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

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

Authorship SCIMAGO INSTITUTIONS RANKINGS

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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