Related Experiment Video
Updated: Nov 27, 2025
Author Spotlight: Advancements in Multiplex Detection of Respiratory Viruses
Published on: November 10, 2023
In silico analysis of mismatches in RT-qPCR assays of 177 SARS-CoV-2 sequences from Brazil
Renan da Silva Santos1, Raissa Souza Caminha Bret1, Ana Cristina de Oliveira Monteiro Moreira1
1Universidade de Fortaleza, Núcleo de Biologia Experimental (NUBEX), Fortaleza, CE, Brasil.
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.
