Paganini Irene, Sani Cristina, Chilleri Chiara, Baccini Michela, Antonelli Alberto, Bisanzi Simonetta, Burroni Elena, Cellai Filippo, Coppi Marco, Mealli Fabrizia, Pompeo Giampaolo, Viti Jessica, Rossolini Gian Maria, Carozzi Francesca M
Regional Laboratory of Cancer Prevention, ISPRO, Florence, Italy.
Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy.
Infect Dis (Lond). 2022 Jul;54(7):478-487. doi: 10.1080/23744235.2022.2044512. Epub 2022 Mar 3.
SARS-CoV-2 pandemic represented a huge challenge for national health systems worldwide. Pooling nasopharyngeal (NP) swabs seems to be a promising strategy, saving time and resources, but it could reduce the sensitivity of the RT-PCR and exacerbate samples management in terms of automation and tracing. In this study, taking advantage of the routine implementation of a screening plan on health workers, we evaluated the feasibility of pool testing for SARS-CoV-2 infection diagnosis in the presence of low viral load samples.
Pools were prepared with an automated instrument, mixing 4, 6 or 20 NP specimens, including one, two or none positive samples. Ct values of positive samples were on average about 35 for the four genes analyzed.
The overall sensitivity of 4-samples and 6-samples pools was 93.1 and 90.0%, respectively. Focussing on pools including one sample with Ct value ≥35 for all analyzed genes, sensitivity decreased to 77.8 and 75.0% for 4- and 6-samples, respectively; pools including two positive samples, resulted positive in any size as well as pools including positive samples with Ct values <35.
Pool testing strategy should account the balance between cost-effectiveness, dilution effect and prevalence of the infection. Our study demonstrated the good performances in terms of sensitivity and saving resources of pool testing mixing 4 or 6 samples, even including low viral load specimens, in a real screening context possibly affected by prevalence fluctuation. In conclusion, pool testing strategy represents an efficient and resources saving surveillance and tracing tool, especially in specific context like schools, even for monitoring changes in prevalence associated to vaccination campaign.
新型冠状病毒肺炎疫情给全球各国卫生系统带来了巨大挑战。合并鼻咽拭子检测似乎是一种很有前景的策略，可节省时间和资源，但这可能会降低逆转录聚合酶链反应（RT-PCR）的灵敏度，并在自动化和追踪方面加剧样本管理的难度。在本研究中，利用对医护人员实施筛查计划的常规操作，我们评估了在存在低病毒载量样本的情况下，合并检测用于新型冠状病毒感染诊断的可行性。
使用自动化仪器将4、6或20个鼻咽标本混合制备样本池，其中包括1个、2个或无阳性样本。所分析的四个基因的阳性样本的Ct值平均约为35。
4样本和6样本样本池的总体灵敏度分别为93.1%和90.0%。对于所有分析基因中包含一个Ct值≥35的样本的样本池，4样本和6样本的灵敏度分别降至77.8%和75.0%；包含两个阳性样本的样本池，无论样本池大小均呈阳性结果，以及包含Ct值<35的阳性样本的样本池也是如此。
合并检测策略应考虑成本效益、稀释效应和感染流行率之间的平衡。我们的研究表明，在实际筛查环境中，即使存在低病毒载量标本，且可能受到流行率波动影响的情况下，混合4或6个样本进行合并检测在灵敏度和节省资源方面表现良好。总之，合并检测策略是一种高效且节省资源的监测和追踪工具，尤其是在学校等特定环境中，甚至可用于监测与疫苗接种活动相关的流行率变化。
