Browsing by Author "Ahmed, K."

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Hospital-based study of the severity and economic burden associated with rotavirus diarrhea in Sri Lanka
(IOS Press, 2009) Chandrasena, N.; Rajindrajith, S.; Ahmed, K.; Pathmeswaran, A.; Nakagomi, O.
Human bocavirus in patients with encephalitis, Sri Lanka, 2009-2010
(Centers for Disease Control and Prevention (CDC), 2013) Mori, D.; Ranawaka, U.; Yamada, K.; Rajindrajith, S.; Miya, K.; Perera, H.K.K.; Matsumoto, T.; Dassanayake, M.; Mitui, M. T.; Mori, H.; Nishizono, A.; Soderlund-Venermo, M.; Ahmed, K.
We identified human bocavirus (HBoV) DNA by PCR in cerebrospinal fluid from adults and children with encephalitis in Sri Lanka. HBoV types 1, 2, and 3 were identified among these cases. Phylogenetic analysis of HBoV1 strain sequences found no subclustering with strains previously identified among encephalitis cases in Bangladesh.
Human-porcine reassortant rotavirus generated by multiple reassortment events in a Sri Lankan child with diarrhea
(Elsevier Science, 2018) Yahiro, T.; Takaki, M.; Chandrasena, T.G.A.N.; Rajindrajith, S.; Isa, H.; Ahmed, K.
A human-porcine reassortant rotavirus, strain R1207, was identified from 74 group A rotaviruses detected in 197 (37.6%) stool samples collected from patients who attended a tertiary care hospital in Ragama, Sri Lanka. This is the first report of a human-porcine reassortant rotavirus in Sri Lanka. The patient was a 12-month-old boy who had been hospitalized with fever and acute diarrhea with a duration of 6 days. The family had pigs at home before the birth of this boy. However, the neighbors still practice pig farming. The genotype constellation of R1207 was G4-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1. This is based on the assignment of all the eleven gene segments a full genome-based genotyping system. R1207 showed a 4-2-3-2 genomic electrophoretic migration pattern, which is characteristic of group A rotaviruses. Our analyses revealed that five (NSP2, NSP4, VP1, VP2, and VP7) of the 11 genes were closely related to the respective genes of porcine strains. Although the remaining six genes (NSP1, NSP3, NSP5, VP3, VP4, and VP6) were related to human strains, with the exception of the gene sequence of NSP1, all of these human strains were human-porcine reassortants. With a genogroup 1 genetic backbone, this strain was possibly formed via multiple genetic reassortments. We do not know whether this strain is circulating in pigs, as no data are available on porcine rotaviruses in Sri Lanka. Surveillance should be strengthened to determine the epidemiology of this genotype of rotavirus in Sri Lanka and to assess whether the infection was limited or sustained by ongoing human-to-human transmission.
Inaccurate identification of rotavirus genotype G9 as genotype G3 strains due to primer mismatch
(BioMed Central, 2012) Mitui, M.T.; Chandrasena, T.G.A.N.; Chan, P.K.S.; Rajindrajith, S.; Nelson, E.A.S.; Leung, T.F.; Nishizono, A.; Ahmed, K.
Reverse transcription (RT)-PCR is now the standard method for typing group A rotaviruses (RVA) to monitor the circulating genotypes in a population. Selection of primers that can accurately type the circulating genotypes is crucial in the context of vaccine introduction and correctly interpreting the impact of vaccination on strain distribution. To our knowledge this study is the first report from Asia of misidentification of genotype G9 as G3 due to a primer-template mismatch. We tested two published G-genotype specific primers sets, designed by Gouvea and colleagues (Set A) and Iturriza-Gomara and colleagues (Set B) on RVA from Hong Kong and Sri Lanka. Among 52 rotaviruses typed as G3 by set A primers, 36 (69.2%) were identified as G9 by nucleotide sequencing and set B primers. Moreover, of 300 rotaviruses tested, 28.3% were untypable by set A primers whereas only 12.3% were untypable by set B primers. Our findings reinforce the need to periodically monitor the primers used for RVA genotyping.
Paediatric rota-virus diarrhoea in Sri Lanka: a preliminary report
(Sri Lanka Medical Association, 2007) Chandrasena, T.G.A.N.; Rajindrajith, S.; Ahmed, K.; Pathmeswaran, A.; Abeyewickreme, W.; Nakagomi, O.
OBJECTIVE: To determine the prevalence, severity and molecular epidemiology of group A rotavirus infections among children hospitalized with diarrhoea in Sri Lanka. DESIGN, SETTINGS AND METHODS: A prospective hospital-based study was conducted in the paediatric units of the Colombo North Teaching Hospital from April 2005 to February 2006. Stool samples of children admitted with diarrhoea were analysed for Group A rotavirus antigen by enzyme linked immunosorbent assay (ELISA) (Rotaclone ®). Samples positive for rotavirus were characterised by electropherotyping (PAGE) and serotyping (reverse transcription-polymerase chain reaction (RT-PCR) respectively. Severity of diarrhoea was assessed by the Vesikari severity score. RESULTS: A total of 341 children [(204 males, mean age 25.7 months (range 1-144)] were studied. Sixty seven (19.6%) had rotavirus diarrhoea. RT-PCR and PAGE were done on 58 rotavirus positive samples. Thirty one samples were PAGE positive with 6 different electropherotypes. RT-PCR revealed the presence of serotypes Gl, G2, G3, G4 and G9 in 7 (12.1%), 16 (27.6%), 2 (3.4%), 2 (3.4%) and 11 (19.0%) samples respectively. Twenty samples (34.5%) were untypable. Severity score assessed in 326 patients revealed a mean score of 13.3 and 11.4 in rotavirus positive and negative diarrhoeas respectively (p<0.05). Presence, frequency and duration of vomiting and duration of diarrhoea were significantly higher in rotavirus infections (p<0.05). CONCLUSIONS: Rotavirus is an important agent of severe paediatric diarrhoea in Sri Lanka. Molecular analysis indicates genetic diversity among group A rotavirus. This study reports for the first time G9 type rotavirus infection in Sri Lanka.
Paediatric rotavirus diarrhoea in Sri Lanka: a preliminary report
(Sri Lanka College of Paediatricians, 2007) Chandrasena, T.G.A.N.; Rajindrajith, S.; Ahmed, K.; Pathmeswaran, A.; Abeyewickreme, W.; Nakagomi, O.
BACKGROUND: Group A rotavirus is the leading cause of acute gastroenteritis in children. Serotypes Gl, G2, G3 and G4 are mainly responsible for human infections. Strain characterization and serotype distribution of rotavirus in a country is an importaa determinant of future vaccine strategy. Information in this regard is scarce in Sri Lanka. OBJECTIVES: To determine the prevalence, severity and molecular epidemiology of rotavirus diarrhoea among children hospitalized with diarrhoea in Sri Lanka. DESIGN, SETTING AND METHOD: A prospective hospital-based study was conducted in the paediatric units of the North Colombo Teaching Hospital from April 2005-February 2006. Stool samples of children admitted with diarrhoea were analyzed for Group A rotavirus antigen by enzyme linked immunosorbent assay (EL1SA) (Rotaclone). Samples positive for rotavirus were characterized electropherotyping (PAGE) and serotyping (reverse transcription-poiymerase chain reaction (RT-PCR)) respectively. Severity of diarrhoea was assessed by the Vesikari severity score. RESULTS: A total of 341 children [204 males mean age 25.7 months (range 1-144)] were studied. Sixty seven (19.6%) had rotavirus diarrhoea. RT-PCR and PAGE were done on 58 rotavirus positive samples. Thirty one were PAGE positive with 6 different electropherotypes. RT-PCR revealed the presence of serotypes Gl, G2, G3, G4 and G9 in 7 (12.1%), 16 (27.6%),2 (3.4%), 2 (3.4%), and 11 (19.0%) samples respectively. Twenty (34.5%) were untypable. Severity score, assessed in 326 patients, revealed a mean score of 13.3 and 11.4 in rotavirus positive and negative patients respectively (p=0.05). Presence frequency and duration of vomiting and duration of diarrhoea were significantly higher in rotavirus diarrhoea (p<0.05). CONCLUSIONS: Rotavirus is an important agent of severe paediatric diarrhoea in Sri Lanka. Molecular analysis indicates genetic diversity among group A rotavirus in Sri Lanka. This study reports for the first time of G9 type rotavirus infection in Sri Lanka.
Projected cost- effectivenes of rotavirus vaccination in Sri Lanka
(The Bulletin of the Sri Lanka College of Microbiologists, 2007) Chandrasena, T.G.A.N.; Rajindrajith, S.; Gunawardane, R.; Adhihetty, D.; Ahmed, K.; Pathmeswaran, A.; Nakagomi, O.
OBJECTIVES: The disease and economic burden of rotavirus infection among children hospitalised for gastroenteritis in Sri Lanka was assessed, in anticipation of the availability of new rotavirus vaccines. METHODS: A prospective gastroenteritis case surveillance was conducted between April 2005-October 2006 at the paediatric units of the Colombo North Teaching Hospital. Stool samples of children admitted with diarrhoea were screened for group A rotavirus antigens by enzyme-immuno assay (ElA)(Rotaclone®).Information regarding medical and non- medical costs during the event was obtained among randomly selected rotavirus cases (n=45) through an interviewer administered questionnaire. Cost effectiveness of universal rotavirus vaccination was investigated assuming a cost Of ≤ US$.7 per vaccine dose (two dose regime) in accordance with the World Bank cost effectiveness standard for low-income countries. RESULTS: Total of 606 children (335 males)[ mean age 27.3 months,(range 1-144) were analyzed. 116 (19.1%) had rotavirus antigens. The prevalence among the 0-5 years age group was 20.8. The average cost per episode of rotavirus gastroenteritis was Rs. 3004(US$ 27). Estimated initial and recurrent expenditure of universal vaccination was US$ 23.7 and five million respectively. Costs saved through averting rotavirus diarrhoea hospitaljsations per year (assuming a vaccine of 100% efficacy) were US$ 0.21 million. Deaths averted were eight per year. CONCLUSION: Universal rotavirus vaccination at 5 US$.7 per dose may not be cost-saving in Srilanka. However decisions regarding vaccine use should be based not only on whether the intervention provides cost savings but also on the value of preventing associated morbidity and mortality.
Rotavirus infections with multiple emerging genotypes in Sri Lanka
(Springer-Verlag, 2010) Ahmed, K.; Batuwanthudawe, R.; Chandrasena, T.G.A.N.; Mitui, M.T.; Rajindrajith, S.; Galagoda, G.; Pun, S.B.; Uchida, R.; Kunii, O.; Moji, K.; Abeysinghe, N.; Nishizono, A.; Nakagomi, O.
Rotavirus diarrhea is an important cause of child mortality in developing countries, but studies on this diarrhea are scarce in Sri Lanka. A prospective study conducted in Sri Lanka on rotavirus infection among children in a hospital setting (n = 611) versus children residing in tsunami camps (n = 52) showed that prevalence of rotavirus infection was comparable, 21.9 and 20%, respectively. The hospital and camps were located in different districts. Analysis of the genotypes of 122 rotaviruses from the hospital and 12 from the camps indicated that G9P[8] was associated with 35 and 33%; G12P[8/nt] with 14.7 and 33%; G3P[8/4/nt] with 17 and 8% and G1P[8/4] with 6.5 and 16.7%. Rotaviruses with G2P[8/4/6] and G4P[8/4] were hospital-associated only, and some rotaviruses (9 and 8% from the hospital and the camps, respectively) were G- and P-nontypable. We conclude from the present study that multiple emerging genotypes were prevalent in Sri Lanka, and children in camps were at risk of developing diarrhea due to rotaviruses
Rotavirus surveillance at the North Colombo Teaching Hospital, Sri Lanka, 2007-2008
(Sri Lanka College of Paediatricians, 2010) Chandrasena, T.G.A.N.; Rajindrajith, S.; Gunawardena, N.K.; Abayawardana, U.A.T.M.; Ranasinghe, S.L.; Nishizono, A.; Moji, K.; Ahmed, K.
INTRODUCTION: Rotavirus disease is a common paediatric problem and accounts for severe dehydrating diarrhoea, a large number of hospital admissions and an annually estimated 600,000 deaths across the world. Prospective Rotavirus surveillance was initiated at the North Colombo Teaching Hospital (NCTH), Sri Lanka from April 2005. The serorype distribution in our previous study was; G9P[S] 35.2%, G12P[8] 14.7%, G3P[4] 17.2%, G2P[8/4/6] 14%, GlP[8/4] 6.5% and G4P[8/4] 3.3%. OBJECTIVE: To describe the serotype distribution of rotavirus responsible for hospitalization at the NCTH. DESIGN, SETTING AND METHOD: A prospective hospital-based study was conducted in the paediatric units of the NCTH from November 2007-October 2008. Stool samples of children admitted with diarrhoea were analyzed for Group A rotavirus antigen by enzyme linked immunosorbent assay (ELISA) (Rotaclone). Stool samples positive for rotavirus were characterized by electropherotyping (PAGE) and serotyping (reverse transcription polymasase chain reaction - RT PCR). RESULTS: Group A rotavirus was detected in 78 (33%) of 231 children less than 5 years of age admitted with diarrhoea. G9, Gl, G2, G3 and G non-typable infections were seen in 33(42%), 31 (40%) 7 (9%), 1 (1.3%) and 4 (5%) respectively. A predominance of G9 serotype (84%) was seen during the initial seven months. Dramatic transition of genotypic predominance to Gl (70%) occurred in the latter half of the year. All Gl, G3 and G9 strains assayed for P genotype contained P8 except two mixed G9 infections which were associated with P4 and PS. In contrast to the previous report, all G2 strains identified were associated with P4 and serotypes G12P [8] and G4P [8/4] were not detected. Polyacrylamide-gel-electrophoresis revealed the presence of El, E2, E3, E4 and E5 electropherotypes with a co-dominance of Eland E5 (30.7%). CONCLUSIONS: During the study period a rising trend in prevalence with a fluctuating genotypic distribution was observed at CNTH, Sri Lanka. The diversity of rotavirus serotypes requires a vaccine that confers adequate homotypic and heterorypic protection against these strains.
Small circular single stranded DNA viral genomes in unexplained cases of human encephalitis, diarrhea, and in untreated sewage
(New York, Academic Press, 2015) Phan, T.G.; Mori, D.; Deng, X.; Rajindrajith, S.; Ranawaka, U.; Fan Ng, T.F.; Bucardo-Rivera, F.; Orlandi, P.; Ahmed, K.; Delwart, E.
Viruses with small circular ssDNA genomes encoding a replication initiator protein can infect a wide range of eukaryotic organisms ranging from mammals to fungi. The genomes of two such viruses, a cyclovirus (CyCV-SL) and gemycircularvirus (GemyCV-SL) were detected by deep sequencing of the cerebrospinal fluids of Sri Lankan patients with unexplained encephalitis. One and three out of 201 CSF samples (1.5%) from unexplained encephalitis patients tested by PCR were CyCV-SL and GemyCV-SL DNA positive respectively. Nucleotide similarity searches of pre-existing metagenomics datasets revealed closely related genomes in feces from unexplained cases of diarrhea from Nicaragua and Brazil and in untreated sewage from Nepal. Whether the tropism of the cyclovirus and gemycircularvirus reported here include humans or other cellular sources in or on the human body remains to be determined.
Spatial epidemiology and hotspots of Rotavirus In children: an analysis and mapping using Geographic Information System
(Sri Lanka College of Paediatricians, 2010) Gunawardena, N.K.; Rajindrajith, S.; Chandrasena, T.G.A.N.; Nishizono, A.; Moji, K.; Ahmed, K.
INTRODUCTION: Rotavirus is a leading cause of acute gastroenteritis in Sri Lanka. Studies from the western world have assessed the seasonal variations of this infection and its association with environmental factors such as rainfall and temperature. However, little is known of its seasonal variation and geographical distribution in Sri Lanka. Areliable and updated distribution map of rotavirus infection is essential for target control strategies and policy making processes. Geographical Information. System (GIS) has previously been used to monitor spatial distribution of diseases and their transmission dynamics. For the first time we describe the spatial epidemiological patterns of rotavirus diarrhoea in Sri Lanka. OBJECTIVE: To study the spatial epidemiological distribution of rotaviral infection among children with diarrhoeal diseases admitted to the North Colombo Teaching Hospital, Ragama. DESIGN, SETTING AND METHOD: This study was carried out in two phases. Phase I, a prospective hospital-based study, was conducted in the North Colombo Teaching Hospital from January 2008 to October 2009 to detect the incidence of rotavirus infection in children with diarrhoea. Stool samples were analyzed for Group A rotavirus antigen by enzyme linked immunosorbent assay (EL1SA) (Rotaclone). During Phase II of the study, patients with rotavirus infection were mapped using geographic coordinates obtained from a hand-held GIS receiver (Trimble Juno SB). Rainfall and temperature data for the years 2008 and 2009 in the Gampaha District were obtained from the Department of Meteorology, Sri Lanka and correlated with the spatial distribution data. RESULTS: In 2008 and 2009, 71 (60.6% males) and 99 (63.6% males) had rotavirus infection respectively. Spatial distribution data showed that most rotavirus infections (78%) presenting to the Teaching Hospital, Ragama were coming from a 10 km radius of catchment area. The hot spots were clustered in and around the marshy land areas of the Gampaha District and 67% use water from their own well or from the well of a neighbour. The peak incidence in both years was between May and July which coincided with the highest rainfall to the area. There was no correlation between environmental temperature and rotavirus infection rates. CONCLUSION: Incidence of rotavirus infection is highest in children living around marshy lands and using water from private sources such as a well.
Surveillance of rotavirus in three hospital settings of Sri Lanka 2007 - 2010
(Sri Lanka College of Microbiologists, 2014) Chandrasena, T.G.A.N.; Rajindrajith, S.; Gunawardena, N.K.; Liyanarachchi, N.; Abeysekera, C.K.; Matsomoto, T.; Yahiro, T.; Nishizono, A.; Ahmed, K.
INTRODUCTION: Rotavirus is an important aetiological agent of childhood diarrhoeas in Sri Lanka. OBJECTIVES: To study the rotavirus epidemiology and genotypic diversity of cases hospitalized in three geographical locations of Sri Lanka, Ragama, Galle and Kandy. MATERIALS AND METHODS: The study was approved by the ethical review board of the Sri Lanka College of Paediatricians. Stool samples were collected from children < 5 years, hospitalized at the Teaching Hospitals at Ragama (RTH) (November 2007 - October 2010) Galle (GTH) and Kandy (KTH) (mid and late 2008) respectively for acute gastroenteritis. Rotavirus was detected using EIA kit, Rotaclone®. A subset of rotavirus positive samples was genotyped by reverse-transcription(Rt)-PCR and polyacrylamide-gel-electrophoresis (PAGE). RESULTS: Stool samples of 1245 children (69.2%, 23.3% and 7.3% from RTH, GTH and KTH respectively) were screened for rotavirus. Of them, 476 were positive by EIA. The overall rate of prevalence of rotavirus infection was 38.2%. The median age of infection ranged from 13-20 months. Rotavirus genotyping was done on 375 (78.8 %) samples. G1 [P8] was the overall dominant strain (44.8%) followed by G9[P8] (10.1%), G2[P4] (5.3%), G3[P8] (3.2%), G1[P6] (2.1%), G12[P6] (1.3%), G2[P8] (1.06%) and 0.26% of G4[P6], G4[P4] and G4[P8]. The G or P serotype was untypable in 25.6% of samples and 5.6% were of mixed-G and P type. PAGE yeilded 25 electropherotypes (E1-E12 and E16-E29), with E5 and E20 causing 19 and 14 percent of infections respectively. The electropherotype could not be determined in 26%. CONCLUSIONS: Rotavirus continues to be an important cause of childhood diarrhoreas in Sri Lanka. Strain G1P8 predominated in all areas during the surveillance period with a notable percentage of mixed-G and P infections. Multiple E types identified indicate increasing strain diversity