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This work was supported by the Agencia Estatal de Investigacion (AEI) (co-supported by FEDER - EU) (Grant PID2022-1393930B-I00 to GG), the CSIC PTI Salud Global (grant SGL2021-03-040 to G.R.) through the NextGenerationEU Fund (regulation 2020/2094) and the Regional Government of Valencia (grant GVA-COVID19/2021/036 to G.R.). J.C.S. and A.G.H.A. are recipients of a pre-doctoral contract from the Generalitat Valenciana (CIACIF-2021-279 and ACIF-2021-202). The central tRNA structure shown in Fig. 4 is adapted from the original figure "The tRNA cloverleaf general" by Yikrazuul under a Creative Commons license (C.C. BY 3.0).

Analysis of institutional authors

Cebria-Mendoza, MariaAuthor

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February 1, 2025
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SARS-CoV-2 remodels the landscape of small non-coding RNAs with infection time and symptom severity

Publicated to:Npj Syst Biol Appl. 10 (1): 41- - 2024-04-17 10(1), DOI: 10.1038/s41540-024-00367-z

Authors: Corell-Sierra, Julia; Marquez-Molins, Joan; Marques, Maria-Carmen; Hernandez-Azurdia, Andrea Gabriela; Montagud-Martinez, Roser; Cebria-Mendoza, Maria; Cuevas, Jose M; Albert, Eliseo; Navarro, David; Rodrigo, Guillermo; Gomez, Gustavo

Affiliations

Clin Univ Hosp, INCLIVA Biomed Res Inst, Microbiol Serv, Valencia 46010, Spain - Author
Linnean Ctr Plant Biol, Uppsala, Sweden - Author
Swedish Univ Agr Sci, Uppsala Bioctr, Dept Plant Biol, Uppsala, Sweden - Author
Univ Valencia, CSIC, Inst Integrat Syst Biol I2SysBio, Paterna 46980, Spain - Author
Univ Valencia, Sch Med, Dept Microbiol, Valencia 46010, Spain - Author
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Abstract

The COVID-19 pandemic caused by the coronavirus SARS-CoV-2 has significantly impacted global health, stressing the necessity of basic understanding of the host response to this viral infection. In this study, we investigated how SARS-CoV-2 remodels the landscape of small non-coding RNAs (sncRNA) from a large collection of nasopharyngeal swab samples taken at various time points from patients with distinct symptom severity. High-throughput RNA sequencing analysis revealed a global alteration of the sncRNA landscape, with abundance peaks related to species of 21-23 and 32-33 nucleotides. Host-derived sncRNAs, including microRNAs (miRNAs), transfer RNA-derived small RNAs (tsRNAs), and small nucleolar RNA-derived small RNAs (sdRNAs) exhibited significant differential expression in infected patients compared to controls. Importantly, miRNA expression was predominantly down-regulated in response to SARS-CoV-2 infection, especially in patients with severe symptoms. Furthermore, we identified specific tsRNAs derived from Glu- and Gly-tRNAs as major altered elements upon infection, with 5' tRNA halves being the most abundant species and suggesting their potential as biomarkers for viral presence and disease severity prediction. Additionally, down-regulation of C/D-box sdRNAs and altered expression of tinyRNAs (tyRNAs) were observed in infected patients. These findings provide valuable insights into the host sncRNA response to SARS-CoV-2 infection and may contribute to the development of further diagnostic and therapeutic strategies in the clinic.

Keywords

Covid-19DatabaseGeneHumansIdentificationMicrornasPandemicsResourceRna, small untranslatedSars-cov-2

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Npj Syst Biol Appl due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2024 there are still no calculated indicators, but in 2023, it was in position 12/66, thus managing to position itself as a Q1 (Primer Cuartil), in the category Mathematical & Computational Biology.

Independientemente del impacto esperado determinado por el canal de difusión, es importante destacar el impacto real observado de la propia aportación.

Según las diferentes agencias de indexación, el número de citas acumuladas por esta publicación hasta la fecha 2025-07-09:

  • WoS: 2
  • Europe PMC: 2

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-07-09:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 7.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 9 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 10.35.
  • The number of mentions on the social network X (formerly Twitter): 24 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.

Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: Sweden.