Mem Inst Oswaldo Cruz, Rio de Janeiro, VOLUME 118 | 2023
Research Articles

A straightforward one-step strategy for SARS-CoV-2 diagnosis and screening of variants of concern: a multicentre study

Marcela Fontana-Maurell1,2, Fernando do Couto Motta3, Monica Barcellos Arruda1, Pedro Cardoso1, Marisa Ribeiro1, Elisabete Andrade1, Daniela T Godoy1, Elaine Costa1, Daniele Rocha1, Paola Cristina Resende3, Marilda Agudo MT Siqueira3, Rodrigo Brindeiro1,2, Patrícia Alvarez1,+, The collaborative study group*

1Fundação Oswaldo Cruz-Fiocruz, Instituto de Tecnologia de Imunobiológicos Bio-Manguinhos, Rio de Janeiro, RJ, Brasil
2Universidade Federal do Rio de Janeiro, Departamento de Genética, Rio de Janeiro, RJ, Brasil
3Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Vírus Respiratório e Sarampo, Rio de Janeiro, RJ, Brasil

DOI: 10.1590/0074-02760220202
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ABSTRACT

BACKGROUND The prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) has changed unevenly over time around the world. Although whole genome sequencing is the gold standard for virus characterisation, the discovery of alpha VOC causing spike gene target failure (SGTF) result, when tested using an reverse transcription real-time polymerase chain reaction (RT-qPCR) assay, has provided a simple tool for tracking the frequencies of variants.
OBJECTIVES The aim of this study was to investigate if a multiplex RT-qPCR assay (BioM 4Plex VOC) could be used to detect SARS-CoV-2 and to perform a VOC screening test in a single reaction tube. Here, we present the multicentre study evaluating this assay.
METHODS Twelve laboratories have participated in the multicentre study. The BioM 4Plex VOC was distributed to them with detailed instructions of how to perform the test. They were asked to test the BioM 4Plex VOC in parallel with their routine Commercial SARS-CoV-2 diagnostic assay. Additionally, they were requested to select SARS-CoV-2-positive samples with genome sequenced and lineage definition according to PANGO lineage classification.
FINDINGS The BioM 4Plex VOC and commercial RT-PCR assay are equally effective in detecting SARS-CoV-2. Results revealed a specificity of 96.5-100% [95% confidence interval (CI)], a sensitivity of 99.8-100% (95% CI), and an accuracy of 99.8-100% (95% CI). A 99% concordance rate was found between results from the BioM 4Plex VOC and that from available genome sequencing data.
MAIN CONCLUSIONS The BioM 4Plex VOC provides an effective solution to detect SARS-CoV-2 infections and screening for VOCs in a single reaction. It is a straightforward method to help us monitor the frequency and distribution of VOCs and develop strategies to better cope with the pandemics.

key words: SARS-CoV-2 diagnosis COVID-19 variants of concern epidemiological surveillance
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*Adriano Abbud, Claudio Tavares Sacchi, Karoline Rodrigues Campos (Adolfo Lutz Institute); Ana Flávia Mendonça, Luiz Augusto Pereira (Central Laboratory - Goiás); Jaqueline Pegoretti Goulart, Anna Clara Gregório Có (Central Laboratory - Espírito Santo); Lidio Gonçalves Lima Neto, Hivylla Lorrana dos Santos Ferreira (Central Laboratory - Maranhão); Maria do Carmo Debur, Guilherme Nardi Becker (Central Laboratory - Paraná); Tatiana Schaffer Gregianini, Richard Steiner Salvato (Central Laboratory - Rio Grande do Sul); Sandra Bianchini Fernandes, Darcita Buerger Rovaris (Central Laboratory - Santa Catarina); Andreia Santos Costa, Márcia Socorro Pereira Cavalcante (Central Laboratory - Amapá); Mirleide Cordeiro dos Santos, Luana Soares Barbagelata (Evandro Chagas Institute); Yasmin Santos Freitas Macêdo, Tiago Gräf (Fiocruz Bahia); Fabio Miyajima, Carlos Leonardo de Aragão Araujo, Joaquim Cesar do Nascimento Sousa Junior (Fiocruz Ceará).

Financial support: Inova Fiocruz/Fundação Oswaldo Cruz (Projects 48111948434181 and 48111255868131).
MF-M and FCM contributed equally to this work.
+ Corresponding author: palvarez@bio.fiocruz.br
ORCID https://orcid.org/ 0000-0003-0313-877X
Received 31 August 2022
Accepted 24 January 2023

HOW TO CITE
Fontana-Maurell M, Motta FC, Arruda MB, Cardoso P, Ribeiro M, Andrade E, et al. A straightforward one-step strategy for SARS-CoV-2 diagnosis and screening of variants of concern: a multicentre study. Mem Inst Oswaldo Cruz. 2023; 118: e220213.

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