Fully automated detection and differentiation of pandemic and endemic coronaviruses (NL63, 229E, HKU1, OC43 and SARS‐CoV‐2) on the hologic panther fusion
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Abstract
The hologic panther fusion (PF) platform provides fully automated CE marked diagnostics for respiratory viruses, including the recently discovered severe acute respiratory syndrome‐coronavirus 2 (SARS‐CoV‐2) by a transcription mediated amplification (TMA) assay, but not for the endemic human coronaviruses (hCoV). Therefore, a laboratory developed test (LDT) comprising a multiplexed reverse transcription polymerase chain reaction (RT‐PCR) protocol that detects and differentiates the four hCoV NL63, 229E, HKU1, and OC43 was adapted on the PF. The novel CE marked Aptima SARS‐CoV‐2 TMA and the LDT for hCoV were validated with 321 diagnostic specimens from the upper and lower respiratory tract in comparison to two SARS‐CoV‐2 RT‐PCRs (PF E‐gene RT‐PCR and genesig RT‐PCR, 157 specimens) or the R‐GENE hCoV/hParaFlu RT‐PCR (164 specimens), respectively. For the endemic hCoV, results were 96.3% concordant with two specimens discordantly positive in the PF and four specimens discordantly positive in the R‐GENE assay. All discordantly positive samples had Ct values between 33 and 39. The PF hCoV LDT identified 23 hCoV positive specimens as NL63, 15 as 229E, 15 as HKU1, and 25 as OC43. The Aptima SARS‐CoV‐2 TMA gave 99.4% concordant results compared to the consensus results with a single specimen discordantly positive. Moreover, 36 samples from proficiency testing panels were detected and typed correctly by both novel methods. In conclusion, the SARS‐CoV‐2 TMA and the LDT for hCoV enhanced the diagnostic spectrum of the PF for all coronaviruses circulating globally for a multitude of diagnostic materials from the upper and lower respiratory tract.
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SciScore for 10.1101/2020.08.31.20185074: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Ethical statement: All 321 diagnostic samples originated from patients who had agreed to the anonymised use of their clinical data at hospital admission (informed consent).
IACUC: As specimens were tested according to diagnostic requests only and medical data were anonymized and analyzed only retrospectively, ethical approval is not required in Germany (confirmed by e-mails of the local ethical committee “Ethikkommission der Medizinischen Hochschule Hannover”, 19th of September, 2019 and 6th of May 2020).Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
No key resources …
SciScore for 10.1101/2020.08.31.20185074: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Ethical statement: All 321 diagnostic samples originated from patients who had agreed to the anonymised use of their clinical data at hospital admission (informed consent).
IACUC: As specimens were tested according to diagnostic requests only and medical data were anonymized and analyzed only retrospectively, ethical approval is not required in Germany (confirmed by e-mails of the local ethical committee “Ethikkommission der Medizinischen Hochschule Hannover”, 19th of September, 2019 and 6th of May 2020).Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Another limitation of the study was that HKU1 was not included in the panel of proficiency testing specimens probably because HKU1 cannot be grown in cell culture easily 40. As the R-GENE assay does not differentiate the endemic hCoV, we could not confirm that a sample positive for HKU1 in the PF LDT truly contains HKU1 RNA but 13 of 15 samples positive for HKU1 were at least confirmed as hCoV positive in the R-GENE assay. Moreover, the primer and probe sequences for HKU1 (and all other hCoVs) that had previously been published 28 were reanalyzed on specificity using Nucleotide Blast (NCBI PubMed). As no homology of the primer and probe sequences with another than the intended corresponding hCoV sequence was detected, we presume classification to be correct. A fast and accurate differentiation of respiratory pathogens in patients with respiratory symptoms is essential to enable sufficient infectious control measures, particularly with regard to the current SARS-CoV-2 pandemic. Together with the PF respiratory panel, 15 different respiratory viruses (Flu A/B, RSV, ParaFlu 1-4, hMPV, AdV, RhV, hCoV NL63/229E/HKU1/OC43 and SARS-CoV-2) can be detected within 4 hours from one single specimen loaded on the PF. Alternatively, a cost saving step by step diagnostic approach is feasible on the PF, e.g. starting with SARS-CoV-2 testing and if negative, testing for other respiratory viruses subsequently.
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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