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-Px-Ix-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hx. The Rotavirus Classification Working 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 (P28-P35), 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 nomenclature system and the NCBI RV resource will offer highly useful tools for investigators to search for, retrieve, and analyze the ever-growing volume of RV genomic data.
Human immunodeficiency virus type-1 (HIV-1), hepatitis B and C and other rapidly evolving viruses are characterized by extremely high levels of genetic diversity. To facilitate diagnosis and the ...development of prevention and treatment strategies that efficiently target the diversity of these viruses, and other pathogens such as human T-lymphotropic virus type-1 (HTLV-1), human herpes virus type-8 (HHV8) and human papillomavirus (HPV), we developed a rapid high-throughput-genotyping system. The method involves the alignment of a query sequence with a carefully selected set of pre-defined reference strains, followed by phylogenetic analysis of multiple overlapping segments of the alignment using a sliding window. Each segment of the query sequence is assigned the genotype and sub-genotype of the reference strain with the highest bootstrap (>70%) and bootscanning (>90%) scores. Results from all windows are combined and displayed graphically using color-coded genotypes. The new Virus-Genotyping Tools provide accurate classification of recombinant and non-recombinant viruses and are currently being assessed for their diagnostic utility. They have incorporated into several HIV drug resistance algorithms including the Stanford (http://hivdb.stanford.edu) and two European databases (http://www.umcutrecht.nl/subsite/spread-programme/ and http://www.hivrdb.org.uk/) and have been successfully used to genotype a large number of sequences in these and other databases. The tools are a PHP/JAVA web application and are freely accessible on a number of servers including: http://bioafrica.mrc.ac.za/rega-genotype/html/ http://lasp.cpqgm.fiocruz.br/virus-genotype/html/ http://jose.med.kuleuven.be/genotypetool/html/.
This paper presents a free and open-source program called PyXRD (short for Python X-ray diffraction) to improve the quantification of complex, poly-phasic mixed-layer phyllosilicate assemblages. The ...validity of the program was checked by comparing its output with Sybilla v2.2.2, which shares the same mathematical formalism. The novelty of this program is the ab initio incorporation of the multi-specimen method, making it possible to share phases and (a selection of) their parameters across multiple specimens. PyXRD thus allows for modelling multiple specimens side by side, and this approach speeds up the manual refinement process significantly. To check the hypothesis that this multi-specimen set-up – as it effectively reduces the number of parameters and increases the number of observations – can also improve automatic parameter refinements, we calculated X-ray diffraction patterns for four theoretical mineral assemblages. These patterns were then used as input for one refinement employing the multi-specimen set-up and one employing the single-pattern set-ups. For all of the assemblages, PyXRD was able to reproduce or approximate the input parameters with the multi-specimen approach. Diverging solutions only occurred in single-pattern set-ups, which do not contain enough information to discern all minerals present (e.g. patterns of heated samples). Assuming a correct qualitative interpretation was made and a single pattern exists in which all phases are sufficiently discernible, the obtained results indicate a good quantification can often be obtained with just that pattern. However, these results from theoretical experiments cannot automatically be extrapolated to all real-life experiments. In any case, PyXRD has proven to be useful when X-ray diffraction patterns are modelled for complex mineral assemblages containing mixed-layer phyllosilicates with a multi-specimen approach.
Establishment of seasonal grazing enclosures has become an important rangeland rehabilitation strategy in semi-arid regions. This study assessed the impact of enclosure age and enclosure management ...on the vegetation composition in the Njemps Flats range unit, Lake Baringo Basin (Kenya). Six communal enclosures (13–23 years since establishment) and six private enclosures (3–17 years since establishment) were selected. Point-line transect and quadrat-based measurements were made of herbaceous cover, functional group relative abundance and standing crop inside the enclosures and in the adjacent open rangeland. Unpalatable forbs and sedges dominated the herbaceous vegetation of the degraded open rangeland. Informal semi-private land ownership reduced open rangeland degradation as shown by a higher cover of surviving annual grasses. Rangeland enclosure fostered regeneration of annual and perennial grasses, and significantly increased grass cover and standing crop. Private and communal enclosure management were equally successful in rehabilitating grass cover. Standing crop in the communal enclosures was fully recovered, but it was sub-optimal in all private enclosures reflecting recent grazing or grass cutting activities. The variability in rehabilitation success highlights the high potential of individual herders’ incentives to promote rangeland rehabilitation but also stresses the importance of more detailed characterisation and monitoring of the enclosure management decisions.
Patients with immune-mediated inflammatory diseases (IMID) such as RA, IBD or psoriasis, are at increased risk of infection, partially because of the disease itself, but mostly because of treatment ...with immunomodulatory or immunosuppressive drugs. In spite of their elevated risk for vaccine-preventable disease, vaccination coverage in IMID patients is surprisingly low. This review summarizes current literature data on vaccine safety and efficacy in IMID patients treated with immunosuppressive or immunomodulatory drugs and formulates best-practice recommendations on vaccination in this population. Especially in the current era of biological therapies, including TNF-blocking agents, special consideration should be given to vaccination strategies in IMID patients. Clinical evidence indicates that immunization of IMID patients does not increase clinical or laboratory parameters of disease activity. Live vaccines are contraindicated in immunocompromized individuals, but non-live vaccines can safely be given. Although the reduced quality of the immune response in patients under immunotherapy may have a negative impact on vaccination efficacy in this population, adequate humoral response to vaccination in IMID patients has been demonstrated for hepatitis B, influenza and pneumococcal vaccination. Vaccination status is best checked and updated before the start of immunomodulatory therapy: live vaccines are not contraindicated at that time and inactivated vaccines elicit an optimal immune response in immunocompetent individuals.
Group A human rotaviruses (RVs) are a major cause of severe gastroenteritis in infants and young children. Yet, aside from the genes encoding serotype antigens (VP7; G-type and VP4; P-type), little ...is known about the genetic make-up of emerging and endemic human RV strains. To gain insight into the diversity and evolution of RVs circulating at a single location over a period of time, we sequenced the eleven-segmented, double-stranded RNA genomes of fifty-one G3P8 strains collected from 1974 to 1991 at Children's Hospital National Medical Center, Washington, D. C. During this period, G1P8 strains typically dominated, comprising on average 56% of RV infections each year in hospitalized children. A notable exception was in the 1976 and 1991 winter seasons when the incidence of G1P8 infections decreased dramatically, a trend that correlated with a significant increase in G3P8 infections. Our sequence analysis indicates that the 1976 season was characterized by the presence of several genetically distinct, co-circulating clades of G3P8 viruses, which contained minor but significant differences in their encoded proteins. These 1976 lineages did not readily exchange gene segments with each other, but instead remained stable over the course of the season. In contrast, the 1991 season contained a single major clade, whose genome constellation was similar to one of the 1976 clades. The 1991 clade may have gained a fitness advantage after reassorting with as of yet unidentified RV strain(s). This study reveals for the first time that genetically distinct RV clades of the same G/P-type can co-circulate and cause disease. The findings from this study also suggest that, although gene segment exchange occurs, most reassortant strains are replaced over time by lineages with preferred genome constellations. Elucidation of the selective pressures that favor maintenance of RVs with certain sets of genes may be necessary to anticipate future vaccine needs.
•
Introduction
•
Methods
•
Results
•
Discussion
•
Conclusion
Consistent evidence underlines the utility of human papillomavirus (HPV) DNA testing in the management of women with equivocal ...cervical cytological abnormalities, but not in case of low‐grade lesions. We performed a meta‐analysis including studies where the high‐risk probe of the Hybrid Capture‐II is used to triage these two cytological categories. The triage test‐positivity rate reflects the colposcopy referral workload.Data were pooled on the HPV test positivity rate in women with atypical squamous cells of undetermined significance (ASCUS/ASC‐US) or low‐grade squamous intraepithelial lesions (LSIL), derived from different cytological classification systems. The meta‐analysis was restricted to studies, published between 1991 and 2007. A random‐effect model was applied for meta‐analytical pooling and the influence of covariates on the HPV positivity rate was analyzed by meta‐regression. The variation by age was assessed within individual studies since age strata were not defined uniformly. On an average, 43% (95% CI: 40–46%) of women with ASCUS/ASC‐US were high‐risk HPV positive (range 23–74%). In women with LSIL, the pooled positivity rate was 76% (95% CI: 71–81%; range 55–89%). In spite of considerable inter‐study heterogeneity, the difference in HPV positivity between the two triage groups was large and highly significant: 32% (95% CI: 27–38%). HPV rates dropped tremendously as age and cutoffs of test positivity increased. Other factors (cytological classification system, country, continent, collection method and year of publication) had no statistically significant impact, except in LSIL triage where HPV positivity was significantly lower in European compared to American studies. Women with LSIL, especially younger women, have high HPV positivity rates suggesting limited utility of reflex HPV triaging these cases. Research is needed to identify more specific methods to triage women with low‐grade squamous cervical lesions.
PDF
