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.
- MeSH
- chřipka lidská * MeSH
- G-kvadruplexy * MeSH
- genom virový MeSH
- genotyp MeSH
- lidé MeSH
- reassortantní viry genetika MeSH
- virus chřipky A, podtyp H1N1 * genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Group A Rotaviruses (RVA) are the leading cause of acute gastroenteritis in children and a major cause of childhood mortality in low-income countries. RVAs are mostly host-specific, but interspecies transmission and reassortment between human and animal RVAs significantly contribute to their genetic diversity. We investigated the VP7 and VP4 genotypes of RVA isolated from 225 stool specimens collected from Czech patients with gastroenteritis during 2016-2019. The most abundant genotypes were G1P[8] (42.7%), G3P[8] (11.1%), G9P[8] (9.8%), G2P[4] (4.4%), G4P[8] (1.3%), G12P[8] (1.3%), and, surprisingly, G8P[8] (9.3%). Sequence analysis of G8P[8] strains revealed the highest nucleotide similarity of all Czech G8 sequences to the G8P[8] rotavirus strains that were isolated in Vietnam in 2014/2015. The whole-genome backbone of the Czech G8 strains was determined with the use of next-generation sequencing as DS-1-like. Phylogenetic analysis of all segments clustered the Czech isolates with RVA strains that were formerly described in Southeast Asia, which had emerged following genetic reassortment between bovine and human RVAs. This is the first time that bovine-human DS1-like G8P[8] strains were detected at a high rate in human patients in Central Europe. Whether the emergence of this unusual genotype reflects the establishment of a new RVA strain in the population requires the continuous monitoring of rotavirus epidemiology.
- MeSH
- antigeny virové genetika MeSH
- feces virologie MeSH
- fylogeneze MeSH
- gastroenteritida epidemiologie virologie MeSH
- genom virový genetika MeSH
- genotyp MeSH
- lidé MeSH
- prevalence MeSH
- reassortantní viry genetika izolace a purifikace MeSH
- RNA virová genetika MeSH
- rotavirové infekce epidemiologie virologie MeSH
- Rotavirus genetika izolace a purifikace MeSH
- skot MeSH
- virové plášťové proteiny genetika MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- skot MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- multicentrická studie MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika MeSH
Viroids are non-coding single-stranded circular RNA molecules that replicate autonomously in infected host plants causing mild to lethal symptoms. Their genomes contain about 250-400 nucleotides, depending on viroid species. Members of the family Pospiviroidae, like the Potato spindle tuber viroid (PSTVd), replicate via an asymmetric rolling-circle mechanism using the host DNA-dependent RNA-Polymerase II in the nucleus, while members of Avsunviroidae are replicated in a symmetric rolling-circle mechanism probably by the nuclear-encoded polymerase in chloroplasts. Viroids induce the production of viroid-specific small RNAs (vsRNA) that can direct (post-)transcriptional gene silencing against host transcripts or genomic sequences. Here, we used deep-sequencing to analyze vsRNAs from plants infected with different PSTVd variants to elucidate the PSTVd quasipecies evolved during infection. We recovered several novel as well as previously known PSTVd variants that were obviously competent in replication and identified common strand-specific mutations. The calculated mean error rate per nucleotide position was less than [Formula: see text], quite comparable to the value of [Formula: see text] reported for a member of Avsunviroidae. The resulting error threshold allows the synthesis of longer-than-unit-length replication intermediates as required by the asymmetric rolling-circle mechanism of members of Pospiviroidae.
