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Iranian Journal of Microbiology
Article . 2020 . Peer-reviewed
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Iranian Journal of Microbiology
Article . 2020
Data sources: DOAJ
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Comparison five primer sets from different genome region of COVID-19 for detection of virus infection by conventional RT-PCR

Authors: Hamid Reza Mollaei; Abass Aghaei Afshar; Davood Kalantar-Neyestanaki; Mehdi Fazlalipour; Behnaz Aflatoonian;

Comparison five primer sets from different genome region of COVID-19 for detection of virus infection by conventional RT-PCR

Abstract

Background and Objectives: The new beta-coronavirus, which caused Severe Acute Respiratory Coronavirus-2 Syndrome (SARS-CoV-2), a major respiratory outbreak in Wuhan, China in December 2019, is now prevalent in many countries around the world. Identifying PCR-based viruses is a well-known and relatively stable protocol. Unfortunately, the high mutation rates may lead to widespread changes in viral nucleic acid sequences, and so using specific primers for PCR can be recom- mended. In this study, we evaluated the power of a conventional RT-PCR to detect SARS-CoV-2 RNA among the five set primer sets. Materials and Methods: The five genomic regions of the Coronavirus SARS-2 virus including Nucleocapsids (N), Enve- lope (E), RNA depended RNA Polymerase (RdRp), ORF1ab and Spike (S) were selected for primer designing. A convention- al RT-PCR was performed to compare sensitivity, specificity and other analytical characteristics of primers designed against two Real Time PCR commercial kits. Results: The result of the comparative analysis showed that the ORF1ab, N and RdRp primers had a sensitivity, specificity and positive predictive value higher than other primers. A significant difference in the analytical sensitivity between the studied primer sets in RT-PCR kits was observed. Conclusion: In this study, the ORF1ab, Nucleocapsid and RdRp regions have the best primers for identifying the SARS- CoV-2 RNA between different genes that have been suggested.

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Keywords

Sars-CoV-2;, COVID-19; Reverse transcription-polymerase chain reaction;, COVID-19;, Specific primer, Microbiology, QR1-502

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
21
Top 10%
Top 10%
Top 10%
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