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Sci Rep
. 2023 Oct 3;13(1):16659.
doi: 10.1038/s41598-023-43204-9. M gene targeted qRT-PCR approach for SARS-CoV-2 virus detection
Md Murshed Hasan Sarkar # 1 , Showti Raheel Naser # 2 , Sanjana Fatema Chowdhury 2 , Md Salim Khan 2 , Md Ahashan Habib 2 , Shahina Akter 2 , Tanjina Akhtar Banu 2 , Barna Goswami 2 , Iffat Jahan 2 , Maksudur Rahman Nayem 3 , Md Akibul Hassan 3 , Md Imran Khan 3 , Mohammad Fazle Alam Rabbi 3 4 , Chowdhury Rafiqul Ahsan 4 , Md Ibrahim Miah 4 , Afzalun Nessa 5 , S M Rashed Ul Islam 5 , Mohammed Atiqur Rahman 5 , Md Aftab Ali Shaikh 6 7 , Md Sharfuddin Ahmed 5
Affiliations
Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) is the gold standard method for SARS-CoV-2 detection, and several qRT-PCR kits have been established targeting different genes of the virus. Due to the high mutation rate of these genes, false negative results arise thus complicating the interpretation of the diagnosis and increasing the need of alternative targets. In this study, an alternative approach for the detection of SARS-CoV-2 viral RNA targeting the membrane (M) gene of the virus using qRT-PCR was described. Performance evaluation of this newly developed in-house assay against commercial qRT-PCR kits was done using clinical oropharyngeal specimens of COVID-19 positive patients. The limit of detection was determined using successive dilutions of known copies of SARS-CoV-2 pseudovirus. The M gene based assay was able to detect a minimum of 100 copies of virus/mL indicating its capacity to detect low viral load. The assay showed comparable accuracy, sensitivity and specificity with commercially available kits while detecting all the variants efficiently. The study concluded that the in-house M gene based assay might be an effective alternative for the currently available commercial qRT-PCR kits.
. 2023 Oct 3;13(1):16659.
doi: 10.1038/s41598-023-43204-9. M gene targeted qRT-PCR approach for SARS-CoV-2 virus detection
Md Murshed Hasan Sarkar # 1 , Showti Raheel Naser # 2 , Sanjana Fatema Chowdhury 2 , Md Salim Khan 2 , Md Ahashan Habib 2 , Shahina Akter 2 , Tanjina Akhtar Banu 2 , Barna Goswami 2 , Iffat Jahan 2 , Maksudur Rahman Nayem 3 , Md Akibul Hassan 3 , Md Imran Khan 3 , Mohammad Fazle Alam Rabbi 3 4 , Chowdhury Rafiqul Ahsan 4 , Md Ibrahim Miah 4 , Afzalun Nessa 5 , S M Rashed Ul Islam 5 , Mohammed Atiqur Rahman 5 , Md Aftab Ali Shaikh 6 7 , Md Sharfuddin Ahmed 5
Affiliations
- PMID: 37789078
- PMCID: PMC10547753
- DOI: 10.1038/s41598-023-43204-9
Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) is the gold standard method for SARS-CoV-2 detection, and several qRT-PCR kits have been established targeting different genes of the virus. Due to the high mutation rate of these genes, false negative results arise thus complicating the interpretation of the diagnosis and increasing the need of alternative targets. In this study, an alternative approach for the detection of SARS-CoV-2 viral RNA targeting the membrane (M) gene of the virus using qRT-PCR was described. Performance evaluation of this newly developed in-house assay against commercial qRT-PCR kits was done using clinical oropharyngeal specimens of COVID-19 positive patients. The limit of detection was determined using successive dilutions of known copies of SARS-CoV-2 pseudovirus. The M gene based assay was able to detect a minimum of 100 copies of virus/mL indicating its capacity to detect low viral load. The assay showed comparable accuracy, sensitivity and specificity with commercially available kits while detecting all the variants efficiently. The study concluded that the in-house M gene based assay might be an effective alternative for the currently available commercial qRT-PCR kits.