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Quasispecies

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https://www.readbyqxmd.com/read/29149077/rna-virus-evolution-via-a-quasispecies-based-model-reveals-a-drug-target-with-a-high-barrier-to-resistance
#1
Richard J Bingham, Eric C Dykeman, Reidun Twarock
The rapid occurrence of therapy-resistant mutant strains provides a challenge for anti-viral therapy. An ideal drug target would be a highly conserved molecular feature in the viral life cycle, such as the packaging signals in the genomes of RNA viruses that encode an instruction manual for their efficient assembly. The ubiquity of this assembly code in RNA viruses, including major human pathogens, suggests that it confers selective advantages. However, their impact on viral evolution cannot be assessed in current models of viral infection that lack molecular details of virus assembly...
November 17, 2017: Viruses
https://www.readbyqxmd.com/read/29118747/emerging-targets-for-developing-t-cell-mediated-vaccines-for-human-immunodeficiency-virus-hiv-1
#2
REVIEW
Danushka K Wijesundara, Charani Ranasinghe, Branka Grubor-Bauk, Eric J Gowans
Human immunodeficiency virus (HIV)-1 has infected >75 million individuals globally, and, according to the UN, is responsible for ~2.1 million new infections and 1.1 million deaths each year. Currently, there are ~37 million individuals with HIV infection and the epidemic has already resulted in 35 million deaths. Despite the advances of anti-retroviral therapy (ART), a cost-effective vaccine remains the best long-term solution to end the HIV-1 epidemic especially given that the vast majority of infected individuals live in poor socio-economic regions of the world such as Sub-Saharan Africa which limits their accessibility to ART...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29116219/a-comparative-study-on-the-characterization-of-hepatitis-b-virus-quasispecies-by-clone-based-sequencing-and-third-generation-sequencing
#3
Jing Li, Mingjie Wang, Demin Yu, Yue Han, Zhitao Yang, Lei Wang, Xinxin Zhang, Feng Liu
Hepatitis B virus (HBV) has a high mutation rate due to the extremely high replication rate and the proofreading deficiency during reverse transcription. The generated variants with genetic heterogeneity are described as viral quasispecies (QS). Clone-based sequencing (CBS) is thought to be the 'gold standard' for assessing QS complexity and diversity of HBV, but an important issue about CBS is cost-effectiveness and laborious. In this study, we investigated the utility of the third-generation sequencing (TGS) DNA sequencing to characterize genetic heterogeneity of HBV QS and assessed the possible contribution of TGS technology in HBV QS studies...
November 8, 2017: Emerging Microbes & Infections
https://www.readbyqxmd.com/read/29112950/single-primer-isothermal-amplification-spia-combined-with-next-generation-sequencing-provides-complete-bovine-coronavirus-genome-coverage-and-higher-sequence-depth-compared-to-sequence-independent-single-primer-amplification-sispa
#4
Mette Myrmel, Veslemøy Oma, Mamata Khatri, Hanne H Hansen, Maria Stokstad, Mikael Berg, Anne-Lie Blomström
Coronaviruses are of major importance for both animal and human health. With the emergence of novel coronaviruses such as SARS and MERS, the need for fast genome characterisation is ever so important. Further, in order to understand the influence of quasispecies of these viruses in relation to biology, techniques for deep-sequence and full-length viral genome analysis are needed. In the present study, we compared the efficiency of two sequence-independent approaches [sequence-independent single primer amplification (SISPA) and single primer isothermal amplification (SPIA, represented by the Ovation kit)] coupled with high-throughput sequencing to generate the full-length genome of bovine coronavirus (BCoV) from a nasal swab...
2017: PloS One
https://www.readbyqxmd.com/read/29100932/evolution-of-equine-influenza-viruses-h3n8-during-a-brazilian-outbreak-2015
#5
Patricia Filippsen Favaro, Wilson Roberto Fernandes, Dilmara Reischak, Paulo Eduardo Brandão, Sheila Oliveira de Souza Silva, Leonardo José Richtzenhain
Equine influenza is one of the major respiratory infectious diseases in horses. An equine influenza virus outbreak was identified in vaccinated and unvaccinated horses in a veterinary school hospital in São Paulo, SP, Brazil, in September 2015. The twelve equine influenza viruses isolated belonged to Florida Clade 1. The hemagglutinin and neuraminidase amino acid sequences were compared with the recent isolates from North and South America and the World Organisation for Animal Health recommended Florida Clade 1 vaccine strain...
October 13, 2017: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/29078745/single-virion-sequencing-of-lamivudine-treated-hbv-populations-reveal-population-evolution-dynamics-and-demographic-history
#6
Yuan O Zhu, Pauline P K Aw, Paola Florez de Sessions, Shuzhen Hong, Lee Xian See, Lewis Z Hong, Andreas Wilm, Chen Hao Li, Stephane Hue, Seng Gee Lim, Niranjan Nagarajan, William F Burkholder, Martin Hibberd
BACKGROUND: Viral populations are complex, dynamic, and fast evolving. The evolution of groups of closely related viruses in a competitive environment is termed quasispecies. To fully understand the role that quasispecies play in viral evolution, characterizing the trajectories of viral genotypes in an evolving population is the key. In particular, long-range haplotype information for thousands of individual viruses is critical; yet generating this information is non-trivial. Popular deep sequencing methods generate relatively short reads that do not preserve linkage information, while third generation sequencing methods have higher error rates that make detection of low frequency mutations a bioinformatics challenge...
October 27, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29077766/peripheral-blood-hiv-1-dna-dynamics-in-antiretroviral-treated-hiv-hcv-co-infected-patients-receiving-directly-acting-antivirals
#7
Gabriella Rozera, Gabriele Fabbri, Patrizia Lorenzini, Ilaria Mastrorosa, Laura Timelli, Mauro Zaccarelli, Alessandra Amendola, Alessandra Vergori, Maria Maddalena Plazzi, Stefania Cicalini, Andrea Antinori, Maria Rosaria Capobianchi, Isabella Abbate, Adriana Ammassari
BACKGROUND: Aim was to determine the dynamics of peripheral blood mononuclear cells (PBMC)- associated total HIV-1 DNA in successfully ART-treated HIV/HCV co-infected patients receiving DAA treatment and to explore possible virological hypotheses underlying the phenomenon. METHODS: Longitudinal, single-centre study measuring total HIV-1 DNA before the start of DAA, at the end of treatment (EOT), and 3 months after treatment. Univariable and multivariable analyses were used to assess factors associated with HIV-1 DNA increase ≥0...
2017: PloS One
https://www.readbyqxmd.com/read/29066544/maternal-but-not-infant-anti-hiv-1-neutralizing-antibody-response-associates-with-enhanced-transmission-and-infant-morbidity
#8
Melissa Ghulam-Smith, Alex Olson, Laura F White, Charles S Chasela, Sascha R Ellington, Athena P Kourtis, Denise J Jamieson, Gerald Tegha, Charles M van der Horst, Manish Sagar
A significant number of infants acquire HIV-1 through their infected mother's breast milk, primarily due to limited access to antiretrovirals. Passive immunization with neutralizing antibodies (nAbs) may prevent this transmission. Previous studies, however, have generated conflicting results about the ability of nAbs to halt mother-to-child transmission (MTCT) and their impact on infant outcomes. This study compared plasma neutralizing activity in exposed infants and the infected mothers (n = 63) against heterologous HIV-1 variants and the quasispecies present in the mother...
October 24, 2017: MBio
https://www.readbyqxmd.com/read/29054249/hiv-1-infected-t-cells-dynamics-and-prognosis-an-evolutionary-game-model
#9
Bahareh Khazaei, Javad Salimi Sartakhti, Mohammad Hossein Manshaei, Quanyan Zhu, Mehdi Sadeghi, Seyed Rasoul Mousavi
BACKGROUND AND OBJECTIVE: Understanding the dynamics of human immunodeficiency virus (HIV) is essential for depicting, developing, and investigating effective treatment strategies. HIV infects several types of immune cells, but its main target is to destroy helper T-cells. In the lymph nodes, the infected T-cells interact with each other and their environment to obtain more resources. According to infectivity and replicative capacity of T-cells in the HIV infection process, they can be divided into four phenotypes...
December 2017: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/29040633/prevalence-of-pre-antiretroviral-treatment-drug-resistance-by-gender-age-and-other-factors-in-hiv-infected-individuals-initiating-therapy-in-kenya-2013-2014
#10
Rachel A Silverman, Ingrid A Beck, Catherine Kiptinness, Molly Levine, Ross Milne, Christine J McGrath, Steve Bii, Barbra A Richardson, Grace John-Stewart, Bhavna Chohan, Samah R Sakr, James N Kiarie, Lisa M Frenkel, Michael H Chung
Background: Pre-antiretroviral-treatment drug resistance (PDR) is a predictor of HIV treatment failure. We determined PDR-prevalence and correlates in a Kenyan cohort. Methods: We conducted a cross-sectional analysis of antiretroviral (ARV) treatment-eligible HIV-infected participants in 2013-2014 at three clinics. PDR was defined as ≥2% mutant-frequency in a participant's HIV-quasispecies at pol codons K103N, Y181C, G190A, M184 V, or K65R by oligonucleotide ligation assay...
October 10, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29029728/software-dedicated-to-virus-sequence-analysis-bioinformatics-goes-viral
#11
Martin Hölzer, Manja Marz
Computer-assisted technologies of the genomic structure, biological function, and evolution of viruses remain a largely neglected area of research. The attention of bioinformaticians to this challenging field is currently unsatisfying in respect to its medical and biological importance. The power of new genome sequencing technologies, associated with new tools to handle "big data", provides unprecedented opportunities to address fundamental questions in virology. Here, we present an overview of the current technologies, challenges, and advantages of Next-Generation Sequencing (NGS) in relation to the field of virology...
2017: Advances in Virus Research
https://www.readbyqxmd.com/read/29029641/sequence-specific-detection-of-different-strains-of-lcmv-in-a-single-sample-using-tentacle-probes
#12
Lina S Franco, Susan A Holechek, Michael R Caplan, Joseph N Blattman
BACKGROUND: Virus infections often result in quasispecies of viral strains that can have dramatic impacts on disease outcomes. However, sequencing of viruses to determine strain composition is time consuming and often cost-prohibitive. Rapid, cost-effective methods are needed for accurate measurement of virus diversity to understand virus evolution and can be useful for experimental systems. METHODS: We have developed a novel molecular method for sequence-specific detection of RNA virus genetic variants called Tentacle Probes...
October 13, 2017: Virology Journal
https://www.readbyqxmd.com/read/29018311/de-novo-genome-assembly-and-single-nucleotide-variations-for-soybean-mosaic-virus-using-soybean-seed-transcriptome-data
#13
Yeonhwa Jo, Hoseong Choi, Miah Bae, Sang-Min Kim, Sun-Lim Kim, Bong Choon Lee, Won Kyong Cho, Kook-Hyung Kim
Soybean is the most important legume crop in the world. Several diseases in soybean lead to serious yield losses in major soybean-producing countries. Moreover, soybean can be infected by diverse viruses. Recently, we carried out a large-scale screening to identify viruses infecting soybean using available soybean transcriptome data. Of the screened transcriptomes, a soybean transcriptome for soybean seed development analysis contains several virus-associated sequences. In this study, we identified five viruses, including soybean mosaic virus (SMV), infecting soybean by de novo transcriptome assembly followed by blast search...
October 2017: Plant Pathology Journal
https://www.readbyqxmd.com/read/28988126/quantitative-characterization-of-hepatitis-delta-virus-genome-edition-by-next-generation-sequencing
#14
Sara Sopena, Cristina Godoy, David Tabernero, Maria Homs, Josep Gregori, Mar Riveiro-Barciela, Alicia Ruiz, Rafael Esteban, Maria Buti, Francisco Rodríguez-Frías
AIM: To determine the capacity of next-generation sequencing (NGS) for quantifying edited and unedited HDV populations, and to confirm if edition is a general phenomenon taking place along the entire HDV region analyzed, as we previously reported (Homs M et al. PLoS One 2016, 11, e0158557). METHODS: Four serum samples from 4 patients with chronic HDV/HBV infection were included in the study. The region selected for analysis covered 360 nucleotides (nt), positions 910-1270 of the HDV genome, which included the HDAg ORF editing site (nt 1014 within codon 196)...
October 4, 2017: Virus Research
https://www.readbyqxmd.com/read/28977510/separation-and-assembly-of-deep-sequencing-data-into-discrete-sub-population-genomes
#15
Konstantinos Karagiannis, Vahan Simonyan, Konstantin Chumakov, Raja Mazumder
Sequence heterogeneity is a common characteristic of RNA viruses that is often referred to as sub-populations or quasispecies. Traditional techniques used for assembly of short sequence reads produced by deep sequencing, such as de-novo assemblers, ignore the underlying diversity. Here, we introduce a novel algorithm that simultaneously assembles discrete sequences of multiple genomes present in populations. Using in silico data we were able to detect populations at as low as 0.1% frequency with complete global genome reconstruction and in a single sample detected 16 resolved sequences with no mismatches...
August 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28968776/archetype-jc-polyomavirus-jcpyv-prevails-in-a-rare-case-of-jcpyv-nephropathy-and-in-stable-renal-transplant-recipients-with-jcpyv-viruria
#16
Hanna M Seppälä, Ilkka T Helanterä, Pia K S Laine, Irmeli T Lautenschlager, Lars G Paulín, Timo J Jahnukainen, Petri O V Auvinen, Eeva Auvinen
Background: JC polyomavirus (JCPyV) is reactivated in approximately 20% of renal transplant recipients, and it may rarely cause JCPyV-associated nephropathy (JCPyVAN). Whereas progressive multifocal leukoencephalopathy of the brain is caused by rearranged neurotropic JCPyV, little is known about viral sequence variation in JCPyVAN owing to the rarity of this condition. Methods: Using single-molecule real-time sequencing, characterization of full-length JCPyV genomes in urine and plasma samples from 1 patient with JCPyVAN and 20 stable renal transplant recipients with JCPyV viruria was attempted...
November 15, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28931691/vertical-transmission-of-hepatitis-c-virus-variable-transmission-bottleneck-and-evidence-of-midgestation-in-utero-infection
#17
Sébastien Fauteux-Daniel, Ariane Larouche, Virginie Calderon, Jonathan Boulais, Chanel Béland, Doris G Ransy, Marc Boucher, Valérie Lamarre, Normand Lapointe, Isabelle Boucoiran, Armelle Le Campion, Hugo Soudeyns
Hepatitis C virus (HCV) can be transmitted from mother to child during pregnancy and childbirth. However, the timing and precise biological mechanisms that are involved in this process are incompletely understood, as are the determinants that influence transmission of particular HCV variants. Here we report results of a longitudinal assessment of HCV quasispecies diversity and composition in 5 cases of vertical HCV transmission, including 3 women coinfected with human immunodeficiency virus type 1 (HIV-1). The population structure of HCV variant spectra based on E2 envelope gene sequences (nucleotide positions 1491 to 1787), including hypervariable regions 1 and 2, was characterized using next-generation sequencing and median-joining network analysis...
December 1, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28931688/a-selective-bottleneck-shapes-the-evolutionary-mutant-spectra-of-enterovirus-a71-during-viral-dissemination-in-humans
#18
Sheng-Wen Huang, Yi-Hui Huang, Huey-Pin Tsai, Pin-Hwa Kuo, Shih-Min Wang, Ching-Chuan Liu, Jen-Ren Wang
RNA viruses accumulate mutations to rapidly adapt to environmental changes. Enterovirus A71 (EV-A71) causes various clinical manifestations with occasional severe neurological complications. However, the mechanism by which EV-A71 evolves within the human body is unclear. Utilizing deep sequencing and haplotype analyses of viruses from various tissues of an autopsy patient, we sought to define the evolutionary pathway by which enterovirus A71 evolves fitness for invading the central nervous system in humans...
December 1, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28910384/correction-rare-hiv-1-transmitted-founder-lineages-identified-by-deep-viral-sequencing-contribute-to-rapid-shifts-in-dominant-quasispecies-during-acute-and-early-infection
#19
Gustavo H Kijak, Eric Sanders-Buell, Agnes-Laurence Chenine, Michael A Eller, Nilu Goonetilleke, Rasmi Thomas, Sivan Leviyang, Elizabeth A Harbolick, Meera Bose, Phuc Pham, Celina Oropeza, Kultida Poltavee, Anne Marie O'Sullivan, Erik Billings, Melanie Merbah, Margaret C Costanzo, Joanna A Warren, Bonnie Slike, Hui Li, Kristina K Peachman, Will Fischer, Feng Gao, Claudia Cicala, James Arthos, Leigh A Eller, Robert J O'Connell, Samuel Sinei, Lucas Maganga, Hannah Kibuuka, Sorachai Nitayaphan, Mangala Rao, Mary A Marovich, Shelly J Krebs, Morgane Rolland, Bette T Korber, George M Shaw, Nelson L Michael, Merlin L Robb, Sodsai Tovanabutra, Jerome H Kim
[This corrects the article DOI: 10.1371/journal.ppat.1006510.].
September 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28879707/analysis-of-hepatitis-c-virus-ns5a-region-in-patients-with-cirrhosis-using-an-ultra-deep-pyrosequencing-method
#20
Fahriye Keskin, Sevgi Ciftci, Filiz Akyuz, Neslihan Abaci, Aris Cakiris, Umit Akyuz, Kadir Demir, Fatih Besisik, Duran Ustek, Sabahattin Kaymakoglu
BACKGROUND: HCV (Hepatitis C Virus) is genetically more diverse than HBV and HIV (Human Immunodeficiency Virus) and exists as quasispecies within infected individuals. This is due to the lack of efficient proofreading of the viral RNA-dependent RNA polymerase. Consequently, quasispecies emerge depending on the mutation rate of the viral polymerase, which may display a high level of genetic variability in a population. In infected individuals, HCV replicates and circulates as quasispecies composed of a complex mixture of different but closely related genomes that undergoes continuous change due to competitive selection and cooperation between arising mutants...
September 1, 2017: Clinical Laboratory
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