In the current analysis, we detected mutations in miR-1307 and miR-8066 only. Additionally, a mutation on miR-129-2-3p was found on only the Icelandic SARS-CoV-2 genome (Table 3). Moreover, miR-129-2-3p is one of the selected miR (Table 1) found only in the Wuhan and Italy genomes, although in less than 5% of the genomes sequenced. These three miRs are potentially involved in mucin type O-glycan biosynthesis, TGF-β signalling pathway, amphetamine addiction, cytokine-cytokine receptor interaction and nicotinate-nicotinamide metabolism. All of these pathways are associated with host responses against SARS-CoV-2, and virus pathogenesis in host cells. The mutations on selected miRs may affect their presence in different strains and may alter their potential host-mediated responses. The remainder of the miRs, presented in Table 3, was found to be conserved. Therefore, our data suggest that either these sequences are crucial for SARS-CoV-2, or their locations are important for the virus to survive. Using the GISAID database, we analysed a sample of viral genomic sequences from several geographical areas for mutations in the potential miR sequences (n = 28–133). The majority of the miRs studied showed very few base changes in these sequences, with <1% overall. MiRs miR-1468-5p and, particularly, miR-1307-3p showed an increased percentage of mutations. All the mutations analysed reduced the microRNA base similarity and decreased the score value to below significance (<70).