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https://www.readbyqxmd.com/read/28073402/deep-sequencing-analysis-of-tick-borne-encephalitis-virus-from-questing-ticks-at-natural-foci-reveals-similarities-between-quasispecies-pools-of-the-virus
#1
Naveed Asghar, John H-O Pettersson, Patrik Dinnetz, Åshild Andreassen, Magnus Johansson
Every year, tick-borne encephalitis virus (TBEV) causes severe central nervous system infection in 10,000 to 15,000 people in Europe and Asia. TBEV is maintained in the environment by an enzootic cycle that requires a tick vector and a vertebrate host, and the adaptation of TBEV to vertebrate and invertebrate environments is essential for TBEV persistence in nature. This adaptation is facilitated by the error-prone nature of the virus' RNA-dependent RNA polymerase that generates genetically distinct virus variants called quasispecies...
January 10, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28072889/in-depth-analysis-of-compartmentalization-of-hiv-1-matrix-protein-p17-in-pbmc-and-plasma
#2
Marina Selleri, Riccardo Dolcetti, Francesca Caccuri, Emanuela Giombini, Gabriella Rozera, Isabella Abbate, Alessia Mammone, Stefania Zanussi, Debora Martorelli, Simona Fiorentini, Arnaldo Caruso, Maria Rosaria Capobianchi
HIV-1 p17 plays an important role in the virus life-cycle and disease pathogenesis. Recent studies indicated a high heterogeneity of p17. A high number of insertions in the p17 carboxy-terminal region have been more frequently detected in patients with non-Hodgkin lymphoma (NHL), suggesting a role of altered p17 in lymphomagenesis. Based on p17 heterogeneity, possible PBMC/plasma compartmentalization of p17 variants was explored by ultra-deep pyrosequencing in five NHL patients. The high variability of p17 with insertions at the carboxy-terminal region was confirmed in plasma and observed for the first time in proviral genomes...
January 9, 2017: New Microbiologica
https://www.readbyqxmd.com/read/28069935/resistance-to-type-1-interferons-is-a-major-determinant-of-hiv-1-transmission-fitness
#3
Shilpa S Iyer, Frederic Bibollet-Ruche, Scott Sherrill-Mix, Gerald H Learn, Lindsey Plenderleith, Andrew G Smith, Hannah J Barbian, Ronnie M Russell, Marcos V P Gondim, Catherine Y Bahari, Christiana M Shaw, Yingying Li, Timothy Decker, Barton F Haynes, George M Shaw, Paul M Sharp, Persephone Borrow, Beatrice H Hahn
Sexual transmission of HIV-1 is an inefficient process, with only one or few variants of the donor quasispecies establishing the new infection. A critical, and as yet unresolved, question is whether the mucosal bottleneck selects for viruses with increased transmission fitness. Here, we characterized 300 limiting dilution-derived virus isolates from the plasma, and in some instances genital secretions, of eight HIV-1 donor and recipient pairs. Although there were no differences in the amount of virion-associated envelope glycoprotein, recipient isolates were on average threefold more infectious (P = 0...
January 9, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28040474/deep-sequencing-in-the-management-of-hepatitis-virus-infections
#4
REVIEW
Josep Quer, Francisco Rodríguez-Frias, Josep Gregori, David Tabernero, Maria Eugenia Soria, Damir García-Cehic, Maria Homs, Albert Bosch, Rosa María Pintó, Juan Ignacio Esteban, Esteban Domingo, Celia Perales
The hepatitis viruses represent a major public health problem worldwide. Procedures for characterization of the genomic composition of their populations, accurate diagnosis, identification of multiple infections, and information on inhibitor-escape mutants for treatment decisions are needed. Deep sequencing methodologies are extremely useful for these viruses since they replicate as complex and dynamic quasispecies swarms whose complexity and mutant composition are biologically relevant traits. Population complexity is a major challenge for disease prevention and control, but also an opportunity to distinguish among related but phenotypically distinct variants that might anticipate disease progression and treatment outcome...
December 28, 2016: Virus Research
https://www.readbyqxmd.com/read/28027000/viroid-quasispecies-revealed-by-deep-sequencing
#5
Joseph R J Brass, Robert A Owens, Jaroslav Matoušek, Gerhard Steger
Viroids are non-coding single-stranded circular RNA molecules that replicate autonomously in infected host plants causing mild to lethal symptoms. Their genomes contain about 250-400 nucleotides, depending on viroid species. Members of the family Pospiviriodeae, like the Potato spindle tuber viroid (PSTVd), replicate via an asymmetric rolling-circle mechanism using the host DNA-dependent RNA-Polymerase II in the nucleus, while members of Avsunviroidae are replicated in a symmetric rolling-circle mechanism probably by the nuclear-encoded polymerase in chloroplasts...
December 27, 2016: RNA Biology
https://www.readbyqxmd.com/read/28024238/forensic-application-of-phylogenetic-analyses-exploration-of-suspected-hiv-1-transmission-case
#6
Marina Siljic, Dubravka Salemovic, Valentina Cirkovic, Ivana Pesic-Pavlovic, Jovan Ranin, Marija Todorovic, Slobodan Nikolic, Djordje Jevtovic, Maja Stanojevic
Transmission of human immunodeficiency virus (HIV) between individuals may have important legal implications and therefore may come to require forensic investigation based upon phylogenetic analysis. In criminal trials results of phylogenetic analyses have been used as evidence of responsibility for HIV transmission. In Serbia, as in many countries worldwide, exposure and deliberate transmission of HIV are criminalized. We present the results of applying state of the art phylogenetic analyses, based on pol and env genetic sequences, in exploration of suspected HIV transmission among three subjects: a man and two women, with presumed assumption of transmission direction from one woman to a man...
December 19, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28012998/viral-small-rnas-reveal-the-genomic-variations-of-three-grapevine-vein-clearing-virus-quasispecies-populations
#7
Susanne Howard, Wenping Qiu
Viral small RNAs (vsRNAs) include viral small interfering RNAs (vsiRNAs) that are initiators and products of RNA silencing, and small RNAs that are derived from viral RNAs with function still unknown. Sequencing of vsRNAs allows assembling of viral genomes and revelation of viral population variations at genomic levels. Grapevine vein clearing virus (GVCV) is a new member of the family Caulimoviridae whose DNA genome is replicated by reverse transcription of pre-genomic RNA molecules. In this short report, three genomic sequences of GVCV were assembled from vsRNAs that were isolated and sequenced from three individual grapevines in commercial vineyards and compared to the GVCV-CHA reference genome...
February 2, 2017: Virus Research
https://www.readbyqxmd.com/read/28011961/genotypic-analysis-of-hcv-1a-by-sequencing-of-the-ns3-proteasic-region-in-simeprevir-therapy-candidates
#8
Alfonso Liberti, Adriana Raddi, Nunzia Cuomo
Each phase of the HCV replication cycle can represent a therapy target. In fact, SIMEPREVIR (SMV) acts as NS3/4A protease inhibitor (PI); its efficacy is, however, reduced in HCV1a patients characterized by NS3Q80K polymorphism. The aim of this work was to design a genotypic analysis of NS3 protease in order to characterize viral quasispecies in HCV 1a patients before starting the SMV therapy. In all, 38 peripheral blood-EDTA samples were collected from patients infected with HCV 1a (RNA > 10,000 cp/ml)...
1, 2016: Le Infezioni in Medicina
https://www.readbyqxmd.com/read/27993149/a-deep-sequencing-reveals-significant-diversity-among-dominant-variants-and-evolutionary-dynamics-of-avian-leukosis-viruses-in-two-infectious-ecosystems
#9
Fanfeng Meng, Xuan Dong, Tao Hu, Shuang Chang, Jianhua Fan, Peng Zhao, Zhizhong Cui
BACKGROUND: As a typical retrovirus, the evolution of Avian leukosis virus subgroup J (ALV-J) in different infectious ecosystems is not characterized, what we know is there are a cloud of diverse variants, namely quasispecies with considerable genetic diversity. This study is to explore the selection of infectious ecosystems on dominant variants and their evolutionary dynamics of ALV-J between DF1 cells and specific-pathogen-free (SPF) chickens. High-throughput sequencing platforms provide an approach for detecting quasispecies diversity more fully...
December 19, 2016: BMC Veterinary Research
https://www.readbyqxmd.com/read/27982069/the-role-of-the-poly-a-tract-in-the-replication-and-virulence-of-tick-borne-encephalitis-virus
#10
Naveed Asghar, Yi-Ping Lee, Emma Nilsson, Richard Lindqvist, Wessam Melik, Andrea Kröger, Anna K Överby, Magnus Johansson
The tick-borne encephalitis virus (TBEV) is a flavivirus transmitted to humans, usually via tick bites. The virus causes tick-borne encephalitis (TBE) in humans, and symptoms range from mild flu-like symptoms to severe and long-lasting sequelae, including permanent brain damage. It has been suggested that within the population of viruses transmitted to the mammalian host, quasispecies with neurotropic properties might become dominant in the host resulting in neurological symptoms. We previously demonstrated the existence of TBEV variants with variable poly(A) tracts within a single blood-fed tick...
December 16, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27975319/deep-sequencing-of-the-hepatitis-b-virus-genome-analysis-of-multiple-samples-by-implementation-of-the-illumina-platform
#11
Quan-Xin Long, Jie-Li Hu, Ai-Long Huang
The quasispecies variation of hepatitis B virus (HBV) was believed to be a viral response to antiviral treatment and host immune pressure. Sanger sequencing was previously the classic approach for quasispecies analysis, but this method was also time-consuming and laborious. Ultra-deep sequencing has been widely used in viral quasispecies research, especially for low-frequency mutation detection. Here we present a multiple samples deep sequencing method employing the Illumina platform to detect HBV quasispecies variation in patient-derived samples...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27959928/an-efficient-microarray-based-genotyping-platform-for-the-identification-of-drug-resistance-mutations-in-majority-and-minority-subpopulations-of-hiv-1-quasispecies
#12
Verónica Martín, Celia Perales, María Fernández-Algar, Helena G Dos Santos, Patricia Garrido, María Pernas, Víctor Parro, Miguel Moreno, Javier García-Pérez, José Alcamí, José Luis Torán, David Abia, Esteban Domingo, Carlos Briones
The response of human immunodeficiency virus type 1 (HIV-1) quasispecies to antiretroviral therapy is influenced by the ensemble of mutants that composes the evolving population. Low-abundance subpopulations within HIV-1 quasispecies may determine the viral response to the administered drug combinations. However, routine sequencing assays available to clinical laboratories do not recognize HIV-1 minority variants representing less than 25% of the population. Although several alternative and more sensitive genotyping techniques have been developed, including next-generation sequencing (NGS) methods, they are usually very time consuming, expensive and require highly trained personnel, thus becoming unrealistic approaches in daily clinical practice...
2016: PloS One
https://www.readbyqxmd.com/read/27920481/new-real-time-pcr-method-to-identify-single-point-mutations-in-hepatitis-c-virus
#13
Qian Chen, Irene Belmonte, Maria Buti, Leonardo Nieto, Damir Garcia-Cehic, Josep Gregori, Celia Perales, Laura Ordeig, Meritxell Llorens, Maria Eugenia Soria, Rafael Esteban, Juan Ignacio Esteban, Francisco Rodriguez-Frias, Josep Quer
AIM: To develop a fast, low-cost diagnostic strategy to identify single point mutations in highly variable genomes such as hepatitis C virus (HCV). METHODS: In patients with HCV infection, resistance-associated amino acid substitutions within the viral quasispecies prior to therapy can confer decreased susceptibility to direct-acting antiviral agents and lead to treatment failure and virological relapse. One such naturally occurring mutation is the Q80K substitution in the HCV-NS3 protease gene, which confers resistance to PI inhibitors, particularly simeprevir...
November 21, 2016: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/27917342/genomic-studies-of-envelope-gene-sequences-from-mosquito-and-human-samples-from-bangkok-thailand
#14
Pannamthip Pitaksajjakul, Surachet Benjathummarak, Hyun Ngoc Son, Supatra Thongrungkiat, Pongrama Ramasoota
Dengue virus (DENV) is an RNA virus showing a high degree of genetic variation as a consequence of its proofreading inability. This variation plays an important role in virus evolution and pathogenesis. Although levels of within-host genetic variation are similar following equilibrium, variation among different hosts is frequently different. To identify dengue quasispecies present among two hosts, we collected patient samples from six acute DENV cases and two pools of Aedes aegypti mosquitoes and analyzed the genetic variation of regions of the viral envelope gene...
2016: SpringerPlus
https://www.readbyqxmd.com/read/27903277/sequence-diversity-of-dengue-virus-type-2-in-brain-and-thymus-of-infected-interferon-receptor-ko-mice-implications-for-dengue-virulence
#15
Priya Dhole, Emi E Nakayama, Akatsuki Saito, Kriengsak Limkittikul, Supranee Phanthanawiboon, Tatsuo Shioda, Takeshi Kurosu
BACKGROUND: We previously reported that a clinical isolate of dengue virus (DENV) is capable of causing acute-phase systemic infection in mice harboring knockouts of the genes encoding type-I and -II interferon IFN receptors (IFN-α/β/γR KO mice); in contrast, other virulent DENV isolates exhibited slow disease progression in this mice, yielding lethal infection around 20 days post-infection (p.i.). In the present study, we sought to clarify the dynamics of slow disease progression by examining disease progression of a type-2 DENV clinical isolate (DV2P04/08) in mice...
November 30, 2016: Virology Journal
https://www.readbyqxmd.com/read/27902354/humoral-immune-system-targets-clonotypic-antibody-associated-hepatitis-c-virus
#16
Amruta S Naik, Brendan A Palmer, Orla Crossbie, Elizabeth Kenny-Walsh, Liam J Fanning
Hypervariable region 1 (HVR1) is one of the potential neutralisation domains in the E2 glycoprotein of Hepatitis C virus (HCV). Point mutations of the HVR1 can lead to humoral immune escape in HCV infected patients. In this study we segregated the chronically infected viraemic sera from HCV infected patients into populations of antibody free virus (AFV) and antibody associated virus (AAV) and mapped potential epitopes within the E1E2 gene junction of AAV sequences (residues 364-430). Furthermore, we generated pseudotyped HCV particles (HCVpp) derived from AAV sequence to assess their infectivity...
November 14, 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27899444/antigen-dependent-competition-shapes-the-local-repertoire-of-tissue-resident-memory-cd8-t-cells
#17
Andreas Muschaweckh, Veit R Buchholz, Anne Fellenzer, Christian Hessel, Paul-Albert König, Sha Tao, Ronny Tao, Mathias Heikenwälder, Dirk H Busch, Thomas Korn, Wolfgang Kastenmüller, Ingo Drexler, Georg Gasteiger
Tissue-resident memory CD8(+) T cells (TRM) constitute a major component of the immune-surveillance system in nonlymphoid organs. Local, noncognate factors are both necessary and sufficient to support the programming of TRM cell fate in tissue-infiltrating T cells. Recent evidence suggests that TCR signals received in infected nonlymphoid tissues additionally contribute to TRM cell formation. Here, we asked how antigen-dependent pathways influence the generation of skin-resident memory T cells that arise from a polyclonal repertoire of cells induced by infection with an antigenically complex virus and recombinant vaccine vector...
December 12, 2016: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/27893822/deciphering-multiplicity-of-hiv-1c-infection-transmission-of-closely-related-multiple-viral-lineages
#18
Vlad Novitsky, Sikhulile Moyo, Rui Wang, Simani Gaseitsiwe, M Essex
BACKGROUND: A single viral variant is transmitted in the majority of HIV infections. However, about 20% of heterosexually transmitted HIV infections are caused by multiple viral variants. Detection of transmitted HIV variants is not trivial, as it involves analysis of multiple viral sequences representing intra-host HIV-1 quasispecies. METHODOLOGY: We distinguish two types of multiple virus transmission in HIV infection: (1) HIV transmission from the same source, and (2) transmission from different sources...
2016: PloS One
https://www.readbyqxmd.com/read/27888038/evidence-of-bottleneck-effect-on-hepatitis-c-virus-transmission-between-a-couple-under-interferon-based-therapy
#19
Rafael Alves da Silva, Isabel Maria Vicente Guedes de Carvalho, Renata Prandini Adum de Matos, Lilian Hiromi Tomonari Yamasaki, Cíntia Bittar, Paula Rahal, Ana Carolina Gomes Jardim
Issues on the correlation of viral genetic diversity and treatment response to the hepatitis C infection remain uncertain. The bottleneck effect dictates the characteristics of the viral population that will establish the infection in a new host and is related to how the immune system and treatment will be effective against the virus. Here we evaluated the phylogenetic characteristics of quasispecies population and the treatment response pattern of a HCV infected couple. We also analyzed whether the viral population of these patients indicated that they were exposed to the same source for primer infection...
January 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/27885563/quasispecies-composition-and-diversity-do-not-reveal-any-predictors-for-chronic-classical-swine-fever-virus-infection
#20
Maria Jenckel, Sandra Blome, Martin Beer, Dirk Höper
Classical swine fever (CSF) can run acute, chronic, and prenatal courses in both domestic pigs and wild boar. Although chronic infections are rare events, their epidemiological impact is very high due to the long-term shedding of virus. So far, little is known about the factors that influence disease course and outcome from either the host or virus's perspective. To elucidate the viral determinants, we analyzed the role of the viral populations for the development of chronic CSF virus (CSFV) infections. Three different animal trials that had led to both chronic and acute infections were chosen for a detailed analysis by deep sequencing...
November 24, 2016: Archives of Virology
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