Correlation of phylogenetic clade diversification and in vitro infectivity differences among Cosmopolitan genotype strains of Chikungunya virus

Cosmopolitan genotypes of Chikungunya virus caused the large-scale febrile disease outbreaks in the last decade in Asian and African continents. Molecular analyses of these strains had revealed significant genetic diversification and occurrence of novel mosquito-adaptive mutations. In the present study we looked into whether the genetic diversification has implications in the infectivity phenotype. A detailed sequence and phylogenetic analyses of these virus strains of Indian Ocean lineage from Kerala, South India from the years 2008 to 2013 identified three distinct genetic clades (I, II and III), which had presence of clade-specific amino acid changes. The E2 envelope protein of the strains from the years 2012 to 2013 had a K252Q or a novel K252H change. This site is reported to affect mosquito cell infectivity. Most of these strains also had the E2 G82R mutation, a mutation previously identified to increase mammalian cell infectivity, and a novel mutation E2 N72S. Positive selection was identified in four sites in the envelope proteins (E1 K211E, A226V and V291I; E2 K252Q/H). In infectivity analysis, we found that strains from clade III had enhanced cytopathogenicity in HEK293 and Vero cells than by strains representing other two clades. These two strains formed smaller sized plaques and had distinctly higher viral protein expression, infectious virus production and apoptosis induction in HEK293 cells. They had novel mutations R171Q in the nsP1; I539S in nsP2; N409T in nsP3; and N72S in E2. Our study identifies a correlation between phylogenetic clade diversification and differences in mammalian cell infectivity phenotype among Cosmopolitan genotype CHIKV strains.     

New dengue virus type 1 genotype in Colombo, Sri Lanka

The number of cases and severity of disease associated with dengue infection in Sri Lanka has been increasing since 1989, when the first epidemic of dengue hemorrhagic fever was recorded. We identified a new dengue virus 1 strain circulating in Sri Lanka that coincided with the 2009 dengue epidemic.     

Dengue virus 3 genotype 1 associated with dengue fever and dengue hemorrhagic fever, Brazil

Dengue serotype 3 viruses were isolated from patients in Brazil from 2002 through 2004. On the basis of phylogenetic analyses, these isolates were assigned genotype 1. This genotype had never been reported in South America before. Its appearance indicates a major risk factor for dengue epidemics and severe disease.     

Emergence of Dengue Virus Serotype 2 Cosmopolitan Genotype,Brazil

We used nanopore sequencing and phylogenetic analyses to identify a cosmopolitan genotype of dengue virus serotype 2 that was isolated from a 56-year-old male patient from the state of Goiás in Brazil. The emergence of a cosmopolitan genotype in Brazil will require risk assessment and surveillance to reduce epidemic potential.     

Disruption of predicted dengue virus type 3 major outbreak cycle coincided with switching of the dominant circulating virus genotype

Dengue is hyperendemic in most of Southeast Asia. In this region, all four dengue virus serotypes are persistently present. Major dengue outbreak cycle occurs in a cyclical pattern involving the different dengue virus serotypes. In Malaysia, since the 1980s, the major outbreak cycles have involved dengue virus type 3 (DENV3), dengue virus type 1 (DENV1) and dengue virus type 2 (DENV2), occurring in that order (DENV3/DENV1/DENV2). Only limited information on the DENV3 cycles, however, have been described. In the current study, we examined the major outbreak cycle involving DENV3 using data from 1985 to 2016. We examined the genetic diversity of DENV3 isolates obtained during the period when DENV3 was the dominant serotype and during the inter-dominant transmission period. Results obtained suggest that the typical DENV3/DENV1/DENV2 cyclical outbreak cycle in Malaysia has recently been disrupted. The last recorded major outbreak cycle involving DENV3 occurred in 2002, and the expected major outbreak cycle involving DENV3 in 2006–2012 did not materialize. DENV genome analyses revealed that DENV3 genotype II (DENV3/II) was the predominant DENV3 genotype (67%–100%) recovered between 1987 and 2002. DENV3 genotype I (DENV3/I) emerged in 2002 followed by the introduction of DENV3 genotype III (DENV3/III) in 2008. These newly emerged DENV3 genotypes replaced DENV3/II, but there was no major upsurge of DENV3 cases that accompanied the emergence of these viruses. DENV3 remained in the background of DENV1 and DENV2 until now. Virus genome sequence analysis suggested that intrinsic differences within the different dengue virus genotypes could have influenced the transmission efficiency of DENV3. Further studies and continuous monitoring of the virus are needed for better understanding of the DENV transmission dynamics in hyperendemic regions.     

Sylvatic dengue virus type 2 activity in humans, Nigeria, 1966

Using phylogenetic analysis of complete virus genomes from human isolates obtained in Nigeria in 1966, we identified sylvatic dengue virus (DENV) strains from 3 febrile patients. This finding extends current understanding of the role of sylvatic DENV in febrile disease and documents another focus of sylvatic DENV transmission in West Africa.     

Genomic mosaicism in two strains of dengue virus type 3

Recombination is a significant factor driving genomic evolution, but it is not well understood in Dengue virus. We used phylogenetic methods to search for recombination in 636 Dengue virus type 3 (DENV-3) genomes and unveiled complex recombination patterns in two strains, which appear to be the outcome of recombination between genotype II and genotype I parental DENV-3 lineages. Our findings of genomic mosaic structures suggest that strand switching during RNA synthesis may be involved in the generation of genetic diversity in dengue viruses.     

Cohesive subgroups and drug user networks in Dhaka City,Bangladesh

The purpose of this paper was to explore group drug taking behaviour in a slum area of Dhaka, Bangladesh. We set out to examine the relationships between those who met, at least weekly, to take illegal drugs together, and how these relationships might shape their drug behaviour. Sociometric and behavioural data were collected using questionnaires via semi-structured interviews. We found that the likelihood of injecting drugs and sharing needles increased with age, duration of group membership and length of drug use. Drug users were classified into two clusters: one was more cohesive and comprised longer-term users, who were more likely to inject drugs and had poorer physical and mental health. The other cluster comprised younger, better educated members who were more transient, less cohesive, less likely to inject drugs and had better health. Qualitative data suggested that members of the first cluster were less accepting of outsiders and confirmed more to group norms. We conclude that emotionally bonded cohesive subgroups acquire norms, which reinforce problematic drug-using behaviour. Thus, health initiatives need to consider group relationships and norms and those initiatives which work with networks may be more effective and more appropriate for low-income countries.     

Perceptions of mothers and use of breastmilk substitutes in Dhaka,Bangladesh

To explore the actual practices and perceptions of giving breastmilk and breastmilk substitutes (BMS), this cross-sectional study was conducted among 326 mothers of low (income/month < Tk 4,000, n = 163) and middle (income/month > Tk 4,000, n = 163) socioeconomic status (SES) with infants aged 6-12 months in Dhaka city during February-April 2001. Qualitative data on perceptions of mothers on appropriate breast-feeding practices were also documented through focus-group discussions (FGDs). The prevalence of exclusive breast-feeding was low in both the socioeconomic groups but was comparatively higher among the mothers of middle SES (3.1% vs 12.3%, p < 0.001), although predominant breast-feeding was high among the mothers of low SES. In addition, the use of BMS was higher among the mothers of middle SES than among the mothers of low SES (55.8% vs. 43.5%, p < 0.001). The majority (62.3%) of the mothers mentioned insufficiency of breastmilk as the main reason for introducing BMS. Perception on appropriate feeding practices was also significantly different between the two groups. Approximately, 90% of the mothers of low SES could not differentiate between infant formula and milk powder compared to 70% of the mothers of middle SES (p < 0.001). The findings of FGDs revealed that some middle-class mothers thought that infant formula was the best food for their infants. Programmes to impart proper knowledge on breast-feeding practices should be strengthened.     

Epidemiology of undernutrition in adults in Dhaka slum households, Bangladesh

OBJECTIVES: To identify socioeconomic, demographic and environmental factors that predict undernutrition in adults in a Dhaka slum population. DESIGN: A panel survey, conducted between 1995 and 1997. A random sample of households was selected. Socioeconomic, demographic and environmental variables were collected monthly by questionnaire and nutritional status was assessed. SETTING: Dhaka slums in Bangladesh. SUBJECTS: A total of 1097 adults surveyed during September-December 1996. MAIN OUTCOME MEASURES: Body mass index (BMI) less than 18.5 kg/m(2). RESULTS: There was a sex difference with female subjects having a significant odds ratio for low BMI compared with male subjects (P<0.03). There was no difference by age for males, but there was a difference by age for female subjects, with women aged 30-39 and 40-49 years having the worst BMI (P<0.04; P<0.04). The Beri Bahd area of residence had the worst BMI (P<0.001). Deficit situation as the self-reported financial situation had the worst BMI (P<0.03). Casual wage workers, unskilled and dependent self-employed individuals had the worst BMI (P<0.005; P<0.003). Not being involved in credit organizations and NGO credit organizations was associated with worst BMI (P<0.008; P<0.03). Those households that had an income of 2000-2499 Taka had the worst BMI (P<0.07). Households with a floor area of 5 m(2) or more per consumption unit had the best BMI (P<0.01). Households without electricity had the worst BMI (P<0.007). Households with tube well water had the worst BMI compared with those with tap water (P<0.001). CONCLUSIONS: Under nutrition was related to demographic, economic, social and environmental factors.     

Cohesive subgroups and drug user networks in Dhaka City, Bangladesh

The purpose of this paper was to explore group drug taking behaviour in a slum area of Dhaka, Bangladesh. We set out to examine the relationships between those who met, at least weekly, to take illegal drugs together, and how these relationships might shape their drug behaviour. Sociometric and behavioural data were collected using questionnaires via semi-structured interviews. We found that the likelihood of injecting drugs and sharing needles increased with age, duration of group membership and length of drug use. Drug users were classified into two clusters: one was more cohesive and comprised longer-term users, who were more likely to inject drugs and had poorer physical and mental health. The other cluster comprised younger, better educated members who were more transient, less cohesive, less likely to inject drugs and had better health. Qualitative data suggested that members of the first cluster were less accepting of outsiders and confirmed more to group norms. We conclude that emotionally bonded cohesive subgroups acquire norms, which reinforce problematic drug-using behaviour. Thus, health initiatives need to consider group relationships and norms and those initiatives which work with networks may be more effective and more appropriate for low-income countries.     

Dietary Patterns and Dietary Adequacy of Street Children in Dhaka,Bangladesh

The negative impact of poverty on the biological well-being of children is well established. The purpose of the present study was to evaluate the impact of the stress of full-time street life on the dietary patterns and dietary adequacy of street children living in Dhaka, Bangladesh. This was accomplished by comparing the nutritional patterns of full-time street children with those of other poor children in Dhaka who also spend their days on the streets but who return to their families at night. There were few differences between groups, possibly due to street children being a select group. However, there were significant sex differences in both groups of children, with boys tending to have more diverse and more adequate diets than girls. The cause of this latter pattern could not be determined with the available data but may involve cultural values favoring males over females.     

Delivery practices of traditional birth attendants in Dhaka slums, Bangladesh

This paper describes associations among delivery-location, training of birth attendants, birthing practices, and early postpartum morbidity in women in slum areas of Dhaka, Bangladesh. During November 1993-May 1995, data on delivery-location, training of birth attendants, birthing practices, delivery-related complications, and postpartum morbidity were collected through interviews with 1,506 women, 489 home-based birth attendants, and audits in 20 facilities where the women from this study gave birth. Associations among maternal characteristics, birth practices, delivery-location, and early postpartum morbidity were specifically explored. Self-reported postpartum morbidity was associated with maternal characteristics, delivery-related complications, and some birthing practices. Dais with more experience were more likely to use potentially-harmful birthing practices which increased the risk of postpartum morbidity among women with births at home. Postpartum morbidity did not differ by birth-location. Safe motherhood programmes must develop effective strategies to discourage potentially-harmful home-based delivery practices demonstrated to contribute to morbidity.     

疏水性区域及稀有密码子对登革2型病毒E基因原核表达影响的分析

登革病毒E蛋白是病毒主要毒力蛋白,带有型特异及属特异抗原决定簇,既能诱导宿主产生保护性的中和抗体,又能诱导产生血凝抑制抗体,与登革出血热(DHF)和登革休克综合征(DSS)的致病机制有关[1].有学者已经利用包括大肠埃希菌、毕赤酵母、昆虫细胞等多种表达系统对其表达条件进行了探讨,由于受未知因素的影响,登革病毒E蛋白的原核重组表达一直不理想[2～4].本研究对登革病毒E蛋白不同区域的原核表达进行了较为系统的分析,探讨疏水性区域及稀有密码子登革病毒E蛋白表达的影响,并对部分区域进行了高效原核表达.广东省科技计划项目(20006836008005);全军医药卫生科研基金资助课题(06MA129)     

Molecular analysis of G3 rotavirus among infants and children in Dhaka City, Bangladesh after 1993

Between 2004 and 2005, 917 fecal specimens were collected from children below age 5 who presented to Child Health Institute for treatment of diarrhoea in Dhaka City, Bangladesh. The specimens were screened by RT-PCR for the presence of group A rotavirus and positive stools genotyped. Group A rotavirus was detected in 307 stools and serotype G3P[8] strains were detected in nine specimens. Sequence analysis clustered the G3 strains into one distinct lineage (lineage I) with other Asian G3 strains. In addition, one amino acid change at position 96 in antigenic region A, similar to lineage II G3 Chinese strains, was noted. To our knowledge this is the first report of serotype G3 strains in Bangladesh since 1993 and the first report of the molecular characterization of these strains.     

Ferritin and Soluble Transferrin Receptors in Type 2 Diabetic and Non-diabetic Post-menopausal Women in Dhaka, Bangladesh

This cross-sectional comparative study was aimed at investigating the iron status of a group of post-menopausal women with and without diabetes. Thirty-five post-menopausal women in each group were selected purposively from among patients attending the out-patient department of Bangladesh Institute of Research and Rehabilitation in Diabetes, Endocrine and Metabolic Disorders (BIRDEM), a specialist hospital, and two of its satellite clinics, all in Dhaka. Patients were enrolled based on their existing records. The subjects were matched on age, menstrual status and fasting status at blood draw. Ferritin, serum soluble transferrin receptors (sTfR) and fasting plasma glucose were measured by standard methods. Dietary information was collected by a specific food frequency questionnaire. No significant difference in plasma ferritin [62.02 ng/ml, (range: 4.68-288.89) vs 54.25 ng/ml (range: 4.58-137.17); p=0.28] was observed between the groups. But a higher level of plasma sTfR was found in diabetic women [(21.12 nmol/l (range: 7.91-39.79) vs 17.63 nmol/l (range: 10.30-110.00); p<0.01]. TFR-F index showed no difference between diabetic and control (p=0.25). Significantly a lower hemoglobin level [10.58±0.67 g/dl vs11.76±1.5 g/dl; p<0.01] was detected in diabetic women. Plasma sTfR (log) did not show any significant association with the dietary parameters and iron indices. No significant association between fasting glucose, ferritin and sTfR was seen except for haemoglobin (r=0.39, p=0.05). Total iron intake recorded was more than the requirement, and was significantly higher in control group [38.11mg/day (range: 19.83-105.63) vs 56.65 mg/day (range: 29.75-109.54); p<0.01)]. More than 97 % of total iron was of plant origin. No differences in heme iron [0.85 mg/day (range: 0.09-4.07) vs. 0.96 mg/day (range: 0.04-4.34), p= 0.17] and vitamin C intake was observed between the groups. Iron indices of non-diabetic women were within the normal range. A higher level of sTfR and a lower level of hemoglobin in diabetic cases is suggestive of iron deficiency anaemia rather than iron overload.     

Infection of young adult mice with dengue virus type 2

Young adult female mice, five to six weeks old, were injected intraperitoneally with 2·5 × 10^6·3 LD₅₀ of dengue-2 virus, New Guinea C strain. The mice were killed on day 1, 2, 3, 4, 5, 6, 7, 10, 14, 21, 28 and 35 respectively. By means of the immunofluorescent antibody technique, viral antigen appeared as irregular granules in the reticuloendothelial cells of liver, lymph nodes and spleen of infected mice on the first day after inoculation and then diminished. From the fifth to sixth day of infection dengue antigen appeared again as homogeneous staining in the cytoplasm of single or groups of mononuclear cells in the lymphatic sinuses only. Later, by the third week of infection, dengue antigen could be seen in the mononuclear cells located in the marginal zone of lymphoid follicle of the spleen, the pattern of staining changing to bright spherical granules. At the same time, the deposition of immune complexes (composed of dengue antigen, mouse gamma and β1C globulin) could be seen in the renal glomeruli of infected mice.Serum antibody to dengue virus was found at low levels, being maximal on the 14th day after infection. Dengue virus was not isolated from the sera or from the infected organs. Granulomatous inflammation developed in lymph nodes and liver of mice infected with dengue virus and in mice inoculated with normal mouse brain suspension. Proliferative glomerular lesion was observed on day 14 after inoculation without definite abnormal urine findings.