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 .

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 organization: Medicum
Staff Services
Viral Zoonosis Research Unit
Department of Virology
Helsinki One Health (HOH)
Emerging Infections Research Group
Veterinary Biosciences
Veterinary Microbiology and Epidemiology
Olli Pekka Vapalahti / Principal Investigator
Date: 2020-10
Language: eng
Number of pages: 4
Belongs to series: Journal of Virological Methods
ISSN: 0166-0934
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
11832 Microbiology and virology
3142 Public health care science, environmental and occupational health
Peer reviewed: Yes
Rights: cc_by_nc_nd
Usage restriction: openAccess
Self-archived version: acceptedVersion

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