Nucleocapsid single point-mutation associated with drop-out on RT-PCR assay for SARS-CoV-2 detection

BMC Infectious Diseases

Research

Roberta Cardoso Petroni¹  Ricardo Andreotti Siqueira¹  Alexandre Rodrigues Marra¹  Silvia Cassiano Oler¹  Deyvid Amgarten¹  João Renato Rebello Pinho¹  Fernanda de Mello Malta¹  Miguel Cendoroglo Neto¹  Luiz Henrique da Silva Nali² 

[1] Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, 05651-901, Sao Paulo, SP, Brazil;Post-Graduation Program in Health Sciences, Santo Amaro University, Rua Prof. Enéas de Siqueira Neto, 340 - Jardim das Imbuias, Sao Paulo, SP, Brazil;

关键词: SARS-CoV-2;    Viral agent;    Genomic data;    Molecular tests;    Vaccines;   

DOI  :  10.1186/s12879-023-08707-w

 received in 2023-07-26, accepted in 2023-10-12,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundSince its beginning, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been a challenge for clinical and molecular diagnostics, because it has been caused by a novel viral agent. Whole-genome sequencing assisted in the characterization and classification of SARS-CoV-2, and it is an essential tool to genomic surveillance aiming to identify potentials hot spots that could impact on vaccine immune response and on virus diagnosis. We describe two cases of failure at the N2 target of the RT-PCR test Xpert® Xpress SARS-CoV-2.MethodsTotal nucleic acid from the Nasopharyngeal (NP) and oropharyngeal (OP) swab samples and cell supernatant isolates were obtained. RNA samples were submitted to random amplification. Raw sequencing data were subjected to sequence quality controls, removal of human contaminants by aligning against the HG19 reference genome, taxonomic identification of other pathogens and genome recovery through assembly and manual curation. RT-PCR test Xpert® Xpress SARS-CoV-2 was used for molecular diagnosis of SARS-CoV-2 infection, samples were tested in duplicates.ResultsWe identified 27 samples positive for SARS-CoV-2 with a nucleocapsid (N) gene drop out on Cepheid Xpert® Xpress SARS-CoV-2 assay. Sequencing of 2 of 27 samples revealed a single common mutation in the N gene C29197T, potentially involved in the failed detection of N target.ConclusionsThis study highlights the importance of genomic data to update molecular tests and vaccines.

【 授权许可】

CC BY   
© BioMed Central Ltd., part of Springer Nature 2023

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