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Quasispecies

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https://www.readbyqxmd.com/read/28422783/lessons-learned-from-humoral-responses-of-hiv-patients
#1
Laura E McCoy, Áine McKnight
PURPOSE OF REVIEW: Since 2009 many broadly neutralizing antibodies against HIV have been identified, yet there is still no vaccine capable of inducing such antibodies in humans. This review considers the early observations of HIV sera neutralization in light of more recent studies and highlights areas for future research. RECENT FINDINGS: Large clinical cohort studies using standardized neutralization assays and pseudoviruses derived from primary isolates have shown that 10-30% of HIV infections result in some level of serum neutralization breadth...
May 2017: Current Opinion in HIV and AIDS
https://www.readbyqxmd.com/read/28401776/molecular-characteristics-of-the-envelope-of-vertically-transmitted-hiv-1-strains-from-infants-with-hiv-infection
#2
Manickam Ashokkumar, Manohar Nesakumar, Cheedarla Narayanaiah, Vidya Vijayan Kk, Babu Hemalatha, Srikanth P Tripathy, Luke Elizabeth Hanna
Mother-to-child transmission of HIV offers a good opportunity to study the dynamics of early viral evolution in the host environment to which the virus has partially adapted. Such studies would throw light on the unique features of the infecting viruses, which will subsequently help to design preventive or therapeutic measures against the newly infecting and evolving strains of HIV. Therefore, we undertook a study to determine the genetic divergence of proviral envelope sequences from the HIV infected infants (< 2 years)...
April 12, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28396522/de-novo-assembly-of-viral-quasispecies-using-overlap-graphs
#3
Jasmijn A Baaijens, Amal Zine El Aabidine, Eric Rivals, Alexander Schönhuth
A viral quasispecies, the ensemble of viral strains populating an infected person, can be highly diverse. For optimal assessment of virulence, pathogenesis, and therapy selection, determining the haplotypes of the individual strains can play a key role. As many viruses are subject to high mutation and recombination rates, high-quality reference genomes are often not available at the time of a new disease outbreak. We present SAVAGE, a computational tool for reconstructing individual haplotypes of intra-host virus strains without the need for a high-quality reference genome...
April 10, 2017: Genome Research
https://www.readbyqxmd.com/read/28396347/serotype-specific-interactions-among-functional-domains-of-dengue-virus-2-non-structural-proteins-ns-5-and-ns3-are-crucial-for-viral-rna-replication
#4
Tadahisa Teramoto, Anuradha Balasubramanian, Kyung H Choi, Radhakrishnan Padmanabhan
Four serotypes of mosquito-borne Dengue virus (DENV), evolved from a common ancestor, are human pathogens of global significance, and there is no vaccine or antiviral drug available. The N-terminal domain of DENV NS5 has guanylyltransferase and methyltransferase (MTase) and the C-terminal region has the polymerase (POL) which are important for 5'-capping and RNA replication. The crystal structure of NS5 showed it as a dimer but the functional evidence for NS5 dimer is lacking. The results of our studies show that the substitution of DENV2 NS5 MTase or POL with that of DENV4 NS5 within DENV2 RNA resulted in severe attenuation of replication in the transfected BHK-21 cells...
April 10, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28395198/propagation-and-some-physiological-effects-of-citrus-bark-cracking-viroid-and-apple-fruit-crinkle-viroid-in-multiple-infected-hop-humulus-lupulus-l
#5
J Matoušek, K Siglová, J Jakše, S Radišek, Joseph R J Brass, T Tsushima, T Guček, G S Duraisamy, T Sano, G Steger
The hop metabolome important for the brewing industry and for medical purposes is endangered worldwide due to multiple viroid infections affecting hop physiology. Combinatorial biolistic hop inoculation with Citrus bark cracking viroid (CBCVd), Apple fruit crinkle viroid (AFCVd), Hop latent viroid, and Hop stunt viroid (HSVd) showed a low CBCVd compatibility with HSVd, while all other viroid combinations were highly compatible. Unlike to other viroids, single CBCVd propagation showed a significant excess of (-) over (+) strands in hop, tomato, and Nicotiana benthamiana, but not in citruses...
March 27, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28394908/natural-non-homologous-recombination-led-to-the-emergence-of-a-duplicated-v3-ns5a-region-in-hcv-1b-strains-associated-with-hepatocellular-carcinoma
#6
Hélène Le Guillou-Guillemette, Adeline Pivert, Elise Bouthry, Cécile Henquell, Odile Petsaris, Alexandra Ducancelle, Pascal Veillon, Sophie Vallet, Sophie Alain, Vincent Thibault, Florence Abravanel, Arielle A Rosenberg, Elisabeth André-Garnier, Jean-Baptiste Bour, Yazid Baazia, Pascale Trimoulet, Patrice André, Catherine Gaudy-Graffin, Dominique Bettinger, Sylvie Larrat, Anne Signori-Schmuck, Hénia Saoudin, Bruno Pozzetto, Gisèle Lagathu, Sophie Minjolle-Cha, Françoise Stoll-Keller, Jean-Michel Pawlotsky, Jacques Izopet, Christopher Payan, Françoise Lunel-Fabiani, Christophe Lemaire
BACKGROUND: The emergence of new strains in RNA viruses is mainly due to mutations or intra and inter-genotype homologous recombination. Non-homologous recombinations may be deleterious and are rarely detected. In previous studies, we identified HCV-1b strains bearing two tandemly repeated V3 regions in the NS5A gene without ORF disruption. This polymorphism may be associated with an unfavorable course of liver disease and possibly involved in liver carcinogenesis. Here we aimed at characterizing the origin of these mutant strains and identifying the evolutionary mechanism on which the V3 duplication relies...
2017: PloS One
https://www.readbyqxmd.com/read/28393875/oldest-varroa-tolerant-honey-bee-population-provides-insight-into-the-origins-of-the-global-decline-of-honey-bees
#7
L E Brettell, S J Martin
The ecto-parasitic mite Varroa destructor has transformed the previously inconsequential Deformed Wing Virus (DWV) into the most important honey bee viral pathogen responsible for the death of millions of colonies worldwide. Naturally, DWV persists as a low level covert infection transmitted between nest-mates. It has long been speculated that Varroa via immunosuppression of the bees, activate a covert infection into an overt one. Here we show that despite Varroa feeding on a population of 20-40 colonies for over 30 years on the remote island of Fernando de Noronha, Brazil no such activation has occurred and DWV loads have remained at borderline levels of detection...
April 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28386078/evolution-of-full-length-genomes-of-hbv-quasispecies-in-sera-of-patients-with-a-coexistence-of-hbsag-and-anti-hbs-antibodies
#8
Tai-Cheng Zhou, Xiao Li, Long Li, Xiao-Fei Li, Liang Zhang, Jia Wei
Although the evolutionary changes of viral quasispecies are correlated to the pathological status of a disease, little is known in the coexistence of hepatitis B surface antigen (HBsAg) and antibodies to these antigens (anti-HBs). To examine evolutionary changes in hepatitis B virus (HBV) and their relationship to the coexistence of HBsAg and anti-HBs antibodies, HBV genomes in patients with a coexistence of HBsAg and anti-HBs antibodies (experimental group) and HBsAg positive without anti-HBs (control group) were assessed...
April 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28382024/current-advances-on-virus-discovery-and-diagnostic-role-of-viral-metagenomics-in-aquatic-organisms
#9
REVIEW
Hetron M Munang'andu, Kizito K Mugimba, Denis K Byarugaba, Stephen Mutoloki, Øystein Evensen
The global expansion of the aquaculture industry has brought with it a corresponding increase of novel viruses infecting different aquatic organisms. These emerging viral pathogens have proved to be a challenge to the use of traditional cell-cultures and immunoassays for identification of new viruses especially in situations where the novel viruses are unculturable and no antibodies exist for their identification. Viral metagenomics has the potential to identify novel viruses without prior knowledge of their genomic sequence data and may provide a solution for the study of unculturable viruses...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28362878/deep-sequencing-is-an-appropriate-tool-for-the-selection-of-unique-hepatitis-c-virus-hcv-variants-after-single-genomic-amplification
#10
Thibault Guinoiseau, Alain Moreau, Guillaume Hohnadel, Nicole Ngo-Giang-Huong, Celine Brulard, Patrick Vourc'h, Alain Goudeau, Catherine Gaudy-Graffin
Hepatitis C virus (HCV) evolves rapidly in a single host and circulates as a quasispecies wich is a complex mixture of genetically distinct virus's but closely related namely variants. To identify intra-individual diversity and investigate their functional properties in vitro, it is necessary to define their quasispecies composition and isolate the HCV variants. This is possible using single genome amplification (SGA). This technique, based on serially diluted cDNA to amplify a single cDNA molecule (clonal amplicon), has already been used to determine individual HCV diversity...
2017: PloS One
https://www.readbyqxmd.com/read/28361288/evolution-of-h5-highly-pathogenic-avian-influenza-sequence-data-indicate-stepwise-changes-in-the-cleavage-site
#11
Celia Abolnik
The genetic composition of an H5 subtype hemagglutinin gene quasispecies, obtained from ostrich tissues that had been infected with H5 subtype influenza virus was analysed using a next generation sequencing approach. The first evidence for the reiterative copying of a poly (U) stretch in the connecting peptide region in the haemagglutinin cleavage site (HACS) by the viral RNA-dependent RNA polymerase (RdRp) is provided. Multiple non-consensus species of RNA were detected in the infected host, corresponding to likely intermediate sequences between the putative low pathogenic precursor nucleotide sequence of the H5 influenza strain and the highly pathogenic avian influenza virus gene sequence...
March 30, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28361286/quasispecies-evolution-of-the-prototypical-genotype-1-porcine-reproductive-and-respiratory-syndrome-virus-early-during-in-vivo-infection-is-rapid-and-tissue-specific
#12
Zen H Lu, Xinglong Wang, Alison D Wilson, Daniel L W Dorey-Robinson, Alan L Archibald, Tahar Ait-Ali, Jean-Pierre Frossard
Porcine reproductive and respiratory syndrome virus (PRRSV) is a major infectious threat to the pig industry worldwide. Increasing evidence suggests that microevolution within a quasispecies population can give rise to high sequence heterogeneity in PRRSV; potentially impacting the pathogenicity of the virus. Here, we report on micro-evolutionary events taking place within the viral quasispecies population in lung and lymph node 3 days post infection (dpi) following experimental in vivo infection with the prototypical Lelystad PRRSV (LV)...
March 30, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28360890/driving-hiv-1-into-a-vulnerable-corner-by-taking-advantage-of-viral-adaptation-and-evolution
#13
REVIEW
Shigeyoshi Harada, Kazuhisa Yoshimura
Anti-retroviral therapy (ART) is crucial for controlling human immunodeficiency virus type-1 (HIV-1) infection. Recently, progress in identifying and characterizing highly potent broadly neutralizing antibodies has provided valuable templates for HIV-1 therapy and vaccine design. Nevertheless, HIV-1, like many RNA viruses, exhibits genetically diverse populations known as quasispecies. Evolution of quasispecies can occur rapidly in response to selective pressures, such as that exerted by ART and the immune system...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28353014/deep-sequencing-analysis-of-quasispecies-in-the-hbv-pre-s-region-and-its-association-with-hepatocellular-carcinoma
#14
An-Ye Zhang, Ching-Lung Lai, Fung-Yu Huang, Wai-Kay Seto, James Fung, Danny Ka-Ho Wong, Man-Fung Yuen
BACKGROUND: The association between the evolution of hepatitis B virus (HBV) quasispecies and the development of hepatocellular carcinoma (HCC) is unknown. METHODS: We used deep sequencing to examine the dynamics of HBV quasispecies and their relationship to HCC development. Thirty-two chronic hepatitis B (CHB) patients with HCC (HCC group) and 32 matched CHB patients without HCC (controls) were recruited. Fourteen patients from each group had serial sera available up to 9 years before the time of the present study...
March 28, 2017: Journal of Gastroenterology
https://www.readbyqxmd.com/read/28331526/impaired-human-immunodeficiency-virus-type-1-replicative-fitness-in-atypical-viremic-non-progressor-individuals
#15
Jan Weber, Richard M Gibson, Lenka Sácká, Dmytro Strunin, Jan Hodek, Jitka Weberová, Marcela Pávová, David J Alouani, Robert Asaad, Benigno Rodriguez, Michael M Lederman, Miguel E Quiñones-Mateu
BACKGROUND: Progression rates from initial HIV-1 infection to advanced AIDS vary significantly among infected individuals. A distinct subgroup of HIV-1-infected individuals-termed viremic non-progressors (VNP) or controllers-do not seem to progress to AIDS, maintaining high CD4(+) T cell counts despite high levels of viremia for many years. Several studies have evaluated multiple host factors, including immune activation, trying to elucidate the atypical HIV-1 disease progression in these patients; however, limited work has been done to characterize viral factors in viremic controllers...
2017: AIDS Research and Therapy
https://www.readbyqxmd.com/read/28327559/quasispecies-of-hepatitis-c-virus-participate-in-cell-specific-infectivity
#16
Takasuke Fukuhara, Satomi Yamamoto, Chikako Ono, Shota Nakamura, Daisuke Motooka, Hiroyuki Mori, Takeshi Kurihara, Asuka Sato, Tomokazu Tamura, Takashi Motomura, Toru Okamoto, Michio Imamura, Toru Ikegami, Tomoharu Yoshizumi, Yuji Soejima, Yoshihiko Maehara, Kazuaki Chayama, Yoshiharu Matsuura
It is well documented that a variety of viral quasispecies are found in the patients with chronic infection of hepatitis C virus (HCV). However, the significance of quasispecies in the specific infectivity to individual cell types remains unknown. In the present study, we analyzed the role of quasispecies of the genotype 2a clone, JFH1 (HCVcc), in specific infectivity to the hepatic cell lines, Huh7.5.1 and Hep3B. HCV RNA was electroporated into Huh7.5.1 cells and Hep3B/miR-122 cells expressing miR-122 at a high level...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28325923/clinical-features-and-viral-quasispecies-characteristics-associated-with-infection-by-the-hepatitis-b-virus-g145r-immune-escape-mutant
#17
Yuan Xue, Ming-Jie Wang, Zhi-Tao Yang, De-Min Yu, Yue Han, Dao Huang, Dong-Hua Zhang, Xin-Xin Zhang
Coexistence of the hepatitis B surface antigen (HBsAg) and hepatitis B surface antibody (anti-HBs) is an uncommon phenomenon, and the underlying mechanisms remain largely unknown. Amino-acid (aa) substitution from glycine to arginine at aa 145 (G145R), in the major hydrophilic region, has been reported in patients with HBsAg and anti-HBs coexistence. However, there is limited knowledge about the clinical features and viral quasispecies characteristics associated with G145R mutant hepatitis B virus (HBV) infection...
March 22, 2017: Emerging Microbes & Infections
https://www.readbyqxmd.com/read/28320417/impaired-human-immunodeficiency-virus-type-1-replicative-fitness-in-atypical-viremic-non-progressor-individuals
#18
Jan Weber, Richard M Gibson, Lenka Sácká, Dmytro Strunin, Jan Hodek, Jitka Weberová, Marcela Pávová, David J Alouani, Robert Asaad, Benigno Rodriguez, Michael M Lederman, Miguel E Quiñones-Mateu
BACKGROUND: Progression rates from initial HIV-1 infection to advanced AIDS vary significantly among infected individuals. A distinct subgroup of HIV-1-infected individuals-termed viremic non-progressors (VNP) or controllers-do not seem to progress to AIDS, maintaining high CD4(+) T cell counts despite high levels of viremia for many years. Several studies have evaluated multiple host factors, including immune activation, trying to elucidate the atypical HIV-1 disease progression in these patients; however, limited work has been done to characterize viral factors in viremic controllers...
March 20, 2017: AIDS Research and Therapy
https://www.readbyqxmd.com/read/28303969/hbv-quasispecies-composition-in-lamivudine-failed-chronic-hepatitis-b-patients-and-its-influence-on-virological-response-to-tenofovir-based-rescue-therapy
#19
Priyanka Banerjee, Abhijit Chakraborty, Rajiv Kumar Mondal, Mousumi Khatun, Somenath Datta, Kausik Das, Pratap Pandit, Souvik Mukherjee, Soma Banerjee, Saurabh Ghosh, Saikat Chakrabarti, Abhijit Chowdhury, Simanti Datta
The present study sought to evaluate the structure of HBV quasispecies in Lamivudine (LMV)-failed chronic hepatitis B (CHB) patients and its impact in defining the subsequent virological responses to Tenofovir (TDF)-based rescue-therapy. By analyzing HBV clones encompassing reverse transcriptase (RT) and surface (S) region from LMV-failed and treatment-naïve CHB patients, we identified 5 classical and 12 novel substitutions in HBV/RT and 9 substitutions in immune-epitopes of HBV/S that were significantly associated with LMV failure...
March 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28301421/persistence-of-hiv-drug-resistance-among-south-african-children-given-nevirapine-to-prevent-mother-to-child-transmission
#20
Ruth Kanthula, Theresa Rossouw, Ute D Feucht, Gisela Van Dyk, Ingrid A Beck, Rachel Silverman, Scott Olson, Christen Salyer, Sharon Cassol, Lisa M Frenkel
OBJECTIVES: We set out to examine the prevalence and persistence of mutations conferring high-level nonnucleoside-reverse-transcriptase (NNRTI)-resistance in a cohort of HIV-infected children who had failed prophylaxis to prevent mother-to-child-transmission (PMTCT). DESIGN: A prospective observational cohort study at the Pediatric HIV Clinic at Kalafong Provincial Tertiary Hospital in Pretoria, South Africa. METHODS: Children referred for initiation of ART were enrolled from July 2010 through February 2013...
March 15, 2017: AIDS
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