Dataset Information

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

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.

SUBMITTER: Santos RDS

PROVIDER: S-EPMC7723368 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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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 RDS Bret Raissa Souza Caminha RSC Moreira Ana Cristina de Oliveira Monteiro ACOM Campos Adriana Rolim AR Silva Angelo Roncalli Alves E ARAE Lima Danielle Malta DM Tavares Kaio Cesar Simiano KCS

Revista da Sociedade Brasileira de Medicina Tropical 20201125

<h4>Introduction</h4>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.<h4>Methods</h4>Here, 177 high-coverage complete SARS-CoV-2 genome sequences from 13 Brazilian states were aligned with 15 WHO recommended PCR assays.<h4>Results</h4>Only 3 of the 15 completely ali ...[more]

PMID: 33263691

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Project description:SARS-CoV-2 variants of concern, demonstrating higher infection rate and lower vaccine effectiveness as compared with the original virus, are important factors propelling the ongoing COVID-19 global outbreak. Therefore, prompt identification of these variants in the environment is essential for pandemic assessment and containment efforts. One well established tool for such viral monitoring is the use of wastewater systems. Here, we describe continuous monitoring of traces of SARS-CoV-2 viruses in the municipal wastewater of a large city in Israel. By observing morbidity fluctuations (during three main COVID-19 surges) occurring in parallel with Pfizer-BioNTech COVID-19 vaccine vaccination rate, compromised immunity was revealed in the current morbidity peak. RT-qPCR assays for the Original (D614G), Alpha and Beta variants had been previously developed and are being employed for wastewater surveillance. In the present study we developed a sensitive RT-qPCR assay designed for the rapid, direct detection of Gamma and Delta variants of concern. Sensitive quantification and detection of the various variants showed the prevalence of the original variant during the first morbidity peak. The dominance of the Alpha variant over the original variant correlated with the second morbidity peak. These variants decreased concurrently with an increase in vaccinations (Feb-March 2021) and the observed decrease in morbidity. The appearance and subsequent rise of the Delta variant became evident and corresponded to the third morbidity peak (June-August 2021). These results suggest a high vaccine neutralization efficiency towards the Alpha variant compared to its neutralization efficiency towards the Delta variant. Moreover, the third vaccination dose (booster) seems to regain neutralization efficiency towards the Delta variant. The developed assays and wastewater-based epidemiology are important tools aiding in morbidity surveillance and disclosing vaccination efforts and immunity dynamics in the community.

Dataset Information

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

Publications

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

Similar Datasets

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