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Translating genomic exploration of the family Polyomaviridae into confident human polyomavirus detection. / Kamminga, Sergio; Sidorov, Igor A.; Tadesse, Michaël et al.

In: iScience, Vol. 25, No. 1, 103613, 21.01.2022.

Research output: Contribution to journalArticleAcademicpeer-review

Harvard

Kamminga, S, Sidorov, IA, Tadesse, M, van der Meijden, E, de Brouwer, C, Zaaijer, HL, Feltkamp, MCW & Gorbalenya, AE 2022, 'Translating genomic exploration of the family Polyomaviridae into confident human polyomavirus detection', iScience, vol. 25, no. 1, 103613. https://doi.org/10.1016/j.isci.2021.103613

APA

Kamminga, S., Sidorov, I. A., Tadesse, M., van der Meijden, E., de Brouwer, C., Zaaijer, H. L., Feltkamp, M. C. W., & Gorbalenya, A. E. (2022). Translating genomic exploration of the family Polyomaviridae into confident human polyomavirus detection. iScience, 25(1), [103613]. https://doi.org/10.1016/j.isci.2021.103613

Vancouver

Author

Kamminga, Sergio ; Sidorov, Igor A. ; Tadesse, Michaël et al. / Translating genomic exploration of the family Polyomaviridae into confident human polyomavirus detection. In: iScience. 2022 ; Vol. 25, No. 1.

BibTeX

@article{071bf93f4ff14965978ac758fb583403,
title = "Translating genomic exploration of the family Polyomaviridae into confident human polyomavirus detection",
abstract = "The Polyomaviridae is a family of ubiquitous dsDNA viruses that establish persistent infection early in life. Screening for human polyomaviruses (HPyVs), which comprise 14 diverse species, relies upon species-specific qPCRs whose validity may be challenged by accelerating genomic exploration of the virosphere. Using this reasoning, we tested 64 published HPyV qPCR assays in silico against the 1781 PyV genome sequences that were divided in targets and nontargets, based on anticipated species specificity of each qPCR. We identified several cases of problematic qPCR performance that were confirmed in vitro and corrected through using degenerate oligos. Furthermore, our study ranked 8 out of 52 tested BKPyV qPCRs as remaining of consistently high quality in the wake of recent PyV discoveries and showed how sensitivity of most other qPCRs could be rescued by annealing temperature adjustment. This study establishes an efficient framework for ensuring confidence in available HPyV qPCRs in the genomic era.",
keywords = "Omics, Virology",
author = "Sergio Kamminga and Sidorov, {Igor A.} and Micha{\"e}l Tadesse and {van der Meijden}, Els and {de Brouwer}, Caroline and Zaaijer, {Hans L.} and Feltkamp, {Mariet C. W.} and Gorbalenya, {Alexander E.}",
note = "Funding Information: This work was supported and funded in part by Sanquin Blood Supply Foundation , a not-for-profit organization, the EU Horizon 2000 EVAg project ( https://www.european-virus-archive.com/ ), and Molecular Diagnostics of Infectious Diseases Working Group, Dutch Association for Medical Microbiology (WDMI/ NVMM , https://www.nvmm.nl/vereniging/commissies-en-werkgroepen/wmdi/ ). IAS and AEG thank Dmitry Samborskiy for help with administrating the VirAliS software. Funding Information: This work was supported and funded in part by Sanquin Blood Supply Foundation, a not-for-profit organization, the EU Horizon 2000 EVAg project (https://www.european-virus-archive.com/), and Molecular Diagnostics of Infectious Diseases Working Group, Dutch Association for Medical Microbiology (WDMI/NVMM, https://www.nvmm.nl/vereniging/commissies-en-werkgroepen/wmdi/). IAS and AEG thank Dmitry Samborskiy for help with administrating the VirAliS software. Conceptualization: AEG and IAS; conceived and designed the research: SK, IAS, AEG, HZ, and MCWF; collected the data: IAS, SK, MT, EM, and CB; contributed analysis tools: IAS, SK, MT, and AEG; analyzed results: SK, IAS, MT, and AEG; wrote the manuscript: SK, IAS, AEG, and MCWF. The authors declare no competing interests. Publisher Copyright: {\textcopyright} 2021 The Author(s)",
year = "2022",
month = jan,
day = "21",
doi = "10.1016/j.isci.2021.103613",
language = "English",
volume = "25",
journal = "iScience",
issn = "2589-0042",
publisher = "Elsevier Inc.",
number = "1",

}

RIS

TY - JOUR

T1 - Translating genomic exploration of the family Polyomaviridae into confident human polyomavirus detection

AU - Kamminga, Sergio

AU - Sidorov, Igor A.

AU - Tadesse, Michaël

AU - van der Meijden, Els

AU - de Brouwer, Caroline

AU - Zaaijer, Hans L.

AU - Feltkamp, Mariet C. W.

AU - Gorbalenya, Alexander E.

N1 - Funding Information: This work was supported and funded in part by Sanquin Blood Supply Foundation , a not-for-profit organization, the EU Horizon 2000 EVAg project ( https://www.european-virus-archive.com/ ), and Molecular Diagnostics of Infectious Diseases Working Group, Dutch Association for Medical Microbiology (WDMI/ NVMM , https://www.nvmm.nl/vereniging/commissies-en-werkgroepen/wmdi/ ). IAS and AEG thank Dmitry Samborskiy for help with administrating the VirAliS software. Funding Information: This work was supported and funded in part by Sanquin Blood Supply Foundation, a not-for-profit organization, the EU Horizon 2000 EVAg project (https://www.european-virus-archive.com/), and Molecular Diagnostics of Infectious Diseases Working Group, Dutch Association for Medical Microbiology (WDMI/NVMM, https://www.nvmm.nl/vereniging/commissies-en-werkgroepen/wmdi/). IAS and AEG thank Dmitry Samborskiy for help with administrating the VirAliS software. Conceptualization: AEG and IAS; conceived and designed the research: SK, IAS, AEG, HZ, and MCWF; collected the data: IAS, SK, MT, EM, and CB; contributed analysis tools: IAS, SK, MT, and AEG; analyzed results: SK, IAS, MT, and AEG; wrote the manuscript: SK, IAS, AEG, and MCWF. The authors declare no competing interests. Publisher Copyright: © 2021 The Author(s)

PY - 2022/1/21

Y1 - 2022/1/21

N2 - The Polyomaviridae is a family of ubiquitous dsDNA viruses that establish persistent infection early in life. Screening for human polyomaviruses (HPyVs), which comprise 14 diverse species, relies upon species-specific qPCRs whose validity may be challenged by accelerating genomic exploration of the virosphere. Using this reasoning, we tested 64 published HPyV qPCR assays in silico against the 1781 PyV genome sequences that were divided in targets and nontargets, based on anticipated species specificity of each qPCR. We identified several cases of problematic qPCR performance that were confirmed in vitro and corrected through using degenerate oligos. Furthermore, our study ranked 8 out of 52 tested BKPyV qPCRs as remaining of consistently high quality in the wake of recent PyV discoveries and showed how sensitivity of most other qPCRs could be rescued by annealing temperature adjustment. This study establishes an efficient framework for ensuring confidence in available HPyV qPCRs in the genomic era.

AB - The Polyomaviridae is a family of ubiquitous dsDNA viruses that establish persistent infection early in life. Screening for human polyomaviruses (HPyVs), which comprise 14 diverse species, relies upon species-specific qPCRs whose validity may be challenged by accelerating genomic exploration of the virosphere. Using this reasoning, we tested 64 published HPyV qPCR assays in silico against the 1781 PyV genome sequences that were divided in targets and nontargets, based on anticipated species specificity of each qPCR. We identified several cases of problematic qPCR performance that were confirmed in vitro and corrected through using degenerate oligos. Furthermore, our study ranked 8 out of 52 tested BKPyV qPCRs as remaining of consistently high quality in the wake of recent PyV discoveries and showed how sensitivity of most other qPCRs could be rescued by annealing temperature adjustment. This study establishes an efficient framework for ensuring confidence in available HPyV qPCRs in the genomic era.

KW - Omics

KW - Virology

UR - http://www.scopus.com/inward/record.url?scp=85122245611&partnerID=8YFLogxK

U2 - 10.1016/j.isci.2021.103613

DO - 10.1016/j.isci.2021.103613

M3 - Article

C2 - 35036862

VL - 25

JO - iScience

JF - iScience

SN - 2589-0042

IS - 1

M1 - 103613

ER -

ID: 21437144