Identification and host response interaction study of SARS-CoV-2 encoded miRNA-like sequences: an in silico approach

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

“…Further validation was done by calculating the MFEs of secondary structures of pre-miRNAs. All the real pre-miRNAs were found to be above the threshold MFE ≤ -20 kcal/mol (shown in Table 1 ) as discussed in previous literature ( Noor, 2021 , Roy, 2021 ). All the predicted fold secondary structures of Reference, Delta, and Omicron real pre-miRNAs can be found in supplementary file 4 .…”

“…Over the years, various efforts were put on by the research community to decipher the role of viral miRNAs in controlling the host gene expressions ( Baruah and Bose, 2019 , Islam et al, 2019 , Islam and Khan, 2021 , Noor, 2021 , Noor, 2022 , Ospina-Bedoya et al, 2014 , Saini, 2018 , Shi, 2014 , Teng, 2015 ). Several studies have been conducted during the last two years for tracing the miRNA's coding potential and their effects on the target genes of humans ( Aydemir et al, 2021 , Khan et al, 2020 , Rahaman et al, 2021 , Roy, 2021 , Saini et al, 2020 , Sarma et al, 2020 , Saçar Demirci and Adan, 2020 ). But owing to considerable mutations or variations in the SARS-COV-2 genome the coding potential of miRNAs could be changed and may affect new targets.…”

miRNA expression in COVID-19

“… ( Sabetian et al, 2021 ) miR-204-5p TMPRSS2 SARS-CoV-miR-029, miR-055, miR-084, miR-027, miR-005, miR-077, miR-060, miR-007 In silico Human genes Expression of human genes mediated by SARS CoV 2 miRNAs affects adaptive hypoxia, neuronal invasion, hormonal imbalances, and induction of cancer pathways. ( Roy et al, 2021 ) miR-146a, miR-155 Bioinformatics Patients with periodontitis and type2 diabetes ACE2 Increased miR 146a, miR 155 due to diabetes and periodontitis in the oral cavity upregulates angiotensin converting enzyme 2 expression and modulates the host antiviral response. ( Roganović, 2021b ) hsa-miR-4778-5p and hsa-miR-4531hsa-miR-6844 hsa-miR627-5p hsa-miR-3674 Bioinformatics ORF1ab miR-6844 is associated with the ORF1ab gene of SARS-CoV-2.…”

PredMHC: An Effective Predictor of Major Histocompatibility Complex Using Mixed Features

“…By using pyrosequencing with high-resolution and Sanger sequencing technology, Shiina et al (2015) genotyped 127 unrelated animals and identified 112 different alleles. Moreover, the International Society for Animal Genetics (ISAG) standardized the nomenclature and established the IPD-MHC database which is used to scientifically manage the MHC allele sequences and genes from nonhuman organisms ( Giuseppe et al, 2017 ; Maccari et al, 2018 ; Ali et al, 2021 ; Burton et al, 2021 ; Karcioglu and Bulut, 2021 ; Roy et al, 2021 ; Safaei et al, 2021 ; Wang et al, 2021 ).…”