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10 results for “Quasispecies”
Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations – application to HIV-1 quasispecies
<p>Pathogen diversity resulting in quasispecies can enable persistence and adaptation to host defenses and therapies. However, accurate quasispecies characterization can be impeded by errors introduced during sample handling and sequencing which can require extensive optimizations to overcome. We present complete laboratory and bioinformatics workflows to overcome many of these hurdles. The Pacific Biosciences single molecule real-time platform was used to sequence PCR amplicons derived from cDNA templates tagged with universal molecular identifiers (SMRT-UMI). Optimized laboratory protocols were developed through extensive testing of different sample preparation conditions to minimize between-template recombination during PCR and the use of UMI allowed accurate template quantitation as well as removal of point mutations introduced during PCR and sequencing to produce a highly accurate consensus sequence from each template. Handling of the large datasets produced from SMRT-UMI sequencing was facilitated by a novel bioinformatic pipeline, Probabilistic Offspring Resolver for Primer IDs (PORPIDpipeline), that automatically filters and parses reads by sample, identifies and discards reads with UMIs likely created from PCR and sequencing errors, generates consensus sequences, checks for contamination within the dataset, and removes any sequence with evidence of PCR recombination or early cycle PCR errors, resulting in highly accurate sequence datasets. The optimized SMRT-UMI sequencing method presented here represents a highly adaptable and established starting point for accurate sequencing of diverse pathogens. These methods are illustrated through characterization of human immunodeficiency virus (HIV) quasispecies.</p>
Intra-host quasispecies reconstructions resemble inter-host variability in transmitted chronic Hepatitis B Virus strains (Dataset)
<p>Data used for publication "Intra-host quasispecies reconstructions resemble inter-host variability in transmitted chronic Hepatitis B Virus strains" submitted to the <em>Journal of Medical Virology</em>. Includes example code and selected sequence, tree, and data files.</p>
Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations – application to HIV-1 quasispecies
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Reduced Complexity of Quasispecies in HBV Surface and Polymerase Genes at Relapses after Antiviral Withdrawal
<p><strong>Figure S1.</strong> The clinical courses of patients included in this study. The longitudinal data of 5 ETV-<strong> (A)</strong> and 2 TDF- <strong>(B)</strong> treated CHB patients are plotted. Black horizontal bar to the top, time-periods when HBeAg was positive; black triangles, time-points when serum samples were obtained before NAs; grey triangles, time-points when serum samples were obtained at relapse after NA withdrawal; black arrows, time-points when patients started to receive NAs; grey arrows, time-points when NAs were withdrawn; black circles, HBV-DNA levels; grey squares, ALT levels.</p> <p> </p> <p><strong>Figure S2.</strong> The HBV genetic heterogeneity in the surface gene analyzed by deep-sequencing. <strong>(A)</strong> The distribution of well-defined functional domains within the surface gene. I, transmembrane domain I (TMD I: s8-22); cytosolic loop (CL: s22-80); II, transmembrane domain II (TMD II: s80-100); major hydrophilic region (MHR: s99-169); antigenic determinant (a determinant) region (located within MHR: s124-147); III, transmembrane domain III (TMD III: s170-192); IV, transmembrane domain IV (TMD IV: s202-224); hydrophobic C-terminus region (HCR: s170-226, includes TMD III-IV and the loop between them). The surface gene variants identified from ETV-treated patients are listed in <strong>(B)</strong> while those identified from TDF-treated patients are listed in <strong>(C)</strong>. Baseline, samples obtained from patients before antiviral treatments; Relapse, samples obtained from patients with virological reactivation after NA withdrawal.</p> <p> </p> <p><strong>Figure S3.</strong> The viral genetic variations in the reverse transcriptase domain of the polymerase gene analyzed by deep-sequencing. <strong>(A)</strong> The functional motifs in the reverse transcriptase domain. G, box G or box I; F, F box or box II: rt37-47; A, box A: rt75-90; B, box B: rt159-182; C, box C: rt201-210; D, box D: rt230-241; E, box E: rt247-257. The variants in the reverse transcriptase domain identified from ETV-treated patients are listed in <strong>(B)</strong> while those identified from TDF-treated patients are listed in <strong>(C)</strong>. Baseline, samples derived from patients before antiviral treatment; Relapse, samples derived from patients with virological relapses after NA withdrawal.</p>
Generation of Anti-HCV Antibodies From Bone Marrow: Defining the Repertoire of Immune Response to HCV Quasispecies
ClinicalTrials.gov study NCT00004851. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Data from: Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake
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Identification of drug- resistance mutations in majority and minority subpopulations of HIV-1 quasispecies
GEO Series GSE90621. Simian-Human immunodeficiency virus. 470 samples. Type: Genome variation profiling by array.
Cyclical quasispecies re-equilibration of dual-tropic measles virus
GEO Series GSE126126. Measles morbillivirus. 10 samples. Type: Expression profiling by high throughput sequencing.
Study of the Role of Dendritic Cells in the Recurrence of Hepatitis C After Liver Transplantation. Analysis of Hepatitis C Virus (HCV) Quasispecies Evolution.
ClinicalTrials.gov study NCT00213707. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Complementation can maintain a quasispecies of drug sensitive and resistant HIV
GEO Series GSE150390. Human immunodeficiency virus 1. 207 samples. Type: Genome variation profiling by high throughput sequencing.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.