Dataset Information

Phylogenetic analysis of rubella viruses identified in Uganda, 2003-2012.

ABSTRACT: Molecular data on rubella viruses are limited in Uganda despite the importance of congenital rubella syndrome (CRS). Routine rubella vaccination, while not administered currently in Uganda, is expected to begin by 2015. The World Health Organization recommends that countries without rubella vaccination programs assess the burden of rubella and CRS before starting a routine vaccination program. Uganda is already involved in integrated case-based surveillance, including laboratory testing to confirm measles and rubella, but molecular epidemiologic aspects of rubella circulation have so far not been documented in Uganda. Twenty throat swab or oral fluid samples collected from 12 districts during routine rash and fever surveillance between 2003 and 2012 were identified as rubella virus RNA positive and PCR products encompassing the region used for genotyping were sequenced. Phylogenetic analysis of the 20 sequences identified 19 genotype 1G viruses and 1 genotype 1E virus. Genotype-specific trees showed that the Uganda viruses belonged to specific clusters for both genotypes 1G and 1E and grouped with similar sequences from neighboring countries. Genotype 1G was predominant in Uganda. More epidemiological and molecular epidemiological data are required to determine if genotype 1E is also endemic in Uganda. The information obtained in this study will assist the immunization program in monitoring changes in circulating genotypes.

SUBMITTER: Namuwulya P

PROVIDER: S-EPMC4269980 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature

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Phylogenetic analysis of rubella viruses identified in Uganda, 2003-2012.

Namuwulya Prossy P Abernathy Emily E Bukenya Henry H Bwogi Josephine J Tushabe Phionah P Birungi Molly M Seguya Ronald R Kabaliisa Theopista T Alibu Vincent P VP Kayondo Jonathan K JK Rivailler Pierre P Icenogle Joseph J Bakamutumaho Barnabas B

Journal of medical virology 20140404 12

Molecular data on rubella viruses are limited in Uganda despite the importance of congenital rubella syndrome (CRS). Routine rubella vaccination, while not administered currently in Uganda, is expected to begin by 2015. The World Health Organization recommends that countries without rubella vaccination programs assess the burden of rubella and CRS before starting a routine vaccination program. Uganda is already involved in integrated case-based surveillance, including laboratory testing to confi ...[more]

PMID: 24700073

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Project description:BackgroundIt is well known that safe delivery in a health facility reduces the risks of maternal and infant mortality resulting from perinatal complications. What is less understood are the factors associated with safe delivery practices. We investigate factors influencing health facility delivery practices while adjusting for multiple other factors simultaneously, spatial heterogeneity, and trends over time.MethodsWe fitted a logistic regression model to Lot Quality Assurance Sampling (LQAS) data from Uganda in a framework that considered individual-level covariates, geographical features, and variations over five time points. We accounted for all two-covariate interactions and all three-covariate interactions for which two of the covariates already had a significant interaction, were able to quantify uncertainty in outputs using computationally intensive cluster bootstrap methods, and displayed outputs using a geographical information system. Finally, we investigated what information could be predicted about districts at future time-points, before the next LQAS survey is carried out. To do this, we applied the model to project a confidence interval for the district level coverage of health facility delivery at future time points, by using the lower and upper end values of known demographics to construct a confidence range for the prediction and define priority groups.ResultsWe show that ease of access, maternal age and education are strongly associated with delivery in a health facility; after accounting for this, there remains a significant trend towards greater uptake over time. We use this model together with known demographics to formulate a nascent early warning system that identifies candidate districts expected to have low prevalence of facility-based delivery in the immediate future.ConclusionsOur results support the hypothesis that increased development, particularly related to education and access to health facilities, will act to increase facility-based deliveries, a factor associated with reducing perinatal associated mortality. We provide a statistical method for using inexpensive and routinely collected monitoring and evaluation data to answer complex epidemiology and public health questions in a resource-poor setting. We produced a model based on this data that explained the spatial distribution of facility-based delivery in Uganda. Finally, we used this model to make a prediction about the future priority of districts that was validated by monitoring and evaluation data collected in the next year.

Project description:BACKGROUND:In China, large-scale outbreaks of severe diarrhea caused by viruses have occurred in pigs since late 2010. To investigate the prevalence and genetic evolution of diarrhea-associated viruses responsible for the outbreaks, a total of 2987 field diarrheal samples collected from 168 pig farms in five provinces in Southern China during 2012-2018 were tested. RESULTS:Porcine epidemic diarrhea virus (PEDV) was most frequently detected virus with prevalence rates between 50.21 and 62.10% in samples, and 96.43% (162/168) in premises, respectively. Porcine deltacoronavirus (PDCoV) was the second prevalent virus with prevalence rates ranging from 19.62 to 29.19% in samples, and 70.24% (118/168) in premises, respectively. Both transmissible gastroenteritis virus (TGEV) and porcine rotavirus (PoRV) were detected at low prevalence rates of < 3% in samples and 10.12% in premises. In this study, we identified a newly emerged swine acute diarrhea syndrome coronavirus (SADS-CoV) in diarrheal samples of piglets from Fujian province in Southern China, and the prevalence rate of SADS-CoV was 10.29% (7/68). Co-infections of these diarrhea-associated viruses were common. The most frequent co-infection was PEDV with PDCoV, with an average detection rate of 12.72% (380/2987, ranging from 8.26-17.33%). Phylogenetic analysis revealed that PEDVs circulating in Southern China during the last 7 years were clustered with the variant strains of PEDV in genotype IIa. The most frequent mutations were present in the collagenase equivalent (COE) and epitope regions of the spike gene of the PEDVs currently circulating in the field. Genetic relationships of PDCoVs were closely related with Chinese strains, other than those present in the USA, South Korea, Thailand and Lao's public. CONCLUSIONS:The findings of this study indicated that variant PEDV, PDCoV, and SADS-CoV were leading etiologic agents of porcine diarrhea, and either mono-infections or co-infections of pathogenic enteric CoVs were common in pigs in Southern China during 2012-2018. Thus, significant attention should be paid in order to effectively prevent and control porcine viral diarrhea.

Dataset Information

Phylogenetic analysis of rubella viruses identified in Uganda, 2003-2012.

Publications

Phylogenetic analysis of rubella viruses identified in Uganda, 2003-2012.

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