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Viral population genetics

Marie-Line Joffret, Patsy M Polston, Richter Razafindratsimandresy, Maël Bessaud, Jean-Michel Heraud, Francis Delpeyroux
Human enteroviruses (EV) consist of more than 100 serotypes classified within four species for enteroviruses (EV-A to -D) and three species for rhinoviruses, which have been implicated in a variety of human illnesses. Being able to simultaneously amplify the whole genome and identify enteroviruses in samples is important for studying the viral diversity in different geographical regions and populations. It also provides knowledge about the evolution of these viruses. Therefore, we developed a rapid, sensitive method to detect and genetically classify all human enteroviruses in mixtures...
2018: Frontiers in Microbiology
Kadir Yeşilbağ, Christine Baechlein, Berfin Kadiroğlu, Eda Baldan Toker, Gizem Alpay, Paul Becher
Hepatitis C virus (HCV), a worldwide distributed human pathogen, causes one of the most important viral infections in human being. HCV is the type species of the genus Hepacivirus (Flaviviridae) in which recently discovered animal viruses i.e. from horses, bats, rodents and cattle are allocated. After preliminary reports in 2015 from German and African cattle, a wide distribution of bovine hepacivirus (BovHepV, Hepacivirus N) was proposed. We investigated the possible presence of BovHepV in serum samples from cattle in different locations of Turkey...
November 2018: Veterinary Microbiology
Gareth Trubl, Ho Bin Jang, Simon Roux, Joanne B Emerson, Natalie Solonenko, Dean R Vik, Lindsey Solden, Jared Ellenbogen, Alexander T Runyon, Benjamin Bolduc, Ben J Woodcroft, Scott R Saleska, Gene W Tyson, Kelly C Wrighton, Matthew B Sullivan, Virginia I Rich
Rapidly thawing permafrost harbors ∼30 to 50% of global soil carbon, and the fate of this carbon remains unknown. Microorganisms will play a central role in its fate, and their viruses could modulate that impact via induced mortality and metabolic controls. Because of the challenges of recovering viruses from soils, little is known about soil viruses or their role(s) in microbial biogeochemical cycling. Here, we describe 53 viral populations (viral operational taxonomic units [vOTUs]) recovered from seven quantitatively derived (i...
September 2018: MSystems
Y K Kiros, H Elinav, A Gebreyesus, H Gebremeskel, J Azar, D Chemtob, H Abreha, D Elbirt, E Shahar, M Chowers, D Turner, Z Grossman, A Haile, R E Sutton, S L Maayan, D Wolday
OBJECTIVES: HIV elite controllers (ECs) are a unique subgroup of HIV-positive patients who are long-term virologically suppressed in the absence of antiretroviral treatment (ART). The prevalence of this subgroup is estimated to be < 1%. Various cohorts of ECs have been described in developed countries, most of which have been demographically heterogeneous. The aim of this study was to identify ECs in two large African cohorts and to estimate their prevalence in a relatively genetically homogenous population...
October 14, 2018: HIV Medicine
Lia van der Hoek, Ernst Verschoor, Martin Beer, Dirk Höper, Kerstin Wernike, Marc Van Ranst, Jelle Matthijnssens, Piet Maes, Patricia Sastre, Paloma Rueda, Jan Felix Drexler, John Barr, Thomas Edwards, Paul Millner, Paul Vermeij, Ad de Groof, Volker Thiel, Ronald Dijkman, Franziska Suter-Riniker, Stephen Leib, Roger Koller, Alban Ramette, Olivier Engler, Christian Beuret
The increase of the human population is accompanied by growing numbers of livestock to feed this population, as well as by an increase of human invasion into natural habitats of wild animals. As a result, both animals and humans are becoming progressively vulnerable to infections with known (zoonotic) pathogens, but are also increasingly exposed to novel viruses. Global trade as well as climate changes can contribute to pathogen transmission, e.g. through import of infected vectors or expansion of habitats for arthropod vectors such as mosquitoes and midges...
September 15, 2018: Virus Research
Alessia Capone, Alessandra Lo Presti, Leonardo Sernicola, Stefania Farcomeni, Flavia Ferrantelli, Maria T Maggiorella, Edward T Mee, Nicola J Rose, Eleonora Cella, Massimo Ciccozzi, Barbara Ensoli, Alessandra Borsetti
Intra-host evolution of human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) has been shown by viral RNA analysis in subjects who naturally suppress plasma viremia to low levels, known as controllers. However, little is known about the variability of proviral DNA and the inter-relationships among contained systemic viremia, rate of reservoir reseeding and specific major histocompatibility complex (MHC) genotypes, in controllers. Here, we analysed the proviral DNA quasispecies of the env V1-V2 region, in PBMCs and in anatomical compartments of 13 long-term controller monkeys after 3...
October 12, 2018: Journal of General Virology
Brett G Dickson, Christine M Albano, Miranda E Gray, Meredith L McClure, David M Theobald, Ranjan Anantharaman, Viral B Shah, Paul Beier, Joe Fargione, Kimberly R Hall, Tabitha A Graves, Josh J Lawler, Paul B Leonard, Caitlin E Littlefield, John Novembre, Carrie Schloss, Nathan Schumaker
Conservation practitioners have long recognized ecological connectivity as a global priority for preserving biodiversity and ecosystem function. In the early years of conservation biology, ecologists extended principles of island biogeography to assess connectivity using measures of source patch proximity and other metrics derivable from binary maps of habitat. From 2006-2008, the late Brad McRae introduced circuit theory to many ecologists and conservation biologists as an alternative approach to model gene flow and the dispersal or movement routes of organisms...
October 11, 2018: Conservation Biology: the Journal of the Society for Conservation Biology
Hod Dana, Ondrej Novak, Michael Guardado-Montesino, James W Fransen, Amy Hu, Bart G Borghuis, Caiying Guo, Douglas S Kim, Karel Svoboda
Calcium imaging is commonly used to measure the neural activity of large groups of neurons in mice. Genetically encoded calcium indicators (GECIs) can be delivered for this purpose using non-invasive genetic methods. Compared to viral gene transfer, transgenic targeting of GECIs provides stable long-term expression and obviates the need for invasive viral injections. Transgenic mice expressing the green GECI GCaMP6 are already widely used. Here we present the generation and characterization of transgenic mice expressing the sensitive red GECI jRGECO1a, driven by the Thy1 promoter...
2018: PloS One
Natalie N Kinloch, Guinevere Q Lee, Jonathan M Carlson, Steven W Jin, Chanson J Brumme, Helen Byakwaga, Conrad Muzoora, Mwebesa B Bwana, Kyle D Cobarrubias, Peter W Hunt, Jeff N Martin, Mary Carrington, David R Bangsberg, P Richard Harrigan, Mark A Brockman, Zabrina L Brumme
The extent to which viral genetic context influences HIV adaptation to Human Leukocyte Antigen (HLA) class I-restricted immune pressures remains incompletely understood. The Ugandan HIV epidemic, where major pandemic group M subtypes A1 and D co-circulate in a single host population, provides an opportunity to investigate this question. We characterized plasma HIV RNA gag, pol and nef sequences, along with host HLA genotypes, in 464 antiretroviral-naïve individuals chronically infected with HIV subtypes A1 or D...
October 10, 2018: Journal of Virology
Su Young Han, Jenny Clarkson, Richard Piet, Allan E Herbison
Developments in optical imaging and optogenetics are transforming the functional investigation of neuronal networks throughout the brain. Recent studies in the neuroendocrine field have used genetic mouse models combined with a variety of light-activated optical tools as well as GCaMP calcium imaging to interrogate the neural circuitry controlling hormone secretion. The present review highlights the benefits and caveats of these approaches for undertaking both acute brain slice and functional studies in vivo...
October 9, 2018: Endocrinology
Jivan Khlghatyan, Clémentine Quintana, Martin Parent, Jean-Martin Beaulieu
Cortical D2 dopamine receptor (Drd2) have mostly been examined in the context of cognitive function regulation and neurotransmission modulation of medial prefrontal cortex by principal neurons and parvalbumin positive, fast-spiking, interneurons in schizophrenia. Early studies suggested the presence of D2 receptors in several cortical areas, albeit with major technical limitations. We used combinations of transgenic reporter systems, recombinase activated viral vectors, quantitative translatome analysis, and high sensitivity in situ hybridization to identify D2 receptor expressing cells and establish a map of their respective projections...
October 6, 2018: Cerebral Cortex
Siyang Liu, Shujia Huang, Fang Chen, Lijian Zhao, Yuying Yuan, Stephen Starko Francis, Lin Fang, Zilong Li, Long Lin, Rong Liu, Yong Zhang, Huixin Xu, Shengkang Li, Yuwen Zhou, Robert W Davies, Qiang Liu, Robin G Walters, Kuang Lin, Jia Ju, Thorfinn Korneliussen, Melinda A Yang, Qiaomei Fu, Jun Wang, Lijun Zhou, Anders Krogh, Hongyun Zhang, Wei Wang, Zhengming Chen, Zhiming Cai, Ye Yin, Huanming Yang, Mao Mao, Jay Shendure, Jian Wang, Anders Albrechtsen, Xin Jin, Rasmus Nielsen, Xun Xu
We analyze whole-genome sequencing data from 141,431 Chinese women generated for non-invasive prenatal testing (NIPT). We use these data to characterize the population genetic structure and to investigate genetic associations with maternal and infectious traits. We show that the present day distribution of alleles is a function of both ancient migration and very recent population movements. We reveal novel phenotype-genotype associations, including several replicated associations with height and BMI, an association between maternal age and EMB, and between twin pregnancy and NRG1...
October 4, 2018: Cell
Amit Kr Chakraborty, Priyanka Mukherjee, Amarjit Karam, Samir Das, Luit Barkalita, Kekungo Puro, Rajkumari Sanjukta, Sandeep Ghatak, Ingudam Sakuntala, Ram Gopal Laha, Prabodh Borah, S V Ngachan, Indu Sharma, Arnab Sen
Introduction: The work has been attempted to detect and genetically characterise the nature of Bovine Viral Diarrhea Virus (BVDV) isolates from the porcine population of the north east. Methods and Material: The samples have been collected over a two year period and are from areas where there is a mixed and integrated rearing of livestock in close proximity. The isolates were identified, cloned and sequenced using BVD specific genomic primers for two important domains viz...
2018: Open Virology Journal
Hui-Ying Ko, Yao-Tsun Li, Day-Yu Chao, Yun-Cheng Chang, Zheng-Rong T Li, Melody Wang, Chuan-Liang Kao, Tzai-Hung Wen, Pei-Yun Shu, Gwong-Jen J Chang, Chwan-Chuen King
Purifying selection during dengue viral infection has been suggested as the driving force of viral evolution and the higher complexity of the intra-host quasi-species is thought to offer an adaptive advantage for arboviruses as they cycle between arthropod and vertebrate hosts. However, very few studies have been performed to investigate the viral genetic changes within (intra-host) and between (inter-host) humans in a spatio-temporal scale. Viruses of different serotypes from various countries imported to Taiwan cause annual outbreaks...
October 2018: PLoS Neglected Tropical Diseases
Zhiqiang Wu, Liang Lu, Jiang Du, Li Yang, Xianwen Ren, Bo Liu, Jinyong Jiang, Jian Yang, Jie Dong, Lilian Sun, Yafang Zhu, Yuhui Li, Dandan Zheng, Chi Zhang, Haoxiang Su, Yuting Zheng, Hongning Zhou, Guangjian Zhu, Hongying Li, Aleksei Chmura, Fan Yang, Peter Daszak, Jianwei Wang, Qiyong Liu, Qi Jin
BACKGROUND: Rodents represent around 43% of all mammalian species, are widely distributed, and are the natural reservoirs of a diverse group of zoonotic viruses, including hantaviruses, Lassa viruses, and tick-borne encephalitis viruses. Thus, analyzing the viral diversity harbored by rodents could assist efforts to predict and reduce the risk of future emergence of zoonotic viral diseases. RESULTS: We used next-generation sequencing metagenomic analysis to survey for a range of mammalian viral families in rodents and other small animals of the orders Rodentia, Lagomorpha, and Soricomorpha in China...
October 3, 2018: Microbiome
Kevin Xu Zhong, Curtis A Suttle, Anne-Claire Baudoux, Evelyne Derelle, Jonathan Colombet, Anna Cho, Jessica Caleta, Christophe Six, Stéphan Jacquet
Pelagic cyanobacteria are key players in the functioning of aquatic ecosystems, and their viruses (cyanophages) potentially affect the abundance and composition of cyanobacterial communities. Yet, there are few well-described freshwater cyanophages relative to their marine counterparts, and in general, few cyanosiphoviruses (family Siphoviridae ) have been characterized, limiting our understanding of the biology and the ecology of this prominent group of viruses. Here, we characterize S-LBS1, a freshwater siphovirus lytic to a phycoerythrin-rich Synechococcus isolate (Strain TCC793)...
2018: Frontiers in Microbiology
David J Duffy, Christine Schnitzler, Lorraine Karpinski, Rachel Thomas, Jenny Whilde, Catherine Eastman, Calvin Yang, Aleksandar Krstic, Devon Rollinson, Bette Zirkelbach, Kelsey Yetsko, Brooke Burkhalter, Mark Q Martindale
Wildlife populations are under intense anthropogenic pressures, with the geographic range of many species shrinking, dramatic reductions in population numbers and undisturbed habitats, and biodiversity loss. It is postulated that we are in the midst of a sixth (Anthropocene) mass extinction event, the first to be induced by human activity. Further, threatening vulnerable species is the increased rate of emerging diseases, another consequence of anthropogenic activities. Innovative approaches are required to help maintain healthy populations until the chronic underlying causes of these issues can be addressed...
2018: Communications biology
Xiaoyu Zhang, Shousheng Liu, Quanjiang Dong, Yongning Xin, Shiying Xuan
The transmembrane 6 superfamily member 2 ( TM6SF2 ) gene E167K variant (rs58542926) was identified by exome-wide association study as a nonsynonymous single nucleotide polymorphism associated with nonalcoholic fatty liver disease. The TM6SF2 E167K variant features a C-to-T substitution at nucleotide 499, encoding a glutamate with lysine change at codon 167 (E167K). TM6SF2 is markedly expressed in the liver, small intestine and kidney, and has been proposed as an important risk factor for diseases associated with lipid metabolism...
September 28, 2018: Journal of Clinical and Translational Hepatology
J R Otieno, E M Kamau, J W Oketch, J M Ngoi, A M Gichuki, Š Binter, G P Otieno, M Ngama, C N Agoti, P A Cane, P Kellam, M Cotten, P Lemey, D J Nokes
The respiratory syncytial virus (RSV) group A variant with the 72-nucleotide duplication in the G gene, genotype ON1, was first detected in Kilifi in 2012 and has almost completely replaced circulating genotype GA2 strains. This replacement suggests some fitness advantage of ON1 over the GA2 viruses in Kilifi, and might be accompanied by important genomic substitutions in ON1 viruses. Close observation of such a new virus genotype introduction over time provides an opportunity to better understand the transmission and evolutionary dynamics of the pathogen...
July 2018: Virus Evolution
Natalia Ramos, Santiago Mirazo, German Botto, Thais Fumaco Teixeira, Samuel Paulo Cibulski, Gustavo Castro, Karina Cabrera, Paulo Michel Roehe, Juan Arbiza
Torque teno sus virus (TTSuV) infection is common worldwide in both healthy and diseased swine and a relationship between this virus and a particular disease in pigs has not been established. This work aimed to investigate the presence of TTSuV1 and TTSuVk2a in Porcine Circovirus type 2 (PCV2)-infected and non-infected domestic pigs and free-living wild boars from Uruguay. Our data evidenced a high frequency of detection and a wide circulation of TTSuV among pig herds and wild boar populations. Furthermore, TTSuV1+TTSuVk2a co-infection was more frequent than single infections in domestic pigs...
October 2018: Veterinary Microbiology
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