Incidence of Non Amplification of N Gene of SARS-CoV-2 using Commercially Available Real Time Polymerase Chain Reaction Kit and its Comparison with Two Other Different Kits
Introduction: Novel Coronavirus Disease-2019 (COVID-19) caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has resulted in an unprecedented global pandemic. Real Time Polymerase Chain Reaction (RT-PCR) tests are being used in the diagnosis of COVID-19 worldwide however mutati...
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| Format: | Article |
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JCDR Research and Publications Private Limited
2022-02-01
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| Series: | Journal of Clinical and Diagnostic Research |
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| Online Access: | https://www.jcdr.net/articles/PDF/15959/52164_CE[Ra1]_F(SL)_PF1(AG_SS)_PFA(AG_KM)_PN(KM).pdf |
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| author | Rajeev Kumar Jain Nagaraj Perumal Deepti Chaurasia Kamlesh Kumar Ahirwar Archa Sharma Rakesh Shrivastava Jaya Lalwani |
| author_facet | Rajeev Kumar Jain Nagaraj Perumal Deepti Chaurasia Kamlesh Kumar Ahirwar Archa Sharma Rakesh Shrivastava Jaya Lalwani |
| author_sort | Rajeev Kumar Jain |
| collection | DOAJ |
| description | Introduction: Novel Coronavirus Disease-2019 (COVID-19) caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has resulted in an unprecedented global pandemic. Real Time Polymerase Chain Reaction (RT-PCR) tests are being used in the diagnosis of COVID-19 worldwide however mutations in the SARS-CoV-2 genome have generated many SARS-CoV-2 genome variants and which may affect the correct Reverse transcriptase-Real time Polymerase Chain Reaction (RT-PCR) diagnosis.
Aim: To confirm and study the incidence of the non amplification of the SARS-CoV-2 Nucleocapsid gene (N gene) target among known SARS-CoV-2 positive samples.
Materials and Methods: This retrospective observational study was carried out at the State Virology Laboratory, Gandhi Medical College, Bhopal, Madhya Pradesh, India, during January to May 2021. During the study period, a total of 159 SARS-CoV-2 positive samples were failed to amplify the N gene target. To investigate the non amplification of N gene target of SARS-CoV-2, a total of 20 samples were selected and retested using the initially used RT-PCR kit (VIRALDTECT RT-PCR kit) and also with the two different RT-PCR kits (TaqPath RT-PCR kit and Hi-PCR RT-PCR kit) which also contain primers/probes for the SARS-CoV-2 N gene target.
Results: Amplification and detection of the SARS-CoV-2 N target gene was not observed in VIRALDTECT RT-PCR test results. In contrast, amplification was detected in the N gene target of SARS-CoV-2 while using the TaqPath and Hi-PCR kits. Obtained results confirm the failure of the annealing of VIRALDTECT kit N gene primer/probe and suggest the possible mutation event in the SARS-CoV-2 N gene among the N gene non amplified samples.
Conclusion: Present study reports, the incidence of non amplification of SARS-CoV-2 N gene, where the RT-PCR kit failed to detect N gene target and seriously affect RT-PCR diagnosis. Hence, the study emphasises the revalidation of commercially available SARS-CoV-2, RT-PCR kits to identify these kinds of failure incidence. |
| first_indexed | 2024-04-10T17:25:55Z |
| format | Article |
| id | doaj.art-6c1ed57451aa4509992798c47ba69e12 |
| institution | Directory Open Access Journal |
| issn | 2249-782X 0973-709X |
| language | English |
| last_indexed | 2024-04-10T17:25:55Z |
| publishDate | 2022-02-01 |
| publisher | JCDR Research and Publications Private Limited |
| record_format | Article |
| series | Journal of Clinical and Diagnostic Research |
| spelling | doaj.art-6c1ed57451aa4509992798c47ba69e122023-02-04T05:28:40ZengJCDR Research and Publications Private LimitedJournal of Clinical and Diagnostic Research2249-782X0973-709X2022-02-01162DM01DM0410.7860/JCDR/2022/52164.15959Incidence of Non Amplification of N Gene of SARS-CoV-2 using Commercially Available Real Time Polymerase Chain Reaction Kit and its Comparison with Two Other Different KitsRajeev Kumar Jain0Nagaraj Perumal1Deepti Chaurasia2Kamlesh Kumar Ahirwar3Archa Sharma4Rakesh Shrivastava5Jaya Lalwani6Scientist-C, Department of Microbiology, Gandhi Medical College, Bhopal, Madhya Pradesh, India.Scientist-B, Department of Microbiology, Gandhi Medical College, Bhopal, Madhya Pradesh, India.Professor, Department of Microbiology, Gandhi Medical College, Bhopal, Madhya Pradesh, India.Assistant Research Officer, Department of Microbiology, Gandhi Medical College, Bhopal, Madhya Pradesh, India.Assistant Professor, Department of Microbiology, Gandhi Medical College, Bhopal, Madhya Pradesh, India.Associate Professor, Department of Microbiology, Gandhi Medical College, Bhopal, Madhya Pradesh, India.Associate Professor, Department of Microbiology, Gandhi Medical College, Bhopal, Madhya Pradesh, India.Introduction: Novel Coronavirus Disease-2019 (COVID-19) caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has resulted in an unprecedented global pandemic. Real Time Polymerase Chain Reaction (RT-PCR) tests are being used in the diagnosis of COVID-19 worldwide however mutations in the SARS-CoV-2 genome have generated many SARS-CoV-2 genome variants and which may affect the correct Reverse transcriptase-Real time Polymerase Chain Reaction (RT-PCR) diagnosis. Aim: To confirm and study the incidence of the non amplification of the SARS-CoV-2 Nucleocapsid gene (N gene) target among known SARS-CoV-2 positive samples. Materials and Methods: This retrospective observational study was carried out at the State Virology Laboratory, Gandhi Medical College, Bhopal, Madhya Pradesh, India, during January to May 2021. During the study period, a total of 159 SARS-CoV-2 positive samples were failed to amplify the N gene target. To investigate the non amplification of N gene target of SARS-CoV-2, a total of 20 samples were selected and retested using the initially used RT-PCR kit (VIRALDTECT RT-PCR kit) and also with the two different RT-PCR kits (TaqPath RT-PCR kit and Hi-PCR RT-PCR kit) which also contain primers/probes for the SARS-CoV-2 N gene target. Results: Amplification and detection of the SARS-CoV-2 N target gene was not observed in VIRALDTECT RT-PCR test results. In contrast, amplification was detected in the N gene target of SARS-CoV-2 while using the TaqPath and Hi-PCR kits. Obtained results confirm the failure of the annealing of VIRALDTECT kit N gene primer/probe and suggest the possible mutation event in the SARS-CoV-2 N gene among the N gene non amplified samples. Conclusion: Present study reports, the incidence of non amplification of SARS-CoV-2 N gene, where the RT-PCR kit failed to detect N gene target and seriously affect RT-PCR diagnosis. Hence, the study emphasises the revalidation of commercially available SARS-CoV-2, RT-PCR kits to identify these kinds of failure incidence.https://www.jcdr.net/articles/PDF/15959/52164_CE[Ra1]_F(SL)_PF1(AG_SS)_PFA(AG_KM)_PN(KM).pdffalse negativitygene mutationsevere acute respiratory syndrome coronavirus-2sequencing |
| spellingShingle | Rajeev Kumar Jain Nagaraj Perumal Deepti Chaurasia Kamlesh Kumar Ahirwar Archa Sharma Rakesh Shrivastava Jaya Lalwani Incidence of Non Amplification of N Gene of SARS-CoV-2 using Commercially Available Real Time Polymerase Chain Reaction Kit and its Comparison with Two Other Different Kits Journal of Clinical and Diagnostic Research false negativity gene mutation severe acute respiratory syndrome coronavirus-2 sequencing |
| title | Incidence of Non Amplification of N Gene of SARS-CoV-2 using Commercially Available Real Time Polymerase Chain Reaction Kit and its Comparison with Two Other Different Kits |
| title_full | Incidence of Non Amplification of N Gene of SARS-CoV-2 using Commercially Available Real Time Polymerase Chain Reaction Kit and its Comparison with Two Other Different Kits |
| title_fullStr | Incidence of Non Amplification of N Gene of SARS-CoV-2 using Commercially Available Real Time Polymerase Chain Reaction Kit and its Comparison with Two Other Different Kits |
| title_full_unstemmed | Incidence of Non Amplification of N Gene of SARS-CoV-2 using Commercially Available Real Time Polymerase Chain Reaction Kit and its Comparison with Two Other Different Kits |
| title_short | Incidence of Non Amplification of N Gene of SARS-CoV-2 using Commercially Available Real Time Polymerase Chain Reaction Kit and its Comparison with Two Other Different Kits |
| title_sort | incidence of non amplification of n gene of sars cov 2 using commercially available real time polymerase chain reaction kit and its comparison with two other different kits |
| topic | false negativity gene mutation severe acute respiratory syndrome coronavirus-2 sequencing |
| url | https://www.jcdr.net/articles/PDF/15959/52164_CE[Ra1]_F(SL)_PF1(AG_SS)_PFA(AG_KM)_PN(KM).pdf |
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