Comparison of Zaire ebolavirus realtime RT-PCRs targeting the nucleoprotein gene

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Jääskeläinen , A J , Sironen , T , Kaloinen , M , Kakkola , L , Julkunen , I , Hewson , R , Weidmann , M W , Mirazimi , A , Watson , R & Vapalahti , O 2020 , ' Comparison of Zaire ebolavirus realtime RT-PCRs targeting the nucleoprotein gene ' , Journal of Virological Methods , vol. 284 , 113941 . https://doi.org/10.1016/j.jviromet.2020.113941

Title: Comparison of Zaire ebolavirus realtime RT-PCRs targeting the nucleoprotein gene
Author: Jääskeläinen, Anne J.; Sironen, Tarja; Kaloinen, Minttu; Kakkola, Laura; Julkunen, Ilkka; Hewson, Roger; Weidmann, Manfred W.; Mirazimi, Ali; Watson, Robert; Vapalahti, Olli
Contributor: University of Helsinki, Medicum
University of Helsinki, Helsinki One Health (HOH)
University of Helsinki, Department of Virology
University of Helsinki, Helsinki One Health (HOH)
Date: 2020-10
Language: eng
Number of pages: 4
Belongs to series: Journal of Virological Methods
ISSN: 0166-0934
URI: http://hdl.handle.net/10138/332637
Abstract: In last five years, the Africa has faced two outbreaks of Zaire ebolavirus. These outbreaks have been the largest so far, and latest outbreak is still ongoing and affecting the Democratic Republic of the Congo. We tested in parallel three different Zaire ebolavirus (EBOV) realtime RT-PCRs targeting the nucleoprotein gene (EBOV NP-RT-qPCRs) described by Trombley et al. (2010); Huang et al. (2012) and Weidmann et al. (2004). These assays are used regularly in diagnostic laboratories. The limit of detection (LOD), intra-assay repeatability using different matrixes, sensitivity and specificity were determined. In addition, the primers and probes were aligned with the sequences available in ongoing and past outbreaks in order to check the mismatches. The specificity of all three EBOV NP-RT-qPCRs were excellent (100 %), and LODs were under or 10 copies per PCR reaction. Intra-assay repeatability was good in all assays, however the Ct-values were bit higher using the EDTA-blood based matrix. All of the primers and probes in EBOV NP-RT-qPCR assays have one or more mismatches in the probes and primers when the 2267 Zaire EBOV NP sequences, including strains Ituri from DRC outbreak (year 2018), was aligned. The EBOV strain of Bikoro (year 2018) circulating in DRC was 100 % match in Trombley and Weidmann assay, but had one mismatch in Huang assay.
Subject: Ebola
Zaire
PCR
Nucleoprotein
RAPID DETECTION
FILOVIRUSES
11832 Microbiology and virology
3142 Public health care science, environmental and occupational health
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