Robust Automation and Point of care IDentification of COVID

As a rapid and definitive diagnosis of SARS-CoV-2 is essential, it is also key to consider that a recent data review has shown that 19% of patients with COVID-19 have co-infections and that these show an association with poor outcomes (JS Musuuza et al. 2021). Due to the benefits in the management of treatment and the timely isolation of infected patients with overlapping clinical symptoms, this highlights the need to identify other common viral and bacterial pathogens. The objective of this study was to evaluate the performance of the Respiratory 1 Panel (RESP003) CE marked kits, developed by GeneFirst (United Kingdom), for multiplex respiratory pathogen testing including 17 common causes of upper-respiratory tract infections and 11 common causes of pneumonia on biobanked clinical samples on the ACSIA - a High Throughput robotic system provided by PrimaDiag (France). The results from this system were assessed against BioFire® FilmArray®, a comparable testing platform used as the gold standard comparator, to determine the clinical sensitivity and specificity of the tests. Results from conventional microbiology techniques were also considered as necessary or required. APHP established a clinical study protocol and has been granted with the necessary approvals for the study. Samples have been formerly screened with FilmArray® or GeneXpert® in order to include the most adequate number of positives and negative cases. Overall, the evaluation criteria for the respiratory panels was: - Clinical sensitivity of the RESP003 test coupled with the ACSIA platform versus the comparator (target: 90%) - Clinical specificity of the RESP003 test coupled with the ACSIA platform in relation to the comparator (target: 98%) - Background noise (white limit) will be also evaluated. The study allowed the constitution of a biobank encompassing all major variants of SARS-CoV-2 samples, along with most of the other respiratory pathogens commonly reported in community acquired respiratory infections. The assay does not yet meet the required sensitivity specification using the automated result call, but the specificity is within range when the automated calling is verified. The reason for the discrepancy between the reference result and the post-biobanking results will be explored to curate and validate the biobank.

鉴于严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）的快速精准诊断至关重要，同时需注意：近期一项数据综述显示，19%的新型冠状病毒肺炎（COVID-19）患者存在合并感染，且这类感染与不良预后相关（JS Musuuza等，2021）。由于优化感染者管理、及时隔离存在重叠临床症状的患者具有重要临床价值，这凸显了识别其他常见病毒及细菌病原体的必要性。

本研究旨在评估由英国GeneFirst公司开发的获得CE认证的Respiratory 1 Panel (RESP003) 呼吸道检测试剂盒的性能：该试剂盒可开展多重呼吸道病原体检测，涵盖17种常见上呼吸道感染致病原与11种常见肺炎致病原，检测样本为搭载于法国PrimaDiag公司提供的ACSIA高通量自动化机器人系统的生物库临床样本。

本研究以BioFire® FilmArray®作为金标准对照的可比检测平台，对该系统的检测结果进行比对，以确定RESP003检测试剂盒的临床灵敏度与特异性；必要时，亦会参考传统微生物学技术的检测结果。

APHP已制定本临床研究的方案，并获得了该研究所需的全部审批资质。所有纳入研究的样本此前均已通过FilmArray®或GeneXpert®完成筛查，以确保纳入足够数量的阳性与阴性病例。

本呼吸道检测试剂盒的评估标准如下：
- 搭载ACSIA平台的RESP003检测试剂盒相较于对照平台的临床灵敏度（预设目标值：90%）
- 搭载ACSIA平台的RESP003检测试剂盒相较于对照平台的临床特异性（预设目标值：98%）
- 同时将评估背景噪音（白限）。

本研究成功构建了包含SARS-CoV-2所有主要变异株样本的生物样本库，同时纳入了社区获得性呼吸道感染中常见的绝大多数其他呼吸道病原体。

采用自动化结果判读时，该检测方法尚未达到预设的灵敏度要求，但经人工验证自动化判读结果后，其特异性处于合格区间内。研究团队将进一步探究参考结果与生物库构建后检测结果之间的差异原因，以整理并验证该生物样本库。