Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2

Author(s):Show less -

Vogels, Chantal B. F. ^[1] ; Breban, Mallery I. ^[1] ; Ott, Isabel M. ^[1] ; Alpert, Tara ^[1] ; Petrone, Mary E. ^[1] ; Watkins, Anne E. ^[1] ; Kalinich, Chaney C. ^[1] ; Earnest, Rebecca ^[1] ; Rothman, Jessica E. ^[1] ; de Jesus, Jaqueline Goes ^{[2, 3]} ; Claro, Ingra Morales ^{[2, 3]} ; Ferreira, Giulia Magalhaes ^{[2, 3, 4]} ; Crispim, Myuki A. E. ^[5] ; Singh, Lavanya ^[6] ; Tegally, Houriiyah ^[6] ; Anyaneji, Ugochukwu J. ^[6] ; Hodcroft, Emma B. ^[7] ; Mason, Christopher E. ^[8] ; Khullar, Gaurav ^[8] ; Metti, Jessica ^[8] ; Dudley, Joel T. ^[8] ; MacKay, Matthew J. ^[8] ; Nash, Megan ^[8] ; Wang, Jianhui ^[9] ; Liu, Chen ^[9] ; Hui, Pei ^[9] ; Murphy, Steven ^[10] ; Neal, Caleb ^[10] ; Laszlo, Eva ^[10] ; Landry, Marie L. ^{[11, 12]} ; Muyombwe, Anthony ^[13] ; Downing, Randy ^[13] ; Razeq, Jafar ^[13] ; de Oliveira, Tulio ^[6] ; Faria, Nuno R. ^{[14, 2, 3, 15]} ; Sabino, Ester C. ^{[2, 3]} ; Neher, Richard A. ^{[16, 17]} ; Fauver, Joseph R. ^[1] ; Grubaugh, Nathan D. ^{[18, 1]} ; Network, Brazil-UK CADDE Genomic ; South, Network Genomic Surveillance

Affiliation:Show less -

^[1] Yale Sch Publ Hlth, Dept Epidemiol Microbial Dis, New Haven, CT 06510 - USA

^[2] Univ Sao Paulo, Dept Molestias Infecciosas & Parasitarias, Fac Med, Sao Paulo - Brazil

^[3] Univ Sao Paulo, Inst Med Trop, Fac Med, Sao Paulo - Brazil

^[4] Univ Fed Uberlandia, Inst Ciencias Biomed, Lab Virol, Uberlandia, MG - Brazil

^[5] Fundacao Hosp Hematol & Hemoterapia Amazonas, Manaus, Amazonas - Brazil

^[6] Univ KwaZulu Natal, KwaZulu Natal Res Innovat & Sequencing Platform K, Sch Lab Med & Med Sci, Durban - South Africa

^[7] Univ Bern, Inst Social & Prevent Med, Bern - Switzerland

^[8] Tempus Labs, Chicago, IL - USA

^[9] Yale Univ, Sch Med, Dept Pathol, New Haven, CT 06510 - USA

^[10] Murphy Med Associates, Greenwich, CT - USA

^[11] Yale Sch Med, Dept Lab Med, New Haven, CT - USA

^[12] Yale Sch Med, Dept Med, New Haven, CT - USA

^[13] Connecticut State Dept Publ Hlth, Rocky Hill, CT - USA

^[14] Univ Oxford, Dept Zool, Oxford - England

^[15] Imperial Coll London, MRC Ctr Global Infect Dis Anal, J IDEA, London - England

^[16] Swiss Inst Bioinformat, Lausanne - Switzerland

^[17] Univ Basel, Biozentrum, Basel - Switzerland

^[18] Yale Univ, Dept Ecol & Evolutionary Biol, New Haven, CT 06520 - USA

• Document type: Journal article
• Source: PLOS BIOLOGY; v. 19, n. 5 MAY 2021.
• Web of Science Citations: 29

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 Delta 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 Delta 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 Delta 3675-3677) in all 3 variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Delta 3675-3677 as the primary target and spike Delta 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. (AU)

• FAPESP's process: 18/14389-0 - Brazil-UK Centre for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE)
• Grantee: Ester Cerdeira Sabino
• Support Opportunities: Research Projects - Thematic Grants