U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SRX341455: NGS of Clinical Metagenomic Datasets Containing Parvo-Like Hybrid Virus (PHV2)
1 ILLUMINA (Illumina MiSeq) run: 2M spots, 497.7M bases, 343.6Mb downloads

Design: BIOSAMPLES accession name title SAMN02338378 PHV-1 non-A-E hepatitis serum cohort SAMN02338379 PHV-2 diarrheic stool from Nigeria SAMN02338380 PHV-3 extracted water Clinical sample sets corresponding to fully sequenced PHV genomes. Diarrheal stool, Nigeria. Seventy-five diarrheic stool samples from Nigeria and 50 from Tunisia were processed for viral NA extraction as previously described (37). Briefly, samples were passed through a 0.45 ?m filter and pretreated with nucleases, followed by NA extraction of 13 sample pools, each containing 5-10 samples, using the QIAamp Viral RNA Mini Kit (Qiagen). Libraries were constructed using the ScriptSeq V2 RNA-Seq Kit (Epicentre) (38) and deep sequenced on an Illumina MiSeq instrument.
Submitted by: University of California, San Francisco
Study: Parvo-like Hybrid Virus Metagenome
show Abstracthide Abstract
NGS metagenomics datasets with sequences corresponding to parvo-like hybrid virus. Next-generation sequencing was used for discovery and de novo assembly of a novel, highly divergent DNA virus at the interface between the Parvoviridae and Circoviridae. The virus, provisionally named “parvovirus-like” hybrid virus (PHV), is nearly identical by sequence to another DNA virus, NIH-CQV, previously reported in Chinese patients with seronegative (non-A-E) hepatitis. Although we initially detected PHV in a wide range of clinical samples, with all strains sharing ~99% nucleotide and amino acid identity with each other and with NIH-CQV, the exact origin of the virus was eventually traced to contaminated silica-binding spin columns used for nucleic acid extraction. Definitive confirmation of the origin of PHV, and presumably NIH-CQV, was obtained by in-depth analyses of water eluted through contaminated spin columns. Analysis of environmental metagenome libraries detected PHV sequences in coastal marine waters of North America, suggesting that a potential association between PHV and diatoms (algae) that generate the silica matrix used in the spin columns may have resulted in inadvertent viral contamination during manufacture. The confirmation of PHV / NIH-CQV as laboratory reagent contaminants and not bona fide infectious agents of humans underscores the rigorous approach needed to establish the validity of new viral genomes discovered by next-generation sequencing.
Sample: diarrheic stool from Nigeria
SAMN02338379 • SRS474560 • All experiments • All runs
Library:
Name: PHV-2
Instrument: Illumina MiSeq
Strategy: OTHER
Source: METAGENOMIC
Selection: RANDOM PCR
Layout: PAIRED
Spot descriptor:
forward151  reverse

Runs: 1 run, 2M spots, 497.7M bases, 343.6Mb
Run# of Spots# of BasesSizePublished
SRR9595551,982,990497.7M343.6Mb2013-08-29

ID:
481173

Supplemental Content

Search details

See more...

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...