The untranslated regions (UTRs) of messenger RNAs (mRNAs) play a crucial role in regulating translational efficiency, stability, and tissue-specific expression. The review describes various applications and challenges of UTR design in the development of gene therapy and mRNA-based therapeutics. UTRs affect critical biological functions, such as mRNA stability, modulation of protein synthesis, and attenuation of immune response. Incorporating tissue-specific microRNA (miRNA)-binding sites into 3′ UTRs might improve precise targeting of transgene expression and minimize off-target effects. Nucleotide modifications (pseudouridine, N1-methyladenosine, and N4-acetylcytidine) in mRNA and UTRs in particular, improve mRNA stability and translational efficiency. At the same time, several challenges remain, such as lack of consensus on UTRs best suited for certain biomedical applications. Current efforts are focused on integrating high-throughput screening, computational modeling, and experimental validation to refine UTR-based therapeutic strategies. The review presents current information on the design of UTRs and their role in therapeutic applications, with special focus on the possibilities and limitations of existing approaches.

Puumala orthohantavirus (PUUV) is a causative agent of haemorrhagic fever with renal syndrome, mainly transmitted through rodent excretions. Classification of PUUV has traditionally been based on the geographic locations of their discovery, but this system faces challenges due to inconsistencies between the names of lineages and their actual distribution. In this study, we propose a quantitative criterion of “10% nucleotide difference” to distinguish PUUV genotypes, resulting in a subdivision of PUUV into twenty-one distinct genotypes. The application of this criterion suggested a further division of the CE, RUS, FIN and N-SCA lineages and was consistent with the current taxonomic position of the S-SCA, LAT, DAN and ALAD lineages. In addition, analysis of reassortment and recombination events showed that PUUV undergoes these processes, but they are relatively rare. Our results emphasise the importance of considering genetic distances in the classification of PUUV and provide a robust criterion for subspecies-level taxonomy.

The taxonomic status of the H17N10 and H18N11 influenza A viruses isolated from bats remains unclear due to the absence of quantitative classification criteria at this taxonomic level. A total of 3328 representative IAV genomes, encompassing all eight protein-coding segments, were analysed. Various genetic distance-based metrics were assessed at the pairwise level, including intra- and intergroup nucleotide distances, dN/dS ratios, and transition/transversion ratios, to facilitate the differentiation of the Alphainfluenzavirus genus into distinct taxa. Pairwise distances for seven of the eight segments (PB2, PB1, PA, NP, M, NA, NS) consistently differentiated the H17–H18 group from H1–H16. Across segments, intergroup nucleotide divergence was consistently above a lower bound of ~25%, with segment-specific values extending to higher levels (up to ~40% in PB2 and PA), while intragroup divergence remained substantially lower. The HA segment did not conform to this pattern, which is consistent with the hypothesis of ancient reassortment. The distribution of pairwise dN/dS values for the PB2, PB1, PA, and NP segments is evidently bimodal. Intergroup comparisons were consistently higher across all segments, whereas intragroup values remained lower. A similar lower boundary of approximately 0.12 was observed across segments, while the upper range of intergroup values varied by gene. Overall, the results support a consistent gene-specific separation pattern. Previously demonstrated absence of reassortment compatibility between bat viruses (H17–H18) and canonical influenza A (H1–H16) viruses indicates that these lineages have evolved independently over an extended period. These consistent genomic patterns provide support for the hypothesis that H17N10 and H18N11 viruses may represent a separate species within the genus Alphainfluenzavirus.

According to classic ideas, new genes emerge from old genes by duplication or horizontal transfer. Analyses of a large number of genomes in recent decades have shown that some genes have no visible homologs and have presumably emerged de novo from previously noncoding sequences. The review considers possible mechanisms of de novo gene formation, the properties of protein sequences encoded by such genes, and features of their expression and selection. The problem of identification of de novo arising gene is discussed separately.