Multicenter Evaluation of the Cepheid Xpert Xpress SARS-CoV-2 Assay for the Detection of SARS-CoV-2 in Oropharyngeal Swab Specimens

Hongyan Hou; Jun Chen; Yueqin Wang; Yanjun Lu; Yaowu Zhu; Bo Zhang; Feng Wang; Lie Mao; Yi-Wei Tang; Bicheng Hu; Yi Ren; Ziyong Sun

摘要

LETTER The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a global health concern that has spread worldwide since December 2019 ( 1 – 4 ). For optimal detection of SARS-CoV-2, the collection and testing of either upper or lower respiratory samples are recommended ( 5 – 7 ). In China, oropharyngeal swab (OPS) specimens have been more widely used than nasopharyngeal swab (NPS) specimens as upper respiratory tract specimens for detection of SARS-CoV-2 during the early stages of COVID-19 outbreak ( 6 ). The Cepheid Xpert Xpress SARS-CoV-2 assay (Cepheid, Sunnyvale, CA) is a rapid, random-access molecular test that detects the pan-sarbecovirus E gene and the N2 region of the N gene as its SARS-CoV-2-specific target. The assay has received United States Food and Drug Administration (FDA) emergency use authorization for nasopharyngeal, nasal, midturbinate, or oropharyngeal swab and nasal wash/aspirate specimens ( 8 ). The Xpert assay has demonstrated good accuracy in SARS-CoV-2 detection in NPS specimens ( 9 ). This study, done in three medical centers in Wuhan, China, aimed to establish performance characteristics of the Xpert Xpress assay in OPS specimens compared to those of commercially available real-time reverse transcription-PCR (RT-PCR) assays approved by the National Medical Products Administration (NMPA) for the detection of SARS-CoV-2 ( 10 , 11 ). A retrospective study was conducted on leftover OPS specimens collected during February to April 2020 that were submitted by clinicians for SARS-CoV-2 testing. The OPS specimens were collected from both sides of the throat as described previously ( 5 , 10 ). An aliquot of OPS specimen was made and stored at ?80°C within 24 h after collection. A total of 285 samples from unique patients were tested from three medical centers and included 99 from Wuhan Tongji Hospital (site 1), 96 from Wuhan Pulmonary Hospital (site 2), and 90 from Wuhan No. 1 Hospital (site 3). Among the patients tested, 159 (55.8%) were males and 126 (44.2%) were females; 220 (77.2%) patients were?≤65?years old, and 65 (22.8%) patients were &65?years old. More than half of the specimens (178; 62.5%) were from inpatients, and 107 (37.5%) specimens were from outpatients. The percentage of outpatients was 62.6% at site 1 and 50% at site 3, but all of the specimens at site 2 were from inpatients. In total, 153 (53.7%) patients were positive and 132 (46.3%) were negative by the first test using the NMPA-approved real-time RT-PCR method. All 285 specimens were tested using the Cepheid Xpert Xpress SARS-CoV-2 assay. The Xpert assay demonstrated a high concordance of 96.1% with the NMPA-PCR methods. The positive percent agreement of the Xpert assay was 96.1% (95% confidence interval [CI], 91.3 to 98.4%), negative percent agreement was 96.2% (95% CI, 90.9 to 98.6%), and the Kappa statistic was 0.92 (95% CI, 0.88 to 0.97) ( Table 1 ). Three additional mixed samples with low, middle, and high threshold cycle ( C _(T) ) levels for SARS-CoV-2 were run by three different staff members on three different days in triplicate using one machine and one lot number of reagents. The coefficients of variation (CVs) of the Xpert assay were 0.86%, 0.73%, and 0.7% for the N2 gene and 0.84%, 0.7%, and 1.95% for the E gene in mixed samples with low, middle, and high C _(T) values, respectively. The Xpert assay showed intratest CVs from 0.2 to 1.17% and 0.21 to 1.27% for the detection of N2 and E genes, respectively. TABLE 1 Xpert Xpress SARS-CoV-2 assay performance versus that of the NMPA-approved RT-PCR method Site No. of results by type ~( a ) PPA ~( b ) (95% CI) NPA ~( c ) (95% CI) Kappa coefficient (95% CI) TP FP FN TN 1 60 5 0 34 100 (92.5–100) 87.2 (71.8–95.2) 0.89 (0.8–0.99) 2 42 0 6 48 87.5 (74.1–94.8) 100 (90.8–100) 0.88 (0.78–0.97) 3 45 0 0 45 100 (90.2–100) 100 (90.2–100) 1.0 (1.0–1.0) Total 147 5 6 127 96.1 (91.3–98.4) 96.2 (90.9–98.6) 0.92 (0.88–0.97) a TP, true positive; FP, false positive; TN, true negative; FN, false negative. b PPA, positive percent agreement. c NPA, negative percent agreement. The upper respiratory samples for RT-PCR tests of SARS-CoV-2 virus included OPS and NPS. Although the positive rates of NPS and sputum were reported as higher than those for OPS, OPS specimens have been more widely used in China ( 5 , 10 ). The OPS specimens were recommended to be collected for real-time RT-PCR assay by the first to fifth editions of the “Guideline of diagnosis and treatment for COVID-19” by the Chinese National Health Commission. Moreover, a swab might have a hard handle, which may cause bleeding when it is inserted into the nostril. This resulted in the dominant use of OPS as upper respiratory specimens in the early COVID-19 outbreak in China. This is, to our knowledge, the first clinical study assessing the Cepheid Xpert Xpress SARS-CoV-2 assay in mainland China. Overall, the Xpert assay demonstrated high positive percent

机译：通过严重急性呼吸综合征冠状病毒2（SARS-COV-2）引起的Coronavirus疾病（Covid-19），是自2019年12月（1 - 4）以来全球蔓延的全球健康问题。为了获得SARS-COV-2的最佳检测，建议使用上呼吸样品的收集和测试（5-7）。在中国，Oropharyngeal Swab（OPS）标本比鼻咽拭子（NPS）标本更广泛地使用，作为上呼吸道试样，用于在Covid-19爆发的早期阶段检测SARS-COV-2（6）。 Cepheid Xpert Xpress SARS-COV-2测定（Cepheid，Sunnyvale，CA）是一种快速，随机接入的分子试验，可检测N基因的Pan-SarboVirus E基因和N2的N2区作为其SARS-COV-2-特定目标。该测定已收到美国食品和药物管理局（FDA）紧急使用鼻咽，鼻，中静脉或口咽拭子和鼻洗涤/吸气标本（8）的授权。 Xpert测定在NPS样本（9）中的SARS-COV-2检测中表现出良好的精度。本研究，在中国武汉的三个医疗中心完成，旨在与国家医疗批准的商业上可获得的实时逆转录-PCR（RT-PCR）测定相比建立OPS标本中的Xpert Xpress测定的性能特征产品施用（NMPA）检测SARS-COV-2（10,11）。在2月至4月20日期间的剩余OPS标本上进行了回顾性研究，该试验由临床医生提交SARS-COV-2测试。如前述（5,10）所述，从喉部的两侧收集OPS样本。制备等分试样并在收集后24小时内储存并储存在α80℃。来自三个医疗中心的三种医疗中心中共有285个样品，其中包括武汉同济医院（武汉肺医院96名（武汉肺医院（2），99名，以及武汉1号医院（遗址3）。在测试的患者中，159名（55.8％）是男性，126名（44.2％）是女性; 220（77.2％）患者？≤65？岁月，65名（22.8％）患者＆ 65岁？岁。超过一半的标本（178; 62.5％）来自住院患者，107例（37.5％）标本来自门诊病人。在部位3和50％的位点为62.6％的门诊患者的百分比，但位点2的所有标本来自住院患者。总共，使用NMPA批准的实时RT-PCR方法第一次试验，153例（53.7％）阳性阳性，132（46.3％）是阴性的。使用Cepheid Xpert Xpress SARS-COV-2测定测试所有285个样本。 XPERT测定与NMPA-PCR方法显示出96.1％的高度一致性。 XPERT测定的阳性百分比达到96.1％（95％置信区间[CI]，91.3至98.4％），负百分比协议为96.2％（95％CI，90.9至98.6％），Kappa统计数为0.92（ 95％CI，0.88至0.97）（表1）。对于SARS-COV-2的三个具有低，中间和高阈值循环（C _（T））水平的三种额外的混合样品在三种不同的日子中，三种不同的工作成员使用一体机和一批试剂进行三次不同的工作成员。对于N2基因的XPERT测定的变化系数（CV）为0.86％，0.73％和0.7％，在混合样品中的0.84％，0.7％和1.95％，在混合样品中，具有低，中间和高C. _（t）值分别。 XPERT测定分别显示肠外CV，分别检测N2和E基因的0.2％至1.17％和0.21至1.27％。表1 XPERT XPRES SARS-COV-2测定性能与NMPA批准的RT-PCR方法的结果〜（a）ppa〜（b）（95％ci）npa〜（c）（95 ％CI）KAPPA系数（95％CI）TP FP FN TN 110 5 0 34 100（92.5-100）87.2（71.8-95.2）0.89（0.8-0.99）2 42 0 6 48 87.5（74.1-94.8）100（ 90.8-100）0.88（0.78-0.97）3 45 0 0 45 100（90.2-100）100（90.2-100）1.0（1.0-1.0）总计147 5 6 127 96.1（91.3-98.4）96.2（90.9-98.6） 0.92（0.88-0.97）TP，真正阳性; FP，假阳性; TN，真实负面; Fn，假阴性。 B PPA，阳性百分比协议。 C NPA，负百分比协议。用于RT-PCR测试的SARS-COV-2病毒的上呼吸样品包括OPS和NPS。尽管据报道，NPS和痰的阳性率高于OPS，但OPS标本在中国（5,10）更广泛使用。建议OPS标本由中国国家卫生委员会的第一个至第五版“Covid-19”的第一个至第五版的实时RT-PCR测定收集。此外，拭子可能具有硬手柄，这在插入鼻孔时可能引起出血。这导致在中国早期Covid-19爆发中主要使用OPS作为上呼吸标本。这是我们的知识，第一个评估中国大陆Cepheid Xpert Xpress SARS-COV-2测定的第一个临床研究。总的来说，XPERT测定显示出高阳性百分比

Multicenter Evaluation of the Cepheid Xpert Xpress SARS-CoV-2 Assay for the Detection of SARS-CoV-2 in Oropharyngeal Swab Specimens

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