencer, Chris Lauber
The family Polyomaviridae encompasses non-enveloped viruses with a circular dsDNA genome that is typically approximately 5000bp in length. Originally isolated from mammals, polyomavirus sequences have now been detected in invertebrates, fish, amphibians, reptiles and birds, although it remains to be determined whether all these animals are genuine hosts. The genomes of all polyomaviruses encode at least two regulatory proteins (large and small tumour antigen) and two structural proteins (capsid proteins VP1 and VP2) whose functions have been defined...
June 17, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28633403/structured-populations-of-sulfolobus-acidocaldarius-with-susceptibility-to-mobile-genetic-elements
#11
Rika E Anderson, Angela Kouris, Christopher H Seward, Kate M Campbell, Rachel J Whitaker
The impact of a structured environment on genome evolution can be determined through comparative population genomics of species that live in the same habitat. Recent work comparing three genome sequences of Sulfolobus acidocaldarius suggested that highly structured, extreme, hot spring environments do not limit dispersal of this thermoacidophile, in contrast to other co-occurring Sulfolobus species. Instead, a high level of conservation among these three S. acidocaldarius genomes was hypothesized to result from rapid, global-scale dispersal promoted by low susceptibility to viruses that sets S...
June 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28630398/hcf-1-encoded-by-baculovirus-acmnpv-is-required-for-productive-nucleopolyhedrovirus-infection-of-non-permissive-tn368-cells
#12
Ami Tachibana, Rina Hamajima, Moe Tomizaki, Takuya Kondo, Yoshie Nanba, Michihiro Kobayashi, Hayato Yamada, Motoko Ikeda
Baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) replicates in both Spodoptera frugiperda Sf21 and Trichoplusia ni Tn368 cells, whereas AcMNPV defective in hcf-1 (host cell-factor 1) gene productively infects only Sf21 cells, indicating that HCF-1 is indispensable for the AcMNPV productive infection of Tn368 cells. Here, we demonstrated that HCF-1 protein transiently expressed in Tn368 cells promotes the DNA synthesis of Hyphantria cunea MNPV (HycuMNPV), Orygia pseudotsugata MNPV and Bombyx mori NPV, which are normally unable to replicate in Tn368 cells...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28630311/a-prokaryotic-viral-sequence-is-expressed-and-conserved-in-mammalian-brain
#13
Yang-Hui Yeh, Vignesh Gunasekharan, Laura Manuelidis
A natural and permanent transfer of prokaryotic viral sequences to mammals has not been reported by others. Circular "SPHINX" DNAs <5 kb were previously isolated from nuclease-protected cytoplasmic particles in rodent neuronal cell lines and brain. Two of these DNAs were sequenced after Φ29 polymerase amplification, and they revealed significant but imperfect homology to segments of commensal Acinetobacter phage viruses. These findings were surprising because the brain is isolated from environmental microorganisms...
June 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28630001/host-influence-in-the-genomic-composition-of-flaviviruses-a-multivariate-approach
#14
Diego Simón, Alvaro Fajardo, Martín Sóñora, Adriana Delfraro, Héctor Musto
Flaviviruses present substantial differences in their host range and transmissibility. We studied the evolution of base composition, dinucleotide biases, codon usage and amino acid frequencies in the genus Flavivirus within a phylogenetic framework by principal components analysis. There is a mutual interplay between the evolutionary history of flaviviruses and their respective vectors and/or hosts. Hosts associated to distinct phylogenetic groups may be driving flaviviruses at different pace and through various sequence landscapes, as can be seen for viruses associated with Aedes or Culex spp...
June 16, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28627851/zika-virus-practical-guidelines
#15
Gilles Eperon, Manuel Schibler, Noémie Wagner, François Chappuis, Isabelle Eperon
Zika virus suddenly emerged in Latin America in 2015‑2016. Congenital malformations have been observed in infected pregnant women, causing a major public health impact in affected countries, particularly in Brazil. In addition, sexual transmission of Zika virus has been well documented. This led to the development of prevention strategies and recommendations for travellers visiting at risk countries. These documents are regularly amended depending on the evolution of scientific knowledge, the epidemiologic trends and the national and international guidelines...
May 3, 2017: Revue Médicale Suisse
https://www.readbyqxmd.com/read/28625667/dynamics-of-pvy-strains-in-field-grown-potato-impact-of-strain-competition-and-ability-to-overcome-host-resistance-mechanisms
#16
Kim Davie, Ross Holmes, Jon Pickup, Christophe Lacomme
Potato virus Y (PVY) is the most important viral pathogen affecting potato crops worldwide. PVY can be transmitted non-persistently by aphids that do not colonize the host plant, resulting in a rapid acquisition and transmission of the virus between plants. PVY exists as a complex of strains that can be distinguished according to their pathogenicity, serology and genomic analysis. While virus incidence remains low in Scottish seed potato crops, PVY has become the increasingly prevalent virus. The monitoring of PVY(N) and PVY° serotypes has revealed a recent shift towards PVY(N) which now accounts for more than 90% of all PVY cases...
June 15, 2017: Virus Research
https://www.readbyqxmd.com/read/28625542/analysis-of-the-codon-usage-of-the-orf2-gene-of-feline-calicivirus
#17
Minghui Zang, Wanting He, Fanshu Du, Gongjian Wu, Bohao Wu, Zhenlei Zhou
Feline calicivirus (FCV) is a highly prevalent pathogen of the domestic cat that causes acute infections of the oral and upper respiratory tract. The E region of the ORF2 protein is responsible for the induction of virus-neutralizing antibodies, thus it is important to understand the codon usage of this gene. Here, analysed 90 coding sequences of ORF2 and show that it undergoes a low codon usage bias. In addition, although mutational bias is one of the factors shaping the codon usage bias of this gene, natural selection plays a more significant role...
June 15, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28623921/genome-wide-analysis-of-codon-usage-bias-in-bovine-coronavirus
#18
Matías Castells, Matías Victoria, Rodney Colina, Héctor Musto, Juan Cristina
BACKGROUND: Bovine coronavirus (BCoV) belong to the genus Betacoronavirus of the family Coronaviridae. BCoV are widespread around the world and cause enteric or respiratory infections among cattle, leading to important economic losses to the beef and dairy industry worldwide. To study the relation of codon usage among viruses and their hosts is essential to understand host-pathogen interaction, evasion from host's immune system and evolution. METHODS: We performed a comprehensive analysis of codon usage and composition of BCoV...
June 17, 2017: Virology Journal
https://www.readbyqxmd.com/read/28623405/genome-dynamics-and-evolution-of-codon-usage-patterns-in-shrimp-viruses
#19
Anuj Tyagi, B T Naveen Kumar, Niraj K Singh
We analysed the genomes and codon usage patterns of seven small (DNA and RNA) shrimp viruses. Effective number of codon (ENC) values indicated moderate (35 < ENC < 50) codon usage bias in shrimp viruses. Correlation analysis between GC compositions at non-synonymous codon and synonymous codon positions (GC1, 2 and GC3) as well as GC3 versus ENC curves indicated varying influences of mutational pressure on codon usage. The presence of deoptimized codons and host-antagonistic codon usage trends in shrimp viruses suggested the adaptation of a slow replication strategy by these viruses to avoid host defences...
June 16, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28622386/alpha-defensin-dependent-enhancement-of-enteric-viral-infection
#20
Sarah S Wilson, Beth A Bromme, Mayumi K Holly, Mayim E Wiens, Anshu P Gounder, Youngmee Sul, Jason G Smith
The small intestinal epithelium produces numerous antimicrobial peptides and proteins, including abundant enteric α-defensins. Although they most commonly function as potent antivirals in cell culture, enteric α-defensins have also been shown to enhance some viral infections in vitro. Efforts to determine the physiologic relevance of enhanced infection have been limited by the absence of a suitable cell culture system. To address this issue, here we use primary stem cell-derived small intestinal enteroids to examine the impact of naturally secreted α-defensins on infection by the enteric mouse pathogen, mouse adenovirus 2 (MAdV-2)...
June 16, 2017: PLoS Pathogens
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