In silico investigation of putative G-quadruplex-forming regions in spike sequence of SARS-CoV-۲ Delta variant

Backgrounds: The ongoing COVID-۱۹ outbreak is now becoming an emerging threat to humanhealth worldwide. SARS-CoV-۲ infection begins through the interaction between spike (S)proteins of virus with the host cellular receptor. Up to now, ۱۱ variants of SARS-CoV-۲ havebeen recognized, and these variants are anticipated to develop while new variants appear.Particular variant of SARS-CoV-۲ is categorized via a class of the prevalent mutations in itsgenome, and the major parts of the described mutations have been reported in Spike protein.Recent studies of RNA viruses have revealed that G-quadruplex structures contribute in severalimportant cellular processes such as recognition of a genome, recombination and HIV-۱ RNAdimerization and packaging. In addition, they could play important role in HIV-۱ transcriptionalsilencing. Furthermore, it has been revealed that G-quadruplex structures act as regulator in thetranslational and immune evasion of Epstein Barr Virus (EBV). Moreover, they might impact thehuman papillomaviruses (HPVs) replication and transcription. G-rich regions in the Zika viralgenome were also recognized to form G-quadruplex structure. The aim of our study was toinvestigate if the spike gene of currently dominant SARS-CoV-۲ Delta variant could form Gquadruplexstructures.Materials and Methods: The high quality and high coverage sequences of Delta (n = ۱۲۷۶) (asof Aguste, ۲۰۲۱) was downloaded from GISAID. The human SARS-CoV-۲ spike proteinsequence from Wuhan-Hu-۱, China (NCBI accession code: YP_۰۰۹۷۲۴۳۹۰.۱)۱ was used asreference sequence to examine the putative G-quadruplex forming sequences. SARS-CoV-۲spike genome of delta variant was analyzed using QGRS Mapper online software(http://bioinformatics.ramapo.edu/QGRS/analyze.php).Results: We found ten G-quadruplex forming sequences with proper G-score. Only one of theG-cores in Delta variants was higher than Wuhan-Hu-۱ reference sequence.Conclusion: Taken together, our analysis of G-quadruplex- forming sequences in SARS-CoV-۲delta variant might provide insights into the design of anti-viral treatment by targeting the Gquadruplexstructures.

کلیدواژه ها:

SARS-COV-۲ ، Delta variant ، G-quadruplex Structures ، QGRS mapper