G-quadruplexes in H1N1 influenza genomes

Abstract

Background Influenza viruses are dangerous pathogens. Seventy-Seven genomes of recently emerged genotype 4 reassortant Eurasian avian-like H1N1 virus (G4-EA-H1N1) are currently available. We investigated the presence and variation of potential G-quadruplex forming sequences (PQS), which can serve as targets for antiviral treatment. Results PQS were identified in all 77 genomes. The total number of PQS in G4-EA-H1N1 genomes was 571. Interestingly, the number of PQS per genome in individual close relative viruses varied from 4 to 12. PQS were not randomly distributed in the 8 segments of the G4-EA-H1N1 genome, the highest frequency of PQS being found in the NP segment (1.39 per 1000 nt), which is considered a potential target for antiviral therapy. In contrast, no PQS was found in the NS segment. Analyses of variability pointed the importance of some PQS; even if genome variation of influenza virus is extreme, the PQS with the highest G4Hunter score is the most conserved in all tested genomes. G-quadruplex formation in vitro was experimentally confirmed using spectroscopic methods. Conclusions The results presented here hint several G-quadruplex-forming sequences in G4-EA-H1N1 genomes, that could provide good therapeutic targets.

Identification and Structural Aspects of G-Quadruplex-Forming Sequences from the Influenza A Virus Genome

“…We found out that 12 PQS motifs are present in the few segments of the IAV genome. It should be noted that one sequence identified in our study, 12KW, was previously found also by Brázda et al [ 20 ], while other potential quadruplex-forming sequences selected by our research groups varied. A possible explanation for this observation is that we identified PQS from influenza A virus vRNA segments using QGRS mapper and G4RNA screener, while Brázda et al utilized in this purpose G4hunter Web tool.…”

“…More recently, some papers described bioinformatics analyses of viral genomes (including human coronaviruses, [ 49 , 50 ] and influenza virus, [ 20 ]) to determine the presence of G-rich regions. In 2020, Bartas et al conducted a systematic and comprehensive analyses to study the occurrence of PQS sites and inverted repeats (IRs) loci in genomes of all known Nidovirales [ 50 ].…”

“…However, location of PQS sites before 3′ UTR, inside 5′ UTR and before mRNA suggests their important regulatory role [ 50 ]. Another study concerning G-quadruplex in H1N1 influenza genomes was performed by Brázda et al [ 20 ]. The comparison of 77 H1N1 influenza genomes provided information on G-quadruplex occurrence, localization and variance.…”

“…The comparison of 77 H1N1 influenza genomes provided information on G-quadruplex occurrence, localization and variance. The results showed that influenza genomes contain several highly conserved PQS, which can be potential therapeutic targets [ 20 ]. Interestingly, in silico analysis of PQS sites in the genome of all the known human-infecting viruses was reported by Lavezzo and co-workers [ 49 ].…”

“…G-quadruplex structures can be intramolecular meaning that one strand folds within itself to form the G-tetrads or intermolecular consisting of two or more strands [ 16 ]. Previously published studies revealed the presence of G4 structures in the genomes of RNA viruses, e.g., Zaire ebolavirus (EBOV) [ 17 ], Zika virus [ 18 ] and more recently also in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [ 19 ] as well as in the IAV [ 20 ]. Apparently, these structures seem to be highly conserved in the viral genomes, indicating their important role in the viral life cycle, for instance during replication.…”