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virus evolution

Sarah E Heath, Sinead Collins
Viruses play important roles in population dynamics and as drivers of evolution in single-celled marine phytoplankton. Viral infection of Ostreococcus tauri often causes cell lysis, but two spontaneously arising resistance mechanisms occur: resistant cells that cannot become infected and resistant producer cells that are infected but not lysed, and which may slowly release viruses. As of yet, little is known about how consistent the effects of viruses on their hosts are across different environments. To measure the effect of host resistance on host growth, and to determine whether this effect is environmentally dependent, we compared the growth and survival of susceptible, resistant and resistant producer O...
October 21, 2016: Environmental Microbiology
Xingguang Li, Junjie Zai, Haizhou Liu, Yi Feng, Fan Li, Jing Wei, Sen Zou, Zhiming Yuan, Yiming Shao
Following its immergence in December 2013, the recent Zaire Ebola virus (EBOV) outbreak in West Africa has spread and persisted for more than two years, making it the largest EBOV epidemic in both scale and geographical region to date. In this study, a total of 726 glycoprotein (GP) gene sequences of the EBOV full-length genome obtained from West Africa from the 2014 outbreak, combined with 30 from earlier outbreaks between 1976 and 2008 were used to investigate the genetic divergence, evolutionary history, population dynamics, and selection pressure of EBOV among distinct epidemic waves...
October 21, 2016: Scientific Reports
Noor-Ul-Huda Ghori, Atif Shafique, Muhammad Qasim Hayat, Sadia Anjum
Hepatitis C Virus (HCV) is the most prevalent human pathogen in Pakistan and is the major cause of liver cirrhosis and hepatocellular carcinoma in infected patients. It has shifted from being hypo-endemic to being hyper-endemic. There was no information about the origin and evolution of the local variants. Here we use newly developed phyloinformatic methods of sequence analysis to conduct the first comprehensive investigation of the evolutionary and biogeographic history in unprecedented detail and breadth...
2016: PloS One
Lucille Arragain, Myrielle Dupont-Rouzeyrol, Olivia O'Connor, Nathalie Sigur, Jean-Paul Grangeon, Emilie Huguon, Clothilde Dechanet, Cécile Cazorla, Ann-Claire Gourinat, Elodie Descloux
: We investigated 10 mother-newborn pairs and found a 90% rate of dengue virus (DENV) transmission during the perinatal period. Here, we describe DENV kinetics in the sera of newborns before the onset of disease. Of the breast-milk samples analyzed, 75% tested positive for DENV. BACKGROUND: Dengue is the most common mosquito-borne viral disease in humans. With this study, we aimed to investigate the risk of vertical (DENV) transmission during the peripartum period and to describe its viral kinetics in serum and breast milk...
October 19, 2016: Journal of the Pediatric Infectious Diseases Society
Uma Sriram, Beth L Hill, Jonathan M Cenna, Larisa Gofman, Nicole C Fernandes, Bijayesh Haldar, Raghava Potula
Methamphetamine (METH) is a widely used psychostimulant that severely impacts the host's innate and adaptive immune systems and has profound immunological implications. T cells play a critical role in orchestrating immune responses. We have shown recently how chronic exposure to METH affects T cell activation using a murine model of lymphocytic choriomeningitis virus (LCMV) infection. Using the TriCOM (trinary state combinations) feature of GemStone™ to study the polyfunctionality of T cells, we have analyzed how METH affected the cytokine production pattern over the course of chronic LCMV infection...
2016: PloS One
Yann J K Bertrand, Magnus Johansson, Peter Norberg
The hypothesis of wide spread reticulate evolution in Tick-Borne Encephalitis virus (TBEV) has recently gained momentum with several publications describing past recombination events involving various TBEV clades. Despite a large body of work, no consensus has yet emerged on TBEV evolutionary dynamics. Understanding the occurrence and frequency of recombination in TBEV bears significant impact on epidemiology, evolution, and vaccination with live vaccines. In this study, we investigated the possibility of detecting recombination events in TBEV by simulating recombinations at several locations on the virus' phylogenetic tree and for different lengths of recombining fragments...
2016: PloS One
Yue Zhang, Richard Potter, William Zhang, Zahra Fakhraai
Recent studies have shown that diffusion on the surface of organic glasses can be many orders of magnitude faster than bulk diffusion. Developing new probes that can readily measure surface diffusion can help study the effect of parameters such as chemical structure, intermolecular interaction, molecules' shape and size on the enhanced surface diffusion. In this study, we develop a novel probe that significantly simplifies these types of studies. Tobacco mosaic virus (TMV) is used as probe particle to measure surface diffusion coefficient of molecular glass N,N'-bis(3-methylphenyl)-N,N'-diphenylbenzidine (TPD)...
October 19, 2016: Soft Matter
Neli Korsun, Svetla Angelova, Ani Teodosieva
AIM: Influenza virological surveillance is an essential tool for studying the evolution of influenza viruses as well as for annual updating of the vaccine composition. The aim of the present study is to analyse the circulation of the influenza viruses in Bulgaria during the four recent post-pandemic seasons. METHODS: A total of 3,681 respiratory samples from patients with influenza like illness (ILI) or acute respiratory illness (ARI) were tested for influenza viruses using Real Time RT-PCR...
September 2016: Central European Journal of Public Health
Utsav Pandey, Andrew S Bell, Daniel W Renner, David A Kennedy, Jacob T Shreve, Chris L Cairns, Matthew J Jones, Patricia A Dunn, Andrew F Read, Moriah L Szpara
The intensification of the poultry industry over the last 60 years facilitated the evolution of increased virulence and vaccine breaks in Marek's disease virus (MDV-1). Full-genome sequences are essential for understanding why and how this evolution occurred, but what is known about genome-wide variation in MDV comes from laboratory culture. To rectify this, we developed methods for obtaining high-quality genome sequences directly from field samples without the need for sequence-based enrichment strategies prior to sequencing...
September 2016: MSphere
Keisuke Yoshihara, Minh Nhat Le, Koo Nagasawa, Hiroyuki Tsukagoshi, Hien Anh Nguyen, Michiko Toizumi, Hiroyuki Moriuchi, Masahiro Hashizume, Koya Ariyoshi, Duc Anh Dang, Hirokazu Kimura, Lay-Myint Yoshida
We performed molecular evolutionary analyses of the G gene C-terminal 3rd hypervariable region of RSV-A genotypes NA1 and ON1 strains from the paediatric acute respiratory infection patients in central Vietnam during the 2010-2012 study period. Time-scaled phylogenetic analyses were performed using Bayesian Markov Chain Monte Carlo (MCMC) method, and pairwise distances (p-distances) were calculated. Bayesian Skyline Plot (BSP) was constructed to analyze the time-trend relative genetic diversity of central Vietnam RSV-A strains...
October 14, 2016: Infection, Genetics and Evolution
David Hamilton, Vinidh Paleri
Morbidity and mortality associated with increasingly radical doses of chemoradiotherapy have led many to question the current standard of care in head and neck cancer. Recently, surgeons have developed minimally invasive, transoral techniques which have demonstrated excellent survival and favourable functional outcomes. Transoral robotic surgery (TORS) is the most recent, cutting edge in the evolution of transoral techniques; TORS allows surgeons unprecedented access to and visualisation of the upper aerodigestive tract...
October 11, 2016: Surgeon: Journal of the Royal Colleges of Surgeons of Edinburgh and Ireland
Bertram Bengsch, Kyong-Mi Chang
Hepatitis B virus (HBV) infection is a major global health challenge. HBV can cause significant morbidity and mortality by establishing acute and chronic hepatitis. Approximately 250 million people worldwide are chronically infected, and more than 2 billion people have been exposed to HBV. Since the discovery of HBV, the advances in our understanding of HBV virology and immunology have translated into effective vaccines and therapies for HBV infection. Although current therapies successfully suppress viral replication but rarely succeed in viral eradication, recent discoveries in HBV virology and immunology provide exciting rationales for novel treatment strategies aiming at HBV cure...
November 2016: Clinics in Liver Disease
Alex S Hartlage, John M Cullen, Amit Kapoor
Hepaciviruses and pegiviruses constitute two closely related sister genera of the family Flaviviridae. In the past five years, the known phylogenetic diversity of the hepacivirus genera has absolutely exploded. What was once an isolated infection in humans (and possibly other primates) has now expanded to include horses, rodents, bats, colobus monkeys, cows, and, most recently, catsharks, shedding new light on the genetic diversity and host range of hepaciviruses. Interestingly, despite the identification of these many animal and primate hepaciviruses, the equine hepaciviruses remain the closest genetic relatives of the human hepaciviruses, providing an intriguing clue to the zoonotic source of hepatitis C virus...
September 29, 2016: Annual Review of Virology
Isabelle Poizot-Martin, Clotilde Allavena, Cyrille Delpierre, Claudine Duvivier, Véronique Obry-Roguet, Carla E Cano, Francine Guillouet de Salvador, David Rey, Pierre Dellamonica, Antoine Cheret, Lise Cuzin, Christine Katlama, André Cabié, Bruno Hoen
The aim of the study was to investigate the impact of first-line combined antiretroviral therapy (cART) regimen on the course of CD8 T-cell counts in human immunodeficiency virus (HIV)-infected patients.A retrospective observational study conducted on the French DAT'AIDS Cohort of HIV-infected patients.We selected 605 patients initiating a first-line cART between 2002 and 2009, and which achieved a sustained undetectable HIV plasma viral load (pVL) for at least 12 months without cART modification. The evolution of CD8 T-cell counts according to cART regimen was assessed...
October 2016: Medicine (Baltimore)
Zobair M Younossi, Haesuk Park, Douglas Dieterich, Sammy Saab, Aijaz Ahmed, Stuart C Gordon
BACKGROUND: New direct-acting antiviral (DAA) therapy has dramatically increased cure rates for patients infected with hepatitis C virus (HCV), but has also substantially raised treatment costs. AIM: The aim of this analysis was to evaluate the therapeutic benefit and net costs (i.e. efficiency frontier) and the quality-adjusted cost of care associated with the evolution of treatment regimens for patients with HCV genotype 1 in the United States. DESIGN: A decision-analytic Markov model...
October 2016: Medicine (Baltimore)
Alberto Zanetto, Alberto Ferrarese, Ilaria Bortoluzzi, Patrizia Burra, Francesco Paolo Russo
The hepatitis B virus (HBV) infects more than 260 million people globally, with increasing incidence, especially in developing countries. Despite antiviral therapies, HBV-related end-stage liver disease remains one of the most important indications for liver transplantation worldwide. Although new available treatments have improved the outcome of patients with both compensated and decompensated liver disease in some specific clinical settings as acute-on-chronic liver failure mortality is still high. Moreover, the incidence of HBV-related hepatocellular carcinoma (HCC) seems to be increasing and represents a major challenge for the transplant team...
October 14, 2016: Annals of Transplantation: Quarterly of the Polish Transplantation Society
Yulin Zhang, Wanyun Gong, Hang Zeng, Ling Wang
Comparative analysis of the genomic sequences of multiple hepatitis E virus (HEV) isolates has revealed extensive genomic diversity among them. Recently, a variety of genetically distinct HEV variants have also been isolated and identified from large numbers of animal species, including birds, rabbits, rats, ferrets, bats, cutthroat trout, and camels, among others. Furthermore, it has been reported that recombination in HEV genomes takes place in animals and in human patients. Also, chronic HEV infection in immunocompromised individuals has revealed the presence of viral strains carrying insertions from human genes...
2016: Advances in Experimental Medicine and Biology
Pauline D Scanlan, Anna M Bischofberger, Alex R Hall
Although experiments indicate that the abiotic environment plays an important role in bacterial interactions with their parasitic viruses (bacteriophages or phages), it is not yet clear how exposure to compounds present in nature alters the impact of phages on bacterial growth and evolution. To address this question we exposed Escherichia coli K12 MG1655, in combination with three lytic phages, to various substances that natural and clinical microbial populations are likely to encounter: bile salts (present in mammalian gastrointestinal tracts), sodium dodecyl sulfate (SDS, a common surfactant in cleaning and hygiene products), and four antibiotics (present at variable concentrations in natural and clinical environments)...
October 12, 2016: FEMS Microbiology Ecology
Edward C Holmes, Gytis Dudas, Andrew Rambaut, Kristian G Andersen
The 2013-2016 epidemic of Ebola virus disease in West Africa was of unprecedented magnitude and changed our perspective on this lethal but sporadically emerging virus. This outbreak also marked the beginning of large-scale real-time molecular epidemiology. Here, we show how evolutionary analyses of Ebola virus genome sequences provided key insights into virus origins, evolution and spread during the epidemic. We provide basic scientists, epidemiologists, medical practitioners and other outbreak responders with an enhanced understanding of the utility and limitations of pathogen genomic sequencing...
October 12, 2016: Nature
Eric R Weiss, Galit Alter, Javier Gordon Ogembo, Jennifer L Henderson, Barbara Tabak, Yasin Bakiş, Mohan Somasundaran, Manuel Garber, Liisa Selin, Katherine Luzuriaga
: The Epstein Barr virus (EBV) gp350 glycoprotein interacts with the cellular receptor to mediate viral entry and is thought to be the major target for neutralizing antibodies. To better understand the role of EBV-specific antibodies in the control of viral replication and evolution of sequence diversity, we measured EBV gp350-specific antibody responses and sequenced the gp350 gene in samples obtained from individuals experiencing primary EBV infection (acute infectious mononucleosis; AIM) and again 6 months later (convalescence, CONV)...
October 12, 2016: Journal of Virology
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