Transmitted drug resistance in recently infected HIV-positive Individuals from four urban locations across Asia (2007–2010) – TASER-S

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Complete Genome Sequences of 13 Human Respiratory Syncytial Virus Subgroup A Strains of Genotypes NA1 and ON1 Isolated in the Philippines

Complete genome sequences of 13 human respiratory syncytial virus strains were determined from samples obtained from children hospitalized in the Philippines between 2012 and 2013 because of acute respiratory infection. We identified amino acid polymorphisms between the NA1 and ON1 genotypes in the P, G, F, and L proteins

Mycobacterium tuberculosis whole genome sequencing provides insights into the Manila strain and drug-resistance mutations in the Philippines.

The Philippines has a high incidence of tuberculosis disease (TB), with an increasing prevalence of multidrug-resistant Mycobacterium tuberculosis (MDR-TB) strains making its control difficult. Although the M. tuberculosis "Manila" ancient lineage 1 strain-type is thought to be prevalent in the country, with evidence of export to others, little is known about the genetic diversity of circulating strains. By whole genome sequencing (WGS) 178 isolates from the Philippines National Drug Resistance Survey, we found the majority (143/178; 80.3%) belonged to the lineage 1 Manila clade, with the minority belonging to lineages 4 (European-American; n = 33) and 2 (East Asian; n = 2). A high proportion were found to be multidrug-resistant (34/178; 19.1%), established through highly concordant laboratory drug susceptibility testing and in silico prediction methods. Some MDR-TB isolates had near identical genomic variation, providing potential evidence of transmission. By placing the Philippine isolates within a phylogeny of global M. tuberculosis (n > 17,000), we established that they are genetically similar to those observed outside the country, including a clade of Manila-like strain-types in Thailand. An analysis of the phylogeny revealed a set of ~200 SNPs that are specific for the Manila strain-type, and a subset can be used within a molecular barcode. Sixty-eight mutations known to be associated with 10 anti-TB drug resistance were identified in the Philippine strains, and all have been observed in other populations. Whilst nine putative streptomycin resistance conferring markers in gid (8) and rrs (1) genes appear to be novel and with functional consequences. Overall, this study provides an important baseline characterisation of M. tuberculosis genetic diversity for the Philippines, and will fill a gap in global datasets and aid the development of a nation-wide database for epidemiological studies and clinical decision making. Further, by establishing a molecular barcode for detecting Manila strains it will assist with the design of diagnostic tools for disease control activities

A Prospective Nested Case-Control Study of Dengue in Infants: Rethinking and Refining the Antibody-Dependent Enhancement Dengue Hemorrhagic Fever Model

Analyses of a prospective case-control study of infant dengue by Daniel Libraty and colleagues casts doubt on the antibody-dependent enhancement model for dengue hemorrhagic fever

フィリピンの小児デングウイルス感染症の重症化に、HLA-A*33:01アレルは防御的に働く

Dengue virus infection is a leading cause of morbidity among children in the Philippines in recent years. In order to investigate the association of HLA Class I and II alleles and dengue disease severity in a cohort of Filipino children, we performed a case control study in 2 hospitals in Metro Manila from June 2008 to December 2009. A total of 250 laboratory confirmed dengue patients and 300 healthy individuals aged 5 to 15 years old were typed for HLA-A, B and DRB1 alleles. The frequency of HLA-A*33:01 was significantly decreased in severe dengue (DHF/ DSS; Pc = 0.0016)) and DSS (Pc = 0.0032) compared to the background population. These findings support a previous study that this allele may confer protection against the severe form of dengue and provide the first evidence of HLA association with dengue in the Philippines. Future studies should be directed in investigating the possible mechanisms of protection.長崎大学学位論文 学位記番号:博(医歯薬)乙第39号 学位授与年月日:平成27年6月3日Author: Edelwisa Segubre Mercado, Fe Esperanza Espino, Ma. Lucila M. Perez, Josie M. Bilar, Jemimah Dawn P. Bajaro, Nguyen Tien Huy, Benilda Q Baello, Mihoko Kikuchi, Kenji HirayamaCitation: PLOS ONE, 10(2), e0115619; 2015Nagasaki University (長崎大学)論文博

Low adiposity during early infancy is associated with a low risk for developing dengue hemorrhagic fever: a preliminary model

Dengue virus (DENV) infections range from asymptomatic or mild illness to a severe and potentially life threatening disease, dengue hemorrhagic fever (DHF). DHF occurs in primary DENV infections during early infancy. A prospective clinical study of DENV infections during infancy was conducted in San Pablo, Philippines. We found that infants who developed DHF with a primary DENV infection had higher WHO weight-for-age z scores before and at the time of infection compared to infants with primary DENV infections who did not develop DHF. In addition, TLR 7/8-stimulated tumor necrosis factor-alpha (TNF-alpha) production from myeloid-derived cells was higher among well-nourished infants. Leptin augmented TLR 7/8-mediated TNF-alpha production in monocytes and decreased intracellular cAMP levels. Circulating leptin levels were elevated during early infancy and correlated with WHO weight-for-age z scores. Our data support a plausible hypothesis as to why well-nourished infants are at risk for developing DHF with their first DENV infection

Molecular detection and characterization of sapovirus in hospitalized children with acute gastroenteritis in the Philippines

AbstractBackgroundHuman sapovirus (SaV) is a causative agent of acute gastroenteritis. Recently, SaV detection has been increasing worldwide due to the emerging SaV genotype I.2. However, SaV infection has not been reported in the Philippines.ObjectivesTo evaluate the prevalence and genetic diversity of SaV in hospitalized children aged less than 5 years with acute gastroenteritis.Study designStool samples were collected from children with acute gastroenteritis at three hospitals in the Philippines from June 2012 to August 2013. SaV was detected by reverse transcription real-time PCR, and the polymerase and capsid gene sequences were analyzed. Full genome sequencing and recombination analysis were performed on possible recombinant viruses.ResultsSaV was detected in 7.0% of the tested stool samples (29/417). In 10 SaV-positive cases, other viruses were also detected, including rotavirus (n=6), norovirus (n=2), and human astrovirus (n=2). Four known SaV genotypes (GI.1 [7], GI.2 [2], GII.1 [12], and GV [2]) and one novel recombinant (n=3) were identified by polymerase and capsid gene sequence analysis. Full genome sequencing revealed that the 5ʹ nontranslated region (NTR) and nonstructural protein region of the novel recombinant were closely related to the GII.1 Bristol/98/UK variant, whereas the structural protein region and 3ʹ NTR were closely related to the GII.4 Kumamoto6/Mar2003/JPN variant.Discussion and conclusionsSaV was regularly detected in hospitalized children due to acute gastroenteritis during the study period. A novel recombinant, SaV GII.1/GII.4, was identified in three cases at two different study sites

Phenotype frequencies of HLA-A, HLA-B and DRB1 and their association with presence or absence of shock in severe dengue.

<p>^aThe number for each locus shows the number of successfully typed samples</p><p>^bCorrected P-values (Pc) were only calculated for loci with P-values less than 0.05</p><p>Phenotype frequencies of HLA-A, HLA-B and DRB1 and their association with presence or absence of shock in severe dengue.</p

Demographic, clinical and laboratory features of dengue patients classified using WHO 1997 classification.

<p>^aDSS vs DF, OR = 2.65 (1.3–5.3), <i>P</i> = 0.005</p><p>^bDSS vs. DF, OR = 3.89 (2.0–7.7), <i>P</i><0.0001 (Abdominal pain/tenderness); DSS vs. DF, OR = 34.17 (8.0 to 145.1), <i>P</i><0.0001, DHF vs. DF, <i>P</i><0.0001 (Clinical fluid accumulation); DSS vs. DF, OR = 2.47 (1.3–4.6), <i>P</i> = 0.0037 (Mucosal bleeding); DSS vs. DF, OR = 4.57(1.8–11.5), <i>P</i> = 0.0004, DHF vs. DF, <i>P</i> = 0.0405 (Increase in hematocrit with decrease in platelet count)</p><p>^cn.d. = not determined</p><p>Demographic, clinical and laboratory features of dengue patients classified using WHO 1997 classification.</p