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https://www.readbyqxmd.com/read/29321314/hla-class-i-downregulation-by-hiv-1-variants-from-subtype-c-transmission-pairs
#1
Zachary Ende, Martin J Deymier, Daniel T Claiborne, Jessica L Prince, Daniela C Mónaco, William Kilembe, Susan A Allen, Eric Hunter
HIV-1 downregulates HLA-A and HLA-B from the surface of infected cells primarily to evade CD8 T cell recognition. HLA-C was thought to remain on the cell surface and bind inhibitory killer immunoglobulin-like receptors, preventing NK cell-mediated suppression. However, a recent study found HIV-1 primary viruses have the capacity to downregulate HLA-C. The goal of this study was to assess the heterogeneity of HLA-A, HLA-B and HLA-C downregulation among full-length primary viruses from six chronically infected and six newly infected individuals from transmission pairs, and to determine whether transmitted/founder variants exhibit common HLA class I downregulation characteristics...
January 10, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29316067/deep-sequencing-shows-low-level-oncogenic-hepatitis-b-virus-variants-persisting-post-liver-transplant-despite-potent-anti-hbv-prophylaxis
#2
Keith Ck Lau, Carla Osiowy, Elizabeth Giles, Beth Lusina, Guido van Marle, Kelly W Burak, Carla S Coffin
Recent studies suggest that withdrawal of hepatitis B immune globulin (HBIG) and nucleos(t)ide analogues (NA) prophylaxis may be considered in HBV surface antigen (HBsAg) negative liver transplant (LT) recipients with a low risk of disease recurrence. However, the frequency of occult HBV infection (OBI) and HBV variants after LT in the current era of potent NA therapy is unknown. 12 LT recipients on prophylaxis were tested in matched plasma and peripheral blood mononuclear cells (PBMC) for HBV quasispecies by in-house nested PCR and next generation sequencing of amplicons...
January 6, 2018: Journal of Viral Hepatitis
https://www.readbyqxmd.com/read/29306002/bovine-viral-diarrhea-virus-genomic-variation-within-persistently-infected-cattle
#3
A Chernick, A Ambagala, K Orsel, J D Wasmuth, G van Marle, F van der Meer
Bovine viral diarrhea virus (BVDV) is a single stranded RNA virus in the family Flaviviridae that causes a form of persistent infection. If a fetus is infected in utero during the first 120days of gestation the resulting calf will be immunotolerant to the infecting strain and maintain the virus for life. These animals are epidemiologically important in maintaining BVDV on farms, but also present a unique opportunity to study quasispecies in vivo in the absence of significant selection by the host adaptive immune response...
January 3, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29304222/quentin-reconstruction-of-disease-transmissions-from-viral-quasispecies-genomic-data
#4
Pavel Skums, Alex Zelikovsky, Rahul Singh, Walker Gussler, Zoya Dimitrova, Sergey Knyazev, Igor Mandric, Sumathi Ramachandran, David Campo, Deeptanshu Jha, Leonid Bunimovich, Elizabeth Costenbader, Connie Sexton, Siobhan O'Connor, Guo-Liang Xia, Yury Khudyakov
Motivation: Genomic analysis has become one of the major tools for disease outbreak investigations. However, existing computational frameworks for inference of transmission history from viral genomic data often do not consider intra-host diversity of pathogens and heavily rely on additional epidemiological data, such as sampling times and exposure intervals. This impedes genomic analysis of outbreaks of highly mutable viruses associated with chronic infections, such as human immunodeficiency virus and hepatitis C virus, whose transmissions are often carried out through minor intra-host variants, while the additional epidemiological information often is either unavailable or has a limited use...
January 1, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29244129/dolutegravir-reshapes-the-genetic-diversity-of-hiv-1-reservoirs
#5
Pierre Gantner, Guinevere Q Lee, David Rey, Thibault Mesplede, Marialuisa Partisani, Christine Cheneau, Geneviève Beck-Wirth, Jean-Pierre Faller, Mahsa Mohseni-Zadeh, Martin Martinot, Mark A Wainberg, Samira Fafi-Kremer
Objectives: Better understanding of the dynamics of HIV reservoirs under ART is a critical step to achieve a functional HIV cure. Our objective was to assess the genetic diversity of archived HIV-1 DNA over 48 weeks in blood cells of individuals starting treatment with a dolutegravir-based regimen. Methods: Eighty blood samples were prospectively and longitudinally collected from 20 individuals (NCT02557997) including: acutely (n = 5) and chronically (n = 5) infected treatment-naive individuals, as well as treatment-experienced individuals who switched to a dolutegravir-based regimen and were either virologically suppressed (n = 5) or had experienced treatment failure (n = 5)...
December 13, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29244009/inference-of-genetic-relatedness-between-viral-quasispecies-from-sequencing-data
#6
Olga Glebova, Sergey Knyazev, Andrew Melnyk, Alexander Artyomenko, Yury Khudyakov, Alex Zelikovsky, Pavel Skums
BACKGROUND: RNA viruses such as HCV and HIV mutate at extremely high rates, and as a result, they exist in infected hosts as populations of genetically related variants. Recent advances in sequencing technologies make possible to identify such populations at great depth. In particular, these technologies provide new opportunities for inference of relatedness between viral samples, identification of transmission clusters and sources of infection, which are crucial tasks for viral outbreaks investigations...
December 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29202874/sensitive-detection-of-hiv-1-resistance-to-zidovudine-and-impact-on-treatment-outcomes-in-low-to-middle-income-countries
#7
Richard M Gibson, Gabrielle Nickel, Michael Crawford, Fred Kyeyune, Colin Venner, Immaculate Nankya, Eva Nabulime, Emmanuel Ndashimye, Art F Y Poon, Robert A Salata, Cissy Kityo, Peter Mugyenyi, Miguel E Quiñones-Mateu, Eric J Arts
BACKGROUND: Thymidine analogs, namely AZT (Zidovudine or Retrovir™) and d4T (Stavudine or Zerit™) are antiretroviral drugs still employed in over 75% of first line combination antiretroviral therapy (cART) in Kampala, Uganda despite aversion to prescribing these drugs for cART in high income countries due in part to adverse events. For this study, we explored how the continued use of these thymidine analogs in cART could impact emergence of drug resistance and impact on future treatment success in Uganda, a low-income country...
December 4, 2017: Infectious Diseases of Poverty
https://www.readbyqxmd.com/read/29149077/rna-virus-evolution-via-a-quasispecies-based-model-reveals-a-drug-target-with-a-high-barrier-to-resistance
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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