Revista da Sociedade Brasileira de Medicina Tropical (Nov 2020)

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

  • Renan da Silva Santos,
  • Raissa Souza Caminha Bret,
  • Ana Cristina de Oliveira Monteiro Moreira,
  • Adriana Rolim Campos,
  • Angelo Roncalli Alves e Silva,
  • Danielle Malta Lima,
  • Kaio Cesar Simiano Tavares

DOI
https://doi.org/10.1590/0037-8682-0657-2020
Journal volume & issue
Vol. 53

Abstract

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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.

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