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https://www.readbyqxmd.com/read/29150926/viral-short-orfs-and-their-possible-functions
#1
REVIEW
Yaara Finkel, Noam Stern-Ginossar, Michal Schwartz
Definition of functional genomic elements is one of the greater challenges of the genomic era. Traditionally, putative short Open Reading Frames (sORFs) coding for less than 100 amino acids were disregarded due to computational and experimental limitations, however it has become clear over the past several years that translation of sORFs is pervasive and serves diverse functions. The development of ribosome profiling, allowing identification of translated sequences genome-wide, revealed wide-spread, previously unidentified translation events...
November 18, 2017: Proteomics
https://www.readbyqxmd.com/read/29150915/epidemiology-of-rhdv2-lagovirus-europaeus-gi-2-in-free-living-wild-european-rabbits-in-portugal
#2
C Rouco, J Abrantes, A Serronha, A M Lopes, E Maio, M J Magalhães, E Blanco, J Bárcena, P J Esteves, N Santos, P C Alves, P Monterroso
As the detection of the first outbreak of a novel aetiological agent of rabbit haemorrhagic disease commonly called RHDV2 or RHDVb (Lagovirus europaeus/GI.2, henceforth GI.2) in France in 2010, the virus rapidly spread throughout continental Europe and nearby islands such as Great Britain, Sardinia, Sicily, the Azores and the Canary Islands among others. The outbreaks of this new lagovirus cause important economic losses in rabbitries, and ecological disruptions by affecting the conservation of rabbit-sensitive top predators...
November 17, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/29149964/chikungunya-infection-in-solid-organ-transplant-recipients
#3
E S Girão, B G Rodrigues Dos Santos, E S do Amaral, P E G Costa, K B Pereira, A H de Araujo Filho, E B Hyppolito, M U Mota, L C B F Marques, C M Costa de Oliveira, S L da Silva, J H P Garcia, P F C B C Fernandes
BACKGROUND: Chikungunya virus (CHIKV) is an emerging mosquito-borne disease that causes acute febrile polyarthralgia and arthritis. CHIKV has spread rapidly to the Americas and, in Brazil, autochthonous cases are increasingly been reported. Solid organ transplant (SOT) recipients who travel to or live in CHIKV endemic areas are under high risk of acquiring the disease. Few data exist regarding the clinical characteristics of CHIKV infections in this population. We report the first case series of CHIKV infection in SOT recipients...
November 2017: Transplantation Proceedings
https://www.readbyqxmd.com/read/29149197/sieve-analysis-of-breakthrough-hiv-1-sequences-in-hvtn-505-identifies-vaccine-pressure-targeting-the-cd4-binding-site-of-env-gp120
#4
Allan C deCamp, Morgane Rolland, Paul T Edlefsen, Eric Sanders-Buell, Breana Hall, Craig A Magaret, Andrew J Fiore-Gartland, Michal Juraska, Lindsay N Carpp, Shelly T Karuna, Meera Bose, Steven LePore, Shana Miller, Annemarie O'Sullivan, Kultida Poltavee, Hongjun Bai, Kalpana Dommaraju, Hong Zhao, Kim Wong, Lennie Chen, Hasan Ahmed, Derrick Goodman, Matthew Z Tay, Raphael Gottardo, Richard A Koup, Robert Bailer, John R Mascola, Barney S Graham, Mario Roederer, Robert J O'Connell, Nelson L Michael, Merlin L Robb, Elizabeth Adams, Patricia D'Souza, James Kublin, Lawrence Corey, Daniel E Geraghty, Nicole Frahm, Georgia D Tomaras, M Juliana McElrath, Lisa Frenkel, Sheila Styrchak, Sodsai Tovanabutra, Magdalena E Sobieszczyk, Scott M Hammer, Jerome H Kim, James I Mullins, Peter B Gilbert
Although the HVTN 505 DNA/recombinant adenovirus type 5 vector HIV-1 vaccine trial showed no overall efficacy, analysis of breakthrough HIV-1 sequences in participants can help determine whether vaccine-induced immune responses impacted viruses that caused infection. We analyzed 480 HIV-1 genomes sampled from 27 vaccine and 20 placebo recipients and found that intra-host HIV-1 diversity was significantly lower in vaccine recipients (P ≤ 0.04, Q-values ≤ 0.09) in Gag, Pol, Vif and envelope glycoprotein gp120 (Env-gp120)...
2017: PloS One
https://www.readbyqxmd.com/read/29149175/the-introduction-of-dengue-follows-transportation-infrastructure-changes-in-the-state-of-acre-brazil-a-network-based-analysis
#5
Raquel Martins Lana, Marcelo Ferreira da Costa Gomes, Tiago França Melo de Lima, Nildimar Alves Honório, Cláudia Torres Codeço
Human mobility, presence and passive transportation of Aedes aegypti mosquito, and environmental characteristics are a group of factors which contribute to the success of dengue spread and establishment. To understand this process, we assess data from dengue national and municipal basins regarding population and demographics, transportation network, human mobility, and Ae. aegypti monitoring for the Brazilian state of Acre since the first recorded dengue case in the year 2000 to the year 2015. During this period, several changes in Acre's transport infrastructure and urbanization have been started...
November 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29149077/rna-virus-evolution-via-a-quasispecies-based-model-reveals-a-drug-target-with-a-high-barrier-to-resistance
#6
Richard J Bingham, Eric C Dykeman, Reidun Twarock
The rapid occurrence of therapy-resistant mutant strains provides a challenge for anti-viral therapy. An ideal drug target would be a highly conserved molecular feature in the viral life cycle, such as the packaging signals in the genomes of RNA viruses that encode an instruction manual for their efficient assembly. The ubiquity of this assembly code in RNA viruses, including major human pathogens, suggests that it confers selective advantages. However, their impact on viral evolution cannot be assessed in current models of viral infection that lack molecular details of virus assembly...
November 17, 2017: Viruses
https://www.readbyqxmd.com/read/29148270/a-g3p-13-porcine-group-a-rotavirus-emerging-in-china-is-a-reassortant-and-a-natural-recombinant-in-the-vp4-gene
#7
Z Jing, X Zhang, H Shi, J Chen, D Shi, H Dong, L Feng
Group A rotaviruses (RVAs) are a major cause of serious intestinal disease in piglets. In this study, a novel pig strain was identified in a stool sample from China. The strain was designated RVA/Pig/China/LNCY/2016/G3P[13] and had a G3-P[13]-I5-R1-C1-M1-A8-N1-T1-E1-H1 genome. The viral protein 7 (VP7) and non-structural protein 4 (NSP4) genes of RVA/Pig/China/LNCY/2016/G3P[13] were closely related to cogent genes of human RVAs, suggesting that a reassortment between pig and human strains had occurred. Recombination analysis showed that RVA/Pig/China/LNCY/2016/G3P[13] is a natural recombinant strain between the P[23] and P[7] RVA strains, and crossover points for recombination were found at nucleotides (nt) 456 and 804 of the VP4 gene...
November 16, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/29146794/evolution-of-neurovirulent-zika-virus
#8
Gavin Screaton, Juthathip Mongkolsapaya
No abstract text is available yet for this article.
November 17, 2017: Science
https://www.readbyqxmd.com/read/29143589/biomarkers-in-the-evolution-of-multiple-sclerosis
#9
Thomas Berger
Nonimaging biomarkers can be applied in differential diagnosis, evaluation of disease progression and therapy monitoring of multiple sclerosis (MS). Presence of oligoclonal IgG bands in cerebrospinal fluid is a diagnostic element and a negative predictor of MS evolution. AQP4 antibodies are pathogenic and diagnostic for neuromyelitis optica spectrum disorder. Antibodies to myelin oligodendrocyte glycoprotein develop in about 50% of predominantly pediatric patients with acute disseminated encephalomyelitis, but their possible role in pathogenesis is unknown...
November 2017: Neurodegenerative Disease Management
https://www.readbyqxmd.com/read/29143492/molecular-epidemiological-survey-and-phylogenetic-analysis-of-bovine-influenza-d-virus-in-japan
#10
H Mekata, M Yamamoto, S Hamabe, H Tanaka, T Omatsu, T Mizutani, B M Hause, T Okabayashi
The influenza D virus, a new member of the Orthomyxoviridae family, is predominantly found in cattle. Although viral pathology and clinical disease in cattle appear mild, this virus plays an important role as a trigger of bovine respiratory disease (BRD). BRD is a costly illness worldwide. Thus, epidemiological surveys of the influenza D virus are necessary. Here, we conducted a molecular epidemiological survey for the influenza D virus in healthy and respiratory-diseased cattle in Japan. We found that 2.1% (8/377) of the cattle were infected with influenza D...
November 16, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/29143488/isolation-and-characterization-of-novel-goose-parvovirus-related-virus-reveal-the-evolution-of-waterfowl-parvovirus
#11
P Li, S Lin, R Zhang, J Chen, D Sun, J Lan, S Song, Z Xie, S Jiang
Short beak and dwarfism syndrome (SBDS) has been constantly breaking out in China since 2015. It is caused by a novel goose parvovirus-related virus (NGPV) and can severely restrict the growth of ducks. In this study, seven NGPV stains were isolated from different regions in China between 2015 and 2016. To better understand the correlation between NGPV and goose parvovirus (GPV), we conducted complete genome sequencing and a comprehensive analysis of the NGPV genome. The phylogenetic and alignment analysis showed that NGPV is a branch of GPV, sharing 92...
November 16, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/29143187/multi-locus-sequence-typing-of-african-swine-fever-viruses-from-endemic-regions-of-kenya-and-eastern-uganda-2011-2013-reveals-rapid-b602l-central-variable-region-evolution
#12
C K Onzere, A D Bastos, E A Okoth, J K Lichoti, E N Bochere, M G Owido, G Ndambuki, M Bronsvoort, R P Bishop
The central variable region (CVR) within the B602L gene of the African swine fever virus (ASFV) is highly polymorphic within the 23 ASFV genotypes defined by sequencing of the C-terminal end of the p72 locus. Sequencing the p54 gene further discriminates ASFV genotypes that are conserved at the p72 locus. Variation in the thymidine kinase locus is a novel additional tool for ASFV genotyping whose application for this purpose is described for the first time herein. We evaluated genetic variation at these four polymorphic loci in 39 ASFV isolates obtained from outbreaks in Kenya and a region of Eastern Uganda between 2011 and 2013...
November 15, 2017: Virus Genes
https://www.readbyqxmd.com/read/29142146/inflammatory-natalizumab-associated-pml-baseline-characteristics-lesion-evolution-and-relation-with-pml-iris
#13
Mike P Wattjes, Martijn T Wijburg, Jeroen van Eijk, Stephan Frequin, Bernard M J Uitdehaag, Frederik Barkhof, Clemens Warnke, Joep Killestein
BACKGROUND AND OBJECTIVE: Natalizumab-associated progressive multifocal leukoencephalopathy (NTZ-PML) patients may show imaging signs suggestive of inflammation at diagnosis ('inflammatory PML'), reminiscent of PML-immune reconstitution inflammatory syndrome (PML-IRIS). We investigated the imaging characteristics of inflammatory NTZ-PML lesions and PML-IRIS to determine differentiating and overlapping features. METHODS: We scored the presence, localisation and pattern of imaging characteristics of inflammation on brain MRI scans of inflammatory NTZ-PML patients...
November 15, 2017: Journal of Neurology, Neurosurgery, and Psychiatry
https://www.readbyqxmd.com/read/29142136/size-composition-and-evolution-of-hiv-dna-populations-during-early-antiretroviral-therapy-and-intensification-with-maraviroc
#14
Antoine Chaillon, Sara Gianella, Steven M Lada, Josué Perez-Santiago, Parris Jordan, Caroline Ignacio, Maile Karris, Douglas Richman, Sanjay R Mehta, Susan J Little, Joel O Wertheim, Davey M Smith
Residual viremia is common during antiretroviral therapy (ART), and could be caused by ongoing low-level virus replication or by release of viral particles from infected cells. ART Intensification should impact ongoing viral propagation but not virion release. Eighteen acutely infected men were enrolled in a randomized controlled trial, and followed for a median of 107 weeks. Participants started ART with (n=9) or without (n=9) intensification with maraviroc (MVC) within 90 days of infection. Levels of HIV DNA and cell-free RNA were quantified by droplet digital PCR...
November 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29141204/characterization-of-the-complete-genome-antigenicity-pathogenicity-tissue-tropism-and-shedding-of-a-recombinant-avian-infectious-bronchitis-virus-with-a-ck-ch-ljl-140901-like-backbone-and-an-s2-fragment-from-a-4-91-like-virus
#15
Lei Jiang, Zongxi Han, Yuqiu Chen, Wenjun Zhao, Junfeng Sun, Yan Zhao, Shengwang Liu
In this study, we isolated an infectious bronchitis virus, designated I1101/16, from broiler breeders in China. Analysis of the S1 gene showed that isolate I1101/16 was genetically close to strain ck/CH/LJL/140901, which belongs to the TW I genotype (also known as lineage GI-7 based on the recent IBV classification), however the S2 gene showed genetic diversity comparing to that of S1 gene. Comparison of the genomic sequences showed that the genome of isolate I1101/16 was similar to that of strain ck/CH/LJL/140901 from the 5' end of the genome to the 5' end of the S2 gene and from the 5' end of the 3a gene to the end of the genome, whereas the remaining parts of the genome sequences were more closely related to those of strain 4/91 than those of ck/CH/LJL/140901, thereby suggesting that recombination might have occurred during the origin of the virus...
November 12, 2017: Virus Research
https://www.readbyqxmd.com/read/29136651/structural-basis-of-glycan-specificity-of-p-19-vp8-implications-for-rotavirus-zoonosis-and-evolution
#16
Yang Liu, Shenyuan Xu, Andrew L Woodruff, Ming Xia, Ming Tan, Michael A Kennedy, Xi Jiang
Recognition of specific cell surface glycans, mediated by the VP8* domain of the spike protein VP4, is the essential first step in rotavirus (RV) infection. Due to lack of direct structural information of virus-ligand interactions, the molecular basis of ligand-controlled host ranges of the major human RVs (P[8] and P[4]) in P[II] genogroup remains unknown. Here, through characterization of a minor P[II] RV (P[19]) that can infect both animals (pigs) and humans, we made an important advance to fill this knowledge gap by solving the crystal structures of the P[19] VP8* in complex with its ligands...
November 14, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/29135988/evolution-of-acute-hepatitis-c-virus-infection-in-a-large-european-city-trends-and-new-patterns
#17
César Garriga, Sandra Manzanares-Laya, Patricia García de Olalla, Pilar Gorrindo, Sabela Lens, Ricard Solà, María Martínez-Rebollar, Montserrat Laguno, Jordi Navarro, Xavier Torras, Mercè Gurguí, María-Jesús Barberá, Josep Quer, Eva Masdeu, Pere Simón, Miriam Ros, Anna de Andrés, Joan A Caylà
The aims of this study were to describe the evolution of acute hepatitis C virus (HCV) infections since 2004 and to determine its associated factors. Acute HCV infections diagnosed in Barcelona from 2004 to 2015 were included. Incidence ratios (IR) were then estimated for sex and age groups. Cases were grouped between 2004-2005, 2006-2011 and 2012-2015, and their incidence rate ratios (IRR) were calculated. In addition, risk factors for acute HCV infection were identified using multinomial logistic regression for complete, available and multiple imputed data...
2017: PloS One
https://www.readbyqxmd.com/read/29134777/epidemiological-investigation-of-h9-avian-influenza-virus-newcastle-disease-virus-tembusu-virus-goose-parvovirus-and-goose-circovirus-infection-of-geese-in-china
#18
X Niu, H Wang, L Wei, M Zhang, J Yang, H Chen, Y Tang, Y Diao
To deepen the knowledge about epidemic prevalence in the goose breeding field, a triplex PCR assay was established, and 478 samples were collected from scaled goose farms in 11 provinces in China. The results of this epidemiological investigation showed that incidence rates of H9 avian influenza and goose circovirus were the highest among five infectious diseases that were evaluated. In addition, the triplex PCR assay established remarkable sensitivity, rapidity and versatility compared to other diagnostic methods...
November 13, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/29133028/evolution-and-postglacial-colonization-of-seewis-hantavirus-with-sorex-araneus-in-finland
#19
Jiaxin Ling, Teemu Smura, Daniel Tamarit, Otso Huitu, Liina Voutilainen, Heikki Henttonen, Antti Vaheri, Olli Vapalahti, Tarja Sironen
Hantaviruses have co-existed with their hosts for millions of years. Seewis virus (SWSV), a soricomorph-borne hantavirus, is widespread in Eurasia, ranging from Central Siberia to Western Europe. To gain insight into the phylogeography and evolutionary history of SWSV in Finland, lung tissue samples of 225 common shrews (Sorex araneus) trapped from different parts of Finland were screened for the presence of SWSV RNA. Forty-two of the samples were positive. Partial small (S), medium (M) and large (L) segments of the virus were sequenced, and analyzed together with all SWSV sequences available in Genbank...
November 10, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29132309/significant-differences-in-terms-of-codon-usage-bias-between-bacteriophage-early-and-late-genes-a-comparative-genomics-analysis
#20
Oriah Mioduser, Eli Goz, Tamir Tuller
BACKGROUND: Viruses undergo extensive evolutionary selection for efficient replication which effects, among others, their codon distribution. In the current study, we aimed at understanding the way evolution shapes the codon distribution in early vs. late viral genes in terms of their expression during different stages in the viral replication cycle. To this end we analyzed 14 bacteriophages and 11 human viruses with available information about the expression phases of their genes. RESULTS: We demonstrated evidence of selection for distinct composition of synonymous codons in early and late viral genes in 50% of the analyzed bacteriophages...
November 13, 2017: BMC Genomics
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