Saravia-Butler Amanda M, Schisler Jonathan C, Taylor Deanne, Beheshti Afshin, Butler Dan, Meydan Cem, Foox Jonathon, Hernandez Kyle, Mozsary Chris, Mason Christopher E, Meller Robert
KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA.
NASA Ames Research Center, Moffett Field, CA 94035, USA.
iScience. 2022 Nov 18;25(11):105310. doi: 10.1016/j.isci.2022.105310. Epub 2022 Oct 7.
We analyzed RNA sequencing data from nasal swabs used for SARS-CoV-2 testing. 13% of 317 PCR-negative samples contained over 100 reads aligned to multiple regions of the SARS-CoV-2 genome. Differential gene expression analysis compares the host gene expression in potential false-negative (FN: PCR negative, sequencing positive) samples to subjects with multiple SARS-CoV-2 viral loads. The host transcriptional response in FN samples was distinct from true negative samples (PCR & sequencing negative) and similar to low viral load samples. Gene Ontology analysis shows viral load-dependent changes in gene expression are functionally distinct; 23 common pathways include responses to viral infections and associated immune responses. GO analysis reveals FN samples had a high overlap with high viral load samples. Deconvolution of RNA-seq data shows similar cell content across viral loads. Hence, transcriptome analysis of nasal swabs provides an additional level of identifying SARS-CoV-2 infection.
我们分析了用于新冠病毒检测的鼻拭子的RNA测序数据。在317份PCR检测呈阴性的样本中，13%含有超过100条与新冠病毒基因组多个区域比对上的 reads。差异基因表达分析将潜在假阴性（FN：PCR阴性，测序阳性）样本中的宿主基因表达与具有多种新冠病毒载量的受试者进行比较。FN样本中的宿主转录反应与真阴性样本（PCR和测序均为阴性）不同，与低病毒载量样本相似。基因本体分析表明，基因表达中病毒载量依赖性变化在功能上是不同的；23条常见途径包括对病毒感染和相关免疫反应的应答。GO分析显示，FN样本与高病毒载量样本有高度重叠。RNA-seq数据的反卷积显示不同病毒载量下细胞含量相似。因此，鼻拭子的转录组分析为识别新冠病毒感染提供了额外的层面。
