Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, Sao Paulo, SP, 05651-901, Brazil.
Post-Graduation Program in Health Sciences, Santo Amaro University, Rua Prof. Enéas de Siqueira Neto, 340 - Jardim das Imbuias, Sao Paulo, SP, Brazil.
BMC Infect Dis. 2023 Oct 23;23(1):714. doi: 10.1186/s12879-023-08707-w.
Since 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.
Total 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.
We 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.
This study highlights the importance of genomic data to update molecular tests and vaccines.
自 SARS-CoV-2 大流行开始以来，临床和分子诊断一直是一个挑战，因为它是由新型病毒引起的。全基因组测序有助于 SARS-CoV-2 的特征描述和分类，是基因组监测的重要工具，旨在确定可能影响疫苗免疫反应和病毒诊断的潜在热点。我们描述了 Xpert® Xpress SARS-CoV-2 RT-PCR 试验中 N2 靶标失败的两个案例。
从鼻咽（NP）和口咽（OP）拭子样本和细胞上清液分离物中获得总核酸。对 RNA 样本进行随机扩增。原始测序数据经过序列质量控制，通过与 HG19 参考基因组进行比对去除人类污染物，对其他病原体进行分类鉴定，并通过组装和人工编辑进行基因组恢复。Xpert® Xpress SARS-CoV-2 RT-PCR 试验用于 SARS-CoV-2 感染的分子诊断，样本进行了重复测试。
我们在 Cepheid Xpert® Xpress SARS-CoV-2 检测中发现了 27 个 N 基因缺失的 SARS-CoV-2 阳性样本。对 27 个样本中的 2 个样本进行测序，发现 N 基因 C29197T 存在单一常见突变，可能与 N 靶标检测失败有关。
本研究强调了基因组数据对于更新分子检测和疫苗的重要性。
