Time series non-Gaussian Bayesian bivariate model applied to data on HMPV and RSV: a case of Dadaab in Kenya.

BACKGROUND: Human metapneumovirus (HMPV) have similar symptoms to those caused by the respiratory syncytial virus (RSV). The modes of transmission and dynamics of time series data still remain poorly understood. Climatic factors have long been suspected to be implicated in impacting on the number of cases for these epidemics. Currently, only a few models satisfactorily capture the dynamics of time series data of these two viruses. Our objective was to assess the presence of influence of high incidences between the viruses and to ascertain whether higher incidences of one virus are influenced by the other. METHODS: In this study, we used a negative binomial model to investigate the relationship between RSV and HMPV while adjusting for climatic factors. We specifically aimed at establishing the heterogeneity in the autoregressive effect to account for the influence between these viruses. RESULTS: In this study, our findings showed that RSV incidence contributed to the severity of HMPV incidence. This was achieved through comparison of 12 models with different structures, including those with and without interaction between climatic factors. The models with climatic factors out-performed those without. CONCLUSIONS: The study has improved our understanding of the dynamics of RSV and HMPV in relation to climatic cofactors thereby setting a platform to devise better intervention measures to combat the epidemics. We conclude that preventing and controlling RSV infection subsequently reduces the incidence of HMPV.

Correction: Sanitation practices and perceptions in Kakuma refugee camp, Kenya: Comparing the status quo with a novel service-based approach.

[This corrects the article DOI: 10.1371/journal.pone.0180864.].

Sanitation practices and perceptions in Kakuma refugee camp, Kenya: Comparing the status quo with a novel service-based approach.

Globally, an estimated 2.5 billion people lack access to improved sanitation. Unimproved sanitation increases the risk of morbidity and mortality, especially in protracted refugee situations where sanitation is based on pit latrine use. Once the pit is full, waste remains in the pit, necessitating the construction of a new latrine, straining available land and funding resources. A viable, sustainable solution is needed. This study used qualitative and quantitative methods to design, implement, and pilot a novel sanitation system in Kakuma refugee camp, Kenya. An initial round of 12 pre-implementation focus group discussions (FGDs) were conducted with Dinka and Somali residents to understand sanitation practices, perceptions, and needs. FGDs and a supplementary pre-implementation survey informed the development of an innovative sanitation management system that incorporated the provision of urine and liquid-diverting toilets, which separate urine and fecal waste, and a service-based sanitation system that included weekly waste collection. The new system was implemented on a pilot scale for 6 weeks. During the implementation, bi-weekly surveys were administered in each study household to monitor user perceptions and challenges. At the end of the pilot, the sanitation system was assessed using a second round of four post-implementation FGDs. Those who piloted the new sanitation system reported high levels of user satisfaction. Reported benefits included odor reduction, insect/pest reduction, the sitting design, the appropriateness for special populations, and waste collection. However, urine and liquid diversion presented a challenge for users who perform anal washing and for women who had experienced female genital mutilation. Refugee populations are often culturally and ethnically diverse. Using residents' input to inform the development of sanitation solutions can increase user acceptability and provide opportunities to improve sanitation system designs based on specific needs.

Evaluation of the Field Performance of ImmunoCard STAT!® Rapid Diagnostic Test for Rotavirus in Dadaab Refugee Camp and at the Kenya-Somalia Border.

AbstractRotavirus commonly causes diarrhea in children, leading to hospitalization and even death. Rapid diagnostic tests are feasible alternatives for determining rotavirus outbreaks in refugee camps that have inadequate laboratory capacity. We evaluated the field performance of ImmunoCard STAT!® Rotavirus (ICS-RV) in Dadaab Refugee Camp and at the Kenya-Somalia border. From May to December 2014, we prospectively enrolled children aged < 5 years hospitalized with acute diarrhea, defined as ≥ 3 episodes of loose stool in 24 hours for < 7 days. Stool samples were collected and tested by trained surveillance clerks using ICS-RV per manufacturer's instructions. The field performance characteristics of ICS-RV were evaluated against the gold standard test, Premier™ Rotaclone® enzyme immunoassay. The operational characteristics were evaluated using World Health Organization (WHO) ASSURED criteria to determine whether ICS-RV is appropriate as a point-of-care test by administering a standard questionnaire and observing surveillance clerks performing the test. We enrolled 213 patients with a median age of 10 months (range = 1-48); 58.2% were male. A total of 71 (33.3%) and 60 (28.2%) patients tested positive for rotavirus infection by immunoassay and ICS-RV, respectively. The sensitivity, specificity, and positive and negative predictive values of ICS-RV compared with the immunoassay were 83.1% (95% confidence interval [CI] = 72.3-91.0), 99.3% (95% CI = 96.1-100), 98.3% (95% CI = 91.1-100), and 92.1% (95% CI = 86.6-95.5), respectively. The ICS-RV fulfilled the WHO ASSURED criteria for point-of-care testing. ICS-RV is a field-ready point-of-care test with good field performance and operational characteristics. It can be useful in determining rotavirus outbreaks in resource-limited settings.

Effect of climate on incidence of respiratory syncytial virus infections in a refugee camp in Kenya: A non-Gaussian time-series analysis.

Respiratory syncytial virus (RSV) is one of the major causes of acute lower respiratory tract infections (ALRTI) in children. Children younger than 1 year are the most susceptible to RSV infection. RSV infections occur seasonally in temperate climate regions. Based on RSV surveillance and climatic data, we developed statistical models that were assessed and compared to predict the relationship between weather and RSV incidence among refugee children younger than 5 years in Dadaab refugee camp in Kenya. Most time-series analyses rely on the assumption of Gaussian-distributed data. However, surveillance data often do not have a Gaussian distribution. We used a generalized linear model (GLM) with a sinusoidal component over time to account for seasonal variation and extended it to a generalized additive model (GAM) with smoothing cubic splines. Climatic factors were included as covariates in the models before and after timescale decompositions, and the results were compared. Models with decomposed covariates fit RSV incidence data better than those without. The Poisson GAM with decomposed covariates of climatic factors fit the data well and had a higher explanatory and predictive power than GLM. The best model predicted the relationship between atmospheric conditions and RSV infection incidence among children younger than 5 years. This knowledge helps public health officials to prepare for, and respond more effectively to increasing RSV incidence in low-resource regions or communities.

Notes from the Field: Splenomegaly of Unknown Etiology in Congolese Refugees Applying for Resettlement to the United States - Uganda, 2015.

Approximately 70,000-90,000 refugees are resettled to the United States each year, and during the next 5 years, 50,000 Congolese refugees are expected to arrive in the United States. The International Organization for Migration (IOM) performs refugee medical examinations overseas for the U.S. Refugee Resettlement Program. In 2014, IOM reported that a large number of U.S.-bound Congolese refugees from Uganda had spleens that were enlarged on examination. During two evaluations of refugee populations in western Uganda in March and July 2015, refugees with splenomegaly on physical examination were offered additional assessment and treatment, including abdominal ultrasonography and laboratory testing. Among 987 persons screened, 145 (14.7%) had splenomegaly and received further testing. Among the 145 patients with splenomegaly, 63.4% were aged 5-17 years (median = 14.8 years). There was some evidence of family clustering, with 33 (22.7%) of the 145 cases occurring in families.

Seroprevalence of Infections with Dengue, Rift Valley Fever and Chikungunya Viruses in Kenya, 2007.

Arthropod-borne viruses are a major constituent of emerging infectious diseases worldwide, but limited data are available on the prevalence, distribution, and risk factors for transmission in Kenya and East Africa. In this study, we used 1,091 HIV-negative blood specimens from the 2007 Kenya AIDS Indicator Survey (KAIS 2007) to test for the presence of IgG antibodies to dengue virus (DENV), chikungunya virus (CHIKV) and Rift Valley fever virus (RVFV).The KAIS 2007 was a national population-based survey conducted by the Government of Kenya to provide comprehensive information needed to address the HIV/AIDS epidemic. Antibody testing for arboviruses was performed on stored blood specimens from KAIS 2007 through a two-step sandwich IgG ELISA using either commercially available kits or CDC-developed assays. Out of the 1,091 samples tested, 210 (19.2%) were positive for IgG antibodies against at least one of the three arboviruses. DENV was the most common of the three viruses tested (12.5% positive), followed by RVFV and CHIKV (4.5% and 0.97%, respectively). For DENV and RVFV, the participant's province of residence was significantly associated (P≤.01) with seropositivity. Seroprevalence of DENV and RVFV increased with age, while there was no correlation between province of residence/age and seropositivity for CHIKV. Females had twelve times higher odds of exposure to CHIK as opposed to DENV and RVFV where both males and females had the same odds of exposure. Lack of education was significantly associated with a higher odds of previous infection with either DENV or RVFV (p <0.01). These data show that a number of people are at risk of arbovirus infections depending on their geographic location in Kenya and transmission of these pathogens is greater than previously appreciated. This poses a public health risk, especially for DENV.

Health care utilization for acute illnesses in an urban setting with a refugee population in Nairobi, Kenya: a cross-sectional survey.

BACKGROUND: Estimates place the number of refugees in Nairobi over 100,000. The constant movement of refugees between countries of origin, refugee camps, and Nairobi poses risk of introduction and transmission of communicable diseases into Kenya. We assessed the care-seeking behavior of residents of Eastleigh, a neighborhood in Nairobi with urban refugees. METHODS: During July and August 2010, we conducted a Health Utilization Survey in Section II of Eastleigh. We used a multistage random cluster sampling design to identify households for interview. A standard questionnaire on the household demographics, water and sanitation was administered to household caretakers. Separate questionnaires were administered to household members who had one or more of the illnesses of interest. RESULTS: Of 785 households targeted for interview, data were obtained from 673 (85.7%) households with 3,005 residents. Of the surveyed respondents, 290 (9.7%) individuals reported acute respiratory illness (ARI) in the previous 12 months, 222 (7.4%) reported fever in the preceding 2 weeks, and 54 (1.8%) reported having diarrhea in the 30 days prior to the survey. Children <5 years old had the highest frequency of all the illnesses surveyed: 17.1% (95% CI 12.2-21.9) reported ARI, 10.0% (95% CI 6.2-13.8) reported fever, and 6.9% (3.8-10.0) reported diarrhea during the time periods specified for each syndrome. Twenty-nine [7.5% (95% CI 4.3-10.7)] hospitalizations were reported among all age groups of those who sought care. Among participants who reported ≥1 illness, 330 (77.0%) sought some form of health care; most (174 [59.8%]) sought health care services from private health care providers. Fifty-five (18.9%) participants seeking healthcare services visited a pharmacy. Few residents of Eastleigh (38 [13.1%]) sought care at government-run facilities, and 24 (8.2%) sought care from a relative, a religious leader, or a health volunteer. Of those who did not seek any health care services (99 [23.0%]), the primary reason was cost (44.8%), followed by belief that the person was not sick enough (34.6%). CONCLUSION: Health care utilization in Eastleigh is high; however, a large proportion of residents opt to seek care at private clinics or pharmacies, despite the availability of accessible government-provided health care services in this area.

Examining strain diversity and phylogeography in relation to an unusual epidemic pattern of respiratory syncytial virus (RSV) in a long-term refugee camp in Kenya.

BACKGROUND: A recent longitudinal study in the Dadaab refugee camp near the Kenya-Somalia border identified unusual biannual respiratory syncytial virus (RSV) epidemics. We characterized the genetic variability of the associated RSV strains to determine if viral diversity contributed to this unusual epidemic pattern. METHODS: For 336 RSV positive specimens identified from 2007 through 2011 through facility-based surveillance of respiratory illnesses in the camp, 324 (96.4%) were sub-typed by PCR methods, into 201 (62.0%) group A, 118 (36.4%) group B and 5 (1.5%) group A-B co-infections. Partial sequencing of the G gene (coding for the attachment protein) was completed for 290 (89.5%) specimens. These specimens were phylogenetically analyzed together with 1154 contemporaneous strains from 22 countries. RESULTS: Of the 6 epidemic peaks recorded in the camp over the period, the first and last were predominantly made up of group B strains, while the 4 in between were largely composed of group A strains in a consecutive series of minor followed by major epidemics. The Dadaab group A strains belonged to either genotype GA2 (180, 98.9%) or GA5 (2, < 1%) while all group B strains (108, 100%) belonged to BA genotype. In sequential epidemics, strains within these genotypes appeared to be of two types: those continuing from the preceding epidemics and those newly introduced. Genotype diversity was similar in minor and major epidemics. CONCLUSION: RSV strain diversity in Dadaab was similar to contemporaneous diversity worldwide, suggested both between-epidemic persistence and new introductions, and was unrelated to the unusual epidemic pattern.

Contraceptive practices and fertility desires among HIV-infected and uninfected women in Kenya: results from a nationally representative study.

BACKGROUND: Prevention of unplanned pregnancies is a critical element in the prevention of mother-to-child transmission of HIV infection, but its potential has not been fully realized. We assessed the utilization of family planning (FP) and fertility desires among women of reproductive age by HIV status. METHODS: We selected a nationally representative sample of households using a stratified 2-stage cluster design and surveyed women aged 15-49 years. We administered questionnaires and examined predictors of current use of FP and desire for children among sexually active women with known HIV infection and women who were HIV uninfected. RESULTS: Of 3583 respondents, 68.2% were currently using FP, and 57.7% did not desire children in the future. Among women who did not desire children in the future, 70.9% reported that they were using FP, including 68.7% of women with known HIV infection and 71.0% of women who were HIV uninfected. Women with known HIV infection had similar odds of using FP as women with no HIV infection (odds ratio, 1.12; 95% confidence interval: 0.81 to 1.54). Women with no HIV infection had significantly higher adjusted odds of desiring future children (adjusted OR, 2.27; 95% confidence interval: 1.31 to 3.93) than women with known HIV infection. CONCLUSIONS: There is unmet need for FP for HIV-infected women, underscoring a gap in the national prevention of mother-to-child transmission of HIV strategy. Efforts to empower HIV-infected women to prevent unintended pregnancies should lead to expanded access to contraceptive methods and take into account women's reproductive intentions.

Epidemic cholera in Kakuma Refugee Camp, Kenya, 2009: the importance of sanitation and soap.

INTRODUCTION: Cholera remains a major public health problem that causes substantial morbidity and mortality in displaced populations due to inadequate or unprotected water supplies, poor sanitation and hygiene, overcrowding, and limited resources. A cholera outbreak with 224 cases and four deaths occurred in Kakuma Refugee Camp in Kenya from September to December 2009. METHODOLOGY: We conducted a case-control study to characterize the epidemiology of the outbreak. Cases were identified by reviewing the hospital registry for patients meeting the World Health Organization (WHO) case definition for cholera. For each case a matched control was selected. A questionnaire focusing on potential risk factors was administered to cases and controls. RESULTS: From 18 September to 15 December 2009, a total of 224 cases were identified and were hospitalised at Kakuma IRC hospital.  Three refugees and one Kenyan national died of cholera. V. cholerae O1, serotype Inaba was isolated in 44 (42%) out of 104 stool specimens collected. A total of 93 cases and 93 matched controls were enrolled in the study. In a multivariate model, washing hands with soap was protective against cholera (adjusted odds ratio [AOR] =0.25[0.09-0.71]; p < 0.01), while presence of dirty water storage containers was a risk factor (AOR=4.39[1.12-17.14]; p=0.03). CONCLUSION: Provision of soap, along with education on hand hygiene and cleaning water storage containers, may be an affordable intervention to prevent cholera.

Epidemiology of respiratory viral infections in two long-term refugee camps in Kenya, 2007-2010.

BACKGROUND: Refugees are at risk for poor outcomes from acute respiratory infections (ARI) because of overcrowding, suboptimal living conditions, and malnutrition. We implemented surveillance for respiratory viruses in Dadaab and Kakuma refugee camps in Kenya to characterize their role in the epidemiology of ARI among refugees. METHODS: From 1 September 2007 through 31 August 2010, we obtained nasopharyngeal (NP) and oropharyngeal (OP) specimens from patients with influenza-like illness (ILI) or severe acute respiratory infections (SARI) and tested them by RT-PCR for adenovirus (AdV), respiratory syncytial virus (RSV), human metapneumovirus (hMPV), parainfluenza viruses (PIV), and influenza A and B viruses. Definitions for ILI and SARI were adapted from those of the World Health Organization. Proportions of cases associated with viral aetiology were calculated by camp and by clinical case definition. In addition, for children < 5 years only, crude estimates of rates due to SARI per 1000 were obtained. RESULTS: We tested specimens from 1815 ILI and 4449 SARI patients (median age = 1 year). Proportion positive for virus were AdV, 21.7%; RSV, 12.5%; hMPV, 5.7%; PIV, 9.4%; influenza A, 9.7%; and influenza B, 2.6%; 49.8% were positive for at least one virus. The annual rate of SARI hospitalisation for 2007-2010 was 57 per 1000 children per year. Virus-positive hospitalisation rates were 14 for AdV; 9 for RSV; 6 for PIV; 4 for hMPV; 5 for influenza A; and 1 for influenza B. The rate of SARI hospitalisation was highest in children < 1 year old (156 per 1000 child-years). The ratio of rates for children < 1 year and 1 to < 5 years old was 3.7:1 for AdV, 5.5:1 for RSV, 4.4:1 for PIV, 5.1:1 for hMPV, 3.2:1 for influenza A, and 2.2:1 for influenza B. While SARI hospitalisation rates peaked from November to February in Dadaab, no distinct seasonality was observed in Kakuma. CONCLUSIONS: Respiratory viral infections, particularly RSV and AdV, were associated with high rates of illness and make up a substantial portion of respiratory infection in these two refugee settings.

Epidemiology of respiratory infections caused by atypical bacteria in two Kenyan refugee camps.

Chlamydia pneumoniae, Mycoplasma pneumoniae, and Legionella spp. are common causes of atypical pneumonia; however, data about these atypical pathogens are limited in the refugee setting. Paired nasopharyngeal and oropharyngeal specimens were collected from patients with respiratory illness presenting to healthcare centers in two refugee camps in Kenya. The specimens were tested for C. pneumoniae, M. pneumoniae, and Legionella spp. as well as eight respiratory viruses. Atypical pathogens were detected in 5.5% of the specimens of which 54% were co-infected with at least one of the eight viruses tested. Patients positive for atypical bacteria co-infected with virus were significantly more likely to have severe acute respiratory illness than patients infected with only atypical bacteria (P = 0.04). While the percentage of atypical pathogens identified was lower than expected, we found a significant relationship between atypical bacterial-viral co-infection and severity of disease in this refugee population.

Epidemic Cholera in Kakuma Refugee Camp; Kenya; 2009: the Importance of Sanitation and Soap

Introduction: Cholera remains a major public health problem that causes substantial morbidity and mortality in displaced populations due to inadequate or unprotected water supplies; poor sanitation and hygiene; overcrowding; and limited resources. A cholera outbreak with 224 cases and four deaths occurred in Kakuma Refugee Camp in Kenya from September to December 2009. Methodology: We conducted a case-control study to characterize the epidemiology of the outbreak. Cases were identified by reviewing the hospital registry for patients meeting the World Health Organization (WHO) case definition for cholera. For each case a matched control was selected. A questionnaire focusing on potential risk factors was administered to cases and controls.Results: From 18 September to 15 December 2009; a total of 224 cases were identified and were hospitalised at Kakuma IRC hospital. Three refugees and one Kenyan national died of cholera. V. cholerae O1; serotype Inaba was isolated in 44 (42) out of 104 stool specimens collected. A total of 93 cases and 93 matched controls were enrolled in the study. In a multivariate model; washing hands with soap was protective against cholera (adjusted odds ratio [AOR] =0.25[0.09-0.71]; p 0.01); while presence of dirty water storage containers was a risk factor (AORConclusion: Provision of soap; along with education on hand hygiene and cleaning water storage containers; may be an affordable intervention to prevent cholera

Comparison of nasopharyngeal and oropharyngeal swabs for the diagnosis of eight respiratory viruses by real-time reverse transcription-PCR assays.

BACKGROUND: Many acute respiratory illness surveillance systems collect and test nasopharyngeal (NP) and/or oropharyngeal (OP) swab specimens, yet there are few studies assessing the relative measures of performance for NP versus OP specimens. METHODS: We collected paired NP and OP swabs separately from pediatric and adult patients with influenza-like illness or severe acute respiratory illness at two respiratory surveillance sites in Kenya. The specimens were tested for eight respiratory viruses by real-time reverse transcription-polymerase chain reaction (qRT-PCR). Positivity for a specific virus was defined as detection of viral nucleic acid in either swab. RESULTS: Of 2,331 paired NP/OP specimens, 1,402 (60.1%) were positive for at least one virus, and 393 (16.9%) were positive for more than one virus. Overall, OP swabs were significantly more sensitive than NP swabs for adenovirus (72.4% vs. 57.6%, p<0.01) and 2009 pandemic influenza A (H1N1) virus (91.2% vs. 70.4%, p<0.01). NP specimens were more sensitive for influenza B virus (83.3% vs. 61.5%, p = 0.02), parainfluenza virus 2 (85.7%, vs. 39.3%, p<0.01), and parainfluenza virus 3 (83.9% vs. 67.4%, p<0.01). The two methods did not differ significantly for human metapneumovirus, influenza A (H3N2) virus, parainfluenza virus 1, or respiratory syncytial virus. CONCLUSIONS: The sensitivities were variable among the eight viruses tested; neither specimen was consistently more effective than the other. For respiratory disease surveillance programs using qRT-PCR that aim to maximize sensitivity for a large number of viruses, collecting combined NP and OP specimens would be the most effective approach.

Unsafe sex among HIV-infected adults in Kenya: results of a nationally representative survey.

OBJECTIVE: Assess factors associated with knowledge of HIV status, sexual activity, and unprotected sex with a partner of unknown or negative HIV status (unsafe sex) among HIV-infected adults in Kenya. DESIGN: Nationally representative Kenya AIDS Indicator Survey among adults aged 15-64 years in 2007. METHODS: A standardized questionnaire was administered and blood samples tested for HIV. We assessed factors associated with knowledge of HIV infection, sexual activity, and unsafe sex. Analyses took into account stratification and clustering in the survey design and estimates were weighted to account for sampling probability. RESULTS: Of 15,853 participants with blood samples, 1104 (6.9%) were HIV infected. Of these, 83.8% did not know their HIV status (56% had never tested; 27.8% reported their last HIV test was negative), and 80.4% were sexually active. Of 861 sexually active adults, 76.9% reported unsafe sex in the past year. Adults who did not know their HIV status were more likely to be sexually active [never tested adjusted odds ratio (AOR): 5.5, 95% confidence interval (CI): 2.8 to 10.7; ever tested, incorrect knowledge AOR: 6.5, CI: 2.1 to 19.6) and to report unsafe sex (never tested AOR: 51.7, CI: 27.3 to 97.6; ever tested, incorrect knowledge of status AOR: 18.6, CI: 8.6 to 40.5) than those who knew their status. CONCLUSIONS: The majority of adults did not know they were infected and engaged in unsafe sex. Adults who knew their HIV status were less likely to be sexually active and report unsafe sex compared with those unaware of their infection. HIV prevention interventions that target HIV-infected adults are urgently needed.