scholarly journals Prevalence, genetic diversity and recombination of species G enteroviruses infecting pigs in Vietnam

2014 ◽  
Vol 95 (3) ◽  
pp. 549-556 ◽  
Author(s):  
Nguyen Van Dung ◽  
Pham Hong Anh ◽  
Nguyen Van Cuong ◽  
Ngo Thi Hoa ◽  
Juan Carrique-Mas ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Untranslated Region ◽  
Study Group ◽  
Group Comparison ◽  
Specific Primers ◽  
Sequence Comparisons ◽  
Detection Rates ◽  
High Frequencies ◽  
Faecal Samples

Picornaviruses infecting pigs, described for many years as ‘porcine enteroviruses’, have recently been recognized as distinct viruses within three distinct genera (Teschovirus, Sapelovirus and Enterovirus). To better characterize the epidemiology and genetic diversity of members of the Enterovirus genus, faecal samples from pigs from four provinces in Vietnam were screened by PCR using conserved enterovirus (EV)-specific primers from the 5′ untranslated region (5′ UTR). High rates of infection were recorded in pigs on all farms, with detection frequencies of approximately 90 % in recently weaned pigs but declining to 40 % in those aged over 1 year. No differences in EV detection rates were observed between pigs with and without diarrhoea [74 % (n = 70) compared with 72 % (n = 128)]. Genetic analysis of consensus VP4/VP2 and VP1 sequences amplified from a subset of EV-infected pigs identified species G EVs in all samples. Among these, VP1 sequence comparisons identified six type 1 and seven type 6 variants, while four further VP1 sequences failed to group with any previously identified EV-G types. These have now been formally assigned as EV-G types 8–11 by the Picornavirus Study Group. Comparison of VP1, VP4/VP2, 3Dpol and 5′ UTRs of study samples and those available on public databases showed frequent, bootstrap-supported differences in their phylogenies indicative of extensive within-species recombination between genome regions. In summary, we identified extremely high frequencies of infection with EV-G in pigs in Vietnam, substantial genetic diversity and recombination within the species, and evidence for a much larger number of circulating EV-G types than currently described.

scholarly journals Genetic diversity of norovirus in children under 5 years of age with acute gastroenteritis from Angola

2018 ◽  
Vol 146 (5) ◽  
pp. 551-557 ◽  
Author(s):  
A. Esteves ◽  
J. Nordgren ◽  
C. Tavares ◽  
F. Fortes ◽  
R. Dimbu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Acute Gastroenteritis ◽  
Target Population ◽  
Continuous Assessment ◽  
Detection Rates ◽  
Faecal Samples ◽  
High Detection ◽  
Paediatric Age ◽  
Genetic Clusters ◽  
Children Under 5

AbstractNorovirus (NoV) is a major cause of acute gastroenteritis (AGE). In this study, we investigated the genetic diversity of NoV strains identified in children under 5 years of age with AGE in four provinces of Angola. Faecal samples from 343 children were screened for NoV by an in house real-time PCR assay and genotyping was performed by partial capsid gene sequencing. NoV was detected in 17.4% (58/334) of the samples, with high detection rates in children <6 months old (19%) and in children aged 12–24 months (23%). Genotype diversity was large, as demonstrated by the 11 identified genotypes. GII.4 was the predominant genotype (20% of all NoV-positive samples), followed by GII.6 (15%), GI.3 (12%), GII.7 (10%) and by other genotypes to a lesser extent. Two GII.4 variants, New Orleans 2009 and Sydney 2012, were detected and several genetic clusters were observed for genotypes GI.3, GII.6 and GII.7. The present study shows high detection rates and genetic diversity of circulating NoV genotypes in paediatric AGE samples from Angola. This information emphasises the importance of continuous assessment of NoV burden and evolution in the target population.

HIV Type 1 Molecular Epidemiology in Cuba: High Genetic Diversity, Frequent Mosaicism, and Recent Expansion of BG Intersubtype Recombinant Forms

2006 ◽  
Vol 22 (8) ◽  
pp. 724-733 ◽  
Author(s):  
Lissette Pérez ◽  
Michael M. Thomson ◽  
María J. Bleda ◽  
Carlos Aragonés ◽  
Zoila González ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Epidemiology ◽  
High Genetic Diversity ◽  
Hiv Type 1

scholarly journals Microsatellite genotyping from faeces of Lontra longicaudis from southern Brazil

2009 ◽  
Vol 99 (1) ◽  
pp. 5-11 ◽  
Author(s):  
Laura I. Weber ◽  
Cintia G. Hildebrand ◽  
Anderson Ferreira ◽  
Gustavo Pedarassi ◽  
José A. Levy ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Conservation Status ◽  
Significant Degree ◽  
Southern Brazil ◽  
High Genetic Diversity ◽  
Low Degree ◽  
Faecal Samples ◽  
High Level ◽  
Degree Of Differentiation ◽  
Lontra Longicaudis

A genetic study of the neotropical river otter Lontra longicaudis (Olfers, 1818), which has an unknown conservation status, was carried out at the Taim Ecological Station and the margins of the Vargas stream, Rio Grande do Sul, southern Brazil. Faecal samples were collected, and DNA was extracted using a silica-guanidine method. Five microsatellite loci were amplified using PCR with heterologous primers previously described for Lutra lutra (Linnaeus, 1758). Sixteen faecal samples out of 29 from Taim and 11 out of 14 from Vargas stream margins contained enough DNA for genetic analysis. A total of 49 different alleles were found at both localities, from which 18 were exclusively found in individuals from Taim and 17 were exclusives from Vargas individuals. The most common allele was the same at both locations for three loci (Lut715, Lut733, and Lut818). A high level of genetic diversity was found at both sites (NeTaim=4.1, HoTaim=0.299, HeTaim=0.681; NeVargas=4.9, HoVargas=0.355, HeVargas=0.724), being higher at the Vargas stream site. A high and significant level of heterozygote deficiency was observed at most loci according to the χ2 test. The homogeneity χ2 test (P<0.001) showed that there were significant differences in the allele frequencies between the two locations. Genotyping for more than one locus was possible in 81.5% of samples, from which only 37% were possible to genotype for more than three loci. A low degree of relatedness was found among individuals from Taim (R=0.055±0.310), but an even lower value of relatedness was found at the Vargas site (R= -0.285±0.440). The significant degree of differentiation (I=0.890; F ST=0.059) found between Taim and Vargas individuals suggests that there is more than one population of otters in the southern extreme of Brazil, which probably are associated with the water body systems found in this region, the Mirim and the Caiuvá/Flores/Mangueira Lagoons. The high genetic diversity and low relatedness found at the Vargas stream, lead us to believe that the Vargas stream may be acting as a corridor between these water bodies for otter dispersion.

scholarly journals Measurement of corneal thickness, optic nerve sheath diameter and retinal nerve fiber layer as potential new non-invasive methods in assessing a risk of cerebral edema in type 1 diabetes in children

2018 ◽  
Vol 55 (12) ◽  
pp. 1295-1301 ◽  
Author(s):  
Krzysztof Jeziorny ◽  
Anna Niwald ◽  
Agnieszka Moll ◽  
Katarzyna Piasecka ◽  
Aleksandra Pyziak-Skupien ◽  
...  
Keyword(s):  
Type 1 Diabetes ◽  
Optic Nerve ◽  
Corneal Thickness ◽  
Optic Nerve Sheath Diameter ◽  
Study Group ◽  
Newly Diagnosed ◽  
Fiber Layer ◽  
Non Invasive ◽  
Nerve Sheath

Abstract Aims Some patients with diabetic ketoacidosis develop cerebral edema (CE) in the course of type 1 diabetes mellitus (T1D), which may result in central nervous system disorders and high mortality. The imperfection of existing neuroimaging techniques for early recognition of CE forces us to search for the new and non-invasive methods. The aim of the study was to assess the usefulness of new methods (pachymetry, transorbital ultrasonography—USG, optical coherence tomography—OCT study) in the assessment of the risk of CE occurrence in children with newly diagnosed T1D. Methods The study group included 50 children with newly diagnosed T1D, 54 patients with long-term T1D as a reference group and 40 children without glucose tolerance disorders as controls. In all subjects, a corneal thickness (CCT) index with pachymeter, optic nerve sheath diameter (ONSD) using transorbital USG and retinal nerve fiber layer (RNFL) during OCT study were measured and compared with selected clinical parameters of T1D. Results In patients from a study group at onset of T1D, the higher CCT (p < 0.001) and ONSD (p < 0.001) values were observed as compared to the results obtained after 48 h of metabolic compensation. The ONSD correlated negatively with pH value (r = − 0.64; p < 0.001), BE (r = − 0.54, p < 0.001) and HCO3− (r = − 0.50; p < 0.001). A positive correlation between RNFL and Na+ levels (r = 0.47; p < 0.005) was also observed. Conclusions Transorbital USG and pachymetry may serve as the potential promising methods for the non-invasive assessment of the increased risk of development of CE in patients with T1D.

scholarly journals Drug Resistance Mutations and Genetic Diversity in Patients Treated for HIV Type 1 Infection in Rural Care Centers in Togo

2016 ◽  
Vol 06 (03) ◽  
pp. 111-115
Author(s):  
Anoumou Dagnra ◽  
Abla Konou ◽  
Mounerou Salou ◽  
Pascal Kodah ◽  
Damobé Kombate ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Drug Resistance ◽  
Resistance Mutations ◽  
Drug Resistance Mutations ◽  
Hiv Type 1 ◽  
Rural Care
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