tetano
Editor, Senior Moderator
PLoS Biol
. 2021 May 7;19(5):e3001236.
doi: 10.1371/journal.pbio.3001236. Online ahead of print.
Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2
Chantal B F Vogels[SUP] 1 [/SUP], Mallery I Breban[SUP] 1 [/SUP], Isabel M Ott[SUP] 1 [/SUP], Tara Alpert[SUP] 1 [/SUP], Mary E Petrone[SUP] 1 [/SUP], Anne E Watkins[SUP] 1 [/SUP], Chaney C Kalinich[SUP] 1 [/SUP], Rebecca Earnest[SUP] 1 [/SUP], Jessica E Rothman[SUP] 1 [/SUP], Jaqueline Goes de Jesus[SUP] 2 [/SUP], Ingra Morales Claro[SUP] 2 [/SUP], Giulia Magalh?es Ferreira[SUP] 2 3 [/SUP], Myuki A E Crispim[SUP] 4 [/SUP], Brazil-UK CADDE Genomic Network; Lavanya Singh[SUP] 5 [/SUP], Houriiyah Tegally[SUP] 5 [/SUP], Ugochukwu J Anyaneji[SUP] 5 [/SUP], Network for Genomic Surveillance in South Africa; Emma B Hodcroft[SUP] 6 [/SUP], Christopher E Mason[SUP] 7 [/SUP], Gaurav Khullar[SUP] 7 [/SUP], Jessica Metti[SUP] 7 [/SUP], Joel T Dudley[SUP] 7 [/SUP], Matthew J MacKay[SUP] 7 [/SUP], Megan Nash[SUP] 7 [/SUP], Jianhui Wang[SUP] 8 [/SUP], Chen Liu[SUP] 8 [/SUP], Pei Hui[SUP] 8 [/SUP], Steven Murphy[SUP] 9 [/SUP], Caleb Neal[SUP] 9 [/SUP], Eva Laszlo[SUP] 9 [/SUP], Marie L Landry[SUP] 10 [/SUP], Anthony Muyombwe[SUP] 11 [/SUP], Randy Downing[SUP] 11 [/SUP], Jafar Razeq[SUP] 11 [/SUP], Tulio de Oliveira[SUP] 5 [/SUP], Nuno R Faria[SUP] 2 12 13 [/SUP], Ester C Sabino[SUP] 2 [/SUP], Richard A Neher[SUP] 14 15 [/SUP], Joseph R Fauver[SUP] 1 [/SUP], Nathan D Grubaugh[SUP] 1 16 [/SUP]
Affiliations
Abstract
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 Coronavirus Disease 2019 (COVID-19) PCR assay because a key deletion in these viruses, spike ?69-70, 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 ?69-70, 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 ?3675-3677) in all 3 variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a ?3675-3677 as the primary target and spike ?69-70 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.
. 2021 May 7;19(5):e3001236.
doi: 10.1371/journal.pbio.3001236. Online ahead of print.
Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2
Chantal B F Vogels[SUP] 1 [/SUP], Mallery I Breban[SUP] 1 [/SUP], Isabel M Ott[SUP] 1 [/SUP], Tara Alpert[SUP] 1 [/SUP], Mary E Petrone[SUP] 1 [/SUP], Anne E Watkins[SUP] 1 [/SUP], Chaney C Kalinich[SUP] 1 [/SUP], Rebecca Earnest[SUP] 1 [/SUP], Jessica E Rothman[SUP] 1 [/SUP], Jaqueline Goes de Jesus[SUP] 2 [/SUP], Ingra Morales Claro[SUP] 2 [/SUP], Giulia Magalh?es Ferreira[SUP] 2 3 [/SUP], Myuki A E Crispim[SUP] 4 [/SUP], Brazil-UK CADDE Genomic Network; Lavanya Singh[SUP] 5 [/SUP], Houriiyah Tegally[SUP] 5 [/SUP], Ugochukwu J Anyaneji[SUP] 5 [/SUP], Network for Genomic Surveillance in South Africa; Emma B Hodcroft[SUP] 6 [/SUP], Christopher E Mason[SUP] 7 [/SUP], Gaurav Khullar[SUP] 7 [/SUP], Jessica Metti[SUP] 7 [/SUP], Joel T Dudley[SUP] 7 [/SUP], Matthew J MacKay[SUP] 7 [/SUP], Megan Nash[SUP] 7 [/SUP], Jianhui Wang[SUP] 8 [/SUP], Chen Liu[SUP] 8 [/SUP], Pei Hui[SUP] 8 [/SUP], Steven Murphy[SUP] 9 [/SUP], Caleb Neal[SUP] 9 [/SUP], Eva Laszlo[SUP] 9 [/SUP], Marie L Landry[SUP] 10 [/SUP], Anthony Muyombwe[SUP] 11 [/SUP], Randy Downing[SUP] 11 [/SUP], Jafar Razeq[SUP] 11 [/SUP], Tulio de Oliveira[SUP] 5 [/SUP], Nuno R Faria[SUP] 2 12 13 [/SUP], Ester C Sabino[SUP] 2 [/SUP], Richard A Neher[SUP] 14 15 [/SUP], Joseph R Fauver[SUP] 1 [/SUP], Nathan D Grubaugh[SUP] 1 16 [/SUP]
Affiliations
- PMID: 33961632
- DOI: 10.1371/journal.pbio.3001236
Abstract
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 Coronavirus Disease 2019 (COVID-19) PCR assay because a key deletion in these viruses, spike ?69-70, 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 ?69-70, 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 ?3675-3677) in all 3 variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a ?3675-3677 as the primary target and spike ?69-70 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.