Surveillance of human calicivirus in Spain.
Ontology highlight
ABSTRACT:
SUBMITTER: Sanchez-Fauquier A
PROVIDER: S-EPMC3320501 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:BackgroundCystic echinococcosis (CE) is an important health problem in many areas of the world including the Mediterranean region. However, the real CE epidemiological situation is not well established. In fact, it is possible that CE is a re-emerging disease due to the weakness of current control programs.MethodologyWe performed a retrospective observational study of inpatients diagnosed with CE from January 2000 to December 2012 in the Western Spain Public Health-Care System.Principal findingsDuring the study period, 5510 cases of CE were diagnosed and 3161 (57.4%) of the cases were males. The age mean and standard deviation were 67.8 ± 16.98 years old, respectively, and 634 patients (11.5%) were younger than 45 years old. A total of 1568 patients (28.5%) had CE as the primary diagnosis, and it was most frequently described in patients <45 years old. Futhermore, a secondary diagnosis of CE was usually found in patients >70 year old associated with other causes of comorbidity. The period incidence rate was 17 cases per 105 person-years and was significantly higher when compared to the incidence declared through the Notifiable Disease System (1.88 cases per 105 person-years; p<0.001).ConclusionsCE in western Spain is an underestimated parasitic disease. It has an active transmission, with an occurrence in pediatric cases, but has decreased in the recent years. The systematic search of Hospital Discharge Records of the National Health System Register (HDR) may be a more accurate method than other methods for the estimation of the incidence of CE in endemic areas.
| S-EPMC4618931 | biostudies-literature
Project description:Epidemiologic data of Herpes Zoster (HZ) disease in Spain are scarce. The objective of this study was to assess the epidemiology of HZ in the Valencian Community (Spain), using outpatient and hospital electronic health databases.Data from 2007 to 2010 was collected from computerized health databases of a population of around 5 million inhabitants. Diagnoses were recorded by physicians using the International Classification of Diseases, 9th Revision, Clinical Modification (ICD-9-CM). A sample of medical records under different criteria was reviewed by a general practitioner, to assess the reliability of codification.The average annual incidence of HZ was 4.60 per 1000 persons-year (PY) for all ages (95% CI: 4.57-4.63), is more frequent in women [5.32/1000PY (95% CI: 5.28-5.37)] and is strongly age-related, with a peak incidence at 70-79 years. A total of 7.16/1000 cases of HZ required hospitalization.Electronic health database used in the Valencian Community is a reliable electronic surveillance tool for HZ disease and will be useful to define trends in disease burden before and after HZ vaccine introduction.
| S-EPMC3851452 | biostudies-other
Project description:Feline calicivirus Genome sequencing and assembly
| PRJNA728105 | ENA
Project description:Feline calicivirus Genome sequencing and assembly
| PRJNA902118 | ENA
Project description:To identify unknown human viruses in the enteric tract, we examined 105 stool specimens from patients with diarrhea in Bangladesh. A novel calicivirus was identified in a sample from 1 patient and subsequently found in samples from 5 other patients. Phylogenetic analyses classified this virus within the proposed genus Recovirus.
| S-EPMC3376821 | biostudies-literature
Project description:Whether animals may act as reservoirs for human caliciviruses is unclear. By sequence analysis of a short fragment of the RNA-dependent RNA polymerase (RdRp) region, porcine sapovirus (SaV) strains that genetically resemble human SaVs have been detected in piglets, but more-informative sequences (capsid gene) were not available for a precise characterization. In this study, the 3' terminus (the 3' end of open reading frame 1 [ORF1], including the polymerase complex and the complete capsid; ORF2; and the 3' untranslated region) of one such human SaV-like strain, 43/06-18p3/2006/It, was determined, revealing that these viruses are more related genetically to human (47.4 to 54.9% amino acid identity) than to animal (35.2 to 44.7% amino acid identity) SaVs in the capsid gene. In addition, the recombination-prone RdRp-capsid junction region was highly conserved with those of human SaVs of genogroup GI. The presence of porcine viruses similar to human SaVs is a significant finding because of the potential for zoonotic infections or generation of porcine/human recombinants.
| S-EPMC2446860 | biostudies-literature
Project description:The molecular epidemiology of HIV-1 is constantly changing, mainly as a result of human migratory flows and the high adaptive ability of the virus. In recent years, Spain has become one of Europe's main destinations for immigrants and one of the western European countries with the highest rates of HIV-positive patients. Using a phylogeographic approach, we have analyzed the relationship between HIV-1 variants detected in immigrant and native populations of the urban area of Madrid. Our project was based on two coincidental facts. First, resistance tests were extended to naïve and newly diagnosed patients, and second, the Spanish government legislated the provision of legal status to many immigrants. This allowed us to obtain a large data set (n = 2,792) from 11 Madrid hospitals of viral pol sequences from the two populations, and with this unique material, we explored the impact of immigration in the epidemiological trends of HIV-1 variants circulating in the largest Spanish city. The prevalence of infections by non-B HIV-1 variants in the studied cohort was 9%, rising to 25% among native Spanish patients. Multiple transmission events involving different lineages and subsubtypes were observed in all the subtypes and recombinant forms studied. Our results also revealed strong social clustering among the most recent immigrant groups, such as Russians and Romanians, but not in those groups who have lived in Madrid for many years. Additionally, we document for the first time the presence of CRF47_BF and CRF38_BF in Europe, and a new BG recombinant form found in Spaniards and Africans is tentatively proposed. These results suggest that the HIV-1 epidemic will evolve toward a more complex epidemiological landscape.
| S-EPMC3187488 | biostudies-literature
Project description:Non-typhoid salmonellosis is a common and problematic foodborne zoonotic disease in which pork and pork products can be an important potential source of infection. To prevent this disease, important efforts to monitor the situation in the main source, livestock, are conducted in most developed countries. In the European Union, European Food Safety Agency (EFSA) and European Center for Disease Control (ECDC) compile information at the member-state level, even though important differences in production systems and surveillance systems exist. Here, Salmonella surveillance systems in one of the main sources of foodborne salmonellosis, swine, and humans in Spain were reviewed to identify potential gaps and discuss potential ways of integration under a "One-Health" approach. Despite the extensive information generated through the surveillance activities, source attribution can be only routinely performed through ad-hoc outbreak investigations, and national reports on human outbreaks do not provide sufficiently detailed information to gain a better understanding of the epidemiology of the pathogen. Human and animal monitoring of Salmonella would benefit from a better exchange of information and collaboration. Analysis of spatio-temporal trends in livestock and humans could help to identify likely sources of infection and to target surveillance efforts in areas with higher prevalence or where specific strains are found.
| S-EPMC6466228 | biostudies-literature
Project description:Salmonella enterica subspecies enterica is one of the most important foodborne pathogens and the causative agent of salmonellosis, which affects both humans and animals producing numerous infections every year. The study and understanding of its epidemiology are key to monitoring and controlling these bacteria. With the development of whole-genome sequencing (WGS) technologies, surveillance based on traditional serotyping and phenotypic tests of resistance is being replaced by genomic surveillance. To introduce WGS as a routine methodology for the surveillance of food-borne Salmonella in the region, we applied this technology to analyze a set of 141 S. enterica isolates obtained from various food sources between 2010 and 2017 in the Comunitat Valenciana (Spain). For this, we performed an evaluation of the most relevant Salmonella typing methods, serotyping and sequence typing, using both traditional and in silico approaches. We extended the use of WGS to detect antimicrobial resistance determinants and predicted minimum inhibitory concentrations (MICs). Finally, to understand possible contaminant sources in this region and their relationship to antimicrobial resistance (AMR), we performed cluster detection combining single-nucleotide polymorphism (SNP) pairwise distances and phylogenetic and epidemiological data. The results of in silico serotyping with WGS data were highly congruent with those of serological analyses (98.5% concordance). Multi-locus sequence typing (MLST) profiles obtained with WGS information were also highly congruent with the sequence type (ST) assignment based on Sanger sequencing (91.9% coincidence). In silico identification of antimicrobial resistance determinants and minimum inhibitory concentrations revealed a high number of resistance genes and possible resistant isolates. A combined phylogenetic and epidemiological analysis with complete genome sequences revealed relationships among isolates indicative of possible common sources for isolates with separate sampling in time and space that had not been detected from epidemiological information. As a result, we demonstrate the usefulness of WGS and in silico methods to obtain an improved characterization of S. enterica enterica isolates, allowing better surveillance of the pathogen in food products and in potential environmental and clinical samples of related interest.
| S-EPMC10215213 | biostudies-literature