A two-step process for in silico screening to assess the performance of qRTPCR kits against variant strains of SARS-CoV-2
Abstract Background Since inception of the COVID-19 pandemic, early detection and isolation of positive cases is one of the key strategies to restrict disease transmission. Real time reverse transcription polymerase chain reaction (qRTPCR) has been the mainstay of diagnosis. Most of the qRTPCR kits...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-11-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-022-08999-3 |
| _version_ | 1797984026751926272 |
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| author | Swati Gupta Amit Kumar Nivedita Gupta Deepak R. Bharti Neeraj Aggarwal Vasanthapuram Ravi |
| author_facet | Swati Gupta Amit Kumar Nivedita Gupta Deepak R. Bharti Neeraj Aggarwal Vasanthapuram Ravi |
| author_sort | Swati Gupta |
| collection | DOAJ |
| description | Abstract Background Since inception of the COVID-19 pandemic, early detection and isolation of positive cases is one of the key strategies to restrict disease transmission. Real time reverse transcription polymerase chain reaction (qRTPCR) has been the mainstay of diagnosis. Most of the qRTPCR kits were designed against the target genes of original strain of SARS-CoV-2. However, with the emergence of variant strains of SARS-CoV-2, sensitivity of the qRTPCR assays has reportedly reduced. In view of this, it is critical to continuously monitor the performance of the qRTPCR kits in the backdrop of variant strains of SARS-CoV-2. Real world monitoring of assay performance is challenging. Therefore, we developed a two-step in-silico screening process for evaluating the performance of various qRTPCR kits used in India. Results We analysed 73 qRT-PCR kits marketed in India, against the two SARS-CoV-2 VoCs. Sequences of both Delta (B.1.617.2) and Omicron (B.1.1.529) VoCs submitted to GISAID within a specific timeframe were downloaded, clustered to identify unique sequences and aligned with primer and probe sequences. Results were analysed following a two-step screening process. Out of 73 kits analysed, seven were unsatisfactory for detection of both Delta and Omicron VoCs, 10 were unsatisfactory for Delta VoC whereas 2 were unsatisfactory for only Omicron VoC. Conclusion Overall, we have developed a useful screening process for evaluating the performance of qRTPCR assays against Delta and Omicron VoCs of SARS-CoV-2 which can be used for detecting SARS-CoV-2 VoCs that may emerge in future and can also be redeployed for other evolving pathogens of public health importance. |
| first_indexed | 2024-04-11T06:56:16Z |
| format | Article |
| id | doaj.art-f66eca985f2648fb95eef57166b0501d |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-11T06:56:16Z |
| publishDate | 2022-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-f66eca985f2648fb95eef57166b0501d2022-12-22T04:39:02ZengBMCBMC Genomics1471-21642022-11-0123111010.1186/s12864-022-08999-3A two-step process for in silico screening to assess the performance of qRTPCR kits against variant strains of SARS-CoV-2Swati Gupta0Amit Kumar1Nivedita Gupta2Deepak R. Bharti3Neeraj Aggarwal4Vasanthapuram Ravi5Division of Epidemiology and Communicable Disease, V. Ramalingaswami Bhawan, Indian Council of Medical ResearchBiomedical Informatics Division, Indian Council of Medical ResearchDivision of Epidemiology and Communicable Disease, V. Ramalingaswami Bhawan, Indian Council of Medical ResearchDepartment of Forensic Medicine & Toxicology, All India Institute of Medical SciencesDivision of Epidemiology and Communicable Disease, V. Ramalingaswami Bhawan, Indian Council of Medical ResearchDepartment of Neurosciences, National Institute of Mental Health and Neuro-SciencesAbstract Background Since inception of the COVID-19 pandemic, early detection and isolation of positive cases is one of the key strategies to restrict disease transmission. Real time reverse transcription polymerase chain reaction (qRTPCR) has been the mainstay of diagnosis. Most of the qRTPCR kits were designed against the target genes of original strain of SARS-CoV-2. However, with the emergence of variant strains of SARS-CoV-2, sensitivity of the qRTPCR assays has reportedly reduced. In view of this, it is critical to continuously monitor the performance of the qRTPCR kits in the backdrop of variant strains of SARS-CoV-2. Real world monitoring of assay performance is challenging. Therefore, we developed a two-step in-silico screening process for evaluating the performance of various qRTPCR kits used in India. Results We analysed 73 qRT-PCR kits marketed in India, against the two SARS-CoV-2 VoCs. Sequences of both Delta (B.1.617.2) and Omicron (B.1.1.529) VoCs submitted to GISAID within a specific timeframe were downloaded, clustered to identify unique sequences and aligned with primer and probe sequences. Results were analysed following a two-step screening process. Out of 73 kits analysed, seven were unsatisfactory for detection of both Delta and Omicron VoCs, 10 were unsatisfactory for Delta VoC whereas 2 were unsatisfactory for only Omicron VoC. Conclusion Overall, we have developed a useful screening process for evaluating the performance of qRTPCR assays against Delta and Omicron VoCs of SARS-CoV-2 which can be used for detecting SARS-CoV-2 VoCs that may emerge in future and can also be redeployed for other evolving pathogens of public health importance.https://doi.org/10.1186/s12864-022-08999-3DeltaOmicronSARS-CoV-2 variantIn silico analysisqRT-PCR kits |
| spellingShingle | Swati Gupta Amit Kumar Nivedita Gupta Deepak R. Bharti Neeraj Aggarwal Vasanthapuram Ravi A two-step process for in silico screening to assess the performance of qRTPCR kits against variant strains of SARS-CoV-2 BMC Genomics Delta Omicron SARS-CoV-2 variant In silico analysis qRT-PCR kits |
| title | A two-step process for in silico screening to assess the performance of qRTPCR kits against variant strains of SARS-CoV-2 |
| title_full | A two-step process for in silico screening to assess the performance of qRTPCR kits against variant strains of SARS-CoV-2 |
| title_fullStr | A two-step process for in silico screening to assess the performance of qRTPCR kits against variant strains of SARS-CoV-2 |
| title_full_unstemmed | A two-step process for in silico screening to assess the performance of qRTPCR kits against variant strains of SARS-CoV-2 |
| title_short | A two-step process for in silico screening to assess the performance of qRTPCR kits against variant strains of SARS-CoV-2 |
| title_sort | two step process for in silico screening to assess the performance of qrtpcr kits against variant strains of sars cov 2 |
| topic | Delta Omicron SARS-CoV-2 variant In silico analysis qRT-PCR kits |
| url | https://doi.org/10.1186/s12864-022-08999-3 |
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