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Short Communication • Rev. Soc. Bras. Med. Trop. 53 • 2020 • https://doi.org/10.1590/0037-8682-0657-2020 linkcopy

Open-access In silico analysis of mismatches in RT-qPCR assays of 177 SARS-CoV-2 sequences from Brazil

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    Abstract

    INTRODUCTION:  Quantitative reverse transcription polymerase chain reaction (RT-qPCR) can detect the severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) in a highly specific manner. However, a decrease in the specificity of PCR assays for their targets may lead to false negative results.

    METHODS:   Here, 177 high-coverage complete SARS-CoV-2 genome sequences from 13 Brazilian states were aligned with 15 WHO recommended PCR assays.

    RESULTS:  Only 3 of the 15 completely aligned to all Brazilian sequences. Ten assays had mismatches in up to 3 sequences and two in many sequences.

    CONCLUSION:  These results should be taken into consideration when using PCR-based diagnostics in Brazil.

    Keywords: SARS-CoV-2; COVID-19; Polymerase chain reaction; Diagnosis; Mismatches

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    Sociedade Brasileira de Medicina Tropical - SBMT Sociedade Brasileira de Medicina Tropical - SBMT, Núcleo de Medicina Tropical – UnB, Sala 43C – 70904-970, E-mails: rsbmt@uftm.edu.br | artes.rsbmt@gmail.com | sbmt@sbmt.org.br , WhatsApp: SBMT (61) 9.9192-6496, WhatsApp: RSBMT (34) 9.9996-5807 - Brasília - DF - Brazil
    E-mail: rsbmt@uftm.edu.br
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