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https://www.readbyqxmd.com/read/28208721/evolution-and-divergence-of-h3n8-equine-influenza-viruses-circulating-in-the-united-kingdom-from-2013-to-2015
#1
Adam Rash, Rachel Morton, Alana Woodward, Olivia Maes, John McCauley, Neil Bryant, Debra Elton
Equine influenza viruses (EIV) are a major cause of acute respiratory disease in horses worldwide and occasionally also affect vaccinated animals. Like other influenza A viruses, they undergo antigenic drift, highlighting the importance of both surveillance and virus characterisation in order for vaccine strains to be kept up to date. The aim of the work reported here was to monitor the genetic and antigenic changes occurring in EIV circulating in the UK from 2013 to 2015 and to identify any evidence of vaccine breakdown in the field...
February 8, 2017: Pathogens
https://www.readbyqxmd.com/read/28207761/the-analysis-of-translation-related-gene-set-boosts-debates-around-origin-and-evolution-of-mimiviruses
#2
REVIEW
Jônatas Santos Abrahão, Rodrigo Araújo, Philippe Colson, Bernard La Scola
The giant mimiviruses challenged the well-established concept of viruses, blurring the roots of the tree of life, mainly due to their genetic content. Along with other nucleo-cytoplasmic large DNA viruses, they compose a new proposed order-named Megavirales-whose origin and evolution generate heated debate in the scientific community. The presence of an arsenal of genes not widespread in the virosphere related to important steps of the translational process, including transfer RNAs, aminoacyl-tRNA synthetases, and translation factors for peptide synthesis, constitutes an important element of this debate...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28202767/genotype-specific-evolution-of-hepatitis-e-virus
#3
Adam B Brayne, Bethany L Dearlove, James S Lester, Sergei L Kosakovsky Pond, Simon D W Frost
Hepatitis E virus (HEV) is the most common cause of acute viral hepatitis globally. HEV comprises four genotypes with different geographic distributions and host ranges. We utilise this natural case-control study for investigating the evolution of zoonotic viruses compared to single host viruses, using 244 near full length HEV genomes. Genome wide estimates of dN/dS located a region of overlapping reading frames, which is subject to positive selection in genotypes 3 and 4. The open reading frames (ORFs) involved have functions related to host-pathogen interaction, so genotype specific evolution of these regions may reflect their fitness...
February 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28198110/emergence-of-a-novel-highly-pathogenic-porcine-reproductive-and-respiratory-syndrome-virus-in-china
#4
J-K Liu, X Zhou, J-Q Zhai, B Li, C-H Wei, A-L Dai, X-Y Yang, M-L Luo
From 2014 to 2015, four novel highly pathogenic PRRS virus (HP-PRRSV) strains named 14LY01-FJ, 14LY02-FJ 15LY01-FJ, and 15LY02-FJ were isolated from high morbidity (100%) and mortality (40%-80%) in piglets and sows in Fujian Province. To further our knowledge about these novel virus strains, we characterized their complete genomes and determined their pathogenicity in piglets. Full-length genome sequencing analysis showed that these four isolates were closely related to type 2 (North American type, NA-type) isolates, with 88...
February 14, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/28194580/hepatitis-c-virus-genotype-3a-in-a-population-of-injecting-drug-users-in-montenegro-bayesian-and-evolutionary-analysis
#5
Boban Mugosa, Eleonora Cella, Alessia Lai, Alessandra Lo Presti, Aletheia Blasi, Zoran Vratnica, Danijela Vujoševic, Erika Ebranati, Dragan Lauševic, Michele Guarino, Gianguglielmo Zehender, Teresa Milano, Stefano Pascarella, Silvia Spoto, Silvia Angeletti, Massimo Ciccozzi
Few reports are available on HCV molecular epidemiology among IDUs in Eastern Europe, and none in Montenegro. The aim of this study was to investigate the HCV genotype distribution in Montenegro among IDUs and to perform Bayesian and evolutionary analysis of the most prevalent HCV genotype circulating in this population. Sixty-four HCV-positive IDUs in Montenegro were enrolled between 2013 and 2014, and the NS5B gene was sequenced. The Bayesian analysis showed that the most prevalent subtype was HCV-3a. Phylogenetic data showed that HCV-3a reached Montenegro in the late 1990s, causing an epidemic that exponentially grew between the 1995 and 2005...
February 13, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28194314/evolutionary-and-functional-implications-of-hypervariable-loci-within-the-skin-virome
#6
Geoffrey D Hannigan, Qi Zheng, Jacquelyn S Meisel, Samuel S Minot, Frederick D Bushman, Elizabeth A Grice
Localized genomic variability is crucial for the ongoing conflicts between infectious microbes and their hosts. An understanding of evolutionary and adaptive patterns associated with genomic variability will help guide development of vaccines and antimicrobial agents. While most analyses of the human microbiome have focused on taxonomic classification and gene annotation, we investigated genomic variation of skin-associated viral communities. We evaluated patterns of viral genomic variation across 16 healthy human volunteers...
2017: PeerJ
https://www.readbyqxmd.com/read/28193550/genetic-characterization-molecular-epidemiology-and-phylogenetic-relationships-of-insect-specific-viruses-in-the-taxon-negevirus
#7
Marcio R T Nunes, María Angélica Contreras-Gutierrez, Hilda Guzman, Livia C Martins, Mayla Feitoza Barbirato, Chelsea Savit, Victoria Balta, Sandra Uribe, Rafael Vivero, Juan David Suaza, Hamilton Oliveira, Joaquin P Nunes Neto, Valeria L Carvalho, Sandro Patroca da Silva, Jedson F Cardoso, Rodrigo Santo de Oliveira, Poliana da Silva Lemos, Thomas G Wood, Steven G Widen, Pedro F C Vasconcelos, Durland Fish, Nikos Vasilakis, Robert B Tesh
The recently described taxon Negevirus is comprised of a diverse group of insect-specific viruses isolated from mosquitoes and phlebotomine sandflies. In this study, a comprehensive genetic characterization, molecular, epidemiological and evolutionary analyses were conducted on nearly full-length sequences of 91 new negevirus isolates obtained in Brazil, Colombia, Peru, Panama, USA and Nepal. We demonstrated that these arthropod restricted viruses are clustered in two major phylogenetic groups with origins related to three plant virus genera (Cilevirus, Higrevirus and Blunevirus)...
February 10, 2017: Virology
https://www.readbyqxmd.com/read/28192520/holding-back-the-tiger-successful-control-program-protects-australia-from-aedes-albopictus-expansion
#8
Mutizwa Odwell Muzari, Gregor Devine, Joseph Davis, Bruce Crunkhorn, Andrew van den Hurk, Peter Whelan, Richard Russell, James Walker, Peter Horne, Gerhard Ehlers, Scott Ritchie
BACKGROUND: The Asian tiger mosquito, Aedes albopictus, is an important vector of dengue, chikungunya and Zika viruses and is a highly invasive and aggressive biter. Established populations of this species were first recognised in Australia in 2005 when they were discovered on islands in the Torres Strait, between mainland Australia and Papua New Guinea. A control program was implemented with the original goal of eliminating Ae. albopictus from the Torres Strait. We describe the evolution of management strategies that provide a template for Ae...
February 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28191658/interpatient-mutational-spectrum-of-human-coronavirus-oc43-revealed-by-illumina-sequencing
#9
Geoffrey J Gorse, Gira B Patel, Xiaofeng Fan
Human coronaviruses (HCoV) are RNA viruses that cause respiratory tract infections with viral replication of limited duration. The host and viral population heterogeneity could influence clinical phenotypes. Employing long RT-PCR with Illumina sequencing, we quantified the gene mutation load at 0.5% mutation frequency for the 4,529 bp-domain spanning the Spike gene (4,086 bp) of HCoV-OC43 in four upper respiratory clinical specimens obtained during acute illness. There were a total of 121 mutations for all four HCoV samples with the average number of mutations at 30...
February 12, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/28187792/evolution-of-rna-and-dna-guided-antivirus-defense-systems-in-prokaryotes-and-eukaryotes-common-ancestry-vs-convergence
#10
REVIEW
Eugene V Koonin
: Complementarity between nucleic acid molecules is central to biological information transfer processes. Apart from the basal processes of replication, transcription and translation, complementarity is also employed by multiple defense and regulatory systems. All cellular life forms possess defense systems against viruses and mobile genetic elements, and in most of them some of the defense mechanisms involve small guide RNAs or DNAs that recognize parasite genomes and trigger their inactivation...
February 10, 2017: Biology Direct
https://www.readbyqxmd.com/read/28185126/zika-virus-and-neuroscience-the-need-for-a-translational-collaboration
#11
Lavínia Schuler-Faccini, Paulo Roehe, Eduardo R Zimmer, André Quincozes-Santos, Adriano M de Assis, Elizabeth Obino Cirne Lima, Jorge Almeida Guimarães, Cesar Victora, Vivaldo Moura Neto, Diogo O Souza
Zika virus (ZIKV) has become a major challenge for scientists and health agencies. ZIKV's involvement with human fetal microcephaly and Guillain-Barré syndrome and its transmission through Aedes africanus and Aedes aegypti mosquitos highlighted the epidemiological and neurological risks associated to ZIKV infection. In 2013, ZIKV arrives in Brazil but the first outbreak in the country was reported in 2015. Here, we used the Web of Science as a search tool for comparing the evolution of world and Brazilian scientific research on dengue virus (DENV)-also present in mosquito-, ZIKV and microcephaly...
February 9, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28182717/error-baseline-rates-of-five-sample-preparation-methods-used-to-characterize-rna-virus-populations
#12
Jeffrey R Kugelman, Michael R Wiley, Elyse R Nagle, Daniel Reyes, Brad P Pfeffer, Jens H Kuhn, Mariano Sanchez-Lockhart, Gustavo F Palacios
Individual RNA viruses typically occur as populations of genomes that differ slightly from each other due to mutations introduced by the error-prone viral polymerase. Understanding the variability of RNA virus genome populations is critical for understanding virus evolution because individual mutant genomes may gain evolutionary selective advantages and give rise to dominant subpopulations, possibly even leading to the emergence of viruses resistant to medical countermeasures. Reverse transcription of virus genome populations followed by next-generation sequencing is the only available method to characterize variation for RNA viruses...
2017: PloS One
https://www.readbyqxmd.com/read/28178932/variability-among-cucurbitaceae-species-melon-cucumber-and-watermelon-in-a-genomic-region-containing-a-cluster-of-nbs-lrr-genes
#13
Jordi Morata, Pere Puigdomènech
BACKGROUND: Cucurbitaceae species contain a significantly lower number of genes coding for proteins with similarity to plant resistance genes belonging to the NBS-LRR family than other plant species of similar genome size. A large proportion of these genes are organized in clusters that appear to be hotspots of variability. The genomes of the Cucurbitaceae species measured until now are intermediate in size (between 350 and 450 Mb) and they apparently have not undergone any genome duplications beside those at the origin of eudicots...
February 8, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28178344/comparative-analysis-estimates-the-relative-frequencies-of-co-divergence-and-cross-species-transmission-within-viral-families
#14
Jemma L Geoghegan, Sebastián Duchêne, Edward C Holmes
The cross-species transmission of viruses from one host species to another is responsible for the majority of emerging infections. However, it is unclear whether some virus families have a greater propensity to jump host species than others. If related viruses have an evolutionary history of co-divergence with their hosts there should be evidence of topological similarities between the virus and host phylogenetic trees, whereas host jumping generates incongruent tree topologies. By analyzing co-phylogenetic processes in 19 virus families and their eukaryotic hosts we provide a quantitative and comparative estimate of the relative frequency of virus-host co-divergence versus cross-species transmission among virus families...
February 8, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28171759/viral-evolution-mummy-virus-challenges-presumed-history-of-smallpox
#15
Joel O Wertheim
Despite evidence of smallpox in antiquity, a new study of a 350 year-old Lithuanian child mummy suggests that the global viral genetic diversity circulating during the 20(th) century was only around 200 years old.
February 6, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28170438/the-effective-rate-of-influenza-reassortment-is-limited-during-human-infection
#16
Ashley Sobel Leonard, Micah T McClain, Gavin J D Smith, David E Wentworth, Rebecca A Halpin, Xudong Lin, Amy Ransier, Timothy B Stockwell, Suman R Das, Anthony S Gilbert, Rob Lambkin-Williams, Geoffrey S Ginsburg, Christopher W Woods, Katia Koelle, Christopher J R Illingworth
We characterise the evolutionary dynamics of influenza infection described by viral sequence data collected from two challenge studies conducted in human hosts. Viral sequence data were collected at regular intervals from infected hosts. Changes in the sequence data observed across time show that the within-host evolution of the virus was driven by the reversion of variants acquired during previous passaging of the virus. Treatment of some patients with oseltamivir on the first day of infection did not lead to the emergence of drug resistance variants in patients...
February 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28167936/small-rna-based-genetic-engineering-for-plant-viral-resistance-application-in-crop-protection
#17
REVIEW
Annum Khalid, Qingling Zhang, Muhammad Yasir, Feng Li
Small RNAs regulate a large set of gene expression in all plants and constitute a natural immunity against viruses. Small RNA based genetic engineering (SRGE) technology had been explored for crop protection against viruses for nearly 30 years. Viral resistance has been developed in diverse crops with SRGE technology and a few viral resistant crops have been approved for commercial release. In this review we summarized the efforts generating viral resistance with SRGE in different crops, analyzed the evolution of the technology, its efficacy in different crops for different viruses and its application status in different crops...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28167595/oropouche-virus-clinical-epidemiological-and-molecular-aspects-of-a-neglected-orthobunyavirus
#18
REVIEW
Jorge Fernando Travassos da Rosa, William Marciel de Souza, Francisco de Paula Pinheiro, Mário Luiz Figueiredo, Jedson Ferreira Cardoso, Gustavo Olszanski Acrani, Márcio Roberto Teixeira Nunes
Oropouche virus (OROV) is an important cause of arboviral illness in Latin American countries, more specifically in the Amazon region of Brazil, Venezuela and Peru, as well as in other countries such as Panama. In the past decades, the clinical, epidemiological, pathological, and molecular aspects of OROV have been published and provide the basis for a better understanding of this important human pathogen. Here, we describe the milestones in a comprehensive review of OROV epidemiology, pathogenesis, and molecular biology, including a description of the first isolation of the virus, the outbreaks during the past six decades, clinical aspects of OROV infection, diagnostic methods, genome and genetic traits, evolution, and viral dispersal...
February 6, 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/28164650/emergence-of-hepatitis-c-virus-genotype-recombinant-forms-2k-1b-in-georgia
#19
Mamuka Zakalashvili, Michael Weizenegger, Jan Bartel, Monika Markowski, Jaba Zarqua, Salome Kavsadze, Ketevan Kvatadze, George Basheleishvili, Tamar Phirtskhalaishvili, Tamar Dzagania, Lela Zangurashvili, Nino Kankia, Nino Jashiashvili, Maka Lomidze, Tengiz Telia, Vakhtang Kerashvili, Maia Zhamutashvili, Nikoloz Abramishvili, Irakli Rtskhiladze, David Metreveli
BACKGROUND: Hepatitis C virus (HCV) evolution is thought to proceed by mutations within the six major genotypes. Studies of HCV recombinant genotypes in different parts of the world have recently been initiated. Only a few cases of recombination have been identified worldwide, predominantly in Eastern Europe and Asia. In 2011 we detected the recombinant form (RF) of a HCV genotype RF_2k/1b in Georgia. Therefore, we reviewed HCV genotyping data of 491 patients with chronic hepatitis C virus infections of our center in Tbilisi over a period of two years...
July 1, 2016: Clinical Laboratory
https://www.readbyqxmd.com/read/28164282/incidence-trends-for-potentially-human-papilloma-virus-related-and-unrelated-head-and-neck-cancers-in-france-using-population-based-cancer-registries-data-1980-2012
#20
Karine Jéhannin-Ligier, Aurélien Belot, Anne-Valérie Guizard, Nadine Bossard, Guy Launoy, Zoé Uhry
Human papilloma virus (HPV) has been recently recognised as a carcinogenic factor for a subset of head and neck cancers (HNC). In Europe, France has one of the highest incidence rates of HNC. The aim of this study is to explore changes in HNC incidence in France, potentially in relation with infection by HPV. HNC were classified into two anatomical groups: potentially HPV-related and HPV- unrelated. Trends over the period 1980-2012 were analysed by an age-period-cohort model based on data from eleven French cancer registries...
February 6, 2017: International Journal of Cancer. Journal International du Cancer
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