{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,28]],"date-time":"2026-01-28T20:53:20Z","timestamp":1769633600451,"version":"3.49.0"},"reference-count":89,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2026,1,28]],"date-time":"2026-01-28T00:00:00Z","timestamp":1769558400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Federal Medical-Biological Agency (FMBA) of Russia"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Transposable elements (TEs) are key regulators of immunity in both health and disease. It has been proven that the activity and transcriptional expression levels of TEs increase during viral infections, correlating with the antiviral response. This study investigates non-LTR TE (LINE, SINE, and SVA) transcriptomic signatures in human PBMCs during infections caused by influenza A virus, HIV, and SARS-CoV-2 (Delta\/Omicron variants) using single-cell RNA sequencing (scRNA-seq) data from 98 patients. In the HIV and SARS-CoV-2 patient cohorts, unique cell-specific TE expression patterns were identified that allow for the differentiation of disease severity, prediction of disease progression, and assessment of the therapy\u2019s efficacy. The expression of LINE elements was found to be more dependent on the nature and course of the disease than that of SINE elements. The most variable TE expression profile was observed in precursor cytotoxic T-lymphocytes (T CD8+ Naive cells), which depended on the virus type and the severity of the viral disease. For this cell type, a bioinformatic analysis of the co-expression regulation of TE transcriptional networks and transcription factors during viral infections was performed. This analysis identified key players among those most involved in virus-specific responses, which could serve as diagnostic biomarkers or therapeutic targets for treating diseases caused by influenza A virus, HIV, and SARS-CoV-2. This work confirms the involvement of non-LTR TEs in mediating antiviral responses. Further research into the mechanisms of TE participation in antiviral defense is necessary to recommend them as potential biomarkers for the diagnosis, monitoring, and assessment of antiviral therapy, or as therapeutic targets for viral infections of various origins.<\/jats:p>","DOI":"10.3390\/ijms27031286","type":"journal-article","created":{"date-parts":[[2026,1,28]],"date-time":"2026-01-28T08:48:04Z","timestamp":1769590084000},"page":"1286","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Single-Cell RNA-Seq Profiling of Transposable Element Expression in Human Peripheral Blood Cells During Viral Infections"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5976-4422","authenticated-orcid":false,"given":"Oleg D.","family":"Fateev","sequence":"first","affiliation":[{"name":"Federal State Budgetary Institution \u201cCenter for Strategic Planning and Management of Biomedical Health Risks\u201d of the Federal Medical-Biological Agency (FSBI \u201cCSP\u201d of FMBA of Russia), Pogodinskaya str. 10, bld. 1, Moscow 119435, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-0380-8144","authenticated-orcid":false,"given":"Vasily E.","family":"Akimov","sequence":"additional","affiliation":[{"name":"Federal State Budgetary Institution \u201cCenter for Strategic Planning and Management of Biomedical Health Risks\u201d of the Federal Medical-Biological Agency (FSBI \u201cCSP\u201d of FMBA of Russia), Pogodinskaya str. 10, bld. 1, Moscow 119435, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0257-6439","authenticated-orcid":false,"given":"Olga V.","family":"Glushkova","sequence":"additional","affiliation":[{"name":"Federal State Budgetary Institution \u201cCenter for Strategic Planning and Management of Biomedical Health Risks\u201d of the Federal Medical-Biological Agency (FSBI \u201cCSP\u201d of FMBA of Russia), Pogodinskaya str. 10, bld. 1, Moscow 119435, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aleksandr V.","family":"Bolbat","sequence":"additional","affiliation":[{"name":"Federal State Budgetary Institution \u201cCenter for Strategic Planning and Management of Biomedical Health Risks\u201d of the Federal Medical-Biological Agency (FSBI \u201cCSP\u201d of FMBA of Russia), Pogodinskaya str. 10, bld. 1, Moscow 119435, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Azat V.","family":"Abdullatypov","sequence":"additional","affiliation":[{"name":"Federal State Budgetary Institution \u201cCenter for Strategic Planning and Management of Biomedical Health Risks\u201d of the Federal Medical-Biological Agency (FSBI \u201cCSP\u201d of FMBA of Russia), Pogodinskaya str. 10, bld. 1, Moscow 119435, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olga A.","family":"Antonova","sequence":"additional","affiliation":[{"name":"Federal State Budgetary Institution \u201cCenter for Strategic Planning and Management of Biomedical Health Risks\u201d of the Federal Medical-Biological Agency (FSBI \u201cCSP\u201d of FMBA of Russia), Pogodinskaya str. 10, bld. 1, Moscow 119435, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vladimir V.","family":"Shiryagin","sequence":"additional","affiliation":[{"name":"Federal State Budgetary Institution \u201cCenter for Strategic Planning and Management of Biomedical Health Risks\u201d of the Federal Medical-Biological Agency (FSBI \u201cCSP\u201d of FMBA of Russia), Pogodinskaya str. 10, bld. 1, Moscow 119435, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0647-5421","authenticated-orcid":false,"given":"Nikolai A.","family":"Bugaev-Makarovsky","sequence":"additional","affiliation":[{"name":"Federal State Budgetary Institution \u201cCenter for Strategic Planning and Management of Biomedical Health Risks\u201d of the Federal Medical-Biological Agency (FSBI \u201cCSP\u201d of FMBA of Russia), Pogodinskaya str. 10, bld. 1, Moscow 119435, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9199-6258","authenticated-orcid":false,"given":"Vladimir S.","family":"Yudin","sequence":"additional","affiliation":[{"name":"Federal State Budgetary Institution \u201cCenter for Strategic Planning and Management of Biomedical Health Risks\u201d of the Federal Medical-Biological Agency (FSBI \u201cCSP\u201d of FMBA of Russia), Pogodinskaya str. 10, bld. 1, Moscow 119435, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anton A.","family":"Keskinov","sequence":"additional","affiliation":[{"name":"Federal State Budgetary Institution \u201cCenter for Strategic Planning and Management of Biomedical Health Risks\u201d of the Federal Medical-Biological Agency 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