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

ERX7140578: 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: 6,836 spots, 17.5M bases, 6.5Mb 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: 10_CSF

SAMEA11459461 • ERS9105381 • All experiments • All runs

Organism: JC polyomavirus

Library:

Name: 10_CSF_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: lung transplant

Experimental Factor: organism part: cerebrospinal fluid

Runs: 1 run, 6,836 spots, 17.5M bases, 6.5Mb

Run	# of Spots	# of Bases	Size	Published
ERR7569989	6,836	17.5M	6.5Mb	2022-01-13

ID:: 19146583

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