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In silico analysis of mismatches in RT-qPCR assays of 177 SARS-CoV-2 sequences from Brazil
Santos, Renan da Silva; Bret, Raissa Souza Caminha; Moreira, Ana Cristina de Oliveira Monteiro; Campos, Adriana Rolim; Silva, Angelo Roncalli Alves e; Lima, Danielle Malta; Tavares, Kaio Cesar Simiano.
  • Santos, Renan da Silva; Universidade de Fortaleza. Núcleo de Biologia Experimental NUBEX. Fortaleza. BR
  • Bret, Raissa Souza Caminha; Universidade de Fortaleza. Núcleo de Biologia Experimental NUBEX. Fortaleza. BR
  • Moreira, Ana Cristina de Oliveira Monteiro; Universidade de Fortaleza. Núcleo de Biologia Experimental NUBEX. Fortaleza. BR
  • Campos, Adriana Rolim; Universidade de Fortaleza. Núcleo de Biologia Experimental NUBEX. Fortaleza. BR
  • Silva, Angelo Roncalli Alves e; Universidade de Fortaleza. Núcleo de Biologia Experimental NUBEX. Fortaleza. BR
  • Lima, Danielle Malta; Universidade de Fortaleza. Núcleo de Biologia Experimental NUBEX. Fortaleza. BR
  • Tavares, Kaio Cesar Simiano; Universidade de Fortaleza. Núcleo de Biologia Experimental NUBEX. Fortaleza. BR
Rev. Soc. Bras. Med. Trop ; 53: e20200657, 2020. tab, graf
Article in English | SES-SP, ColecionaSUS, LILACS | ID: biblio-1143868
ABSTRACT
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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Full text: Available Index: LILACS (Americas) Main subject: Genome, Viral / Coronavirus Infections / Betacoronavirus Type of study: Diagnostic study Limits: Humans Country/Region as subject: South America / Brazil Language: English Journal: Rev. Soc. Bras. Med. Trop Year: 2020 Type: Article Institution/Affiliation country: Universidade de Fortaleza/BR

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Full text: Available Index: LILACS (Americas) Main subject: Genome, Viral / Coronavirus Infections / Betacoronavirus Type of study: Diagnostic study Limits: Humans Country/Region as subject: South America / Brazil Language: English Journal: Rev. Soc. Bras. Med. Trop Year: 2020 Type: Article Institution/Affiliation country: Universidade de Fortaleza/BR