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Quasispecies

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https://www.readbyqxmd.com/read/28931691/vertical-transmission-of-hepatitis-c-virus-variable-transmission-bottleneck-and-evidence-of-mid-gestation-in-utero-infection
#1
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 biologic 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 HIV-1. The population structure of HCV variant spectra based on E2 envelope gene sequences (nucleotide positions 1491-1787), including hypervariable regions 1 and 2, was characterized using next-generation sequencing and median joining network analysis...
September 20, 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
#2
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...
September 20, 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
#3
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
#4
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
https://www.readbyqxmd.com/read/28870671/relationship-between-serum-hbv-rna-levels-and-intrahepatic-viral-as-well-as-histologic-activity-markers-in-entecavir-treated-patients
#5
Jing Wang, Yiqi Yu, Guojun Li, Chuan Shen, Zhefeng Meng, Jianming Zheng, Yanhong Jia, Shaolong Chen, Xiao Zhang, MengQi Zhu, Jiangjiang Zheng, Zhangzhang Song, Jing Wu, Lingyun Shao, Peiyu Qian, Xiaona Mao, Xuanyi Wang, Yuxian Huang, Caiyan Zhao, Jiming Zhang, Chao Qiu, Wenhong Zhang
BACKGROUND: In diagnostics, serum hepatitis B virus (HBV)-RNA levels are valuable when the HBV-DNA load in circulation is effectively suppressed by nucleos(t)ide analogue (NUC) therapy. This study aimed to determine the intrahepatic viral replication activity reflected in serum HBV-RNA and whether HBV-RNA contributes to liver histological changes in NUC-treated patients. METHODS: A cross-sectional set of serum and liver biopsy samples was obtained from entecavir-treated patients with undetectable levels of serum HBV-DNA...
September 1, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28860476/quantifying-perinatal-transmission-of-hepatitis-b-viral-quasispecies-by-tag-linkage-deep-sequencing
#6
Yushen Du, Xiumei Chi, Chong Wang, Jing Jiang, Fei Kong, Hongqing Yan, Xiaomei Wang, Jie Li, Nicholas C Wu, Lei Dai, Tian-Hao Zhang, Sara Shu, Jian Zhou, Janice M Yoshizawa, Xinmin Li, Debika Bhattacharya, Ting-Ting Wu, Junqi Niu, Ren Sun
Despite full immunoprophylaxis, mother-to-child transmission (MTCT) of Hepatitis B Virus still occurs in approximately 2-5% of HBsAg positive mothers. Little is known about the bottleneck of HBV transmission and the evolution of viral quasispecies in the context of MTCT. Here we adopted a newly developed tag linkage deep sequencing method and analyzed the quasispecies of four MTCT pairs that broke through immunoprophylaxis. By assigning unique tags to individual viral sequences, we accurately reconstructed HBV haplotypes in a region of 836 bp, which contains the major immune epitopes and drug resistance mutations...
August 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28774407/the-virological-aspects-of-hepatitis-b
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
In the large majority of cases, HIV infection is 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 nontransmitter mothers, 48 transmitter mothers, and 47 infected infants were assayed in an HIV-1-inducible green fluorescent protein reporter cell line...
September 1, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28635289/exploring-the-drug-resistance-of-hcv-protease
#15
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
#16
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
#17
Frederic Bertels, Chaitanya S Gokhale, Arne Traulsen
Mobile genetic elements can be found in almost all genomes. Possibly the most common nonautonomous mobile genetic elements in bacteria are repetitive extragenic palindromic doublets forming hairpins (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...
August 2017: Genetics
https://www.readbyqxmd.com/read/28613145/two-novel-dromedary-camel-bocaparvoviruses-from-dromedaries-in-the-middle-east-with-unique-genomic-features
#18
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
#19
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
#20
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
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