Heiman Wertheim and colleagues discuss a network that aims to improve infectious disease management through integrated, collaborative clinical research in South East Asia.
BackgroundHand, foot and mouth disease (HFMD) has become a major public health problem across the Asia-Pacific region, and is commonly caused by enterovirus A71 (EV-A71) and coxsackievirus A6 (CV-A6), CV-A10 and CV-A16. Generating pathogen whole-genome sequences is essential for understanding their evolutionary biology. The frequent replacements among EV serotypes and a limited numbers of available whole-genome sequences hinder the development of overlapping PCRs for whole-genome sequencing.We developed and evaluated a non-ribosomal random PCR (rPCR) and next-generation sequencing based assay for sequence-independent whole-genome amplification and sequencing of HFMD pathogens. A total of 16 EV-A71/CV-A6/CV-A10/CV-A16 PCR positive rectal/throat swabs (Cp values: 20.9–33.3) were used for assay evaluation.ResultsOur assay evidently outperformed the conventional rPCR in terms of the total number of EV-A71 reads and the percentage of EV-A71 reads: 2.6 % (1275/50,000 reads) vs. 0.1 % (31/50,000) and 6 % (3008/50,000) vs. 0.9 % (433/50,000) for two samples with Cp values of 30 and 26, respectively. Additionally the assay could generate genome sequences with the percentages of coverage of 94–100 % of 4 different enterovirus serotypes in 73 % of the tested samples, representing the first whole-genome sequences of CV-A6/10/16 from Vietnam, and could assign correctly serotyping results in 100 % of 24 tested specimens. In all but three the obtained consensuses of two replicates from the same sample were 100 % identical, suggesting that our assay is highly reproducible.ConclusionsIn conclusion, we have successfully developed a non-ribosomal rPCR and next-generation sequencing based assay for sensitive detection and direct whole-genome sequencing of HFMD pathogens from clinical samples.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-016-0580-9) contains supplementary material, which is available to authorized users.
BackgroundThe influenza A virus is an RNA virus that is responsible for seasonal epidemics worldwide with up to five million cases of severe illness and 500,000 deaths annually according to the World Health Organization estimates. The factors associated with severe diseases are not well defined, but more severe disease is more often seen among persons aged >65 years, infants, pregnant women, and individuals of any age with underlying health conditions.Methodology/Principal FindingsUsing gene expression microarrays, the transcriptomic profiles of influenza-infected patients with severe (N = 11), moderate (N = 40) and mild (N = 83) symptoms were compared with the febrile patients of unknown etiology (N = 73). We found that influenza-infected patients, regardless of their clinical outcomes, had a stronger induction of antiviral and cytokine responses and a stronger attenuation of NK and T cell responses in comparison with those with unknown etiology. More importantly, we found that both interferon and ubiquitination signaling were strongly attenuated in patients with the most severe outcomes in comparison with those with moderate and mild outcomes, suggesting the protective roles of these pathways in disease pathogenesis.Conclusion/SignificancesThe attenuation of interferon and ubiquitination pathways may associate with the clinical outcomes of influenza patients.
hepatitis C virus (HCV) infection in Vietnam in 2016. Since then, Hospital for Tropical Diseases (HTD), Ho Chi Minh City, Vietnam introduced DAAs based treatment for all newly presented chronic HCV patients. Here, we report the sociodemographic, clinical, biochemical, and virologic characteristics of patients and the direct medical cost associated with DAAs treatment. METHODS: We conducted a retrospective cross-sectional study among chronic HCV patients attended at HTD from March 2016 to October 2017 and treated with DAAs. We used an extract of the patient's electronic medical record containing demographics, clinical presentations, laboratory results, drug prescription, and cost of treatment at the hospital for data analysis. RESULTS: 2817 chronic HCV patient received DAAs treatment during the study period. The mean age was 55.0 years, and 54.9% (1546/2817) of the patients were female. HCV genotype 1, 2, 3 and 6 prevalence was 32.1% (904/2817), 12.7% (359/2817), 0.4% (10/2817), and 54.7% (1542/2817) respectively. The mean HCV viral load was 3.1 × 10 6 copies/ml, including 46.9% (1322/2817) had ≥10 6 copies/ml. 70.64% (1990/2817) and 16.15% (455/28817) of the patients received Sofosbuvir (SOF)/Ledipasvir (LDV) ± Ribavirin (RBV) and SOF/Daclatasvir (DCV) ± RBV therapy respectively.
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