tetano
Editor, Senior Moderator
Sci Rep
. 2023 Feb 9;13(1):2342.
doi: 10.1038/s41598-023-28275-y.
Evaluation of RT-PCR assays for detection of SARS-CoV-2 variants of concern
Sourav Dutta Dip[SUP] #[/SUP][SUP] 1 [/SUP], Shovon Lal Sarkar[SUP] #[/SUP][SUP] 1 [/SUP], Md Ali Ahasan Setu[SUP] 1 [/SUP], Prosanto Kumar Das[SUP] 1 [/SUP], Md Hasan Ali Pramanik[SUP] 1 [/SUP], A S M Rubayet Ul Alam[SUP] 1 [/SUP], Hassan M Al-Emran[SUP] 2 [/SUP], M Anwar Hossain[SUP] 3 4 [/SUP], Iqbal Kabir Jahid[SUP] 5 6 [/SUP]
Affiliations
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic has been considered with great importance on correct screening procedure. The detection efficiency of recent variants of concern were observed by comparing 5 commercial RT-PCR kits and a SYBR-green method developed and validated in our laboratory. The RNA was extracted from nasopharyngeal samples from suspected COVID-19 patients and RT-PCR assay was performed according to the instruction of the respective manufacturers. The specificity and sensitivity of Maccura kit was 81.8% and 82.5%, A*Star kit was 100% and 75.4%, Da An Gene kit was 100% and 68.4%, Sansure kit was 54.5% and 91.2% and TaqPath kit was 100% and 70.2% respectively. Our in house SYBR-Green method showed a consistent detection result with 90.9% specificity and 91.2% sensitivity. We also found that detection kits targeting more genes showed better accuracy which facilitates less false positive results (< 20%). Our study found a significant difference (p < 0.005) in Ct value reported for common target genes shared by the RT-PCR kits in relation with different variants of COVID-19 infection. Recent variants of concerns contain more than 30 mutations in the spike proteins including 2 deletion and a unique insertion mutation by which makes detection of these variants difficult and these facilitates the variants to escape from being detected.
. 2023 Feb 9;13(1):2342.
doi: 10.1038/s41598-023-28275-y.
Evaluation of RT-PCR assays for detection of SARS-CoV-2 variants of concern
Sourav Dutta Dip[SUP] #[/SUP][SUP] 1 [/SUP], Shovon Lal Sarkar[SUP] #[/SUP][SUP] 1 [/SUP], Md Ali Ahasan Setu[SUP] 1 [/SUP], Prosanto Kumar Das[SUP] 1 [/SUP], Md Hasan Ali Pramanik[SUP] 1 [/SUP], A S M Rubayet Ul Alam[SUP] 1 [/SUP], Hassan M Al-Emran[SUP] 2 [/SUP], M Anwar Hossain[SUP] 3 4 [/SUP], Iqbal Kabir Jahid[SUP] 5 6 [/SUP]
Affiliations
- PMID: 36759632
- DOI: 10.1038/s41598-023-28275-y
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic has been considered with great importance on correct screening procedure. The detection efficiency of recent variants of concern were observed by comparing 5 commercial RT-PCR kits and a SYBR-green method developed and validated in our laboratory. The RNA was extracted from nasopharyngeal samples from suspected COVID-19 patients and RT-PCR assay was performed according to the instruction of the respective manufacturers. The specificity and sensitivity of Maccura kit was 81.8% and 82.5%, A*Star kit was 100% and 75.4%, Da An Gene kit was 100% and 68.4%, Sansure kit was 54.5% and 91.2% and TaqPath kit was 100% and 70.2% respectively. Our in house SYBR-Green method showed a consistent detection result with 90.9% specificity and 91.2% sensitivity. We also found that detection kits targeting more genes showed better accuracy which facilitates less false positive results (< 20%). Our study found a significant difference (p < 0.005) in Ct value reported for common target genes shared by the RT-PCR kits in relation with different variants of COVID-19 infection. Recent variants of concerns contain more than 30 mutations in the spike proteins including 2 deletion and a unique insertion mutation by which makes detection of these variants difficult and these facilitates the variants to escape from being detected.