Rotavirus vaccination started in Slovenia in 2007 on a voluntarily basis. The vaccination rate is relatively low (up to 27%) and no increasing trend is observed. We present rotavirus genotype distribution among children hospitalized for rotavirus gastroenteritis in Slovenia. Eight consecutive rotavirus seasons were followed, from 2005/06 to 2012/13, and 113 strains of the most common rotavirus genotypes were randomly selected for molecular characterization of rotavirus VP7 and VP4 (VP8*) genome segments. During the vaccine introduction period, from 2007 to 2013, rotavirus genotype prevalences changed, with G1P[8] decreasing from 74.1% to 8.7% between 2007/08 and 2010/11 seasons, replaced by G4P[8] and G2P[4], with up to 52.0% prevalence. Comparable analysis of VP7 and VP8* genome fragments within G1P[8] genotype lineages revealed considerable differences for rotavirus strains circulating before and during the vaccination period. The G1P[8] rotavirus strains from the pre-vaccination period clustered in a phylogenetic tree within Rotarix - like VP7 and VP8* lineages. However, since 2007, the majority of G1P[8] strains have shifted to distant genetic lineages with lower nucleotide (88.1-94.0% for VP7 and 86.6-91.1% for VP8*) and amino acid (93.8-95.2% for VP7 and 85.3-94.6% for VP8*) identities to the vaccine Rotarix strain. This change also resulted in a different deduced amino acid profile at the major VP7 and VP8* antigenic epitopes.
COBISS.SI-ID: 31479769
A novel orthoreovirus was isolated from stool sample of a child, hospitalized for acute gastroenteritis, sharing the highest symilarity to recently described strains in Italian and German bats. A successful approach was described, combining classical methods in virology and modern molecular method (next generation sequencing, NGS), for effective and timely diagnostics of viral infections. In addition, novel approach was presented for sample pre-treatment, including concentrating and purifying of viruses with a chromatographic method, enabling improved target nucleic acid recovery in NGS.
COBISS.SI-ID: 2886735
The objective of our study was to assess the significance of HCoVs in the etiology of acute gastroenteritis (AGE) in children (6 years of age. Stool samples and nasopharyngeal (NP) swabs collected from 260 children hospitalized for AGE and 157 otherwise healthy control children were tested for the presence of four HCoVs using molecular methods. HCoVs were more frequent in patients with AGE than in controls (23/260, 8.8% versus 4/151, 2.6%; odds ratio, OR 3.3; 95% confidence interval, CI 1.3– 10.0; P = 0.01). Although HCoVs were more frequently detected in patients with AGE than in the control group, high prevalence of HCoVs in NP swabs compounded by their low occurrence in stool samples and detection of other viruses in stool samples, indicate that HCoVs probably play only a minor role in causing gastrointestinal illness in children (6 years old.
COBISS.SI-ID: 30419417
Group A rotaviruses can infect both humans and animals. Individual rotavirus strains can occasionally cross species barriers and might hereby contribute tothe emergence of new genotypes in heterologous hosts. The incidence and impact of zoonotic rotavirus are not well defined, and one reason for this is a lack of data about strains circulating in suspected reservoir animal hosts. In this study we report the incidence, genetic diversity, and molecular epidemiology of rotaviruses detected in domestic cattle and swine in 6 European countries. From 2003 to 2007, 1101 and more than 2000 faecal specimens were collected from swine and cattle, both healthy and diarrhoeic, and tested for rotaviruses. Viruses from positive stools were genotyped and a subset of strains was characterized by nucleotide sequencing and phylogenetic analysis of the VP7 (G) and VP4 (P) genes. Rotaviruses were detected in 43% ofbovine samples and in 14% of porcine samples. In cattle, 10 different combinations of G and P types were identified and the most common strains wereG6Pš11đ and G6Pš5đ. In swine, the number of identified G-P combinations was higher (n=21), however, no single combination was predominant across Europe. Newly described genotype specificities, Pš27đ and Pš32đ, were identified in swine. When compared at the nucleotide sequence level, the identified porcine rotavirus strains and contemporary human strains grouped together phylogenetically, whereas bovine rotavirus strains formed separate clades. These data demonstrate large genetic diversity of porcine and bovine rotavirus strains across Europe, and suggest that livestock herds may serve aspotential reservoirs for human infections.
COBISS.SI-ID: 29078745
During the rotavirus strain surveillance in Slovenia, G6P[11] bovine rotavirusstrain was detected in a 5 months old boy with gastroenteritis. The strain was enrolled in a whole genome sequence analysis to determine its genome segment composition and genetic characteristics. Genotype composition for the whole genome was G6-P[11]-I2-R2-C2-M2-A13-N2-T6-E2-H3, reflecting similarities with bovine rotavirus strains. The bovine origin of the strain was confirmed in all genome segments, showing the highest nucleotide identity with bovine rotavirus strains and clustering together with bovine rotavirus strains in phylogenetic analysis. This is the first bovine G6P[11] rotavirus strain with the whole genome analysis and the first report on rotavirus G6P[11] genotype detected in humans.
COBISS.SI-ID: 30182617