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Research Article
Joshua Stuart
University of California, Santa Cruz
Corresponding Author
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This work is licensed under a CC BY 4.0 License. Read Full License
The SARS-CoV-2 pandemic has challenged humankind’s ability to quickly determine the cascade of health effects caused by a novel infection. Even with the unprecedented speed at which vaccines were developed and introduced into society, identifying therapeutic interventions and drug targets for patients infected with the virus remains important as new strains of the virus may evolve, or future coronaviruses may emerge, that are resistant to current vaccines. The application of transcriptomic RNA sequencing of infected samples may shed new light on the pathways involved in viral mechanisms and host responses. We describe the application of “dual RNA-seq” analysis to consider both the host and pathogen transcriptomes simultaneously, to investigate for the first time the co-regulation of human and SARS-CoV-2 genes. Together with differential expression analysis, we describe the tissue specificity of SARS-CoV-2 expression, an inferred lipopolysaccharide response, and co-regulation of CXCL’s, SPRR’s, S100’s with SARS-CoV-2 expression. Lipopolysaccharide response pathways in particular offer promise for future therapeutic research and the prospect of subgrouping patients based on chemokine expression that may help explain the vastly different reactions patients have to infection. Taken together these findings illuminate previously unappreciated SARS-CoV-2 expression signatures, identify new therapeutic considerations, and contribute a pipeline for studying multi-transcriptome systems.
Keywords
SARS-CoV-2, COVID-19, CXCL’s, SPRR’s, S100’s, Lipopolysaccharide response
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No competing interests reported.
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On 02 Apr, 2021
Reviewer #3 agreed
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Reviewer #11 agreed
On 02 Apr, 2021
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On 02 Apr, 2021
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This preprint is under consideration at Scientific Reports. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research Article
Joshua Stuart
University of California, Santa Cruz
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Under Review
Version 1
Posted 19 Mar, 2021
No community comments so far
Review #1 received
Received 13 Apr, 2021
Review #3 received
Received 13 Apr, 2021
Review #2 received
Received 13 Apr, 2021
Reviewer #8 agreed
On 02 Apr, 2021
Reviewer #1 agreed
On 02 Apr, 2021
Reviewer #4 agreed
On 02 Apr, 2021
Reviewer #2 agreed
On 02 Apr, 2021
Reviewer #9 agreed
On 02 Apr, 2021
Reviewer #3 agreed
On 02 Apr, 2021
Reviewer #11 agreed
On 02 Apr, 2021
Reviewer #10 agreed
On 02 Apr, 2021
Reviewers invited
Invitations sent on 30 Mar, 2021
Editor assigned
On 30 Mar, 2021
Editor invited
On 10 Mar, 2021
Submission checks complete
On 10 Mar, 2021
First submitted
On 04 Mar, 2021
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
The SARS-CoV-2 pandemic has challenged humankind’s ability to quickly determine the cascade of health effects caused by a novel infection. Even with the unprecedented speed at which vaccines were developed and introduced into society, identifying therapeutic interventions and drug targets for patients infected with the virus remains important as new strains of the virus may evolve, or future coronaviruses may emerge, that are resistant to current vaccines. The application of transcriptomic RNA sequencing of infected samples may shed new light on the pathways involved in viral mechanisms and host responses. We describe the application of “dual RNA-seq” analysis to consider both the host and pathogen transcriptomes simultaneously, to investigate for the first time the co-regulation of human and SARS-CoV-2 genes. Together with differential expression analysis, we describe the tissue specificity of SARS-CoV-2 expression, an inferred lipopolysaccharide response, and co-regulation of CXCL’s, SPRR’s, S100’s with SARS-CoV-2 expression. Lipopolysaccharide response pathways in particular offer promise for future therapeutic research and the prospect of subgrouping patients based on chemokine expression that may help explain the vastly different reactions patients have to infection. Taken together these findings illuminate previously unappreciated SARS-CoV-2 expression signatures, identify new therapeutic considerations, and contribute a pipeline for studying multi-transcriptome systems.
Figure 1
Figure 2
Figure 3
Figure 4
This preprint is available for download as a PDF.
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