Host transcriptional responses in nasal swabs identifies potential SARS-CoV-2 infection in PCR negative patients
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 ne...
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Veröffentlicht in: | iScience 2022-10 |
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Format: | Artikel |
Sprache: | eng |
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Zusammenfassung: | 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 ontology analysis reveals FN samples had a high overlap with high viral load samples. Deconvolution of RNA-seq data show similar cell content across viral loads. Hence, transcriptome analysis of nasal swabs provides an additional level of identifying SARS-CoV-2 infection. |
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ISSN: | 2589-0042 |
DOI: | 10.1016/j.isci.2022.105310 |