The Perils of Pathogen Discovery: Origin of a Novel Parvovirus-Like Hybrid Genome Traced to Nucleic Acid Extraction Spin Columns

被引:189
作者
Naccache, Samia N. [1 ,2 ]
Greninger, Alexander L. [1 ,2 ]
Lee, Deanna [1 ,2 ]
Coffey, Lark L. [3 ]
Tung Phan [3 ]
Rein-Weston, Annie [1 ,2 ]
Aronsohn, Andrew [4 ]
Hackett, John, Jr. [5 ]
Delwart, Eric L. [1 ,3 ]
Chiu, Charles Y. [1 ,2 ,6 ]
机构
[1] Univ Calif San Francisco, Dept Lab Med, San Francisco, CA 94143 USA
[2] UCSF Abbott Viral Diagnost & Discovery Ctr, San Francisco, CA USA
[3] Blood Syst Res Inst, San Francisco, CA USA
[4] Univ Chicago, Med Ctr, Ctr Liver Dis, Chicago, IL 60637 USA
[5] Abbott Diagnost, Abbott Pk, IL USA
[6] Univ Calif San Francisco, Dept Med, Div Infect Dis, San Francisco, CA USA
基金
美国国家卫生研究院;
关键词
VIRUSES; HEPATITIS; DNA; DISEASE; IDENTIFICATION; CONTAMINATION; SOFTWARE; CHILDREN; DIATOMS; SAMPLES;
D O I
10.1128/JVI.02323-13
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
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 detected 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 similar to 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.
引用
收藏
页码:11966 / 11977
页数:12
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