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https://www.readbyqxmd.com/read/28774407/the-virological-aspects-of-hepatitis-b
#1
REVIEW
Zina S Valaydon, Stephen A Locarnini
Human hepatitis B virus (HBV) is a hepatotropic virus that is responsible for a significant burden of disease, causing liver disease and hepatocellular carcinoma. It is a small DNA virus with a replication strategy that is similar to that of a retrovirus. HBV is prone to mutagenesis and under the influence of diverse selection pressures, has evolved into a pool of quasispecies, genotypes and mutants, which confers a significant survival advantage. The genome is small, circular, and compact but has a complex replication strategy...
June 2017: Best Practice & Research. Clinical Gastroenterology
https://www.readbyqxmd.com/read/28759651/rare-hiv-1-transmitted-founder-lineages-identified-by-deep-viral-sequencing-contribute-to-rapid-shifts-in-dominant-quasispecies-during-acute-and-early-infection
#2
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
In order to inform the rational design of HIV-1 preventive and cure interventions it is critical to understand the events occurring during acute HIV-1 infection (AHI). Using viral deep sequencing on six participants from the early capture acute infection RV217 cohort, we have studied HIV-1 evolution in plasma collected twice weekly during the first weeks following the advent of viremia. The analysis of infections established by multiple transmitted/founder (T/F) viruses revealed novel viral profiles that included: a) the low-level persistence of minor T/F variants, b) the rapid replacement of the major T/F by a minor T/F, and c) an initial expansion of the minor T/F followed by a quick collapse of the same minor T/F to low frequency...
July 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28750044/hcv-replication-in-gastrointestinal-mucosa-potential-extra-hepatic-viral-reservoir-and-possible-role-in-hcv-infection-recurrence-after-liver-transplantation
#3
Giovanna Russelli, Paola Pizzillo, Gioacchin Iannolo, Floriana Barbera, Fabio Tuzzolino, Rosa Liotta, Mario Traina, Giovanni Vizzini, Bruno Gridelli, Ester Badami, Pier Giulio Conaldi
PURPOSE: Hepatitis C virus (HCV) predominantly infects hepatocytes, although it is known that receptors for viral entry are distributed on a wide array of target cells. Chronic HCV infection is indeed characterized by multiple non-liver manifestations, suggesting a more complex HCV tropism extended to extrahepatic tissues and remains to be fully elucidated. In this study, we investigated the gastrointestinal mucosa (GIM) as a potential extrahepatic viral replication site and its contribution to HCV recurrence...
2017: PloS One
https://www.readbyqxmd.com/read/28740221/escape-from-humoral-immunity-is-associated-with-treatment-failure-in-hiv-1-infected-patients-receiving-long-term-antiretroviral-therapy
#4
Yabo Ouyang, Qianqian Yin, Wei Li, Zhenpeng Li, Desheng Kong, Yanling Wu, Kunxue Hong, Hui Xing, Yiming Shao, Shibo Jiang, Tianlei Ying, Liying Ma
Interindividual heterogeneity in the disease progression of HIV-1-infected patients receiving long-term antiretroviral therapy suggests that some host-related factors may have limited treatment efficacy. To understand the nature of factors contributing to treatment failure, we performed a retrospective cohort study of 45 chronically HIV-1-infected individuals sharing a similar demographics and route of infection, compared the differences between virologically suppressed (VS) and treatment failure (TF) patients with respect to clinical, immunological and virological characteristics...
July 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28732199/catch-shiny-droplets-in-suspension-finding-the-needle-in-a-haystack
#5
Nina V Hein-Fuchs, Renate König
In a recent issue of Cell Chemical Biology, Chaipan et al. (2017) described a high-throughput screening methodology to identify epitopes on HIV-1 particles recognized by broadly neutralizing antibodies. The approach utilizes a droplet-based microfluidics platform combining robust phenotypic single-virus sorting with next-generation sequencing of viral quasispecies.
July 20, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/28680115/identification-of-hcv-resistant-variants-against-direct-acting-antivirals-in-plasma-and-liver-of-treatment-na%C3%A3-ve-patients
#6
V Stalin Raj, Gadissa Bedada Hundie, Anita C Schürch, Saskia L Smits, Suzan D Pas, Sophie Le Pogam, Harry L A Janssen, Rob J de Knegt, Albert D M E Osterhaus, Isabel Najera, Charles A Boucher, Bart L Haagmans
Current standard-of-care treatment of chronically infected hepatitis C virus (HCV) patients involves direct-acting antivirals (DAA). However, concerns exist regarding the emergence of drug -resistant variants and subsequent treatment failure. In this study, we investigate potential natural drug-resistance mutations in the NS5B gene of HCV genotype 1b from treatment-naïve patients. Population-based sequencing and 454 deep sequencing of NS5B gene were performed on plasma and liver samples obtained from 18 treatment- naïve patients...
July 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28650844/long-term-persistence-of-hcv-ns5a-resistance-associated-substitutions-after-treatment-with-the-hcv-ns5a-inhibitor-ledipasvir-without-sofosbuvir
#7
David Wyles, Alessandra Mangia, Wendy Cheng, Stephen Shafran, Christian Schwabe, Wen Ouyang, Charlotte Hedskog, John McNally, Diana M Brainard, Brian P Doehle, Evguenia Svarovskaia, Michael D Miller, Hongmei Mo, Hadas Dvory-Sobol
BACKGROUND: Data on persistence of NS5A resistance associated substitutions (RASs) may have implications for resistance testing approaches and selection of initial and retreatment strategies. METHODS: Long-term persistence of NS5A RASs in HCV genotype (GT) 1 infected subjects (n=76) who did not achieve sustained virologic response after receiving ledipasvir (LDV) without sofosbuvir (SOF) and were subsequently enrolled in an ongoing 3-year follow-up registry study was investigated by population or deep sequencing...
June 26, 2017: Antiviral Therapy
https://www.readbyqxmd.com/read/28637761/mother-to-child-hiv-transmission-bottleneck-selects-for-consensus-virus-with-lower-gag-protease-driven-replication-capacity
#8
Vanessa L Naidoo, Jaclyn K Mann, Christie Noble, Emily Adland, Jonathan M Carlson, Jake Thomas, Chanson J Brumme, Christina F Thobakgale-Tshabalala, Zabrina L Brumme, Mark A Brockman, Philip J R Goulder, Thumbi Ndung'u
HIV infection is in the large majority of cases established by a single variant and understanding the characteristics of successfully transmitted variants is relevant to prevention strategies. Few studies have investigated the viral determinants of mother-to-child transmission. To determine the impact of Gag-protease driven viral replication capacity on mother-to-child transmission, the replication capacities of 148 recombinant viruses encoding plasma derived Gag-protease from 53 non-transmitter mothers, 48 transmitter mothers and 47 infected infants were assayed in an HIV-1 inducible green fluorescent protein reporter cell line...
June 21, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28635289/exploring-the-drug-resistance-of-hcv-protease
#9
Garima Jindal, Dibyendu Mondal, Arieh Warshel
Hepatitis C virus (HCV) currently affects several million people across the globe. One of the major classes of drugs against HCV inhibits the NS3/4A protease of the polyprotein chain. Efficacy of these drugs is severely limited due to the high mutation rate that results in several genetically related quasispecies. The molecular mechanism of drug resistance is frequently deduced from structural studies and binding free energies. However, prediction of new mutations requires the evaluation of both binding free energy of the drug as well as the parameters (kcat and KM) for the natural substrate...
July 5, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28634353/coronavirus-hku15-in-respiratory-tract-of-pigs-and-first-discovery-of-coronavirus-quasispecies-in-5-untranslated-region
#10
Patrick Cy Woo, Susanna Kp Lau, Chi-Ching Tsang, Candy Cy Lau, Po-Chun Wong, Franklin Wn Chow, Jordan Yh Fong, Kwok-Yung Yuen
Coronavirus HKU15 is a deltacoronavirus that was discovered in fecal samples of pigs in Hong Kong in 2012. Over the past three years, Coronavirus HKU15 has been widely detected in pigs in East/Southeast Asia and North America and has been associated with fatal outbreaks. In all such epidemiological studies, the virus was generally only detected in fecal/intestinal samples. In this molecular epidemiology study, we detected Coronavirus HKU15 in 9.6% of the nasopharyngeal samples obtained from 249 pigs in Hong Kong...
June 21, 2017: Emerging Microbes & Infections
https://www.readbyqxmd.com/read/28630115/discovering-complete-quasispecies-in-bacterial-genomes
#11
Frederic Bertels, Chaitanya S Gokhale, Arne Traulsen
Mobile genetic elements can be found in almost all genomes. Possibly the most common non-autonomous mobile genetic elements in bacteria are REPINs that can occur hundreds of times within a genome. The sum of all REPINs in a genome can be viewed as an evolving population because REPINs replicate and mutate. In contrast to most other biological populations, we know the exact composition of the REPIN population and the sequence of each member of the population. Here, we model the evolution of REPINs as quasispecies...
June 19, 2017: Genetics
https://www.readbyqxmd.com/read/28613145/two-novel-dromedary-camel-bocaparvoviruses-from-dromedaries-in-the-middle-east-with-unique-genomic-features
#12
Patrick C Y Woo, Susanna K P Lau, Hoi-Wah Tsoi, Nissy Georgy Patteril, Hazel C Yeung, Sunitha Joseph, Emily Y M Wong, Rubeena Muhammed, Franklin W N Chow, Ulrich Wernery, Kwok-Yung Yuen
The recent emergence of Middle East respiratory syndrome (MERS) coronavirus and its discovery from dromedary camels has boosted interest in the search for novel viruses in dromedaries. While bocaparvoviruses are known to infect various animals, it was not known that they exist in dromedaries. In this study, we describe the discovery of two novel dromedary camel bocaparvoviruses (DBoVs), DBoV1 and DBoV2, from dromedary faecal samples in Dubai. Among 667 adult dromedaries and 72 dromedary calves, 13.9 % of adult dromedaries and 33...
June 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28595635/the-pepper-virome-natural-co-infection-of-diverse-viruses-and-their-quasispecies
#13
Yeonhwa Jo, Hoseong Choi, Sang-Min Kim, Sun-Lim Kim, Bong Choon Lee, Won Kyong Cho
BACKGROUND: The co-infection of diverse viruses in a host plant is common; however, little is known about viral populations and their quasispecies in the host. RESULTS: Here, we report the first pepper viromes that were co-infected by different types of viral genomes. The pepper viromes are dominated by geminivirus DNA-A followed by a novel carlavirus referred to as Pepper virus A. The two pepper cultivars share similar viral populations and replications. However, the quasispecies for double-stranded RNA virus and two satellite DNAs were heterogeneous and homogenous in susceptible and resistant cultivars, respectively, indicating the quasispecies of an individual virus depends on the host...
June 8, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28595606/detection-of-a-genetic-footprint-of-the-sofosbuvir-resistance-associated-substitution-s282t-after-hcv-treatment-failure
#14
Andreas Walker, Sandra Filke, Nadine Lübke, Martin Obermeier, Rolf Kaiser, Dieter Häussinger, Jörg Timm, Hans H Bock
BACKGROUND: The major resistance-associated substitution for sofosbuvir (S282T) in HCV NS5B causes severe viral fitness costs and rapidly reverts back to prototype in the absence of selection pressure. Accordingly, resistance against sofosbuvir is rarely detected even in patients after treatment failure. CASE PRESENTATION: We report a case of a GT3a infected patient with viral breakthrough under SOF/DCV therapy. At the time of breakthrough the RAS S282T was predominant in NS5B and then rapidly disappeared during follow-up by week 12 after treatment...
June 8, 2017: Virology Journal
https://www.readbyqxmd.com/read/28591184/occult-hepatitis-b-virus-infection-in-hiv-positive-patients-at-a-tertiary-healthcare-unit-in-eastern-india
#15
Debraj Saha, Ananya Pal, Neelakshi Sarkar, Dipanwita Das, Jason T Blackard, Subhasish Kamal Guha, Bibhuti Saha, Runu Chakravarty
Occult HBV infection (OBI), defined by the presence of HBV DNA in absence of hepatitis B surface antigen (HBsAg), is a significant concern in the HIV-infected population. Of 441 HIV+/HBsAg- patients analyzed, the overall prevalence of OBI was 6.3% (28/441). OBI was identified in 21 anti-HBc positives (17.8%), as well as among those who lacked any HBV-specific serological markers (2.2%). Comparison with HIV/HBV co-infection revealed that the levels of CD4, ALT, and HBV DNA were significantly lower during occult infection...
2017: PloS One
https://www.readbyqxmd.com/read/28547382/comparative-analysis-of-cherry-virus-a-genome-sequences-assembled-from-deep-sequencing-data
#16
Prasad Kesanakurti, Mark Belton, Hanaa Saeed, Heidi Rast, Ian Boyes, Michael Rott
Cherry virus A (CVA) is a ubiquitous graft-transmissible virus that mainly infects Prunus spp. Next-generation sequencing was applied to 39 tree fruit specimens infected with CVA, and 75 full and 16 partial-length CVA genome sequences were assembled. Phylogenetic analysis of these and 11 previously sequenced CVA genomes resulted in six major clusters with no observable relationship between the host and the assembled genome sequences. Recombination analysis detected four recombinants. Consistent single-nucleotide polymorphism (SNP) patterns were observed between the 75 full-length genomes and their sequence clouds, which supports a quasispecies model for CVA evolution...
May 25, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28539654/quasispecies-composition-and-evolution-of-a-typical-zika-virus-clinical-isolate-from-suriname
#17
Sander van Boheemen, Ali Tas, S Yahya Anvar, Rebecca van Grootveld, Irina C Albulescu, Martijn P Bauer, Mariet C Feltkamp, Peter J Bredenbeek, Martijn J van Hemert
The arthropod-borne Zika virus (ZIKV) is currently causing a major international public health threat in the Americas. This study describes the isolation of ZIKV from the plasma of a 29-year-old female traveler that developed typical symptoms, like rash, fever and headache upon return from Suriname. The complete genome sequence including the 5' and 3' untranslated regions was determined and phylogenetic analysis showed the isolate clustering within the Asian lineage, close to other viruses that have recently been isolated in the Americas...
May 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28483405/quasispecies-characteristics-in-mother-to-child-transmission-of-hepatitis%C3%A2-b%C3%A2-virus-by-next-generation-sequencing
#18
Guifeng Yang, Zhihua Liu, Juncheng Yang, Kangxian Luo, Ying Xu, Haitang He, Qunfang Fu, Shouyi Yu, Zhanhui Wang
OBJECTIVES: To identify within-host quasispecies characteristics of hepatitis B virus (HBV) in mothers and children infected via mother-to-child transmission (MTCT). METHODS: Using next-generation sequencing (NGS), we analyzed sequences within the non-overlapping pre-core/core (pre-C/C) gene in 37 mother-child pairs. RESULTS: Phylogenetic and Highlighter analyses suggested that both a single strain and multiple distinct strains may be transmitted in MTCT of HBV...
May 5, 2017: Journal of Infection
https://www.readbyqxmd.com/read/28464889/highly-divergent-patterns-of-genetic-diversity-and-evolution-in-proviral-quasispecies-from-hiv-controllers
#19
Suwellen S D de Azevedo, Diogo Gama Caetano, Fernanda H Côrtes, Sylvia L M Teixeira, Karina Dos Santos Silva, Brenda Hoagland, Beatriz Grinsztejn, Valdilea G Veloso, Mariza G Morgado, Gonzalo Bello
BACKGROUND: Ongoing intra-host HIV-1 evolution has been shown in individuals that naturally suppress the viremia to low levels (HIV controllers) by the analysis of the RNA in plasma compartment. Detection of evolution at the DNA proviral compartment in HIV controllers, however, has been more challenging and the precise correlation between the systemic viral suppression level and rate of reservoir's reseeding in those individuals is not fully understood. In this sense, we examined the proviral DNA quasispecies by single genome amplification of the env gene in a cohort of 23 HIV controllers from Brazil, divided in three groups, according to the level of systemic viral suppression: (1) elite controllers with persistent undetectable viral load (PEC, n = 6); (2) elite controllers with occasional episodes of transient (51-400 copies/mL) viremia (EEC, n = 7); and (3) viremic controllers with persistent low-level (80-2000 copies/mL) viremia (VC, n = 10)...
May 2, 2017: Retrovirology
https://www.readbyqxmd.com/read/28446139/de-novo-assembly-of-highly-polymorphic-metagenomic-data-using-in-situ-generated-reference-sequences-and-a-novel-blast-based-assembly-pipeline
#20
You-Yu Lin, Chia-Hung Hsieh, Jiun-Hong Chen, Xuemei Lu, Jia-Horng Kao, Pei-Jer Chen, Ding-Shinn Chen, Hurng-Yi Wang
BACKGROUND: The accuracy of metagenomic assembly is usually compromised by high levels of polymorphism due to divergent reads from the same genomic region recognized as different loci when sequenced and assembled together. A viral quasispecies is a group of abundant and diversified genetically related viruses found in a single carrier. Current mainstream assembly methods, such as Velvet and SOAPdenovo, were not originally intended for the assembly of such metagenomics data, and therefore demands for new methods to provide accurate and informative assembly results for metagenomic data...
April 26, 2017: BMC Bioinformatics
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