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https://www.readbyqxmd.com/read/28340349/structure-reveals-mechanisms-of-viral-suppressors-that-intercept-a-crispr-rna-guided-surveillance-complex
#1
Saikat Chowdhury, Joshua Carter, MaryClare F Rollins, Sarah M Golden, Ryan N Jackson, Connor Hoffmann, Lyn'Al Nosaka, Joseph Bondy-Denomy, Karen L Maxwell, Alan R Davidson, Elizabeth R Fischer, Gabriel C Lander, Blake Wiedenheft
Genetic conflict between viruses and their hosts drives evolution and genetic innovation. Prokaryotes evolved CRISPR-mediated adaptive immune systems for protection from viral infection, and viruses have evolved diverse anti-CRISPR (Acr) proteins that subvert these immune systems. The adaptive immune system in Pseudomonas aeruginosa (type I-F) relies on a 350 kDa CRISPR RNA (crRNA)-guided surveillance complex (Csy complex) to bind foreign DNA and recruit a trans-acting nuclease for target degradation. Here, we report the cryo-electron microscopy (cryo-EM) structure of the Csy complex bound to two different Acr proteins, AcrF1 and AcrF2, at an average resolution of 3...
March 23, 2017: Cell
https://www.readbyqxmd.com/read/28340348/the-evolutionary-pathway-to-virulence-of-an-rna-virus
#2
Adi Stern, Ming Te Yeh, Tal Zinger, Matt Smith, Caroline Wright, Guy Ling, Rasmus Nielsen, Andrew Macadam, Raul Andino
Paralytic polio once afflicted almost half a million children each year. The attenuated oral polio vaccine (OPV) has enabled world-wide vaccination efforts, which resulted in nearly complete control of the disease. However, poliovirus eradication is hampered globally by epidemics of vaccine-derived polio. Here, we describe a combined theoretical and experimental strategy that describes the molecular events leading from OPV to virulent strains. We discover that similar evolutionary events occur in most epidemics...
March 23, 2017: Cell
https://www.readbyqxmd.com/read/28340335/experimental-evolution-to-study-virus-emergence
#3
Nathan D Grubaugh, Kristian G Andersen
Understanding how viruses adapt to new environments and acquire new phenotypes is critical for developing comprehensive responses to outbreaks. By studying the emergence of vaccine-derived poliovirus outbreaks, Stern et al. describe how a combination of sequence analysis and experimental evolution can be used to reveal adaptive pathways.
March 23, 2017: Cell
https://www.readbyqxmd.com/read/28338950/non-replicative-rna-recombination-of-an-animal-plus-strand-rna-virus-in-the-absence-of-efficient-translation-of-viral-proteins
#4
Maximiliane Kleine Büning, Denise Meyer, Sophia Austermann-Busch, Gleyder Roman-Sosa, Tillmann Rümenapf, Paul Becher
RNA recombination is a major driving force for the evolution of RNA viruses and is significantly implicated in the adaptation of viruses to new hosts, changes of virulence, as well as in the emergence of new viruses including drug-resistant and escape mutants. However, the molecular details of recombination in animal RNA viruses are only poorly understood. In order to determine whether viral RNA recombination depends on translation of viral proteins, a non-replicative recombination system was established which is based on cotransfection of cells with synthetic bovine viral diarrhea virus (family Flaviviridae) RNA genome fragments either lacking the internal ribosome entry site required for cap-independent translation or lacking almost the complete polyprotein coding region...
March 11, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28338832/evidence-of-translation-efficiency-adaptation-of-the-coding-regions-of-the-bacteriophage-lambda
#5
Eli Goz, Oriah Mioduser, Alon Diament, Tamir Tuller
Deciphering the way gene expression regulatory aspects are encoded in viral genomes is a challenging mission with ramifications related to all biomedical disciplines. Here, we aimed to understand how the evolution shapes the bacteriophage lambda genes by performing a high resolution analysis of ribosomal profiling data and gene expression related synonymous/silent information encoded in bacteriophage coding regions.We demonstrated evidence of selection for distinct compositions of synonymous codons in early and late viral genes related to the adaptation of translation efficiency to different bacteriophage developmental stages...
February 28, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28332654/vp1-sequencing-protocol-for-foot-and-mouth-disease-virus-molecular-epidemiology
#6
N J Knowles, J Wadsworth, K Bachanek-Bankowska, D P King
Nucleotide sequences of field strains of foot and mouth disease virus (FMDV) contribute to our understanding of the distribution and evolution of viral lineages that circulate in different regions of the world. This paper outlines a practical reversetranscription polymerase chain reaction (RT-PCR) and sequencing strategy that can be used to generate RNA sequences encoding the VP1 (1D) region of FMDV. The protocol contains a panel of PCR and sequencing primers that can be selected to characterise genetically diverse isolates representing all seven FMDV serotypes...
December 2016: Revue Scientifique et Technique
https://www.readbyqxmd.com/read/28332643/virus-mutations-and-their-impact-on-vaccination-against-infectious-bursal-disease-gumboro-disease
#7
A Boudaoud, B Mamache, W Tombari, A Ghram
Infectious bursal disease (also known as Gumboro disease) is an immunosuppressive viral disease specific to chickens. In spite of all the information amassed on the antigenic and immunological characteristics of the virus, the disease has not yet been brought fully under control. It is still prevalent in properly vaccinated flocks carrying specific antibodies at levels normally high enough to prevent the disease. Common causes apart, failure of vaccination against infectious bursal disease is associated mainly with early vaccination in flocks of unknown immune status and with the evolution of viruses circulating in the field, leading to antigenic drift and a sharp rise in pathogenicity...
December 2016: Revue Scientifique et Technique
https://www.readbyqxmd.com/read/28332348/molecular-epidemiology-of-hiv
#8
REVIEW
Bum Sik Chin
During the evolution of human immunodeficiency virus (HIV), transmissions between humans and primates resulted in multiple HIV lineages in humans. This evolution has been rapid, giving rise to a complex classification and allowing for worldwide spread and intermixing of subtypes, which has consequently led to dozens of circulating recombinant forms. In the Republic of Korea, 12,522 cases of HIV infection have been reported between 1985, when AIDS was first identified, and 2015. This review focuses on the evolution of HIV infection worldwide and the molecular epidemiologic characteristics of HIV in Korea...
March 22, 2017: Infection & Chemotherapy
https://www.readbyqxmd.com/read/28331993/molecular-characterization-and-phylogenetic-analysis-of-human-influenza-a-viruses-isolated-in-iran-during-the-2014-2015-season
#9
Elham Moasser, Farida Behzadian, Afagh Moattari, Fatemeh Fotouhi, Amir Rahimi, Hassan Zaraket, Seyed Younes Hosseini
Influenza A viruses are an important cause of severe infectious diseases in humans and are characterized by their fast evolution rate. Global monitoring of these viruses is critical to detect newly emerging variants during annual epidemics. Here, we sought to genetically characterize influenza A/H1N1pdm09 and A/H3N2 viruses collected in Iran during the 2014-2015 influenza season. A total of 200 nasopharyngeal swabs were collected from patients with influenza-like illnesses. Swabs were screened for influenza A and B using real-time PCR...
March 22, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28331600/bacterial-cell-to-cell-signaling-promotes-the-evolution-of-resistance-to-parasitic-bacteriophages
#10
Pierre Moreau, Stephen P Diggle, Ville-Petri Friman
The evolution of host-parasite interactions could be affected by intraspecies variation between different host and parasite genotypes. Here we studied how bacterial host cell-to-cell signaling affects the interaction with parasites using two bacteria-specific viruses (bacteriophages) and the host bacterium Pseudomonas aeruginosa that communicates by secreting and responding to quorum sensing (QS) signal molecules. We found that a QS-signaling proficient strain was able to evolve higher levels of resistance to phages during a short-term selection experiment...
March 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28331089/diversity-distribution-and-evolution-of-tomato-viruses-in-china-uncovered-by-small-rna-sequencing
#11
Chenxi Xu, Xuepeng Sun, Angela Taylor, Chen Jiao, Yimin Xu, Xiaofeng Cai, Xiaoli Wang, Chenhui Ge, Guanghui Pan, Quanxi Wang, Zhangjun Fei, Quanhua Wang
Tomato is a major vegetable crop that has tremendous popularity. However, viral disease is still a major factor limiting tomato production. Here we report the tomato virome identified through sequencing small RNAs of 170 field-grown samples collected in China. A total of 22 viruses were identified including both well-documented and newly detected viruses. The tomato viral community is dominated by a few species, and they exhibit polymorphisms and recombination in the genomes with coldspots and hotspots. Most samples were co-infected by multiple viruses and the majority of identified viruses are positive-sense single-stranded RNA viruses...
March 22, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28331087/feline-immunodeficiency-virus-evolutionarily-acquires-two-proteins-vif-and-protease-capable-of-antagonizing-feline-apobec3
#12
Rokusuke Yoshikawa, Junko S Takeuchi, Eri Yamada, Yusuke Nakano, Naoko Misawa, Yuichi Kimura, Fengrong Ren, Takayuki Miyazawa, Yoshio Koyanagi, Kei Sato
The interplay between viral and host proteins has been well studied to elucidate virus-host interactions and their relevance to virulence. Mammalian genes encode apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) proteins, which act as intrinsic restriction factors against lentiviruses. To overcome APOBEC3-mediated anti-viral actions, lentiviruses have evolutionarily acquired an accessory protein, viral infectivity factor (Vif), and Vif degrades host APOBEC3 proteins via a ubiquitin/proteasome-dependent pathway...
March 22, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28331081/multiple-sources-of-genetic-diversity-of-influenza-a-viruses-during-the-hajj
#13
Joanna C A Cobbin, Mohammad Alfelali, Osamah Barasheed, Janette Taylor, Dominic E Dwyer, Jen Kok, Robert Booy, Edward C Holmes, Harunor Rashid
Outbreaks of respiratory virus infection at mass gatherings pose significant health risks to attendants, host communities and ultimately the global population if they help facilitate viral emergence. However, little is known about the genetic diversity, evolution and patterns of viral transmission during mass gatherings, particularly how much diversity is generated by in situ transmission compared to that imported from other locations. Here we describe the genomic-scale evolution of influenza A viruses sampled from the Hajj at Makkah during 2013-2015...
March 22, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28328987/a-novel-recombinant-variant-of-latent-membrane-protein-1-from-epstein-barr-virus-in-argentina-denotes-phylogeographical-association
#14
Magdalena Gantuz, Mario Alejandro Lorenzetti, Paola Andrea Chabay, María Victoria Preciado
AIM: To study LMP1 variants distribution among children with EBV+ malignant and benign conditions as well as in healthy carriers. METHODS: Oral secretions and blood cells from 31 children with IM, and biopsies from 14 EBV+ reactive lymphoid hyperplasia and 33 EBV+ lymphomas were included. LMP1 was amplified by nested PCR and sequenced. Phylogenetic reconstructions were made under Maximun Likelihood, Bayesian and coalescent algorithms. RESULTS: Six clades were defined (China1, China2, Med-, Alaskan, B95...
2017: PloS One
https://www.readbyqxmd.com/read/28327527/emerging-interaction-patterns-in-the-emiliania-huxleyi-ehv-system
#15
Eliana Ruiz, Monique Oosterhof, Ruth-Anne Sandaa, Aud Larsen, António Pagarete
Viruses are thought to be fundamental in driving microbial diversity in the oceanic planktonic realm. That role and associated emerging infection patterns remain particularly elusive for eukaryotic phytoplankton and their viruses. Here we used a vast number of strains from the model system Emiliania huxleyi/Emiliania huxleyi Virus to quantify parameters such as growth rate (µ), resistance (R), and viral production (Vp) capacities. Algal and viral abundances were monitored by flow cytometry during 72-h incubation experiments...
March 22, 2017: Viruses
https://www.readbyqxmd.com/read/28325935/a-comparison-study-of-zika-virus-outbreaks-in-french-polynesia-colombia-and-the-state-of-bahia-in-brazil
#16
Daihai He, Daozhou Gao, Yijun Lou, Shi Zhao, Shigui Ruan
Zika virus (ZIKV) disease outbreaks occurred in French Polynesia in 2013-2014 and in Brazil and Colombia in 2015-2016, respectively. Using our recently developed ZIKV disease model, we simulated the reported ZIKV infection cases from French Polynesia, Colombia and the State of Bahia of Brazil. Moreover, we estimated that the infection attack rates were 78.0% (95% confidence interval (CI): 63.5-86.3%) in French Polynesia which closely matches a previous serological study; 20.8% (95% CI: 1.1-50.0%) in Colombia which suggests that the attack rate was most likely less than 50%; and 32...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28325923/clinical-features-and-viral-quasispecies-characteristics-associated-with-infection-by-the-hepatitis-b-virus-g145r-immune-escape-mutant
#17
Yuan Xue, Ming-Jie Wang, Zhi-Tao Yang, De-Min Yu, Yue Han, Dao Huang, Dong-Hua Zhang, Xin-Xin Zhang
Coexistence of the hepatitis B surface antigen (HBsAg) and hepatitis B surface antibody (anti-HBs) is an uncommon phenomenon, and the underlying mechanisms remain largely unknown. Amino-acid (aa) substitution from glycine to arginine at aa 145 (G145R), in the major hydrophilic region, has been reported in patients with HBsAg and anti-HBs coexistence. However, there is limited knowledge about the clinical features and viral quasispecies characteristics associated with G145R mutant hepatitis B virus (HBV) infection...
March 22, 2017: Emerging Microbes & Infections
https://www.readbyqxmd.com/read/28325372/is-predominant-clonal-evolution-a-common-evolutionary-adaptation-to-parasitism-in-pathogenic-parasitic-protozoa-fungi-bacteria-and-viruses
#18
M Tibayrenc, F J Ayala
We propose that predominant clonal evolution (PCE) in microbial pathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure. The main features of PCE are (1) strong linkage disequilibrium, (2) the widespread occurrence of stable genetic clusters blurred by occasional bouts of genetic exchange ('near-clades'), (3) the existence of a "clonality threshold", beyond which recombination is efficiently countered by PCE, and near-clades irreversibly diverge...
2017: Advances in Parasitology
https://www.readbyqxmd.com/read/28324177/a-detailed-analysis-of-codon-usage-patterns-and-influencing-factors-in-zika-virus
#19
Niraj K Singh, Anuj Tyagi
Recent outbreaks of Zika virus (ZIKV) in Africa, Latin America, Europe, and Southeast Asia have resulted in serious health concerns. To understand more about evolution and transmission of ZIKV, detailed codon usage analysis was performed for all available strains. A high effective number of codons (ENC) value indicated the presence of low codon usage bias in ZIKV. The effect of mutational pressure on codon usage bias was confirmed by significant correlations between nucleotide compositions at third codon positions and ENCs...
March 21, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28322924/evolutionary-trends-of-resistance-mutational-patterns-of-hbv-reverse-transcriptase-over-years-2002-2012-of-different-treatment-regimens-the-legacy-of-lamivudine-adefovir-combination-treatment
#20
Donatella Vincenti, Pierluca Piselli, Mariacarmela Solmone, Gianpiero D'Offizi, Maria R Capobianchi, Stefano Menzo
Antiviral therapy has revolutionized treatment of chronic HBV infections. First generation compounds, lamivudine and adefovir, displayed a high rate of treatment failures, and have been replaced by more potent compounds with high genetic barrier to resistance. However, the evolution of the virus towards resistance due the use of first generation compounds may still provide useful information for a better management of current antivirals. A single center sequence database including 705 HBV reverse transcriptase sequences from patients failing antiviral treatments (2002-2012) has been statistically analyzed to highlight viral evolution in relationship to the use of antiviral compounds and to their associations/sequencing in those years...
March 16, 2017: Antiviral Research
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