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Viral evolution

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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/28332654/vp1-sequencing-protocol-for-foot-and-mouth-disease-virus-molecular-epidemiology
#2
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
#3
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/28331089/diversity-distribution-and-evolution-of-tomato-viruses-in-china-uncovered-by-small-rna-sequencing
#4
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
#5
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
#6
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/28328797/activation-senescence-and-inflammation-markers-in-hiv-patients-association-with-renal-function
#7
Alexandra Ozanne, Pierre Duffau, Frédéric-Antoine Dauchy, Claire Rigothier, Cécile Terrien, Estibaliz Lazaro, Charles Cazanave, Sylvie Lawson-Ayayi, Fabrice Bonnet, Patrick Blanco, Linda Wittkop, Isabelle Pellegrin
OBJECTIVES: To assess the association between immune-activation (IA), immune-senescence (IS), inflammation biomarkers and renal function measured by estimated glomerular function rate (eGFR) at inclusion and its evolution over a 3-years follow-up in HIV-infected patients with undetectable viral load. DESIGN: The CIADIS (Chronic Immune Activation anD Senescence) sub-study consecutively included patients between October 2011 and May 2013 enrolled in the ANRS CO3 Aquitaine observational cohort...
March 21, 2017: AIDS
https://www.readbyqxmd.com/read/28327527/emerging-interaction-patterns-in-the-emiliania-huxleyi-ehv-system
#8
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/28325923/clinical-features-and-viral-quasispecies-characteristics-associated-with-infection-by-the-hepatitis-b-virus-g145r-immune-escape-mutant
#9
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/28325903/whole-genome-analysis-of-human-papillomavirus-types-16-18-and-58-isolated-from-cervical-precancer-and-cancer-samples-in-chinese-women
#10
Ying Liu, Yaqi Pan, Weijiao Gao, Yang Ke, Zheming Lu
Human papillomavirus (HPV) types 16, 18 and 58 are ranked the top three high-risk HPV types for cervical intraepithelial neoplasia (CIN) and invasive carcinoma. We aimed to evaluate the diversity of HPV16, HPV18, and HPV58 genetic variants by HPV capture technology combined with next generation sequencing. 295, 73, and 148 variations were observed in 51 HPV16, 7 HPV18, and 11 HPV58 genomes, respectively. HPV16 isolates were predominantly of the A variant lineage, and sublineage A4 (Asian) was the most common...
March 21, 2017: Scientific Reports
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
#11
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
https://www.readbyqxmd.com/read/28320935/triad-of-human-cellular-proteins-irf2-fam111a-and-rfc3-restrict-replication-of-orthopoxvirus-spi-1-host-range-mutants
#12
Debasis Panda, Daniel J Fernandez, Madhu Lal, Eugen Buehler, Bernard Moss
Viruses and their hosts can reach balanced states of evolution ensuring mutual survival, which makes it difficult to appreciate the underlying dynamics. To uncover hidden interactions, virus mutants that have lost defense genes may be used. Deletion of the gene that encodes serine protease inhibitor 1 (SPI-1) of rabbitpox virus and vaccinia virus, two closely related orthopoxviruses, prevents their efficient replication in human cells, whereas certain other mammalian cells remain fully permissive. Our high-throughput genome-wide siRNA screen identified host factors that prevent reproduction and spread of the mutant viruses in human cells...
March 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28316597/insights-of-phage-host-interaction-in-hypersaline-ecosystem-through-metagenomics-analyses
#13
Amir Mohaghegh Motlagh, Ananda S Bhattacharjee, Felipe H Coutinho, Bas E Dutilh, Sherwood R Casjens, Ramesh K Goel
Bacteriophages, as the most abundant biological entities on Earth, place significant predation pressure on their hosts. This pressure plays a critical role in the evolution, diversity, and abundance of bacteria. In addition, phages modulate the genetic diversity of prokaryotic communities through the transfer of auxiliary metabolic genes. Various studies have been conducted in diverse ecosystems to understand phage-host interactions and their effects on prokaryote metabolism and community composition. However, hypersaline environments remain among the least studied ecosystems and the interaction between the phages and prokaryotes in these habitats is poorly understood...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28315552/cancer-immunotherapy-an-evidence-based-overview-and-implications-for-practice
#14
Virginia Bayer, Beau Amaya, Diane Baniewicz, Colleen Callahan, Lisa Marsh, Asia S McCoy
BACKGROUND: Significant research progress has been made in immunotherapies since the mid-1990s, and this rapid evolution necessitates evidence-based education on immunotherapies, their pathophysiology, and their toxicities to provide safe, effective care.
. OBJECTIVES: The aim of this article is to provide an evidence-based overview, with implications for practice, of checkpoint inhibitors, monoclonal antibodies, oncolytic viral therapies, and chimeric antigen receptor T-cell therapies...
April 1, 2017: Clinical Journal of Oncology Nursing
https://www.readbyqxmd.com/read/28315475/evolution-of-the-ability-to-modulate-host-chemokine-networks-via-gene-duplication-in-human-cytomegalovirus-hcmv
#15
Jessica A Scarborough, John R Paul, Juliet V Spencer
Human cytomegalovirus (HCMV) is a widespread pathogen that is particularly skillful at evading immune detection and defense mechanisms, largely due to extensive co-evolution with its host. One aspect of this co-evolution involves the acquisition of virally encoded G protein-coupled receptors (GPCRs) with homology to the chemokine receptor family. GPCRs are the largest family of cell surface proteins, found in organisms from yeast to humans, and they regulate a variety of cellular processes including development, sensory perception, and immune cell trafficking...
March 14, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28295052/dynamic-circulation-and-genetic-exchange-of-a-shrew-borne-hantavirus-imjin-virus-in-the-republic-of-korea
#16
Seung-Ho Lee, Won-Keun Kim, Jin Sun No, Jeong-Ah Kim, Jin Il Kim, Se Hun Gu, Heung-Chul Kim, Terry A Klein, Man-Seong Park, Jin-Won Song
Hantaviruses (family Bunyaviridae) are enveloped negative-sense tripartite RNA viruses. The natural hosts of hantaviruses include rodents, shrews, moles, and bats. Imjin virus (MJNV) is a shrew-borne hantavirus identified from the Ussuri white-toothed shrews (Crocidura lasiura) in the Republic of Korea (ROK) and China. We have isolated MJNV and determined its prevalence and molecular diversity in Gyeonggi province, ROK. However, the distribution and phylogeography of MJNV in other regions of ROK remain unknown...
March 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28294087/a-large-outbreak-of-acute-gastroenteritis-in-shippensburg-pennsylvania-1972-revisited-evidence-for-common-source-exposure-to-a-recombinant-gii-pg-gii-3-norovirus
#17
J A Johnson, G I Parra, E A Levenson, K Y Green
Historical outbreaks can be an important source of information in the understanding of norovirus evolution and epidemiology. Here, we revisit an outbreak of undiagnosed gastroenteritis that occurred in Shippensburg, Pennsylvania in 1972. Nearly 5000 people fell ill over the course of 10 days. Symptoms included diarrhea, vomiting, stomach cramps, and fever, lasting for a median of 24 h. Using current techniques, including next-generation sequencing of full-length viral genomic amplicons, we identified an unusual norovirus recombinant (GII...
March 15, 2017: Epidemiology and Infection
https://www.readbyqxmd.com/read/28291233/lysogeny-in-nature-mechanisms-impact-and-ecology-of-temperate-phages
#18
Cristina Howard-Varona, Katherine R Hargreaves, Stephen T Abedon, Matthew B Sullivan
Viruses that infect bacteria (phages) can influence bacterial community dynamics, bacterial genome evolution and ecosystem biogeochemistry. These influences differ depending on whether phages establish lytic, chronic or lysogenic infections. Although the first two produce virion progeny, with lytic infections resulting in cell destruction, phages undergoing lysogenic infections replicate with cells without producing virions. The impacts of lysogeny are numerous and well-studied at the cellular level, but ecosystem-level consequences remain underexplored compared to those of lytic infections...
March 14, 2017: ISME Journal
https://www.readbyqxmd.com/read/28289418/fighting-viral-infections-and-virus-driven-tumors-with-cytotoxic-cd4-t-cells
#19
REVIEW
Elena Muraro, Anna Merlo, Debora Martorelli, Michela Cangemi, Silvia Dalla Santa, Riccardo Dolcetti, Antonio Rosato
CD4(+) T cells have been and are still largely regarded as the orchestrators of immune responses, being able to differentiate into distinct T helper cell populations based on differentiation signals, transcription factor expression, cytokine secretion, and specific functions. Nonetheless, a growing body of evidence indicates that CD4(+) T cells can also exert a direct effector activity, which depends on intrinsic cytotoxic properties acquired and carried out along with the evolution of several pathogenic infections...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28288206/an-in-vivo-system-for-directed-experimental-evolution-of-rabbit-haemorrhagic-disease-virus
#20
Robyn N Hall, Lorenzo Capucci, Markus Matthaei, Simona Esposito, Peter J Kerr, Michael Frese, Tanja Strive
The calicivirus Rabbit haemorrhagic disease virus (RHDV) is widely used in Australia as a biocontrol agent to manage wild European rabbit (Oryctolagus cuniculus) populations. However, widespread herd immunity limits the effectiveness of the currently used strain, CAPM V-351. To overcome this, we developed an experimental platform for the selection and characterisation of novel RHDV strains. As RHDV does not replicate in cell culture, variant viruses were selected by serially passaging a highly virulent RHDV field isolate in immunologically naïve laboratory rabbits that were passively immunised 18-24 hours post-challenge with a neutralising monoclonal antibody...
2017: PloS One
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