Variant-Specific tRNA-Derived Fragments Induced By Severe Acute Respiratory Syndrome Coronavirus 2: Implications for Disease Outcome Differentiation

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a critical global health challenge, with many molecular mechanisms of pathogenesis remaining unclear. Among small noncoding RNAs, tRNA-derived RNA fragments (tRFs) have gained attention for their roles in viral infections. We previously reported significant alterations in tRFs originating from the 5′-end of tRNAs (tRF5s) in nasopharyngeal swab (NPS) specimens from patients infected with the SARS-CoV-2 alpha variant. Building upon this work, we collected 209 NPS specimens between late 2021 and February 2023. This cohort of specimens includes patients with delta or omicron variants (BA.1, BA.5, XBB.1.5) and negative controls. We investigated the expression of five tRF5s (tRF5-GlnCTG, tRF5-CysGCA, tRF5-ValCAC, tRF5-GlyCCC2, and tRF5-GlyGCC) in this cohort and observed distinct induction patterns across the different viral variants. tRF5-ValCAC, which we previously reported was induced by the alpha variant, was absent among later variants. tRF5-GlnCTG was consistently elevated by multiple variants (alpha, delta, and BA.1), while the induction diminished in BA.5 and XBB.1.5. tRF5-GlyCCC2 induction had not been observed until the BA.1 wave; its induction initially occurred in the pediatric population with BA.1 or BA.5, and later within both pediatric and adult populations with XBB.1.5. Subsequently, cytokines/chemokines within these NPS specimens were measured via Bio-plex. We found several tRF5 levels correlated with viral gene expression. Functional studies suggested that these tRF5s regulate the replication of their corresponding SARS-CoV-2 variants. In summary, our findings offer insights into their functional roles in viral replication and their potential as biomarkers.