Sequel sequencing; JC polyomavirus whole genome sequencing at the sin... - SRA

ERX7140577: Sequel sequencing; JC polyomavirus whole genome sequencing at the single molecule level reveals emerging viral populations in Progressive Multifocal Leucoencephalopathy
1 PACBIO_SMRT (Sequel) run: 2,101 spots, 6.9M bases, 2.9Mb downloads

Design: JC polyomavirus whole genome sequencing at the single molecule level reveals emerging viral populations in Progressive Multifocal Leucoencephalopathy

Submitted by: Biomics Platform, Institut Pasteur

Study: JC polyomavirus whole genome sequencing at the single molecule level reveals emerging viral populations in Progressive Multifocal Leucoencephalopathy

PRJEB49243 • ERP133727 • All experiments • All runs

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JC polyomavirus (circular genome) contains two opposite coding regions separated by the regulator non-coding control region (NCCR). NCCR rearrangements and missense mutations in the viral capsid protein VP1 gene differentiate JCV prototype genomes recovered from PML lesions from archetype urine strains. To further investigate the emerging variability of JCV populations in PML, we deep sequenced JCV whole genome recovered from CNS and/or urine samples from HIV- and non HIV-infected PML patients, using single-molecule real-time sequencing (PacBio, Paci?c Biosciences). Phylogenetic analysis showed that PML strains distributed among 6 of 7 known genotypes. Whole genome single molecule sequencing provides insight in the genesis of JCV neurotropic populations.

Sample: 8_urine

SAMEA11459460 • ERS9105380 • All experiments • All runs

Organism: JC polyomavirus

Library:

Name: 8_urine_s

Instrument: Sequel

Strategy: AMPLICON

Source: GENOMIC

Selection: PCR

Layout: SINGLE

Construction protocol: All clinical samples were collected in the frame of standard virology diagnosis procedures, and were independently obtained to confirm JCV infection in immune depressed patients suspected with PML (progressive multifocal leukoencephalopathy). All metadata apart from organism pertains to the host from which the sample was derived QIAsymphony SP, QIAGEN Barcoded libraries were prepared using the Procedure & Checklist \"Preparing Amplicon Libraries\" using PacBio Barcoded Adapters for Multiplex SMRT Sequencing protocol (3.0 chemistry)

Experiment attributes:

Experimental Factor: disease: HIV infection

Experimental Factor: organism part: urine

Runs: 1 run, 2,101 spots, 6.9M bases, 2.9Mb

Run	# of Spots	# of Bases	Size	Published
ERR7569988	2,101	6.9M	2.9Mb	2022-01-13

ID:: 19146582

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