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

Mollaie, Hamidreza; Afshar, Abbas Aghaei; Kalantar-Neyestanaki, Davood; Fazlalipour, Mehdi

doi:10.18502/ijm.v12i3.3234

Cited by 29 publications

(33 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In this study, the primers designed by Mollaei et al (14) were used for diagnosis of SARS-CoV-2 RNA from the patients and the N gene (87%) had high analytical sensitivity for detection of SARS-CoV-2, whereas the ORF1ab gene was slightly less sensitive (82%). Therefore, the best gene for identifying cases of SARS-CoV-2 is the N gene, ORF1ab is the second-best option after this gene.…”

Section: Discussionmentioning

confidence: 95%

See 1 more Smart Citation

Detection of SARS-CoV-2 using five primer sets

Karagöz

Tutun

Arslantaş

et al. 2020

Ankara Üniversitesi Veteriner Fakültesi Dergisi

View full text Add to dashboard Cite

A novel coronavirus (SARS-CoV-2) outbreak, responsible for a pneumonia-associated respiratory disorder (COVID-19), has started in early December 2019 in Wuhan, China, and has rapidly spread around the world. Rapid and accurate diagnostic testing plays a crucial role in tackling the COVID-19 pandemic. In this study, it was aimed to compare 5 primer sets designed to amplify different regions for the detection of SARS-CoV-2 and to perform sequence analysis. Conventional RT-PCR was carried out using primers targeting different regions of the virus genome including ORF1ab, Envelope (E), RNA-dependent RNA polymerase (RdRp), Spike (S) and Nucleocapsid (N) genes for the diagnosis of COVID-19. DNA sequence of ORF1ab gene from each sample were compared with the DNA sequence data of SARS-CoV-2 stored in the GenBank and ORF1ab phylogenetic tree was constructed. The amplicon sizes of ORF1ab, S, E, N and RdRp genes were 588 bp, 440 bp, 145 bp, 323 bp and 196 bp, respectively. The 2019-nCoV RNA was detected from 74% of total samples from RdRp gene, 87% for N gene, 74% for S gene, 61% for E gene and 82% for ORF1ab region. The ORF1ab sequences of SARS-CoV-2 from 82 patients were had 100% identity to the sequence of Wuhan isolate and among themselves. The phylogenetic analysis revealed that all isolates formed a cluster. The results of this study suggest that the N region is the best for SARS-CoV-2 identification.

show abstract

Section: Discussionmentioning

confidence: 95%

“…One study showed that the N gene was to be performing well for SARS-CoV-2 diagnosis (8). Another study showed that the ORF1ab, N and RdRp primers had sensitivity, specificity and positive predictive value higher than other primer (S gene, E gene) (14).…”

Section: Discussionmentioning

confidence: 99%

Detection of SARS-CoV-2 using five primer sets

Karagöz

Tutun

Arslantaş

et al. 2020

Ankara Üniversitesi Veteriner Fakültesi Dergisi

View full text Add to dashboard Cite

show abstract

“…The sensitivity, specificity, and positive predictive value of ORF1Ab, N and RDRP primers were higher than those of other primers. Using ORF1ab, N and RdRp primers for RT-PCR analysis can quickly, sensitively, and specifically detect COVID-19 in patients with pneumonia [ 15 ].…”

Section: Sars-cov-2 Laboratory Detection Methodsmentioning

confidence: 99%

Research progress in laboratory detection of SARS-CoV-2

Wang

Xiang

et al. 2021

Ir J Med Sci

View full text Add to dashboard Cite

Background Nucleic acid testing is a reliable method for diagnosing viral infection in clinical samples. However, when the number of cases is huge and there are individual differences in the virus itself, the probability of false-negative results increases. With the advancement in research on the new coronavirus, new detection technologies that use serum-specific antibodies as detection targets have been developed. These detection technologies have high efficiency and shorter turnaround time, which ultimately shortens the time required for diagnosis. This article summarizes the methods that have been reported to date for the detection of the new coronavirus and discusses their principles and technical characteristics. Aims Compare the advantages and disadvantages of various SARS-CoV-2 detection methods and analyze their principles. Methods Searched reports on SARS-CoV-2 detection methods published so far, extracted the data and analyzed them. Use the primer blast function of NCBI to analyze the primers used in qRT-PCR detection. Results The detection sensitivity was the highest when nucleocapsid protein gene was used as the target, reaching 96.6%. The detection efficiency of the remaining targets ranged from 66.7% to 96.0%. Various new detection methods, like Serum specific antibody detection, can speed up the test time. However, due to the complexity of the method and higher testing requirements, it seems that it cannot be used as a complete replacement for qRT-PRC testing. Conclusions With the advancement of technology and the improvement of methods, the detection methods of SARSCoV-2 have become more mature. These advances provided great help to the detection of SARS-CoV-2.

show abstract

“…In general, the E gene is used to screen pan-sarbecovirus and the RdRp and the N gene are used to confirm SARS-CoV-2 infection [46] . The related sensitivity and specificity were reported as 96.6% and 100% for Nucleocapsids, 96% and 100% for ORF1ab and 95.7% and 88.9 for RdRp, respectively [47] , [48] . Hoang Quoc Cuong and colleagues compared three different sets of primer-probe targeting E gene from TIB-Molbiol, IDT, and Phu Sa using two different PCR mixes including Invitrogen SuperScript III One-Step RT-PCR and LightCycler Multiplex RNA Virus Master.…”

Section: Analytical Errorsmentioning

confidence: 99%