A1 Refereed original research article in a scientific journal
Comparison of Zaire ebolavirus realtime RT-PCRs targeting the nucleoprotein gene
Authors: Anne J Jääskeläinen, Tarja Sironen, Minttu Kaloinen, Laura Kakkola, Ilkka Julkunen, Roger Hewson, Manfred W Weidmann, Ali Mirazimi, Robert Watson, Olli Vapalahti
Publisher: ELSEVIER
Publication year: 2020
Journal: Journal of Virological Methods
Journal name in source: JOURNAL OF VIROLOGICAL METHODS
Journal acronym: J VIROL METHODS
Article number: ARTN 113941
Volume: 284
Number of pages: 4
ISSN: 0166-0934
eISSN: 1879-0984
DOI: https://doi.org/10.1016/j.jviromet.2020.113941(external)
Self-archived copy’s web address: https://helda.helsinki.fi/bitstream/handle/10138/332637/Jaaskelainen_Zaire.pdf?sequence=1(external)
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.
