In April 2008, a nucleotide-sequence-based, complete genome classification system was developed for group A rotaviruses (RVs). This system assigns a specific genotype to each of the 11 genome segments of a particular RV strain according to established nucleotide percent cutoff values. Using this approach, the genome of individual RV strains are given the complete descriptor of Gx-P[x]-Ix-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hx. The Rotavirus ClassificationWorking Group (RCWG) was formed by scientists in the field to maintain, evaluate and develop the RV genotype classification system, in particular to aid in the designation of new genotypes. Since its conception, the group has ratified 51 new genotypes: as of April 2011, new genotypes for VP7 (G20-G27), VP4 (Pš28đ-Pš35đ), VP6 (I12-I16), VP1 (R5-R9), VP2 (C6-C9), VP3(M7-M8), NSP1 (A15-A16), NSP2 (N6-N9), NSP3 (T8-T12), NSP4 (E12-E14) and NSP5/6 (H7-H11) have been defined for RV strains recovered from humans, cows, pigs, horses, mice, South American camelids (guanaco), chickens, turkeys, pheasants, bats and a sugar glider. With increasing numbers of complete RV genome sequences becoming available, a standardized RV strain nomenclature system is needed, and the RCWG proposes that individual RV strains are named as follows: RV group/species of origin/country of identification/common name/year of identification/G- and P-type. In collaboration with the National Center for Biotechnology Information (NCBI), the RCWG is also working on developing a RV-specific resource for the deposition of nucleotide sequences. This resource will provide useful information regarding RV strains, including,but not limited to, the individual gene genotypes and epidemiological and clinical information. Together, the proposed nomenclaturesystem and the NCBI RV resource will offer highly useful tools forinvestigators to search for, retrieve, and analyze the ever-growing volume of RV genomic data.
D.03 Membership in foreign/international boards/committees
COBISS.SI-ID: 28690649Rotaviruses are the main infectious agent of acute gastroenteritis in children under the age of 5 years. Worldwide, rotaviruses are responsible for high mortality in this age group as World Health Organization estimate 453.000 deaths to be caused by rotavirus infection. In this lecture we present a review of the zoonotic potential of rotaviruses, their diversity found in human and animal rotavirus strains and findings of interspecies transmission studies and genetic mechanisms influencing the high viral variability in nature.
B.04 Guest lecture
COBISS.SI-ID: 29045465With the advent and the rapid evolution of next-generation sequencing (NGS) platforms, the possibilities of discovering new viruses and viral strains and of performing high scale virus population studies have broadened dramatically. Despite NGS can produce massive amounts of sequence data, viral sequences are often present in minor quantities within a vast background of host ones. The removal of host nucleic acids and simultaneous enrichment of viruses still remains a challenge. CIM monoliths are chromatographic supports that have been successfully used for the purification and/or concentration of different plant, human and animal viruses. In this work we assessed the potential advantages of using CIM monoliths to enrich a putative reoviruses present in different samples (stool and cell culture supernatant) before applying them to NGS in a Ion Torrent platform. The inclusion of a CIM purification step using a gradient elution resulted in an increase of the virus specific reads linked to a decrease in background nucleic acids, which facilitated the post sequencing data analysis. Such virus enriching strategy using CIM monoliths proved to have the potential of improving virus oriented NGS applications and thus it will also be tested for other virus cases and NGS platforms.
B.03 Paper at an international scientific conference
COBISS.SI-ID: 31472601Gastroenteritis is still one of the major cause of childhood mortality in developing countries and the leading cause of hospitalizations in developed countries. Despite improvements in microbiological diagnostic procedures, an estimated 30% of all cases remain undiagnosed. The aim of the presented work was to show a practical case of the new molecular technique, next generation sequencing (NGS), introduced in gastroenteritis diagnostics to fill the diagnostic gap. Stool samples of hospitalized children were screened for most prevalent bacterial, parasitic and viral causes using pathogen specific molecular methods. Only negative samples were included in metagenomic analysis. In total 292 stool samples were screened in our study and in 90.75% of them the etiology was determined successfully, using pathogen-specific molecular tests. In 14 additional samples (4.8%) a possible viral cause was detected after the next-generation sequence and bioinformatics analysis. We found genetic variants of recombinant enteroviruses, noroviruses, sapoviruses, novel astroviruses and a new candidate species of picobirnavirus in stool samples that were of indeterminate etiology. Subsequent clinical studies are now required to determine the prevalence and disease association of these viruses. We have shown in our study that Next Generation Sequencing is an important tool in pathogen discovery and viral diagnostics, as no other method combines satisfactory sensitivity, specificity and »catch all« approach.
F.17 Transfer of existing technologies, know-how, methods and procedures into practice
COBISS.SI-ID: 31024089