Dataset Information

Nucleocapsid (N) Gene Mutations of SARS-CoV-2 Can Affect Real-Time RT-PCR Diagnostic and Impact False-Negative Results.

ABSTRACT: The current COVID-19 pandemic demands massive testing by Real-time RT-PCR (Reverse Transcription Polymerase Chain Reaction), which is considered the gold standard diagnostic test for the detection of the SARS-CoV-2 virus. However, the virus continues to evolve with mutations that lead to phenotypic alterations as higher transmissibility, pathogenicity or vaccine evasion. Another big issue are mutations in the annealing sites of primers and probes of RT-PCR diagnostic kits leading to false-negative results. Therefore, here we identify mutations in the N (Nucleocapsid) gene that affects the use of the GeneFinder COVID-19 Plus RealAmp Kit. We sequenced SARS-CoV-2 genomes from 17 positive samples with no N gene detection but with RDRP (RNA-dependent RNA polymerase) and E (Envelope) genes detection, and observed a set of three different mutations affecting the N detection: a deletion of 18 nucleotides (Del28877-28894), a substitution of GGG to AAC (28881-28883) and a frameshift mutation caused by deletion (Del28877-28878). The last one cause a deletion of six AAs (amino acids) located in the central intrinsic disorder region at protein level. We also found this mutation in 99 of the 14,346 sequenced samples by the Sao Paulo state Network for Pandemic Alert of Emerging SARS-CoV-2 variants, demonstrating the circulation of the mutation in Sao Paulo, Brazil. Continuous monitoring and characterization of mutations affecting the annealing sites of primers and probes by genomic surveillance programs are necessary to maintain the effectiveness of the diagnosis of COVID-19.

SUBMITTER: Lesbon JCC

PROVIDER: S-EPMC8707239 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature

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Nucleocapsid (N) Gene Mutations of SARS-CoV-2 Can Affect Real-Time RT-PCR Diagnostic and Impact False-Negative Results.

Lesbon Jéssika Cristina Chagas JCC Poleti Mirele Daiana MD de Mattos Oliveira Elisângela Chicaroni EC Patané José Salvatore Leister JSL Clemente Luan Gaspar LG Viala Vincent Louis VL Ribeiro Gabriela G Giovanetti Marta M de Alcantara Luiz Carlos Junior LCJ Teixeira Olivia O Nonato Maria Cristina MC de Lima Loyze Paola Oliveira LPO Martins Antonio Jorge AJ Dos Santos Barros Claudia Renata CR Marqueze Elaine Cristina EC de Souza Todão Bernardino Jardelina J Moretti Debora Botequio DB Brassaloti Ricardo Augusto RA de Lello Rocha Campos Cassano Raquel R Mariani Pilar Drummond Sampaio Correa PDSC Slavov Svetoslav Nanev SN Dos Santos Rafael Bezerra RB Rodrigues Evandra Strazza ES Santos Elaine Vieira EV Borges Josiane Serrano JS de La Roque Debora Glenda Lima DGL Kitajima Joao Paulo JP Santos Bibiana B Assato Patricia Akemi PA da Silva da Costa Felipe Allan FA Banho Cecilia Artico CA Sacchetto Livia L Moraes Marilia Mazzi MM Palmieri Melissa M da Silva Fabiana Erica Vilanova FEV Grotto Rejane Maria Tommasini RMT Souza-Neto Jayme A JA Nogueira Mauricio Lacerda ML Coutinho Luiz Lehman LL Calado Rodrigo Tocantins RT Calado Rodrigo Tocantins RT Neto Raul Machado RM Covas Dimas Tadeu DT Kashima Simone S Elias Maria Carolina MC Sampaio Sandra Coccuzzo SC Fukumasu Heidge H

Viruses 20211210 12

The current COVID-19 pandemic demands massive testing by Real-time RT-PCR (Reverse Transcription Polymerase Chain Reaction), which is considered the gold standard diagnostic test for the detection of the SARS-CoV-2 virus. However, the virus continues to evolve with mutations that lead to phenotypic alterations as higher transmissibility, pathogenicity or vaccine evasion. Another big issue are mutations in the annealing sites of primers and probes of RT-PCR diagnostic kits leading to false-negati ...[more]

PMID: 34960743

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Project description:BackgroundA false-negative case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is defined as a person with suspected infection and an initial negative result by reverse transcription-polymerase chain reaction (RT-PCR) test, with a positive result on a subsequent test. False-negative cases have important implications for isolation and risk of transmission of infected people and for the management of coronavirus disease 2019 (COVID-19). We aimed to review and critically appraise evidence about the rate of RT-PCR false-negatives at initial testing for COVID-19.MethodsWe searched MEDLINE, EMBASE, LILACS, as well as COVID-19 repositories, including the EPPI-Centre living systematic map of evidence about COVID-19 and the Coronavirus Open Access Project living evidence database. Two authors independently screened and selected studies according to the eligibility criteria and collected data from the included studies. The risk of bias was assessed using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. We calculated the proportion of false-negative test results using a multilevel mixed-effect logistic regression model. The certainty of the evidence about false-negative cases was rated using the GRADE approach for tests and strategies. All information in this article is current up to July 17, 2020.ResultsWe included 34 studies enrolling 12,057 COVID-19 confirmed cases. All studies were affected by several risks of bias and applicability concerns. The pooled estimate of false-negative proportion was highly affected by unexplained heterogeneity (tau-squared = 1.39; 90% prediction interval from 0.02 to 0.54). The certainty of the evidence was judged as very low due to the risk of bias, indirectness, and inconsistency issues.ConclusionsThere is substantial and largely unexplained heterogeneity in the proportion of false-negative RT-PCR results. The collected evidence has several limitations, including risk of bias issues, high heterogeneity, and concerns about its applicability. Nonetheless, our findings reinforce the need for repeated testing in patients with suspicion of SARS-Cov-2 infection given that up to 54% of COVID-19 patients may have an initial false-negative RT-PCR (very low certainty of evidence).Systematic review registrationProtocol available on the OSF website: https://tinyurl.com/vvbgqya.

Dataset Information

Nucleocapsid (N) Gene Mutations of SARS-CoV-2 Can Affect Real-Time RT-PCR Diagnostic and Impact False-Negative Results.

Publications

Nucleocapsid (N) Gene Mutations of SARS-CoV-2 Can Affect Real-Time RT-PCR Diagnostic and Impact False-Negative Results.

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