{"doi":"10.3389/fmolb.2022.821137","title":"Changes of Small Non-coding RNAs by Severe Acute Respiratory Syndrome Coronavirus 2 Infection","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.","journal":"Frontiers in Molecular Biosciences","year":2022,"id":249318,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":28,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9585,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":326644,"name":"Eun‐Jin Choi","orcid":"0000-0001-9690-7501","position":1,"is_corresponding":false},{"id":396905,"name":"Binbin Wang","orcid":"0000-0002-1597-5930","position":2,"is_corresponding":false},{"id":44752,"name":"Ke Zhang","orcid":"0000-0002-6153-6912","position":3,"is_corresponding":false},{"id":398464,"name":"Awadalkareem Adam","orcid":null,"position":4,"is_corresponding":false},{"id":587566,"name":"Gengming Huang","orcid":null,"position":5,"is_corresponding":false},{"id":332765,"name":"Leo Tunkle","orcid":null,"position":6,"is_corresponding":false},{"id":889017,"name":"Philip Huang","orcid":"0000-0002-0194-3882","position":7,"is_corresponding":false},{"id":889738,"name":"Rohit Goru","orcid":null,"position":8,"is_corresponding":false},{"id":889506,"name":"Isabella Imirowicz","orcid":"0009-0007-6100-2594","position":9,"is_corresponding":false},{"id":699673,"name":"Leanne E. Henry","orcid":"0009-0003-7554-079X","position":10,"is_corresponding":false},{"id":326648,"name":"Inhan Lee","orcid":"0000-0001-5840-3900","position":11,"is_corresponding":false},{"id":655605,"name":"Jianli Dong","orcid":"0000-0001-8929-6132","position":12,"is_corresponding":false},{"id":314672,"name":"Tian Wang","orcid":"0000-0001-8111-2773","position":13,"is_corresponding":false},{"id":326649,"name":"Xiaoyong Bao","orcid":"0000-0002-6884-2584","position":14,"is_corresponding":false},{"id":326646,"name":"Wenzhe Wu","orcid":"0000-0002-8030-3698","position":0,"is_corresponding":true}],"reference_count":57,"raw_metadata":null,"created_at":"2026-07-19T00:24:19.356023Z","pmid":"35281271","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}