Changes of Small Non-coding RNAs by Severe Acute Respiratory Syndrome Coronavirus 2 Infection
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Abstract
The ongoing pandemic of coronavirus disease 2019 (COVID-19), which results from the rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a significant global public health threat, with molecular mechanisms underlying its pathogenesis largely unknown. In the context of viral infections, small non-coding RNAs (sncRNAs) are known to play important roles in regulating the host responses, viral replication, and host-virus interaction. Compared with other subfamilies of sncRNAs, including microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), tRNA-derived RNA fragments (tRFs) are relatively new and emerge as a significant regulator of host-virus interactions. Using T4 PNK‐RNA‐seq, a modified next-generation sequencing (NGS), we found that sncRNA profiles in human nasopharyngeal swabs (NPS) samples are significantly impacted by SARS-CoV-2. Among impacted sncRNAs, tRFs are the most significantly affected and most of them are derived from the 5′-end of tRNAs (tRF5). Such a change was also observed in SARS-CoV-2-infected airway epithelial cells. In addition to host-derived ncRNAs, we also identified several small virus-derived ncRNAs (svRNAs), among which a svRNA derived from CoV2 genomic site 346 to 382 (sv-CoV2-346) has the highest expression. The induction of both tRFs and sv-CoV2-346 has not been reported previously, as the lack of the 3′-OH ends of these sncRNAs prevents them to be detected by routine NGS. In summary, our studies demonstrated the involvement of tRFs in COVID-19 and revealed new CoV2 svRNAs.
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SciScore for 10.1101/2021.12.16.472982: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: The protocol was approved by institutional review boards (IRB) of UTMB at Galveston, under the IRB protocol # 02-089 and 03-385. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Viral stocks were prepared by propagation in Vero E6 cells. Vero E6suggested: RRID:CVCL_XD71)Viral infection: To infect A549-ACE2 cells in monolayer culture, the cells were seeded into the 24-well plate 24 h prior to the infection to allow the cells to reach 80∼90% confluence in the following day. A549-ACE2suggested: NoneSoftware and Algorithms Sente… SciScore for 10.1101/2021.12.16.472982: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: The protocol was approved by institutional review boards (IRB) of UTMB at Galveston, under the IRB protocol # 02-089 and 03-385. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Viral stocks were prepared by propagation in Vero E6 cells. Vero E6suggested: RRID:CVCL_XD71)Viral infection: To infect A549-ACE2 cells in monolayer culture, the cells were seeded into the 24-well plate 24 h prior to the infection to allow the cells to reach 80∼90% confluence in the following day. A549-ACE2suggested: NoneSoftware and Algorithms Sentences Resources NPS samples were transported to the Molecular Pathology laboratory, directed by Dr. Jianli Dong, in universal viral transport media, and subjected to SARS-CoV-2 test using Abbott m2000 SARS-CoV-2 RT-PCR assay. Abbottsuggested: (Abbott, RRID:SCR_010477)Our in-house small RNA database includes 1) these tRFs, 2) miR/snoR sequences downloaded from the UCSC genome browser, and 3) piRNA sequences downloaded from piRBase (http://www.regulatoryrna.org/database/piRNA/). UCSC genome browsersuggested: (UCSC Genome Browser, RRID:SCR_005780)The cleaned input reads were mapped to our in-house small RNA database using bowtie2 (v2.4.1) allowing two mismatches (option m -1). bowtie2suggested: (Bowtie 2, RRID:SCR_016368)Raw read counts were normalized with the DEseq2 median of ratios method. DEseq2suggested: (DESeq2, RRID:SCR_015687)Statistical analysis: The experimental results were analyzed using Graphpad Prism 5 software. Graphpad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:We are aware that our study has some limitations, such as T4 PNK-RNA-seq cannot restore and catch all the type ncRNAs. Although the sample size of patients is limited, our methods enabled us to identify tRF signatures of SARS-CoV-2 infection. Our methods also enabled us to find several new SARS-CoV-2-encoded sncRNAs, whose functions and biogenesis will be studied in the near future.
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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