The DOI matches its Crossref record; 60 of the 60 references it cites were found in a registry or an index.
The Perils of Pathogen Discovery: Origin of a Novel Parvovirus-Like Hybrid Genome Traced to Nucleic Acid Extraction Spin Columns
Open accessAbstract
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.
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Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C., et al. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts199 · Cited by 20,027
Isolation of a Novel Coronavirus from a Man with Pneumonia in Saudi Arabia
Zaki, A. M., van Boheemen, S., Bestebroer, T. M., Osterhaus, A. D. M. E., & Fouchier, R. A. M. (2012) · New England Journal of Medicine · doi:10.1056/nejmoa1211721 · Cited by 5,735
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., He, G., Chen, Y., Pan, Q., Liu, Y., et al. (2012) · Gigascience · doi:10.1186/2047-217x-1-18 · Cited by 5,307
Rapid and simple method for purification of nucleic acids
Boom, R., Sol, C. J., Salimans, M. M., Jansen, C. L., Wertheim-van Dillen, P. M., & van der Noordaa, J. (1990) · Journal of Clinical Microbiology · doi:10.1128/jcm.28.3.495-503.1990 · Cited by 5,266
Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R., Wilke, A., et al. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-386 · Cited by 3,565
Clonal Integration of a Polyomavirus in Human Merkel Cell Carcinoma
Feng, H., Shuda, M., Chang, Y., & Moore, P. S. (2008) · Science · doi:10.1126/science.1152586 · Cited by 3,208
CDD: a Conserved Domain Database for the functional annotation of proteins
Marchler-Bauer, A., Lu, S., Anderson, J. B., Chitsaz, F., Derbyshire, M. K., DeWeese-Scott, C., Fong, J. H., Geer, L. Y., Geer, R. C., Gonzales, N. R., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1189 · Cited by 3,159
Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative
Anisimova, M., & Gascuel, O. (2006) · Systematic Biology · doi:10.1080/10635150600755453 · Cited by 2,693
Suttle, C. A. (2005) · Nature · doi:10.1038/nature04160 · Cited by 2,176
Genomic analysis identifies association of Fusobacterium with colorectal carcinoma
Kostic, A. D., Gevers, D., Pedamallu, C. S., Michaud, M., Duke, F., Earl, A. M., Ojesina, A. I., Jung, J., Bass, A. J., Tabernero, J., et al. (2012) · Genome Research · doi:10.1101/gr.126573.111 · Cited by 1,960
Cited by
Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection
Gu, W., Miller, S., & Chiu, C. Y. (2019) · Annual Review of Pathology: Mechanisms of Disease · doi:10.1146/annurev-pathmechdis-012418-012751 · Cited by 1,458
Self-citationContamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations
Eisenhofer, R., Minich, J. J., Marotz, C., Cooper, A., Knight, R., & Weyrich, L. S. (2019) · Trends in Microbiology · doi:10.1016/j.tim.2018.11.003 · Cited by 1,146
Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing
Wilson, M. R., Naccache, S. N., Samayoa, E., Biagtan, M., Bashir, H., Yu, G., Salamat, S. M., Somasekar, S., Federman, S., Miller, S., et al. (2014) · New England Journal of Medicine · doi:10.1056/nejmoa1401268 · Cited by 977
Self-citationBlauwkamp, T. A., Thair, S., Rosen, M. J., Blair, L., Lindner, M. S., Vilfan, I. D., Kawli, T., Christians, F. C., Venkatasubrahmanyam, S., Wall, G. D., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-018-0349-6 · Cited by 962
Simner, P. J., Miller, S., & Carroll, K. C. (2018) · Clinical Infectious Diseases · doi:10.1093/cid/cix881 · Cited by 821
Metadata
- Authors
- Naccache, S. N., Greninger, A. L., Lee, D., Coffey, L. L., Phan, T., Rein-Weston, A., Aronsohn, A., Hackett, J., Delwart, E. L., & Chiu, C. Y.
- Venue
- Journal of Virology
- Publisher
- American Society for Microbiology
- Published
- 2013-11-15
- Volume
- 87
- Issue
- 22
- Pages
- 11966-11977
- ISSN
- 0022-538X (ISSN-L)
- 1098-5514
- OpenAlex
- W2120490381
- Cited by
- 255
- References
- 60
- FWCI
- 10.76
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Naccache, S. N., Greninger, A. L., Lee, D., Coffey, L. L., Phan, T., Rein-Weston, A., Aronsohn, A., Hackett, J., Delwart, E. L., & Chiu, C. Y. (2013). The Perils of Pathogen Discovery: Origin of a Novel Parvovirus-Like Hybrid Genome Traced to Nucleic Acid Extraction Spin Columns. Journal of Virology. https://doi.org/10.1128/jvi.02323-13
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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