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In silico analysis of mismatches in RT-qPCR assays of 177 SARS-CoV-2 sequences from Brazil.
Rev Soc Bras Med Trop. 2020; 53:e20200657.RS

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.

Authors+Show Affiliations

Universidade de Fortaleza, Núcleo de Biologia Experimental (NUBEX), Fortaleza, CE, Brasil.Universidade de Fortaleza, Núcleo de Biologia Experimental (NUBEX), Fortaleza, CE, Brasil.Universidade de Fortaleza, Núcleo de Biologia Experimental (NUBEX), Fortaleza, CE, Brasil.Universidade de Fortaleza, Núcleo de Biologia Experimental (NUBEX), Fortaleza, CE, Brasil.Universidade de Fortaleza, Núcleo de Biologia Experimental (NUBEX), Fortaleza, CE, Brasil.Universidade de Fortaleza, Núcleo de Biologia Experimental (NUBEX), Fortaleza, CE, Brasil.Universidade de Fortaleza, Núcleo de Biologia Experimental (NUBEX), Fortaleza, CE, Brasil.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

33263691

Citation

Santos, Renan da Silva, et al. "In Silico Analysis of Mismatches in RT-qPCR Assays of 177 SARS-CoV-2 Sequences From Brazil." Revista Da Sociedade Brasileira De Medicina Tropical, vol. 53, 2020, pp. e20200657.
Santos RDS, Bret RSC, Moreira ACOM, et al. In silico analysis of mismatches in RT-qPCR assays of 177 SARS-CoV-2 sequences from Brazil. Rev Soc Bras Med Trop. 2020;53:e20200657.
Santos, R. D. S., Bret, R. S. C., Moreira, A. C. O. M., Campos, A. R., Silva, A. R. A. E., Lima, D. M., & Tavares, K. C. S. (2020). In silico analysis of mismatches in RT-qPCR assays of 177 SARS-CoV-2 sequences from Brazil. Revista Da Sociedade Brasileira De Medicina Tropical, 53, e20200657. https://doi.org/10.1590/0037-8682-0657-2020
Santos RDS, et al. In Silico Analysis of Mismatches in RT-qPCR Assays of 177 SARS-CoV-2 Sequences From Brazil. Rev Soc Bras Med Trop. 2020;53:e20200657. PubMed PMID: 33263691.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - In silico analysis of mismatches in RT-qPCR assays of 177 SARS-CoV-2 sequences from Brazil. AU - Santos,Renan da Silva, AU - Bret,Raissa Souza Caminha, AU - Moreira,Ana Cristina de Oliveira Monteiro, AU - Campos,Adriana Rolim, AU - Silva,Angelo Roncalli Alves E, AU - Lima,Danielle Malta, AU - Tavares,Kaio Cesar Simiano, Y1 - 2020/11/25/ PY - 2020/09/25/received PY - 2020/10/28/accepted PY - 2020/12/2/entrez PY - 2020/12/3/pubmed PY - 2020/12/15/medline SP - e20200657 EP - e20200657 JF - Revista da Sociedade Brasileira de Medicina Tropical JO - Rev Soc Bras Med Trop VL - 53 N2 - 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. SN - 1678-9849 UR - https://www.unboundmedicine.com/medline/citation/33263691/In_silico_analysis_of_mismatches_in_RT_qPCR_assays_of_177_SARS_CoV_2_sequences_from_Brazil_ L2 - https://www.scielo.br/scielo.php?script=sci_arttext&pid=S0037-86822020000100668&lng=en&nrm=iso&tlng=en DB - PRIME DP - Unbound Medicine ER -