Center for Molecular Dynamics Nepal

Kathmandu, Nepal

Center for Molecular Dynamics Nepal

Kathmandu, Nepal
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PubMed | Mountain Gorilla Veterinary Project Inc., University of California at Davis and Center for Molecular Dynamics Nepal
Type: Journal Article | Journal: PLoS neglected tropical diseases | Year: 2015

Free-ranging nonhuman primates are frequent sources of zoonotic pathogens due to their physiologic similarity and in many tropical regions, close contact with humans. Many high-risk disease transmission interfaces have not been monitored for zoonotic pathogens due to difficulties inherent to invasive sampling of free-ranging wildlife. Non-invasive surveillance of nonhuman primates for pathogens with high potential for spillover into humans is therefore critical for understanding disease ecology of existing zoonotic pathogen burdens and identifying communities where zoonotic diseases are likely to emerge in the future. We developed a non-invasive oral sampling technique using ropes distributed to nonhuman primates to target viruses shed in the oral cavity, which through bite wounds and discarded food, could be transmitted to people. Optimization was performed by testing paired rope and oral swabs from laboratory colony rhesus macaques for rhesus cytomegalovirus (RhCMV) and simian foamy virus (SFV) and implementing the technique with free-ranging terrestrial and arboreal nonhuman primate species in Uganda and Nepal. Both ubiquitous DNA and RNA viruses, RhCMV and SFV, were detected in oral samples collected from ropes distributed to laboratory colony macaques and SFV was detected in free-ranging macaques and olive baboons. Our study describes a technique that can be used for disease surveillance in free-ranging nonhuman primates and, potentially, other wildlife species when invasive sampling techniques may not be feasible.


Bam K.,Center for Molecular Dynamics Nepal | Rajbhandari R.M.,Center for Molecular Dynamics Nepal | Karmacharya D.B.,Center for Molecular Dynamics Nepal | Dixit S.M.,Center for Molecular Dynamics Nepal
BMC Health Services Research | Year: 2015

Background: Anti Retroviral Therapy (ART) is the cornerstone for comprehensive health sector response to Human Immunodeficiency Virus (HIV) treatment, care and support. Adherence of at least 95% is needed to keep HIV under control, as per World Health Organization (WHO) guidelines. This study was aimed at identifying the overall adherence level of, and barriers and facilitators to adherence for patients taking ART in different clinics in all five development regions of Nepal. Methods: A descriptive cross-sectional study was conducted among ART clients receiving free ART from Government of Nepal ART clinics. A total of 435 clients taking ART from twelve ART clinics in different regions of Nepal, aged fifteen years and above were interviewed on one-and-one basis using questionnaires developed in reference to Adult AIDS Clinical Trial Group (AACTG) toolkit among them data from 404 were analyzed after cleaning. Data was entered and analyzed using Statistical Package for Social Sciences (SPSS) software where the P value of∈<∈0.05 was accepted as being statistically significant. Results: The overall adherence in the last month (missed less than three pills total) was 94.8% (383 out of 404). The main barrier to ART adherence was the fear of side effects (among 61.9% of the non adherent population) which included dizziness (18.1%) and headaches (15.4%). The standard wristwatch (39%) was found to be the most useful aid in enabling timely consumption of medication. Educational status (P∈=∈0.018), drug using habits (P∈=∈0.039) and the conducive environment at ART clinics (P∈=∈0.004) were significantly associated with ART adherence. Conclusion: Improving better adherence may require a more holistic approach to treatment regimen and adapting it to patient daily routines. This study identifies issues such as pill count for assessing adherence, better access to health care facilities by clients, better access to medication, as well as improved nutritional support issues for better adherence by the population in the future. © 2015 Bam et al.; licensee BioMed Central.


Manandhar S.,Center for Molecular Dynamics Nepal | Bhusal C.L.,Nepal Health Research Council | Ghimire U.,Nepal Health Research Council | Singh S.P.,Nepal Health Research Council | And 2 more authors.
Malaria Journal | Year: 2013

Background: Malaria is a major public health problem in Nepal inflicted primarily by the parasite Plasmodium vivax, - the only species responsible for relapse cases in Nepal. Knowledge on its relapse rate is important for successful malaria control, but is lacking in Nepal. The information on circulating predominant genotypes of P. vivax is equally relevant for high endemic districts of Nepal to understand the transmission dynamics of the parasite and to uncover the coverage and efficacy of potential vaccine beforehand. Methods. A prospective observational study with a six months follow-up period was conducted from August 2010 to May 2011 in four health centres of Kailali and Kanchanpur districts of Nepal to access the relapse/re-infection rate of P. vivax. The prevalence and heterogeneity of its genotypes were identified by PCR-RFLP assay targeting central repeat region of circumsporozoite protein (Pvcsp). Results: In total, 137 cases microscopically suspected to have P. vivax infection were enrolled in the study. Of these, 23 cases (17%) were detected for the relapse/ re-infection-during a six-month period, with a high proportion being male cases of age group 11-20 years. For genotyping, 100 whole blood samples were analysed, of which 95% of the parasite isolates were found to be of VK210 genotype. The minor genotype VK247 existed either in isolation or as mixed infection with VK210 in rest of the samples. Conclusions: The relapse/re-infection rate of 17% was determined for P. vivax in Kailali and Kanchanpur districts of Nepal. A heterogeneous Pvcsp genotypic distribution of P. vivax was detected with VK210 being a predominant type, suggesting a complex transmission dynamics of the parasite. Expanding such study in other endemic regions of Nepal would help provide a complete picture on relapse/re-infection rate and parasite genotypic variability that can help in effective control and management of malaria in Nepal. © 2013 Manandhar et al.; licensee BioMed Central Ltd.


Aryal A.,Massey University | Brunton D.,Massey University | Ji W.,Massey University | Karmacharya D.,Center for Molecular Dynamics Nepal | And 4 more authors.
Journal of Mammalogy | Year: 2014

The snow leopard (Panthera uncia) is an endangered carnivore of southern and central Asia. Approximate 10% of the global population occurs in the Himalayan region of Nepal. The snow leopard is thought to be in decline because of human-snow leopard conflicts, poaching, habitat loss and fragmentation, decreasing prey populations, and a lack of awareness and enforcement of conservation legislation. In this study, we used habitat surveys and genetic analyses of putative snow leopard scats to estimate the abundance, habitat preferences, and diet profile of the snow leopard in the Annapurna Conservation Area, Nepal. Cliffs, grassland, and shrubland at high elevation (3,000-5,000 m) were the preferred habitats of snow leopards. Eighty-three percent of collected scats collected were verified to be from snow leopards using mitochondrial DNA cytochrome-b species-specific polymerase chain reaction assays. Sixty-two percent of the scats were successfully genotyped using 6 microsatellite markers, and identified as having originated from 5 different individuals. The dispersion of multiple scats from the same individual suggested minimum movement ranges of 89.4 km2 for males and 59.3 km2 for females. Estimated population density was 1.9 individuals/100 km2 and 22 snow leopards were estimated to inhabit the upper Mustang region. Microhistological analysis of scats (n = 248) revealed that blue sheep (Pseudois nayaur) was the primary wild prey (63%), and livestock also contributed significantly (18%) to snow leopard diet. We used a multipronged strategy for assessing conservation options for this rare carnivore and compared our findings with those pertaining to other predators of the region that share similar habitats and resources. The findings from this study will be helpful in managing snow leopards and similar carnivore populations across the snow leopard's entire geographic range. © 2014 American Society of Mammalogists.


Upreti S.R.,Child Health Division | Gurung S.,World Health Organization | Patel M.,Centers for Disease Control and Prevention | Dixit S.M.,Center for Molecular Dynamics Nepal | And 6 more authors.
Vaccine | Year: 2014

Background: In Nepal, an estimated 2-4% of the population has chronic hepatitis B virus (HBV) infection. To combat this problem, from 2002 to 2004, a national three dose hepatitis B vaccination program was implemented to decrease infection rates among children. The program does not currently include a birth dose to prevent perinatal HBV transmission. In 2012, to assess the impact of the program, we conducted a serosurvey among children born before and after vaccine introduction. Methods: In 2012, a cross-sectional nationally representative stratified cluster survey was conducted to estimate hepatitis B surface antigen (HBsAg) prevalence among children born from 2006 to 2007 (post-vaccine cohort) and among children born from 2000 to 2002 (pre-vaccine cohort). Demographic data, as well as written and oral vaccination history were collected. All children were tested for HBsAg; mothers of HBsAg positive children were also tested. Furthermore, we evaluated the field sensitivity and specificity of the SD Bioline HBsAg rapid diagnostic test by comparing results with an enzyme immunoassay. Results: Among 2181 post-vaccination cohort children with vaccination data by either card or recall, 86% (95% confidence interval [CI] 77-95%) received ≥3 hepatitis B vaccine doses. Of 1200 children born in the pre-vaccination cohort, 0.28% (95% CI 0.09-0.85%) were positive for HBsAg; of 2187 children born in the post-vaccination cohort, 0.13% (95% CI 0.04-0.39%) were positive for HBsAg (p= 0.39). Of the six children who tested positive for HBsAg, two had mothers who were positive for HBsAg. Finally, we found the SD Bioline HBsAg rapid diagnostic test to have a sensitivity of 100% and a specificity of 100%. Conclusions: This is the first nationally representative hepatitis B serosurvey conducted in Nepal. Overall, a low burden of chronic HBV infection was found in children born in both the pre and post-vaccination cohorts. Current vaccination strategies should be continued. © 2014.


Dixit S.,Center for Molecular Dynamics Nepal
Journal of Nepal Health Research Council | Year: 2011

V. cholera types have been implicated often in a number of occasions in diarrhoeal outbreaks in Nepal. The recent outbreak in Far Western Nepal, 2009, was also attributed primarily to V. cholera. Molecular tools were used for the first time on some of the samples from the outbreak to screen for major pathogens present in those samples. A commercial multiplex PCR kit based bacterial enteropathogen screening assessment was carried out on 33 human stool samples from areas of a diarrhoeal outbreak in Nepal. A total of 10 pathogenic bacterial strains at the genus level were targeted using primers provided by the manufacturer. Bacterial pathogens were detected in 23 samples (69.7%). Vibrio species was detected at an overall frequency of 36.4% followed by Aeromonas spp (33.3%) and Shigella spp (15.2%) along with Verocytotoxin producing E. coli (VTEC) family (15.2%). The frequency of singly occurring pathogen in all samples was 18.2% with most of the bacterial pathogens detected in combination with other pathogens at a frequency of 60.6%. The study also shows that majority 73 (86%) of the research centers didn't start the research yet. This first ever molecular screening study shows that bacterial screening is indeed possible in diarrhoeal samples. The results obtained from this study will enable monitoring of future such outbreaks using similar techniques.


Karmacharya D.,Center for Molecular Dynamics Nepal | Yu D.,Massachusetts General Hospital | Dixit S.,Center for Molecular Dynamics Nepal | Rajbhandari R.,Center for Molecular Dynamics Nepal | And 4 more authors.
AIDS Research and Therapy | Year: 2012

Background: The true prevalence of HIV and other sexually transmitted diseases among street children in Nepal is virtually unknown while information on related behavioural risk factors in this population is non-existent. The risk of HIV infection among street children and adolescents may be especially high due to their marginalized social and economic conditions. This study was conducted to determine the prevalence of HIV infection among a sample of street children and youth of Kathmandu and to identify risk factors associated with HIV infection in this group.A sample of street children and youth was recruited based on the purposive sampling of ten streets in Kathmandu, Nepal, known to have a high density of street children and youth. A total of 251 street children (aged 11-16 years) and youth (aged 17-24 years) were enrolled, with informed consent, from November, 2008 through June, 2009. Most of the participants (95%) were male. Case status was determined by serological assessment of HIV status; data on risk factors were obtained using structured survey interviews. HIV prevalence and rates of a number of behavioural risk factors suspected to play a role in HIV transmission among street children and youth were determined, including unprotected sex, intravenous drug use, and other risky sex and substance use behaviours.Results: Among the 251 children and youth, we found an overall HIV prevalence of 7.6%. As the sample size of females was small (n = 13) and the behavioural risk factors are likely to be quite different for boys and girls, we conducted separate analyses by gender. As our small sample of females is unlikely to be representative and lacks power for statistical testing, our report focuses on the results for the males surveyed.The strongest behavioural risk factor to emerge from this study was intravenous drug use; 30% of the male subjects were injecting drug users and 20% of those were HIV positive. Furthermore, frequency of drug injection was a highly significant predictor with a dose-response relationship; males reporting occasional injection drug use were nearly 9 times more likely to be HIV positive than never users, while weekly drug injectors had over 46 times the risk of non-users, controlling for exposure to group sex, the only other significant risk factor in the multivariate model.Conclusions: This sample of street children and youth of Kathmandu has a nearly 20-fold higher prevalence of HIV infection than the general population of Nepal (0.39%). The children and youth engage in number of high risk behaviours, including intravenous drug use, putting them at significant risk of contracting HIV and other sexually transmitted infections. © 2012 Karmacharya et al.; licensee BioMed Central Ltd.


Karmacharya D.B.,Center for Molecular Dynamics Nepal | Thapa K.,World Wildlife Fund | Shrestha R.,World Wildlife Fund | Dhakal M.,Ministry of Forests and Soil Conservation | Janecka J.E.,Texas A&M University
BMC Research Notes | Year: 2011

Background: The endangered snow leopard is found throughout major mountain ranges of Central Asia, including the remote Himalayas. However, because of their elusive behavior, sparse distribution, and poor access to their habitat, there is a lack of reliable information on their population status and demography, particularly in Nepal. Therefore, we utilized noninvasive genetic techniques to conduct a preliminary snow leopard survey in two protected areas of Nepal. Results: A total of 71 putative snow leopard scats were collected and analyzed from two different areas; Shey Phoksundo National Park (SPNP) in the west and Kangchanjunga Conservation Area (KCA) in the east. Nineteen (27%) scats were genetically identified as snow leopards, and 10 (53%) of these were successfully genotyped at 6 microsatellite loci. Two samples showed identical genotype profiles indicating a total of 9 individual snow leopards. Four individual snow leopards were identified in SPNP (1 male and 3 females) and five (2 males and 3 females) in KCA. Conclusions: We were able to confirm the occurrence of snow leopards in both study areas and determine the minimum number present. This information can be used to design more in-depth population surveys that will enable estimation of snow leopard population abundance at these sites. © 2011 Karmacharya et al; licensee BioMed Central Ltd.


PubMed | Trichandra Multiple College, German Society for International Cooperation, SPARSHA Nepal, St Xavier College and Center for Molecular Dynamics Nepal
Type: Journal Article | Journal: PloS one | Year: 2015

As part of a comprehensive health care programme for people who use drugs in Nepal, HIV and viral hepatitis B and C status--including risk factors, HCV-genotypes and co-infections--as well as two IL28B Single-nucleotide polymorphisms (SNPs) were assessed for a random sample of 401 people who inject drugs in three regions of Nepal: mid-western Terrai (Nepalgunj), the eastern region (Dharan, Biratnagar) and the central region (Kathmandu, Lalitpur and Chitwan). Individuals were included who showed at least a minimum of health care seeking behaviour. This latter criterion was defined by being registered with any organisation offering health services. The average age of the participants was 30.5 yrs, and the average length of intravenous drug use was 8.5 yrs. The prevalence rates of HBsAg, anti-HIV antibodies and HCV-RNA were 3.5%, 13.8% and 41.9%, respectively. Spontaneous HCV clearance was evident in 16% of all of those who tested positive for anti-HCV antibodies. Independent risk factors for HCV-RNA positivity were age, gender, geographical region, duration of injecting drug use, history of imprisonment and HIV co-infection. In the age group 24 yrs, the rate of spontaneous HCV clearance was 43.5%. Overall, 59.8% of HCV infections were caused by HCV genotype 3 and 40.2% by HCV genotype 1. No other HCV genotypes were identified in this study. The IL28B SNP rs12979860 and rs8099917 were identified in 122 patients, and 75.4% of all participants had both favourable genotypes rs12979860 C/C and rs8099917 T/T.


PubMed | Centers for Disease Control and Prevention, World Health Organization, Child Health Division, National Public Health Laboratory and Center for Molecular Dynamics Nepal
Type: Journal Article | Journal: Vaccine | Year: 2014

In Nepal, an estimated 2-4% of the population has chronic hepatitis B virus (HBV) infection. To combat this problem, from 2002 to 2004, a national three dose hepatitis B vaccination program was implemented to decrease infection rates among children. The program does not currently include a birth dose to prevent perinatal HBV transmission. In 2012, to assess the impact of the program, we conducted a serosurvey among children born before and after vaccine introduction.In 2012, a cross-sectional nationally representative stratified cluster survey was conducted to estimate hepatitis B surface antigen (HBsAg) prevalence among children born from 2006 to 2007 (post-vaccine cohort) and among children born from 2000 to 2002 (pre-vaccine cohort). Demographic data, as well as written and oral vaccination history were collected. All children were tested for HBsAg; mothers of HBsAg positive children were also tested. Furthermore, we evaluated the field sensitivity and specificity of the SD Bioline HBsAg rapid diagnostic test by comparing results with an enzyme immunoassay.Among 2181 post-vaccination cohort children with vaccination data by either card or recall, 86% (95% confidence interval [CI] 77-95%) received 3 hepatitis B vaccine doses. Of 1200 children born in the pre-vaccination cohort, 0.28% (95% CI 0.09-0.85%) were positive for HBsAg; of 2187 children born in the post-vaccination cohort, 0.13% (95% CI 0.04-0.39%) were positive for HBsAg (p=0.39). Of the six children who tested positive for HBsAg, two had mothers who were positive for HBsAg. Finally, we found the SD Bioline HBsAg rapid diagnostic test to have a sensitivity of 100% and a specificity of 100%.This is the first nationally representative hepatitis B serosurvey conducted in Nepal. Overall, a low burden of chronic HBV infection was found in children born in both the pre and post-vaccination cohorts. Current vaccination strategies should be continued.

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