Dimcheff Derek E, Valesano Andrew L, Rumfelt Kalee E, Fitzsimmons William J, Blair Christopher, Mirabelli Carmen, Petrie Joshua G, Martin Emily T, Bhambhani Chandan, Tewari Muneesh, Lauring Adam S
Division of Hospital Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
Division of Infectious Disease, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
medRxiv. 2021 Mar 1:2021.02.25.21252493. doi: 10.1101/2021.02.25.21252493.
Understanding viral load in patients infected with SARS-CoV-2 is critical to epidemiology and infection control. Previous studies have demonstrated that SARS-CoV-2 RNA can be detected for many weeks after symptom onset. The clinical significance of this finding is unclear and, in most patients, likely does not represent active infection. There are, however, patients who shed infectious virus for weeks. Detection of subgenomic RNA transcripts expressed by SARS-CoV-2 has been proposed to represent productive infection and may be a tractable marker for monitoring infectivity. Here, we use RT-PCR to quantify total and subgenomic nucleocapsid (N) and envelope (E) transcripts in 190 SARS-CoV-2 positive samples collected on hospital admission. We relate these findings to duration of symptoms. We find that all transcripts decline at the same rate; however, subgenomic E becomes undetectable before other transcripts. In Kaplan-Meier analysis the median duration of symptoms to a negative test is 14 days for sgE and 25 days for sgN. There is a linear decline in subgenomic RNA compared to total RNA suggesting subgenomic transcript copy number is highly dependent on copy number of total transcripts. The mean difference between total N and subgenomic N is 16-fold (4.0 cycles) and the mean difference between total E and sub-genomic E is 137-fold (7.1 cycles). This relationship is constant over duration of symptoms allowing prediction of subgenomic copy number from total copy number. Although Subgenomic E is undetectable at a time that may more closely reflect the duration of infectivity, its utility in determining active infection may be no more useful than a copy number threshold determined for total transcripts.
了解感染严重急性呼吸综合征冠状病毒2（SARS-CoV-2）患者的病毒载量对于流行病学和感染控制至关重要。先前的研究表明，症状出现后数周仍可检测到SARS-CoV-2 RNA。这一发现的临床意义尚不清楚，在大多数患者中，这可能并不代表活跃感染。然而，有患者会持续数周排出传染性病毒。有人提出，检测SARS-CoV-2表达的亚基因组RNA转录本可代表有生产性的感染，并且可能是监测传染性的一个易于处理的标志物。在此，我们使用逆转录聚合酶链反应（RT-PCR）对190份入院时采集的SARS-CoV-2阳性样本中的总核衣壳（N）和包膜（E）转录本以及亚基因组核衣壳和包膜转录本进行定量。我们将这些发现与症状持续时间相关联。我们发现所有转录本均以相同速率下降；然而，亚基因组E在其他转录本之前就无法检测到。在卡普兰-迈耶分析中，亚基因组E检测呈阴性的症状中位持续时间为14天，亚基因组N为25天。与总RNA相比，亚基因组RNA呈线性下降，这表明亚基因组转录本拷贝数高度依赖于总转录本拷贝数。总N与亚基因组N的平均差异为16倍（4.0个循环），总E与亚基因组E的平均差异为137倍（7.1个循环）。这种关系在症状持续期间保持不变，从而可以根据总拷贝数预测亚基因组拷贝数。尽管亚基因组E在可能更准确反映传染性持续时间的时间点无法检测到，但其在确定活跃感染方面的效用可能并不比为总转录本确定的拷贝数阈值更有用。
