Sentis Célia, Parraud Delphine, Billaud Geneviève, Valette Martine, Bouscambert-Duchamp Maude, Lina Bruno, Morfin Florence, Gaymard Alexandre
Hospices Civils de Lyon, Institut des Agents Infectieux, service de Virologie, Laboratoire Associé au Centre National de Référence des Virus des Infections Respiratoires, Lyon, France.
CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, Lyon, France.
J Med Virol. 2025 May;97(5):e70363. doi: 10.1002/jmv.70363.
SARS-CoV-2 clinical samples can be detected as positive for a long period of time using real-time RT-PCR, even when patients are no longer infectious. Viral culture is the gold standard for assessing a patient's infectivity, but it is a time-consuming technique and lacks sensitivity. SARS-CoV-2 subgenomic RNA (sgRNA) detection has been used as a proxy for assessing the infectivity but only a limited number of studies have described its use in vitro and in clinical samples. This study aimed to evaluate the correlation between results from viral culture, genomic RT-PCR (gRT-PCR), and subgenomic RT-PCR (sgRT-PCR) during in vitro infection and in clinical samples. In vitro viral replication kinetics showed that both genomic RNA (gRNA) and subgenomic RNA (sgRNA) levels remained stable up to 21 days in the absence of replication-competent virus. Using clinical samples, sgRNA was detected in 87.5% of culture-positive samples, demonstrating better performances than gRT-PCR (Positive predictive value (PPV) 93.3% and Negative predictive value (NPV) of 87.5%) and an almost perfect agreement with culture results (Cohen κ = 0.81 [95% CI: 0.66-0.95]). These findings suggest that testing for sgRNA and/or using a gRNA Ct cut-off of 21.2 could be used as a proxy to determine the presence of SARS-CoV-2 replication-competent virus.
即使患者不再具有传染性，使用实时逆转录聚合酶链反应（RT-PCR）仍可在很长一段时间内检测到严重急性呼吸综合征冠状病毒2（SARS-CoV-2）临床样本呈阳性。病毒培养是评估患者传染性的金标准，但它是一项耗时的技术且缺乏敏感性。SARS-CoV-2亚基因组RNA（sgRNA）检测已被用作评估传染性的替代方法，但仅有有限数量的研究描述了其在体外和临床样本中的应用。本研究旨在评估体外感染和临床样本中病毒培养、基因组RT-PCR（gRT-PCR）和亚基因组RT-PCR（sgRT-PCR）结果之间的相关性。体外病毒复制动力学表明，在没有具有复制能力的病毒的情况下，基因组RNA（gRNA）和亚基因组RNA（sgRNA）水平在长达21天的时间内保持稳定。使用临床样本，在87.5%的培养阳性样本中检测到sgRNA，其表现优于gRT-PCR（阳性预测值（PPV）为93.3%，阴性预测值（NPV）为87.5%），并且与培养结果几乎完全一致（科恩κ系数=0.81[95%置信区间：0.66-0.95]）。这些发现表明，检测sgRNA和/或使用gRNA循环阈值（Ct）为21.2可作为确定是否存在具有SARS-CoV-2复制能力病毒的替代方法。
