The Open COVID Journal

: Background: The SARS-CoV-2 emergence in 2019 has caused health, safety, and socioeconomic issues worldwide. Current testing prioritizes viral RNA detection, requiring specialized techniques, training, and time periods, resulting in significant testing limitations. Viral infection can cause changes in host cell gene expression, which vary from virus to virus. Recent research has suggested that SARS-CoV-2-induced gene expression modulations in infected human cells may be differentiated from expressions elicited by other acute respiratory illnesses. Data in this study highlight specific genes that are differentially expressed during SARS-CoV-2 infection. This novel application of individual sample analysis, in connection with global databases, provides robust data for genes that are specifically modulated during SARS-CoV-2 infection. This expression profile would be valuable for SARS-CoV-2 testing, prevention, treatment, and basic virology research. Methods: Previously collected COVID-19 surveillance-testing samples from cadets at the United States Air Force Academy were used to quantify the expression of 19 target genes using direct primer-mediated qRTPCR. Additionally, samples were analyzed with RNA-seq to assess the different transcriptomes between uninfected and SARS-CoV-2-infected samples. Results were compared with national databases to confirm the agreement between findings. Results: A total of 19 genes were identified to be altered

Studies included in review (n = 18) Reports of included studies (n = 2) Selection process 8 Specify the methods used to decide whether a study met the inclusion criteria of the review, including how many reviewers screened each record and each report retrieved, whether they worked independently, and if applicable, details of automation tools used in the process.

LINE 156-172
Data collection process 9 Specify the methods used to collect data from reports, including how many reviewers collected data from each report, whether they worked independently, any processes for obtaining or confirming data from study investigators, and if applicable, details of automation tools used in the process.

LINE 156-172
Data items 10a List and define all outcomes for which data were sought. Specify whether all results that were compatible with each outcome domain in each study were sought (e.g. for all measures, time points, analyses), and if not, the methods used to decide which results to collect.
LINE 161-172 10b List and define all other variables for which data were sought (e.g. participant and intervention characteristics, funding sources). Describe any assumptions made about any missing or unclear information.

LINE 150-172
Study risk of bias assessment 11 Specify the methods used to assess risk of bias in the included studies, including details of the tool(s) used, how many reviewers assessed each study and whether they worked independently, and if applicable, details of automation tools used in the process.

LINE 156-172
Effect measures 12 Specify for each outcome the effect measure(s) (e.g. risk ratio, mean difference) used in the synthesis or presentation of results.

N/A
Synthesis methods 13a Describe the processes used to decide which studies were eligible for each synthesis (e.g. tabulating the study intervention characteristics and comparing against the planned groups for each synthesis (item #5)).

LINE 150-171
13b Describe any methods required to prepare the data for presentation or synthesis, such as handling of missing summary statistics, or data conversions.
N/A 13c Describe any methods used to tabulate or visually display results of individual studies and syntheses.
N/A 13d Describe any methods used to synthesize results and provide a rationale for the choice(s). If metaanalysis was performed, describe the model(s), method(s) to identify the presence and extent of statistical heterogeneity, and software package(s) used.

N/A
13e Describe any methods used to explore possible causes of heterogeneity among study results (e.g. subgroup analysis, meta-regression).

NA 13f
Describe any sensitivity analyses conducted to assess robustness of the synthesized results. N/A

Reporting bias assessment 14
Describe any methods used to assess risk of bias due to missing results in a synthesis (arising from reporting biases).

N/A
Certainty assessment 15 Describe any methods used to assess certainty (or confidence) in the body of evidence for an outcome.

Study selection 16a
Describe the results of the search and selection process, from the number of records identified in the search to the number of studies included in the review, ideally using a flow diagram.

LINE 174-184
16b Cite studies that might appear to meet the inclusion criteria, but which were excluded, and explain why they were excluded.