Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2.
With the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants that may increase transmissibility and/or cause escape from immune responses, there is an urgent need for the targeted surveillance of circulating lineages. It was found that the B.1.1.7 (also 501Y.V1) varian...
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Public Library of Science (PLoS)
2021-05-01
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| Online Access: | https://doi.org/10.1371/journal.pbio.3001236 |
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| author | Chantal B F Vogels Mallery I Breban Isabel M Ott Tara Alpert Mary E Petrone Anne E Watkins Chaney C Kalinich Rebecca Earnest Jessica E Rothman Jaqueline Goes de Jesus Ingra Morales Claro Giulia Magalhães Ferreira Myuki A E Crispim Brazil-UK CADDE Genomic Network Lavanya Singh Houriiyah Tegally Ugochukwu J Anyaneji Network for Genomic Surveillance in South Africa Emma B Hodcroft Christopher E Mason Gaurav Khullar Jessica Metti Joel T Dudley Matthew J MacKay Megan Nash Jianhui Wang Chen Liu Pei Hui Steven Murphy Caleb Neal Eva Laszlo Marie L Landry Anthony Muyombwe Randy Downing Jafar Razeq Tulio de Oliveira Nuno R Faria Ester C Sabino Richard A Neher Joseph R Fauver Nathan D Grubaugh |
| author_facet | Chantal B F Vogels Mallery I Breban Isabel M Ott Tara Alpert Mary E Petrone Anne E Watkins Chaney C Kalinich Rebecca Earnest Jessica E Rothman Jaqueline Goes de Jesus Ingra Morales Claro Giulia Magalhães Ferreira Myuki A E Crispim Brazil-UK CADDE Genomic Network Lavanya Singh Houriiyah Tegally Ugochukwu J Anyaneji Network for Genomic Surveillance in South Africa Emma B Hodcroft Christopher E Mason Gaurav Khullar Jessica Metti Joel T Dudley Matthew J MacKay Megan Nash Jianhui Wang Chen Liu Pei Hui Steven Murphy Caleb Neal Eva Laszlo Marie L Landry Anthony Muyombwe Randy Downing Jafar Razeq Tulio de Oliveira Nuno R Faria Ester C Sabino Richard A Neher Joseph R Fauver Nathan D Grubaugh |
| author_sort | Chantal B F Vogels |
| collection | DOAJ |
| description | With the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants that may increase transmissibility and/or cause escape from immune responses, there is an urgent need for the targeted surveillance of circulating lineages. It was found that the B.1.1.7 (also 501Y.V1) variant, first detected in the United Kingdom, could be serendipitously detected by the Thermo Fisher TaqPath COVID-19 PCR assay because a key deletion in these viruses, spike Δ69-70, would cause a "spike gene target failure" (SGTF) result. However, a SGTF result is not definitive for B.1.1.7, and this assay cannot detect other variants of concern (VOC) that lack spike Δ69-70, such as B.1.351 (also 501Y.V2), detected in South Africa, and P.1 (also 501Y.V3), recently detected in Brazil. We identified a deletion in the ORF1a gene (ORF1a Δ3675-3677) in all 3 variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Δ3675-3677 as the primary target and spike Δ69-70 to differentiate, we designed and validated an open-source PCR assay to detect SARS-CoV-2 VOC. Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence and spread of B.1.1.7, B.1.351, and P.1. |
| format | Article |
| id | doaj-art-df6ae3b174fb4117b9adacb18f55fee4 |
| institution | OA Journals |
| issn | 1544-9173 1545-7885 |
| language | English |
| publishDate | 2021-05-01 |
| publisher | Public Library of Science (PLoS) |
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| series | PLoS Biology |
| spelling | doaj-art-df6ae3b174fb4117b9adacb18f55fee42025-08-20T02:23:08ZengPublic Library of Science (PLoS)PLoS Biology1544-91731545-78852021-05-01195e300123610.1371/journal.pbio.3001236Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2.Chantal B F VogelsMallery I BrebanIsabel M OttTara AlpertMary E PetroneAnne E WatkinsChaney C KalinichRebecca EarnestJessica E RothmanJaqueline Goes de JesusIngra Morales ClaroGiulia Magalhães FerreiraMyuki A E CrispimBrazil-UK CADDE Genomic NetworkLavanya SinghHouriiyah TegallyUgochukwu J AnyanejiNetwork for Genomic Surveillance in South AfricaEmma B HodcroftChristopher E MasonGaurav KhullarJessica MettiJoel T DudleyMatthew J MacKayMegan NashJianhui WangChen LiuPei HuiSteven MurphyCaleb NealEva LaszloMarie L LandryAnthony MuyombweRandy DowningJafar RazeqTulio de OliveiraNuno R FariaEster C SabinoRichard A NeherJoseph R FauverNathan D GrubaughWith the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants that may increase transmissibility and/or cause escape from immune responses, there is an urgent need for the targeted surveillance of circulating lineages. It was found that the B.1.1.7 (also 501Y.V1) variant, first detected in the United Kingdom, could be serendipitously detected by the Thermo Fisher TaqPath COVID-19 PCR assay because a key deletion in these viruses, spike Δ69-70, would cause a "spike gene target failure" (SGTF) result. However, a SGTF result is not definitive for B.1.1.7, and this assay cannot detect other variants of concern (VOC) that lack spike Δ69-70, such as B.1.351 (also 501Y.V2), detected in South Africa, and P.1 (also 501Y.V3), recently detected in Brazil. We identified a deletion in the ORF1a gene (ORF1a Δ3675-3677) in all 3 variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Δ3675-3677 as the primary target and spike Δ69-70 to differentiate, we designed and validated an open-source PCR assay to detect SARS-CoV-2 VOC. Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence and spread of B.1.1.7, B.1.351, and P.1.https://doi.org/10.1371/journal.pbio.3001236 |
| spellingShingle | Chantal B F Vogels Mallery I Breban Isabel M Ott Tara Alpert Mary E Petrone Anne E Watkins Chaney C Kalinich Rebecca Earnest Jessica E Rothman Jaqueline Goes de Jesus Ingra Morales Claro Giulia Magalhães Ferreira Myuki A E Crispim Brazil-UK CADDE Genomic Network Lavanya Singh Houriiyah Tegally Ugochukwu J Anyaneji Network for Genomic Surveillance in South Africa Emma B Hodcroft Christopher E Mason Gaurav Khullar Jessica Metti Joel T Dudley Matthew J MacKay Megan Nash Jianhui Wang Chen Liu Pei Hui Steven Murphy Caleb Neal Eva Laszlo Marie L Landry Anthony Muyombwe Randy Downing Jafar Razeq Tulio de Oliveira Nuno R Faria Ester C Sabino Richard A Neher Joseph R Fauver Nathan D Grubaugh Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2. PLoS Biology |
| title | Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2. |
| title_full | Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2. |
| title_fullStr | Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2. |
| title_full_unstemmed | Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2. |
| title_short | Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2. |
| title_sort | multiplex qpcr discriminates variants of concern to enhance global surveillance of sars cov 2 |
| url | https://doi.org/10.1371/journal.pbio.3001236 |
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