title: The perils of pathogen discovery: origin of a novel parvovirus-like hybrid genome traced to nucleic acid extraction spin columns.
abstract: 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 ∼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.
authors.affiliation: Department of Laboratory Medicine, University of California, San Francisco, California, USA.
authors.forename: Samia N
authors.initials: SN
authors.lastname: Naccache
authors.forename: Alexander L
authors.initials: AL
authors.lastname: Greninger
authors.forename: Deanna
authors.initials: D
authors.lastname: Lee
authors.forename: Lark L
authors.initials: LL
authors.lastname: Coffey
authors.forename: Tung
authors.initials: T
authors.lastname: Phan
authors.forename: Annie
authors.initials: A
authors.lastname: Rein-Weston
authors.forename: Andrew
authors.initials: A
authors.lastname: Aronsohn
authors.forename: John
authors.initials: J
authors.lastname: Hackett
authors.forename: Eric L
authors.initials: EL
authors.lastname: Delwart
authors.forename: Charles Y
authors.initials: CY
authors.lastname: Chiu
mesh_terms: D002678:Chimera; D018136:Circoviridae / Q000235:genetics*; D018173:Circoviridae Infections / Q000235:genetics* / Q000821:virology; D004279:DNA, Viral / Q000235:genetics / Q000302:isolation & purification*; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D010322:Parvoviridae Infections / Q000235:genetics* / Q000821:virology; D017992:Parvovirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D010802:Phylogeny
chemical_list: D004279:DNA, Viral
references.citation: BMC Infect Dis. 2010 Aug 20;10:246
references.pmid: 20727151
references.citation: Ann Nutr Metab. 1990;34(4):216-20
references.pmid: 2400203
references.citation: Clin Infect Dis. 2006 Dec 15;43(12):1565-77
references.pmid: 17109290
references.citation: Environ Microbiol. 2012 Jan;14(1):162-76
references.pmid: 21914098
references.citation: J Virol. 2005 Dec;79(23):14781-92
references.pmid: 16282478
references.citation: J Gen Virol. 2009 Oct;90(Pt 10):2418-2424
references.pmid: 19570956
references.citation: Bioinformatics. 2012 Jun 15;28(12):1647-9
references.pmid: 22543367
references.citation: J Clin Microbiol. 2011 Sep;49(9):3422-4
references.pmid: 21734024
references.citation: J Virol. 2010 Feb;84(4):1674-82
references.pmid: 20007276
references.citation: Methods Mol Biol. 2009;537:113-37
references.pmid: 19378142
references.citation: ISME J. 2012 Feb;6(2):273-84
references.pmid: 21833038
references.citation: J Virol. 2010 Jun;84(12):6033-40
references.pmid: 20375174
references.citation: PLoS One. 2013 Apr 29;8(4):e62083
references.pmid: 23637969
references.citation: Transfusion. 2009 Aug;49 Suppl 2:1S-29S
references.pmid: 19686562
references.citation: Science. 2011 Nov 11;334(6057):814-7
references.pmid: 21940862
references.citation: PLoS One. 2011;6(8):e23484
references.pmid: 21876752
references.citation: Gigascience. 2012 Dec 27;1(1):18
references.pmid: 23587118
references.citation: J Clin Microbiol. 1999 Aug;37(8):2557-63
references.pmid: 10405401
references.citation: Vet J. 2011 Jul;189(1):72-6
references.pmid: 20817515
references.citation: PLoS Pathog. 2011 Nov;7(11):e1002369
references.pmid: 22114553
references.citation: PLoS One. 2010 Oct 18;5(10):e13381
references.pmid: 20976137
references.citation: mBio. 2013 Apr 16;4(2):e00084
references.pmid: 23592261
references.citation: Microbiol Mol Biol Rev. 2012 Sep;76(3):667-84
references.pmid: 22933565
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D546-51
references.pmid: 21045053
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D225-9
references.pmid: 21109532
references.citation: Virol J. 2013 Feb 13;10:54
references.pmid: 23402347
references.citation: N Engl J Med. 2012 Nov 8;367(19):1814-20
references.pmid: 23075143
references.citation: BMC Bioinformatics. 2008 Sep 19;9:386
references.pmid: 18803844
references.citation: J Gen Virol. 2011 Jun;92(Pt 6):1302-1308
references.pmid: 21367985
references.citation: J Clin Microbiol. 2003 Jul;41(7):3452-3
references.pmid: 12843121
references.citation: PLoS Pathog. 2009 May;5(5):e1000455
references.pmid: 19478873
references.citation: Science. 2008 Feb 22;319(5866):1096-100
references.pmid: 18202256
references.citation: J Eukaryot Microbiol. 2013 Mar-Apr;60(2):179-91
references.pmid: 23360210
references.citation: Transfusion. 2012 Feb;52(2):307-16
references.pmid: 22023235
references.citation: Biologicals. 2013 May;41(3):129-30
references.pmid: 23622811
references.citation: Science. 2011 Jul 1;333(6038):97-101
references.pmid: 21628392
references.citation: Proc Natl Acad Sci U S A. 2013 Jun 18;110(25):10264-9
references.pmid: 23716702
references.citation: PLoS One. 2012;7(2):e30875
references.pmid: 22355331
references.citation: Nat Rev Microbiol. 2013 Feb;11(2):133-41
references.pmid: 23268232
references.citation: Curr Opin Microbiol. 2013 Aug;16(4):468-78
references.pmid: 23725672
references.citation: PLoS Pathog. 2012 Sep;8(9):e1002924
references.pmid: 23028323
references.citation: Retrovirology. 2010 Dec 20;7:110
references.pmid: 21171978
references.citation: PLoS One. 2012;7(9):e44954
references.pmid: 23028701
references.citation: PLoS One. 2011;6(6):e21362
references.pmid: 21738642
references.citation: PLoS One. 2012;7(11):e49449
references.pmid: 23166671
references.citation: Retrovirology. 2010 Dec 20;7:109
references.pmid: 21171973
references.citation: J Virol. 2011 Nov;85(22):11697-708
references.pmid: 21900163
references.citation: G3 (Bethesda). 2013 May 20;3(5):865-80
references.pmid: 23550143
references.citation: Science. 2011 Jul 1;333(6038):94-7
references.pmid: 21628393
references.citation: Cold Spring Harb Perspect Biol. 2011 Jan 01;3(1):a006833
references.pmid: 21421910
references.citation: J Clin Microbiol. 1990 Mar;28(3):495-503
references.pmid: 1691208
references.citation: Proc Natl Acad Sci U S A. 2013 Apr 9;110(15):E1407-15
references.pmid: 23509292
references.citation: J Microbiol. 2008 Jun;46(3):235-43
references.pmid: 18604491
references.citation: Virus Res. 2002 Jul;87(1):79-87
references.pmid: 12135792
references.citation: JAMA. 1990 Jan 5;263(1):77-8
references.pmid: 2104549
references.citation: Retrovirology. 2010 Dec 20;7(1):111
references.pmid: 21171979
references.citation: J Clin Microbiol. 2011 Sep;49(9):3268-75
references.pmid: 21715589
references.citation: Emerg Infect Dis. 1998 Jul-Sep;4(3):382-9
references.pmid: 9716951
references.citation: Genome Res. 2012 Feb;22(2):292-8
references.pmid: 22009990
references.citation: mBio. 2012 Sep 18;3(5):
references.pmid: 22991430
references.citation: Microbiol Mol Biol Rev. 2010 Sep;74(3):363-77
references.pmid: 20805403
references.citation: Nature. 2005 Sep 15;437(7057):356-61
references.pmid: 16163346
references.citation: N Engl J Med. 2008 Mar 6;358(10):991-8
references.pmid: 18256387
references.citation: Dev Cell. 2001 Aug;1(2):291-302
references.pmid: 11702787
references.citation: J Virol. 2009 May;83(9):4642-51
references.pmid: 19211756
references.citation: Syst Biol. 2006 Aug;55(4):539-52
references.pmid: 16785212