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https://www.readbyqxmd.com/read/29244017/implications-of-segment-mismatch-for-influenza-a-virus-evolution
#1
Maria C White, Anice C Lowen
Influenza A virus (IAV) is an RNA virus with a segmented genome. These viral properties allow for the rapid evolution of IAV under selective pressure, due to mutation occurring from error-prone replication and the exchange of gene segments within a co-infected cell, termed reassortment. Both mutation and reassortment give rise to genetic diversity, but constraints shape their impact on viral evolution: just as most mutations are deleterious, most reassortment events result in genetic incompatibilities. The phenomenon of segment mismatch encompasses both RNA- and protein-based incompatibilities between co-infecting viruses and results in the production of progeny viruses with fitness defects...
December 15, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/29243070/extensive-evolution-analysis-of-the-global-chikungunya-virus-strains-revealed-the-origination-of-chikv-epidemics-in-pakistan-in-2016
#2
Junming Shi, Zhengyuan Su, Zhaojun Fan, Jun Wang, Siqing Liu, Bo Zhang, Hongping Wei, Shoukat Jehan, Nadia Jamil, Shu Shen, Fei Deng
Chikungunya virus (CHIKV) is a mosquito-borne virus that causes epidemics widely in the world especially in the tropical and subtropical regions. Phylogenetic analysis has found that the CHIKV lineages were associated with the spatial and temporal distributions, which were related to the virus adaption to the major mosquito species and their distributions. In this study, we reported the complete genome sequences of eight CHIKV isolates from the outbreak in Pakistan last year. Then we reviewed the evolutionary history using extensive phylogenetic analysis, analyzed lineagespecific substitutions in viral proteins, and characterized the spreading pathway of CHIKV strains including the Pakistani strains...
December 11, 2017: Virologica Sinica
https://www.readbyqxmd.com/read/29241646/hiv-population-level-adaptation-can-rapidly-diminish-the-impact-of-a-partially-effective-vaccine
#3
Joshua T Herbeck, Kathryn Peebles, Paul T Edlefsen, Morgane Rolland, James T Murphy, Geoffrey S Gottlieb, Neil Abernethy, James I Mullins, John E Mittler, Steven M Goodreau
BACKGROUND: Development of an HIV vaccine might be essential to ending the HIV/AIDS pandemic. However, vaccines can result in the emergence and spread of vaccine-resistant strains. Indeed, analyses of breakthrough infections in the HIV phase 3 vaccine trial RV144 identified HIV genotypes with differential rates of transmission in vaccine and placebo recipients. We hypothesized that, for HIV vaccination programs based on partially effective vaccines similar to RV144, HIV adaptation will rapidly diminish the expected vaccine impact...
December 11, 2017: Vaccine
https://www.readbyqxmd.com/read/29240811/whole-genome-analyses-of-human-adenovirus-type-55-emerged-in-tibet-sichuan-and-yunnan-in-china-in-2016
#4
Wenbo Wang, Yuan Liu, Yifan Zhou, Liangqi Gu, Lin Zhang, Xuelian Zhang, Maomao Chen, Ziying Zou, Wei Qiu, Xiaobing Hu, Quanshui Fan
Three outbreaks of acute respiratory disease occurred at military camps in 2016 at Tibet, Sichuan and Yunnan province, China. The pathogen induced these three outbreaks were all confirmed as HAdV-55 by genotype-specific PCR. The outbreak in Tibet was the first report that HAdV-55 occurred in the high altitude (HA, above sea level 3658 m). This study aims to determine the gene variation and evolution characteristics of these viral strains. Three strains of adenoviruses, LS89/Tibet/2016 (GenBank accession no...
2017: PloS One
https://www.readbyqxmd.com/read/29237841/mammalian-adaptation-of-an-avian-influenza-a-virus-involves-stepwise-changes-in-ns1
#5
C Chauché, A Nogales, H Zhu, D Goldfarb, A I Ahmad Shanizza, Q Gu, C R Parrish, L Martínez-Sobrido, J F Marshall, P R Murcia
Influenza A viruses (IAVs) are common pathogens of birds that occasionally establish endemic infections in mammals. The processes and mechanisms that result in IAV mammalian adaptation are poorly understood. The viral non-structural 1 (NS1) protein counteracts the interferon (IFN) response, a central component of the host-species barrier.We characterised the NS1 proteins of equine influenza virus (EIV), a mammalian IAV lineage of avian origin. We showed that evolutionary distinct NS1s counteract the IFN response using different and mutually exclusive mechanisms: while the NS1s of early EIVs block general gene expression by binding to the cellular polyadenylation specific factor 30 (CPSF30), NS1s from more evolved EIVs specifically block the induction of IFN-stimulated genes by interfering with the JAK/STAT pathway...
December 13, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29237837/molecular-dynamics-and-mode-of-transmission-of-koala-retrovirus-korv-as-it-invades-and-spreads-through-a-wild-queensland-koala-population
#6
Bonnie Chaban, Vanissa A Ong, Jonathan Hanger, Peter Timms
The recent acquisition of a novel retrovirus (KoRV) by koalas (Phascolarctos cinereus) has created new opportunities for retroviral research and new challenges for koala conservation. There are currently two major subtypes of KoRV; KoRV-A, which is believed to be endogenous only in koalas from the northern part of Australia, and KoRV-B, which appears to be exogenous. Understanding and management of these subtypes requires population-level studies of their prevalence and diversity, especially when co-infected in the same population, and investigations of their modes of transmission in the wild...
December 13, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29237831/maintenance-of-ap-2-dependent-functional-activities-of-nef-restricts-pathways-of-immune-escape-from-cd8-t-lymphocyte-responses
#7
Blake Schouest, Andrea M Weiler, Sanath Kumar Janaka, T Alix Myers, Arpita Das, Sarah C Wilder, Jessica Furlott, Melody Baddoo, Erik K Flemington, Eva G Rakasz, David T Evans, Thomas C Friedrich, Nicholas J Maness
Nef-specific CD8+ T lymphocytes (CD8TL) are linked to extraordinary control of primate lentiviral replication, but the mechanisms underlying their efficacy remain largely unknown. The immunodominant, Mamu-B*017:01+ restricted Nef195-203MW9 epitope in SIVmac239 partially overlaps a sorting motif important for interactions with host AP-2 proteins and, hence, downmodulation of several host proteins including Tetherin (CD317/BST-2), CD28, CD4, SERINC3, and SERINC5. We reasoned that CD8TL-driven evolution in this epitope might compromise Nef's ability to modulate these important molecules...
December 13, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29237829/unexpected-functional-divergence-of-bat-influenza-virus-ns1-proteins
#8
Hannah L Turkington, Mindaugas Juozapaitis, Nikos Tsolakos, Eugenia Corrales-Aguilar, Martin Schwemmle, Benjamin G Hale
Recently, two influenza A virus (FLUAV) genomes were identified in Central and South American bats. These sequences exhibit notable divergence from classical FLUAV counterparts, and functionally, bat FLUAV glycoproteins lack canonical receptor binding and destroying activity. Nevertheless, other features that distinguish these viruses from classical FLUAVs have yet to be explored. Here, we studied the viral non-structural protein, NS1, a virulence factor that modulates host signaling to promote efficient propagation...
December 13, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29237726/transmission-evolution-and-endogenization-lessons-learned-from-recent-retroviral-invasions
#9
REVIEW
Alex D Greenwood, Yasuko Ishida, Sean P O'Brien, Alfred L Roca, Maribeth V Eiden
Viruses of the subfamily Orthoretrovirinae are defined by the ability to reverse transcribe an RNA genome into DNA that integrates into the host cell genome during the intracellular virus life cycle. Exogenous retroviruses (XRVs) are horizontally transmitted between host individuals, with disease outcome depending on interactions between the retrovirus and the host organism. When retroviruses infect germ line cells of the host, they may become endogenous retroviruses (ERVs), which are permanent elements in the host germ line that are subject to vertical transmission...
March 2018: Microbiology and Molecular Biology Reviews: MMBR
https://www.readbyqxmd.com/read/29237241/the-p-patens-chromosome-scale-assembly-reveals-moss-genome-structure-and-evolution
#10
Daniel Lang, Kristian K Ullrich, Florent Murat, Jörg Fuchs, Jerry Jenkins, Fabian B Haas, Mathieu Piednoel, Heidrun Gundlach, Michiel Van Bel, Rabea Meyberg, Cristina Vives, Jordi Morata, Aikaterini Symeonidi, Manuel Hiss, Wellington Muchero, Yasuko Kamisugi, Omar Saleh, Guillaume Blanc, Eva L Decker, Nico van Gessel, Jane Grimwood, Richard D Hayes, Sean W Graham, Lee E Gunter, Stuart McDaniel, Sebastian N W Hoernstein, Anders Larsson, Fay-Wei Li, Pierre-Francois Perroud, Jeremy Phillips, Priya Ranjan, Daniel S Rokshar, Carl J Rothfels, Lucas Schneider, Shengqiang Shu, Dennis W Stevenson, Fritz Thümmler, Michael Tillich, Juan Carlos Villarreal A, Thomas Widiez, Gane Ka-Shu Wong, Ann Wymore, Yong Zhang, Andreas D Zimmer, Ralph S Quatrano, Klaus F X Mayer, David Goodstein, Josep M Casacuberta, Klaas Vandepoele, Ralf Reski, Andrew C Cuming, Jerry Tuskan, Florian Maumus, Jérome Salse, Jeremy Schmutz, Stefan A Rensing
The draft genome of the moss model, Physcomitrella patens, comprised approximately 2,000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes...
December 13, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29236688/evolution-of-a-designed-protein-assembly-encapsulating-its-own-rna-genome
#11
Gabriel L Butterfield, Marc J Lajoie, Heather H Gustafson, Drew L Sellers, Una Nattermann, Daniel Ellis, Jacob B Bale, Sharon Ke, Garreck H Lenz, Angelica Yehdego, Rashmi Ravichandran, Suzie H Pun, Neil P King, David Baker
The challenges of evolution in a complex biochemical environment, coupling genotype to phenotype and protecting the genetic material, are solved elegantly in biological systems by the encapsulation of nucleic acids. In the simplest examples, viruses use capsids to surround their genomes. Although these naturally occurring systems have been modified to change their tropism and to display proteins or peptides, billions of years of evolution have favoured efficiency at the expense of modularity, making viral capsids difficult to engineer...
December 13, 2017: Nature
https://www.readbyqxmd.com/read/29234320/increasing-the-clinical-potential-and-applications-of-anti-hiv-antibodies
#12
REVIEW
Casey K Hua, Margaret E Ackerman
Preclinical and early human clinical studies of broadly neutralizing antibodies (bNAbs) to prevent and treat HIV infection support the clinical utility and potential of bNAbs for prevention, postexposure prophylaxis, and treatment of acute and chronic infection. Observed and potential limitations of bNAbs from these recent studies include the selection of resistant viral populations, immunogenicity resulting in the development of antidrug (Ab) responses, and the potentially toxic elimination of reservoir cells in regeneration-limited tissues...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29232958/architect-hiv-combo-ag-ab%C3%A2-and-realtime%C3%A2-hiv-1-assays-detect-diverse-hiv-strains-in-clinical-specimens
#13
Mary A Rodgers, Ana S Vallari, Julie Yamaguchi, Vera Holzmayer, Barbara Harris, Coumba Toure-Kane, Souleymane M'Boup, Samar Badreddine, Carole McArthur, Nicaise Ndembi, Dora Ngum Mbanya, Lazare Kaptué, Gavin Cloherty
Periodic evaluation of the impact of viral diversity on diagnostic tests is critical to ensure current technologies are keeping pace with viral evolution. To determine whether HIV diversity impacts the ARCHITECT HIV Combo Ag/Ab (HIV Combo) or RealTime HIV-1 (RT) assays, a set of N=199 HIV clinical specimens from Cameroon, Senegal, Saudi Arabia, and Thailand were sequenced and tested in both assays. The panel included historical Group N and P specimens and a newly identified Group N specimen. These and specimens classified as H, U/URF, CRF01, 02, 06, 09, 11, 13, 18, 22, 37, and 43 were detected by both the RT assay (1...
December 12, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/29231176/tensorcalculator-exploring-the-evolution-of-mechanical-stress-in-the-ccmv-capsid
#14
Olga Kononova, Farkhad Maksudov, Kenneth A Marx, Valeri Barsegov
A new computational methodology for accurate numerical calculation of the Cauchy stress tensor, stress invariants, principal stress components, von Mises and Tresca tensors is developed. The methodology is based on the atomic stress approach which permits the calculation of stress tensors, widely used in continuum mechanics modeling of materials properties, using the output from the MD simulations of discrete atomic and Cα-based coarse-grained structural models of biological particles. The methodology mapped into software package TensorCalculator was successfully applied to the empty Cowpea Chlorotic Mottle virus (CCMV) shell to explore the evolution of mechanical stress in this mechanically-tested specific example of a soft virus capsid...
December 12, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/29226181/a-bioreactor-method-to-generate-high-titer-genetically-stable-clinical-isolate-human-cytomegalovirus
#15
Victoria R Saykally, Luke I Rast, Jeff Sasaki, Seung-Yong Jung, Cynthia Bolovan-Fritts, Leor S Weinberger
Human cytomegalovirus (HCMV) infection is a major cause of morbidity and mortality in transplant patients and a leading cause of congenital birth defects (Saint Louis, 2016). Vaccination and therapeutic studies often require scalable cell culture production of wild type virus, represented by clinical isolates. Obtaining sufficient stocks of wild-type clinical HCMV is often labor intensive and inefficient due to low yield and genetic loss, presenting a barrier to studies of clinical isolates. Here we report a bioreactor method based on continuous infection, where retinal pigment epithelial (ARPE-19) cells adhered to microcarrier beads are infected in a bioreactor and used to produce high-titers of clinical isolate HCMV that maintain genetic integrity of key viral tropism factors and the viral genome...
November 5, 2017: Bio-protocol
https://www.readbyqxmd.com/read/29226104/hepatitis-e-a-literature-review
#16
REVIEW
Juliana Ayres de Alencar Arrais Guerra, Katia Cristina Kampa, Daphne Gonçalves Benatti Morsoletto, Alcindo Pissaia Junior, Cláudia Alexandra Pontes Ivantes
Hepatitis E is the fifth known form of human viral hepatitis. Although not very common in our clinical practice, the incidence in Western countries is increasing. Infection with the hepatitis E virus (HEV) may be related to acute illness, liver failure, chronic hepatitis and cirrhosis. HEV itself is an RNA virus, with eight described genotypes (HEV 1-8), four of which more commonly affect humans and have, thus, been better studied. Besides liver manifestations, genotype 3 is also related to extra-hepatic manifestations, such as neurological, renal and rheumatological...
December 28, 2017: Journal of Clinical and Translational Hepatology
https://www.readbyqxmd.com/read/29224715/ebola-virus-disease-biological-and-diagnostic-evolution-from-2014-to-2017
#17
A Mérens, C Bigaillon, D Delaune
The Ebola virus disease outbreak observed in West Africa from March 2014 to June 2016 has led to many fundamental and applied research works. Knowledge of this virus has substantially increased. Treatment of many patients in epidemic countries and a few imported cases in developed countries led to developing new diagnostic methods and to adapt laboratory organization and biosafety precautions to perform conventional biological analyses. Clinical and biological monitoring of patients infected with Ebola virus disease helped to determine severity criteria and bad prognosis markers...
December 7, 2017: Médecine et Maladies Infectieuses
https://www.readbyqxmd.com/read/29223945/-heart-transplantation-in-an-hiv-infected-patient
#18
Pablo Mouras, Laura Barcán, César Belziti, Rodolfo Pizarro, Noelia Mañez, Ricardo Marenchino
Because of its own unfavourable evolution, HIV infection was until recently considered a contraindication for organ transplantation. The introduction of highly active antiretroviral therapy prolonged the life expectancy of these patients and allowed the manifestation of disorders directly or indirectly related to HIV infection, mainly liver, kidney and cardiovascular diseases. We present a case of cardiac transplantation due to dilated cardiomyopathy that was performed in a patient with a recently detected HIV infection...
2017: Medicina
https://www.readbyqxmd.com/read/29220671/structural-comparison-among-the-2013-2017-avian-influenza-a-h5n6-hemagglutinin-proteins-a-computational-study-with-epidemiological-implications
#19
Marni E Cueno, Izuho Suzuki, Shiori Shimotomai, Takuma Yokoyama, Kai Nagahisa, Kenichi Imai
Avian influenza viruses easily spread allowing viral re-assortment to simply occur which in-turn increases the potential for a pandemic. A novel 2013 H5N6 influenza strain was detected among the avian population and was reported to continuously evolve, however, this was never structurally demonstrated. Here, we elucidated the putative structural evolution of the novel H5N6 influenza strain. Throughout this study, we analyzed 2013-2017 H5N6 HA protein models. Model quality was first verified before further analyses and structural comparison was made using superimposition...
November 28, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29220409/acquisition-of-functions-on-the-outer-capsid-surface-during-evolution-of-double-stranded-rna-fungal-viruses
#20
Carlos P Mata, Daniel Luque, Josué Gómez-Blanco, Javier M Rodríguez, José M González, Nobuhiro Suzuki, Said A Ghabrial, José L Carrascosa, Benes L Trus, José R Castón
Unlike their counterparts in bacterial and higher eukaryotic hosts, most fungal viruses are transmitted intracellularly and lack an extracellular phase. Here we determined the cryo-EM structure at 3.7 Å resolution of Rosellinia necatrix quadrivirus 1 (RnQV1), a fungal double-stranded (ds)RNA virus. RnQV1, the type species of the family Quadriviridae, has a multipartite genome consisting of four monocistronic segments. Whereas most dsRNA virus capsids are based on dimers of a single protein, the ~450-Å-diameter, T = 1 RnQV1 capsid is built of P2 and P4 protein heterodimers, each with more than 1000 residues...
December 8, 2017: PLoS Pathogens
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