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A novel ORF1a-based SARS-CoV-2 RT-PCR assay to resolve inconclusive samples
BACKGROUND: India bears the second largest burden of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. A multitude of reverse transcription polymerase chain reaction (RT-PCR) detection assays with disparate gene targets, including automated high-throughput platforms, are availa...
Autores principales: | , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The Authors. Published by Elsevier Ltd on behalf of International Society for Infectious Diseases.
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8036167/ https://www.ncbi.nlm.nih.gov/pubmed/33852938 http://dx.doi.org/10.1016/j.ijid.2021.04.006 |
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author | Jawade, Ketki Sinha, Akhauri Yash Bhagat, Sharad Bhowmick, Shilpa Chauhan, Bhagyashree Kaginkar, Snehal Palav, Harsha Kasarpalkar, Nandini Devadiga, Pratik Karandikar, Kalyani Agrawal, Sachee Shastri, Jayanthi Munne, Kiran Bhor, Vikrant M. Mahale, Smita D. Bhowmik, Subhanjan Jagtap, Dhanashree Patel, Vainav |
author_facet | Jawade, Ketki Sinha, Akhauri Yash Bhagat, Sharad Bhowmick, Shilpa Chauhan, Bhagyashree Kaginkar, Snehal Palav, Harsha Kasarpalkar, Nandini Devadiga, Pratik Karandikar, Kalyani Agrawal, Sachee Shastri, Jayanthi Munne, Kiran Bhor, Vikrant M. Mahale, Smita D. Bhowmik, Subhanjan Jagtap, Dhanashree Patel, Vainav |
author_sort | Jawade, Ketki |
collection | PubMed |
description | BACKGROUND: India bears the second largest burden of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. A multitude of reverse transcription polymerase chain reaction (RT-PCR) detection assays with disparate gene targets, including automated high-throughput platforms, are available. Varying concordance and interpretation of diagnostic results in this setting can result in significant reporting delays, leading to suboptimal disease management. This article reports the development of a novel ORF1a-based SARS-CoV-2 RT-PCR assay – Viroselect – that shows high concordance with conventional assays and the ability to resolve inconclusive results generated during the peak of the epidemic in Mumbai, India. METHODS: A unique target region within SARS-CoV-2 ORF1a – the non-structural protein 3 (nsp3) region – was used to design and develop the assay. This hypervariable region (1923–3956) between SARS-CoV-2, SARS-CoV-1 and Middle East respiratory syndrome coronavirus was utilized to design the primers and probes for the RT-PCR assay. The concordance of this assay with commonly used emergency use authorization (US Food and Drug Administration) manual kits and an automated high-throughput testing platform was evaluated. Further, a retrospective analysis was carried out using Viroselect on samples reported as ‘inconclusive’ between April and October 2020. RESULTS: In total, 701 samples were tested. Concordance analysis of 477 samples demonstrated high overall agreement of Viroselect with both manual (87.6%) and automated (84.7%) assays. Also, in the retrospective analysis of 224 additional samples reported as ‘inconclusive’, Viroselect was able to resolve 100% (19/19) and 93.7% (192/205) of samples which had inconclusive results on manual and automated high-throughput platforms, respectively. CONCLUSION: Viroselect had high concordance with conventional assays, both manual and automated, and has potential to resolve inconclusive samples. |
format | Online Article Text |
id | pubmed-8036167 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | The Authors. Published by Elsevier Ltd on behalf of International Society for Infectious Diseases. |
record_format | MEDLINE/PubMed |
spelling | pubmed-80361672021-04-12 A novel ORF1a-based SARS-CoV-2 RT-PCR assay to resolve inconclusive samples Jawade, Ketki Sinha, Akhauri Yash Bhagat, Sharad Bhowmick, Shilpa Chauhan, Bhagyashree Kaginkar, Snehal Palav, Harsha Kasarpalkar, Nandini Devadiga, Pratik Karandikar, Kalyani Agrawal, Sachee Shastri, Jayanthi Munne, Kiran Bhor, Vikrant M. Mahale, Smita D. Bhowmik, Subhanjan Jagtap, Dhanashree Patel, Vainav Int J Infect Dis Article BACKGROUND: India bears the second largest burden of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. A multitude of reverse transcription polymerase chain reaction (RT-PCR) detection assays with disparate gene targets, including automated high-throughput platforms, are available. Varying concordance and interpretation of diagnostic results in this setting can result in significant reporting delays, leading to suboptimal disease management. This article reports the development of a novel ORF1a-based SARS-CoV-2 RT-PCR assay – Viroselect – that shows high concordance with conventional assays and the ability to resolve inconclusive results generated during the peak of the epidemic in Mumbai, India. METHODS: A unique target region within SARS-CoV-2 ORF1a – the non-structural protein 3 (nsp3) region – was used to design and develop the assay. This hypervariable region (1923–3956) between SARS-CoV-2, SARS-CoV-1 and Middle East respiratory syndrome coronavirus was utilized to design the primers and probes for the RT-PCR assay. The concordance of this assay with commonly used emergency use authorization (US Food and Drug Administration) manual kits and an automated high-throughput testing platform was evaluated. Further, a retrospective analysis was carried out using Viroselect on samples reported as ‘inconclusive’ between April and October 2020. RESULTS: In total, 701 samples were tested. Concordance analysis of 477 samples demonstrated high overall agreement of Viroselect with both manual (87.6%) and automated (84.7%) assays. Also, in the retrospective analysis of 224 additional samples reported as ‘inconclusive’, Viroselect was able to resolve 100% (19/19) and 93.7% (192/205) of samples which had inconclusive results on manual and automated high-throughput platforms, respectively. CONCLUSION: Viroselect had high concordance with conventional assays, both manual and automated, and has potential to resolve inconclusive samples. The Authors. Published by Elsevier Ltd on behalf of International Society for Infectious Diseases. 2021-05 2021-04-11 /pmc/articles/PMC8036167/ /pubmed/33852938 http://dx.doi.org/10.1016/j.ijid.2021.04.006 Text en © 2021 The Authors. Published by Elsevier Ltd on behalf of International Society for Infectious Diseases. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active. |
spellingShingle | Article Jawade, Ketki Sinha, Akhauri Yash Bhagat, Sharad Bhowmick, Shilpa Chauhan, Bhagyashree Kaginkar, Snehal Palav, Harsha Kasarpalkar, Nandini Devadiga, Pratik Karandikar, Kalyani Agrawal, Sachee Shastri, Jayanthi Munne, Kiran Bhor, Vikrant M. Mahale, Smita D. Bhowmik, Subhanjan Jagtap, Dhanashree Patel, Vainav A novel ORF1a-based SARS-CoV-2 RT-PCR assay to resolve inconclusive samples |
title | A novel ORF1a-based SARS-CoV-2 RT-PCR assay to resolve inconclusive samples |
title_full | A novel ORF1a-based SARS-CoV-2 RT-PCR assay to resolve inconclusive samples |
title_fullStr | A novel ORF1a-based SARS-CoV-2 RT-PCR assay to resolve inconclusive samples |
title_full_unstemmed | A novel ORF1a-based SARS-CoV-2 RT-PCR assay to resolve inconclusive samples |
title_short | A novel ORF1a-based SARS-CoV-2 RT-PCR assay to resolve inconclusive samples |
title_sort | novel orf1a-based sars-cov-2 rt-pcr assay to resolve inconclusive samples |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8036167/ https://www.ncbi.nlm.nih.gov/pubmed/33852938 http://dx.doi.org/10.1016/j.ijid.2021.04.006 |
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