The viral load of SARS-CoV-2 in clinical samples as measured by the primary diagnostic tool of RT-PCR is an imperfect readout for infection potential as most targeted assays designed for sensitivity, indiscriminately detect short and long RNA fragments, although infectivity is embodied only in the whole virus and its intact genome. Here, we used next-generation sequencing (NGS) to characterize 155 clinical samples and show sensitive and quantitative detection of viral RNA which confirmed subgenomic RNA in 57.6% of samples and provided a novel method to determine relative integrity of viral RNA in samples. The relative abundance of long fragments quantified as a viral fragmentation score was positively associated with viral load and inversely related to time from disease onset. An empirically determined score cut-off for presence of substantially fragmented RNA was able to identify 100% of samples collected after 8 days of illness with poor infection potential in line with current clinical understanding of infectiousness of SARS-CoV-2. The quantification of longer fragments in addition to existing short targets in an NGS or RT-PCR-based assay could provide a valuable readout of infection potential simultaneous to the detection of any fragments of SARS-CoV-2 RNA in test samples.

中文翻译：

---

与传染性相关的临床样本中SARS-CoV-2的病毒片段签名。

通过RT-PCR的主要诊断工具测量的临床样品中SARS-CoV-2的病毒载量对于感染潜力而言是不完美的读数，因为大多数针对性分析旨在提高灵敏度，不加区别地检测长短RNA片段，尽管体现了传染性仅存在于整个病毒及其完整基因组中。在这里，我们使用下一代测序（NGS）表征了155个临床样品，并显示了对病毒RNA的灵敏和定量检测，这证实了57.6％的样品中的亚基因组RNA，并提供了确定样品中病毒RNA相对完整性的新方法。定量为病毒片段分数的长片段的相对丰度与病毒载量呈正相关，与疾病发作的时间呈负相关。根据实际确定的SARS-CoV-2传染性的临床理解，凭经验确定的存在明显片段化的RNA的得分临界值能够确定100％患病8天后收集的样本，其潜在感染力较差。在基于NGS或RT-PCR的分析中，除了现有的短靶标外，对更长片段的定量分析还可以提供对感染潜力的有价值的读数，同时可以检测测试样品中的SARS-CoV-2 RNA的任何片段。