NDLI: SARS-CoV2 RT-PCR assays: In vitro comparison of 4 WHO approved protocols on clinical specimens and its implications for real laboratory practice through variant emergence

Content Provider	Springer Nature : BioMed Central
Author	Gdoura, Mariem Abouda, Imen Mrad, Mehdi Ben Dhifallah, Imen Belaiba, Zeineb Fares, Wasfi Chouikha, Anissa Khedhiri, Maroua Layouni, Kaouther Touzi, Henda Sadraoui, Amel Hammemi, Walid Meddeb, Zina Hogga, Nahed Ben Fadhel, Sihem Haddad-Boubaker, Sondes Triki, Henda
Abstract	Introduction RT-PCR testing on nasopharyngeal swabs is a key component in the COVID-19 fighting, provided to use sensitive and specific SARS-CoV2 genome targets. In this study, we aimed to evaluate and to compare 4 widely used WHO approved RT-PCR protocols on real clinical specimens, to decrypt the reasons of the diverging results and to propose recommendations for the choice of the genome targets. Methods 260 nasopharyngeal samples were randomly selected among the samples tested between Week-16, 2020 and week-16 2021, in the Institut Pasteur de Tunis, Tunisia, one of the referent laboratories of COVID-19 in Tunisia. All samples were tested by Charité, Berlin protocol (singleplex envelop (E) and singleplex RNA-dependent RNA polymerase (RdRp)), Hong Kong Universiy, China protocol (singleplex nucleoprotein (N) and singleplex Open reading frame Orf1b), commercial test DAAN Gene® (using the CDC China protocol), (triplex N, Orf1ab with internal control) and Institut Pasteur Paris protocol (IPP) (triplex IP2(nsp9) and IP4 (nsp12) with internal control). For IPP, a selection from samples positive by IP2 but negative with IP4 was re-tested by exactly the same protocol but this time in singleplex. New results were described and analyzed. Results In vitro analysis showed discordant results in 29.2% of cases (76 out of 260). The most discordant protocol is DAAN Gene® due to the false positive late signals with N target. Discordant results between the two protocol’s targets are more frequent when viral load are low (high Ct values). Our results demonstrated that the multiplexing has worsened the sensitivity of the IP4 target. Conclusion We provide concise recommendations for the choice of the genome targets, the interpretation of the results and the alarm signals which makes suspect a gene mutation.
Related Links	https://virologyj.biomedcentral.com/counter/pdf/10.1186/s12985-022-01784-4.pdf
Ending Page	9
Page Count	9
Starting Page	1
File Format	HTM / HTML
DOI	10.1186/s12985-022-01784-4
Journal	Virology Journal
Issue Number	1
Volume Number	19
Language	English
Publisher	BioMed Central
Publisher Date	2022-03-28
Access Restriction	Open
Subject Keyword	Virology SARS-CoV2 COVID-19 RT-PCR Variant Diagnosis Sensitivity In vitro False positive False negative
Content Type	Text
Resource Type	Article
Subject	Virology Infectious Diseases
Journal Impact Factor	4/2023
5-Year Journal Impact Factor	3.8/2023

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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