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Gupta S, Kumar A, Gupta N, Bharti DR, Aggarwal N, Ravi V. A two-step process for in silico screening to assess the performance of qRTPCR kits against variant strains of SARS-CoV-2. BMC Genomics 2022; 23:755. [DOI: 10.1186/s12864-022-08999-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022] Open
Abstract
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.
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Mani K, Thirumalmuthu K, Kathiresan DS, Ramalingam S, Sankaran R, Jeyaraj S. In-silico analysis of Covid-19 genome sequences of Indian origin: Impact of mutations in identification of SARS-Co-V2. Mol Cell Probes 2021; 58:101748. [PMID: 34146663 PMCID: PMC8214951 DOI: 10.1016/j.mcp.2021.101748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/29/2021] [Accepted: 06/12/2021] [Indexed: 11/16/2022]
Abstract
Covid-19 disease caused by SARS-CoV-2 is still being transmitted in developed and developing countries irrespective of healthcare setups. India with 1.3 billion people in the world is severely affected by Covid-19 with 11.3 million cases and 157 000 deaths so far. We have assessed the mismatches in WHO recommended rRT-PCR assays primer and probe binding regions against SARS-CoV-2 Indian genome sequences through in-silico bioinformatics analysis approach. Primers and probe sequences belonging to CN-CDC-ORF1ab from China and HKU-ORF1b from Hong Kong targeting ORF1ab gene while NIH-TH-N from Thailand, HKU-N from Hong Kong and US-CDCN-2 from USA targeting N genes displayed accurate matches (>98.3%) with the 2019 novel corona virus sequences from India. On the other hand, none of the genomic sequences displayed exact match with the primer/probe sequences belonging to Charité-ORF1b from Germany targeting ORF1ab gene. We think it will be worthwhile to release this information to the clinical and medical communities working in Indian Covid-19 frontline taskforce to tackle the recently emerging Covid-19 outbreaks as of March-2021.
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Affiliation(s)
- Kabilan Mani
- PSG Center for Molecular Medicine & Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore, Tamil Nadu, 641 004, India; PSG Centre for Genetics and Molecular Biology, Off Avinashi Road, Peelamedu, Coimbatore, Tamil Nadu, 641 004, India
| | - Kannan Thirumalmuthu
- Lipid and Nutrition Laboratory, Department of Lipid Science, Council of Scientific and Industrial Research-Central Food Technological Research Institute, Mysuru, India
| | - Divya Sri Kathiresan
- PSG Center for Molecular Medicine & Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore, Tamil Nadu, 641 004, India; PSG Centre for Genetics and Molecular Biology, Off Avinashi Road, Peelamedu, Coimbatore, Tamil Nadu, 641 004, India
| | - Sudha Ramalingam
- PSG Center for Molecular Medicine & Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore, Tamil Nadu, 641 004, India; PSG Centre for Genetics and Molecular Biology, Off Avinashi Road, Peelamedu, Coimbatore, Tamil Nadu, 641 004, India; Department of Community Medicine, PSG Institute of Medical Sciences and Research, 641004, Coimbatore, Tamil Nadu, India
| | - Ramalingam Sankaran
- PSG Center for Molecular Medicine & Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore, Tamil Nadu, 641 004, India; PSG Centre for Genetics and Molecular Biology, Off Avinashi Road, Peelamedu, Coimbatore, Tamil Nadu, 641 004, India; Department of Pharmacology, PSG Institute of Medical Sciences and Research, 641 004, Coimbatore, Tamil Nadu, India
| | - Sankarganesh Jeyaraj
- PSG Center for Molecular Medicine & Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore, Tamil Nadu, 641 004, India; PSG Centre for Genetics and Molecular Biology, Off Avinashi Road, Peelamedu, Coimbatore, Tamil Nadu, 641 004, India.
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Elaswad A, Fawzy M. Mutations in Animal SARS-CoV-2 Induce Mismatches with the Diagnostic PCR Assays. Pathogens 2021; 10:371. [PMID: 33808783 PMCID: PMC8003424 DOI: 10.3390/pathogens10030371] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023] Open
Abstract
Recently, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was detected in several animal species. After transmission to animals, the virus accumulates mutations in its genome as adaptation to the new animal host progresses. Therefore, we investigated whether these mutations result in mismatches with the diagnostic PCR assays and suggested proper modifications to the oligo sequences accordingly. A comprehensive bioinformatic analysis was conducted using 28 diagnostic PCR assays and 793 publicly available SARS-CoV-2 genomes isolated from animals. Sixteen out of the investigated 28 PCR assays displayed at least one mismatch with their targets at the 0.5% threshold. Mismatches were detected in seven, two, two, and six assays targeting the ORF1ab, spike, envelope, and nucleocapsid genes, respectively. Several of these mismatches, such as the deletions and mismatches at the 3' end of the primer or probe, are expected to negatively affect the diagnostic PCR assays resulting in false-negative results. The modifications to the oligo sequences should result in stronger template binding by the oligos, better sensitivity of the assays, and higher confidence in the result. It is necessary to monitor the targets of diagnostic PCR assays for any future mutations that may occur as the virus continues to evolve in animals.
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Affiliation(s)
- Ahmed Elaswad
- Department of Animal Wealth Development, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Mohamed Fawzy
- Department of Virology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
- Middle East for Vaccines (ME VAC®), Sharquia 44813, Egypt
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Khan KA, Cheung P. Evaluation of the Sequence Variability within the PCR Primer/Probe Target Regions of the SARS-CoV-2 Genome. Bio Protoc 2020; 10:e3871. [PMID: 33659508 PMCID: PMC7842606 DOI: 10.21769/bioprotoc.3871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 11/02/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; initially named 2019-nCoV) is responsible for the recent coronavirus disease (COVID-19) pandemic, and polymerase chain reaction (PCR) is the current standard method for diagnosis from patient samples. As PCR assays are prone to sequence mismatches due to mutations in the viral genome, it is important to verify the genomic variability at primer/probe binding regions periodically. This step-by-step protocol describes a bioinformatics approach for an extensive evaluation of the sequence variability within the primer/probe target regions of the SARS-CoV-2 genome. The protocol can be applied to any molecular diagnostic assay of choice using freely available software programs and the ready-to-use multiple sequence alignment (MSA) file provided. Graphic abstract Overview of the sequence tracing protocol. The figure was created using the Library of Science and Medical Illustrations from somersault18:24 licensed under a CC BY-NC-SA 4.0 license (https://creativecommons.org/licenses/by-nc-sa/4.0/). Video abstract: https://youtu.be/M1lV1liWE9k.
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Affiliation(s)
| | - Peter Cheung
- Department of Biology, York University, Toronto, Canada
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Khan KA, Cheung P. Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome. ROYAL SOCIETY OPEN SCIENCE 2020; 7:200636. [PMID: 32742701 PMCID: PMC7353963 DOI: 10.1098/rsos.200636] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 05/27/2020] [Indexed: 05/29/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; initially named as 2019-nCoV) is responsible for the recent COVID-19 pandemic and polymerase chain reaction (PCR) is the current standard method for its diagnosis from patient samples. This study conducted a reassessment of published diagnostic PCR assays, including those recommended by the World Health Organization (WHO), through the evaluation of mismatches with publicly available viral sequences. An exhaustive evaluation of the sequence variability within the primer/probe target regions of the viral genome was performed using more than 17 000 viral sequences from around the world. The analysis showed the presence of mutations/mismatches in primer/probe binding regions of 7 assays out of 27 assays studied. A comprehensive bioinformatics approach for in silico inclusivity evaluation of PCR diagnostic assays of SARS-CoV-2 was validated using freely available software programs that can be applied to any diagnostic assay of choice. These findings provide potentially important information for clinicians, laboratory professionals and policy-makers.
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Affiliation(s)
- Kashif Aziz Khan
- Department of Biology, York University, 4700 Keele Street, Toronto, CanadaM3 J 1P3
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