Identification of a SARS-CoV-2 virus-encoded small non-coding RNA in association with the neurological disorders in COVID-19 patients

Viral and host small RNA transcriptome analysis of SARS-CoV-1 and SARS-CoV-2-infected human cells reveals novel viral short RNAs

“…Important, the svRNAs we found were much more abundant than previously reported viral miRNAs such as CvmiR-5 (which was detected in serum of COVID-19 patients) [Zhao et al, 2022], CoV2-miR-O7a.1, and CoV2-miR-O7a.2. In the datasets we analyzed, these viral miRNAs were 100-1000-fold lower than svRNAs derived from the sense viral RNA strand and 10-100-fold lower than svRNAs derived from the antisense strand.…”

“…These results were confirmed by Singh et al, who detected CoV2-miR-O7a.1 and its isoform CoV2-miR-O7a.2 in infected Caco-2 and A549-ACE2 cells [Singh et al, 2022]. Finally, CvmiR-5 was identified as a viral miRNA encoded in ORF1a [Zhao et al, 2022]. In the SRR11550027 and SRR11550028 datasets (small RNAseq of cells 24h post-infection) only a small number of these viral miRNA sequences were found.…”

“…Generation of small RNA species from viral RNA genomes has been shown for multiple pathogens [Perez et al, 2010, Parameswaran et al, 2010] including coronaviruses [Morales et al, 2017]. However, previous studies investigating small RNA transcriptomes from SARS-CoV-1 and SARS-CoV-2 infected cells utilized ligation-based library preparation protocols for deep sequencing that captured predominantly 5’-Phosporylated/3’-OH RNA molecules such as microRNA [Pawlica et al, 2021; Singh et al, 2022; Zhao et al, 2022]. In contrast, one recent publication used a ligation-independent technique [Wyler et al, 2021] but limited analysis to the Argonaute-associated small RNAs including miRNA and vault RNA.…”

In silico analysis of genomic landscape of SARS-CoV-2 and its variant of concerns (Delta and Omicron) reveals changes in the coding potential of miRNAs and their target genes

“…Moreover, due to a myriad of post-COVID complications that are affecting multiple organs, the disease is now considered a systemic illness and results in increased morbidity ( Chippa et al, 2022 ). The evidence of SARS-CoV-2 encoded miRNAs in virus pathogenesis and disease etiology has been deciphered by many recent works ( Li, 2022 , Merino, 2021 , Zhao, 2022 , Zhu, 2021 ). However, due to considerable mutations in the SARS-CoV-2 genome, the miRNAs coding potential may be altered and thus may affect the pathophysiology.…”

MicroRNA Networks in Cognition and Dementia

“…Using this transcriptome profile, identifying the miRNA targets of differentially expressed mRNAs could uncover novel miRNA–mRNA pathways activated in response to viral infection in the central nervous system. Indeed, a recent study found that the SARS-CoV-2 virus encodes a miRNA, CvmiR-5-5p [ 89 ]. Moreover, bioinformatics analysis of the CvmiR-5-5p sequence suggests that it targets genes involved in neurogenesis, neuron development, and neuron differentiation.…”