Dataset Information

Phylogeography of recently emerged DENV-2 in southern Viet Nam.

ABSTRACT: Revealing the dispersal of dengue viruses (DENV) in time and space is central to understanding their epidemiology. However, the processes that shape DENV transmission patterns at the scale of local populations are not well understood, particularly the impact of such factors as human population movement and urbanization. Herein, we investigated trends in the spatial dynamics of DENV-2 transmission in the highly endemic setting of southern Viet Nam. Through a phylogeographic analysis of 168 full-length DENV-2 genome sequences obtained from hospitalized dengue cases from 10 provinces in southern Viet Nam, we reveal substantial genetic diversity in both urban and rural areas, with multiple lineages identified in individual provinces within a single season, and indicative of frequent viral migration among communities. Focusing on the recently introduced Asian I genotype, we observed particularly high rates of viral exchange between adjacent geographic areas, and between Ho Chi Minh City, the primary urban center of this region, and populations across southern Viet Nam. Within Ho Chi Minh City, patterns of DENV movement appear consistent with a gravity model of virus dispersal, with viruses traveling across a gradient of population density. Overall, our analysis suggests that Ho Chi Minh City may act as a source population for the dispersal of DENV across southern Viet Nam, and provides further evidence that urban areas of Southeast Asia play a primary role in DENV transmission. However, these data also indicate that more rural areas are also capable of maintaining virus populations and hence fueling DENV evolution over multiple seasons.

SUBMITTER: Rabaa MA

PROVIDER: S-EPMC2910671 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature

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Phylogeography of recently emerged DENV-2 in southern Viet Nam.

Rabaa Maia A MA Ty Hang Vu Thi VT Wills Bridget B Farrar Jeremy J Simmons Cameron P CP Holmes Edward C EC

PLoS neglected tropical diseases 20100727 7

Revealing the dispersal of dengue viruses (DENV) in time and space is central to understanding their epidemiology. However, the processes that shape DENV transmission patterns at the scale of local populations are not well understood, particularly the impact of such factors as human population movement and urbanization. Herein, we investigated trends in the spatial dynamics of DENV-2 transmission in the highly endemic setting of southern Viet Nam. Through a phylogeographic analysis of 168 full-l ...[more]

PMID: 20668540

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Project description:BackgroundSince 1962, enterovirus D68 (EV-D68) has been implicated in multiple outbreaks and sporadic cases of respiratory infection worldwide, but especially in the USA and Europe with an increasing frequency between 2010 and 2014. We describe the detection, associated clinical features and molecular characterization of EV-D68 in central and southern Viet Nam between 2009 and 2015.MethodsEnterovirus/rhinovirus PCR positive respiratory or CSF samples taken from children and adults with respiratory/central nervous system infections in Viet Nam were tested by an EV-D68 specific PCR. The included samples were derived from 3 different observational studies conducted at referral hospitals across central and southern Viet Nam between 2009 and 2015. Whole-genome sequencing was carried out using a MiSeq based approach. Phylogenetic reconstruction and estimation of evolutionary rate and recombination were carried out in BEAST and Recombination Detection Program, respectively.ResultsEV-D68 was detected in 21/625 (3.4%) enterovirus/rhinovirus PCR positive respiratory samples but in none of the 15 CSF. All the EV-D68 patients were young children (age range: 11.8 - 24.5 months) and had moderate respiratory infections. Phylogenetic analysis suggested that the Vietnamese sequences clustered with those from Asian countries, of which 9 fell in the B1 clade, and the remaining sequence was identified within the A2 clade. One intra sub-clade recombination event was detected, representing the second reported recombination within EV-D68. The evolutionary rate of EV-D68 was estimated to be 5.12E -3 substitutions/site/year. Phylogenetic analysis indicated that the virus was imported into Viet Nam in 2008.ConclusionsWe have demonstrated for the first time EV-D68 has been circulating at low levels in Viet Nam since 2008, associated with moderate acute respiratory infection in children. EV-D68 in Viet Nam is most closely related to Asian viruses, and clusters separately from recent US and European viruses that were suggested to be associated with acute flaccid paralysis.

Project description:Fusarium is one of the most important fungal genera of plant pathogens that affect the cultivation of a wide range of crops. Agricultural losses caused by Fusariumoxysporumf.sp.cubense (Foc) directly affect the income, subsistence, and nourishment of thousands of farmers worldwide. For Viet Nam, predictions on the impact of Foc for the future are dramatic, with an estimated loss in the banana production area of 8% within the next five years and up to 71% within the next 25 years. In the current study, we applied a combined morphological-molecular approach to assess the taxonomic identity and phylogenetic position of the different Foc isolates collected in northern Viet Nam. In addition, we aimed to estimate the proportion of the different Fusarium races infecting bananas in northern Viet Nam. The morphology of the isolates was investigated by growing the collected Fusarium isolates on four distinct nutritious media (PDA, SNA, CLA, and OMA). Molecular phylogenetic relationships were inferred by sequencing partial rpb1, rpb2, and tef1a genes and adding the obtained sequences into a phylogenetic framework. Molecular characterization shows that c. 74% of the Fusarium isolates obtained from infected banana pseudostem tissue belong to F.tardichlamydosporum. Compared to F.tardichlamydosporum, F.odoratissimum accounts for c.10% of the Fusarium wilt in northern Viet Nam, demonstrating that Foc TR4 is not yet a dominant strain in the region. Fusariumcugenangense - considered to cause Race 2 infections among bananas - is only found in c. 10% of the tissue material that was obtained from infected Vietnamese bananas. Additionally, one of the isolates cultured from diseased bananas was phylogenetically not positioned within the F.oxysporum species complex (FOSC), but in contrast, fell within the Fusariumfujikuroi species complex (FFSC). As a result, a possible new pathogen for bananas may have been found. Besides being present on several ABB 'Tay banana', F.tardichlamydosporum was also derived from infected tissue of a wild Musalutea, showing the importance of wild bananas as a possible sink for Foc.

Project description:BACKGROUND:Evidence-based practice (EBP) enhances healthcare services and keeps providers current with best practices. EBP has been adopted and spread worldwide. However, people will not apply it if they do not know, understand, or believe it. Few studies have considered EBP application in Viet Nam. This study explores whether Vietnamese physical therapists' attitude, knowledge, skills toward EBP and barriers to its use make them ready to implement its practice. METHODS:A survey questionnaire was sent directly to physical therapists in governmental healthcare organizations in Ho Chi Minh City, Viet Nam, from July to October, 2017. It consisted of 41 closed- and open-ended questions related to knowledge, attitude, behaviors, frequency of use, and barriers of EBP and the demographic characteristics of participants. Descriptive statistics and significant correlations were determined from Chi-Square statistics or odds ratios between the variables. RESULTS:The return rate was 93% (421 out of 453). Eliminated were 40 responses inconsistent with inclusion criteria. The 381 eligible participants were more female (62%) than male, about 53% had vocational degrees, less than 1% had M.S. degrees. Participants reported a positive attitude toward EBP. An incongruity existed between knowledge/ skills of EBP and the frequency of using its 5 steps. English competence was the most critical barrier to applying EBP. The significant associations between attitude and knowledge, and demographical attributes indicated that younger therapists with lower educational degrees had less knowledge of EBP and they rarely employed the application and analytical steps 4 and 5. CONCLUSIONS:The incongruity between knowledge and use of EBP may result from the lack of EBP in academic education. The skills of reading professional articles in the English language and understanding and applying the steps of EBP should be emphasized in academic physical therapy programs. Additionally, policy makers should consider the number of patients a day per physical therapist which impacts EBP use and the quality of healthcare service.

Dataset Information

Phylogeography of recently emerged DENV-2 in southern Viet Nam.

Publications

Phylogeography of recently emerged DENV-2 in southern Viet Nam.

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