Last data update: Jun 03, 2024. (Total: 46935 publications since 2009)
Records 1-21 (of 21 Records) |
Query Trace: Waiboci L [original query] |
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Efficacy of a solar concentrator to Inactivate E. coli and C. perfringens spores in latrine waste in Kenya
Murphy JL , Ayers T , Foote A , Woods E , Wamola N , Fagerli K , Waiboci L , Mugoh R , Mintz ED , Zhao K , Marano N , O'Reilly CE , Hill VR . Sci Total Environ 2019 691 401-406 Alternative sanitation options are needed for effective waste management in low-income countries where centralized, large-scale waste treatment is not easily achievable. A newly designed solar concentrator technology utilizes solar thermal energy to treat feces contained in drums. This pilot study assessed the efficacy of the new design to inactivate microbes in 13 treatment drums under field conditions in Kenya. Three-quarters of the drums contained <1000E. coli/g of total solids following 6h of solar thermal treatment and inactivation of thermotolerant C. perfringens spores ranged from <1.8 to >5.0log10. Nearly all (94%) samples collected from treatment drums achieved thermophilic temperatures (>50 degrees C) during the treatment period, however this alone did not ensure samples met the WHO E. coli guideline; higher, sustained thermophilic temperatures tended to be more effective in reaching this guideline. The newly designed solar concentrator was capable of inactivating thermotolerant, environmentally-stable microorganisms as, or possibly more, efficiently than a previous design. Additional data are needed to better characterize how temperature, time, and other parameters affect the ability of the solar concentrator to inactivate microbes in feces. |
Identification and characterization of influenza A viruses in selected domestic animals in Kenya, 2010-2012.
Munyua P , Onyango C , Mwasi L , Waiboci LW , Arunga G , Fields B , Mott JA , Cardona CJ , Kitala P , Nyaga PN , Njenga MK . PLoS One 2018 13 (2) e0192721 BACKGROUND: Influenza A virus subtypes in non-human hosts have not been characterized in Kenya. We carried out influenza surveillance in selected domestic animals and compared the virus isolates with isolates obtained in humans during the same period. METHODS: We collected nasal swabs from pigs, dogs and cats; oropharyngeal and cloacal swabs from poultry; and blood samples from all animals between 2010 and 2012. A standardized questionnaire was administered to farmers and traders. Swabs were tested for influenza A by rtRT-PCR, virus isolation and subtyping was done on all positive swabs. All sera were screened for influenza A antibodies by ELISA, and positives were evaluated by hemagglutination inhibition (HI). Full genome sequencing was done on four selected pig virus isolates. RESULTS: Among 3,798 sera tested by ELISA, influenza A seroprevalence was highest in pigs (15.9%; 172/1084), 1.2% (3/258) in ducks, 1.4% (1/72) in cats 0.6% (3/467) in dogs, 0.1% (2/1894) in chicken and 0% in geese and turkeys. HI testing of ELISA-positive pig sera showed that 71.5% had positive titers to A/California/04/2009(H1N1). Among 6,289 swabs tested by rRT-PCR, influenza A prevalence was highest in ducks [1.2%; 5/423] and 0% in cats and turkeys. Eight virus isolates were obtained from pig nasal swabs collected in 2011 and were determined to be A(H1N1)pdm09 on subtyping. On phylogenetic analysis, four hemagglutinin segments from pig isolates clustered together and were closely associated with human influenza viruses that circulated in Kenya in 2011. CONCLUSION: Influenza A(H1N1)pdm09 isolated in pigs was genetically similar to contemporary human pandemic influenza virus isolates. This suggest that the virus was likely transmitted from humans to pigs, became established and circulated in Kenyan pig populations during the study period. Minimal influenza A prevalence was observed in the other animals studied. |
Which influenza vaccine formulation should be used in Kenya? A comparison of influenza isolates from Kenya to vaccine strains, 2007-2013
Waiboci LW , Mott JA , Kikwai G , Arunga G , Xu X , Mayieka L , Emukule GO , Muthoka P , Njenga MK , Fields BS , Katz MA . Vaccine 2016 34 (23) 2593-601 INTRODUCTION: Every year the World Health Organization (WHO) recommends which influenza virus strains should be included in a northern hemisphere (NH) and a southern hemisphere (SH) influenza vaccine. To determine the best vaccine formulation for Kenya, we compared influenza viruses collected in Kenya from April 2007 to May 2013 to WHO vaccine strains. METHODS: We collected nasopharyngeal and oropharyngeal (NP/OP) specimens from patients with respiratory illness, tested them for influenza, isolated influenza viruses from a proportion of positive specimens, tested the isolates for antigenic relatedness to vaccine strains, and determined the percentage match between circulating viruses and SH or NH influenza vaccine composition and schedule. RESULTS: During the six years, 7.336 of the 60,072 (12.2%) NP/OP specimens we collected were positive for influenza: 30,167 specimens were collected during the SH seasons and 3717 (12.3%) were positive for influenza; 2903 (78.1%) influenza A, 902 (24.2%) influenza B, and 88 (2.4%) influenza A and B positive specimens. We collected 30,131 specimens during the NH seasons and 3978 (13.2%) were positive for influenza; 3181 (80.0%) influenza A, 851 (21.4%) influenza B, and 54 (1.4%) influenza A and B positive specimens. Overall, 362/460 (78.7%) isolates from the SH seasons and 316/338 (93.5%) isolates from the NH seasons were matched to the SH and the NH vaccine strains, respectively (p<0.001). Overall, 53.6% and 46.4% SH and NH vaccines, respectively, matched circulating strains in terms of vaccine strains and timing. CONCLUSION: In six years of surveillance in Kenya, influenza circulated at nearly equal levels during the SH and the NH influenza seasons. Circulating viruses were matched to vaccine strains. The vaccine match decreased when both vaccine strains and timing were taken into consideration. Either vaccine formulation could be suitable for use in Kenya but the optimal timing for influenza vaccination needs to be determined. |
Uptake and effectiveness of a trivalent inactivated influenza vaccine in children in urban and rural Kenya, 2010-2012
Katz MA , Lebo E , Emukule GO , Otieno N , Caselton DL , Bigogo G , Njuguna H , Muthoka PM , Waiboci LW , Widdowson MA , Xu X , Njenga MK , Mott JA , Breiman RF . Pediatr Infect Dis J 2015 35 (3) 322-9 BACKGROUND: In Africa, recent surveillance has demonstrated a high burden of influenza, but influenza vaccine is rarely used. In Kenya, a country with a tropical climate, influenza has been shown to circulate year-round, like in other tropical countries. METHODS: During three months in 2010 and 2011, and two months in 2012, the Kenya Medical Research Institute/CDC-Kenya offered free injectable trivalent inactivated influenza vaccine to children 6 months-10 years old in two resource-poor communities in Kenya - Kibera andLwak (total population ~50,000). We conducted a case-control study to evaluate vaccine effectiveness (VE)in preventing laboratory-confirmed influenza associated with influenza-like illness and acute lower respiratory illness. RESULTS: Of 52,000 eligible children, 41%, 48%, and 51% received at least one vaccine in 2010, 2011, and 2012, respectively; 30%, 36%, and 38% were fully vaccinated. VE among fully vaccinated children was 57% (95% CI = 29-74%) during a 6-month follow-up period, 39% (95% CI = 17-56%) during a 9-month follow-up period, and 48% (95% CI = 32-61%) during a 12-month follow-up period. For the 12-month follow-up period, VE was statistically significant in children < 5 years and children 5 years old < 10 years old (50% and 46%, respectively). CONCLUSIONS: In Kenya, parents of nearly half of eligible children under 10 years old chose to get their children vaccinated with a free influenza vaccine. During a 12-month follow-up period the vaccine was moderately effective in preventing medically attended influenza-associated respiratory illness. |
Serologic evidence of the geographic distribution of bacterial zoonotic agents in Kenya, 2007
Omballa VO , Musyoka RN , Vittor AY , Wamburu KB , Wachira CM , Waiboci LW , Abudo MU , Juma BW , Kim AA , Montgomery JM , Breiman RF , Fields BS . Am J Trop Med Hyg 2015 94 (1) 43-51 Diseases of zoonotic origin contribute to the burden of febrile illnesses in developing countries. We evaluated serologic evidence of exposure to Bacillus anthracis, Brucella spp., spotted fever group rickettsioses (SFGR), and typhus group rickettsioses (TGR) from samples of persons aged 15-64 years collected during a nationwide human immunodeficiency virus (HIV) serosurvey conducted in 2007 in Kenya. The seropositivity observed for pathogens was B. anthracis 11.3% (141/1,091), Brucella spp. 3.0% (27/968), SFGR 23.3% (191/770), and TGR 0.6% (12/770). On univariate analysis, seropositivity for each pathogen was significantly associated with the following risk factors: B. anthracis with province of residence; Brucella spp. with sex, education level, and wealth; SFGR with age, education level, wealth, and province of residence; and TGR with province of residence. On multivariate analysis, seropositivity remained significantly associated with wealth and province for B. anthracis; with sex and age for Brucella spp; and with sex, education level, and province of residence for SFGR whereas TGR had no significance. High IgG seropositivity to these zoonotic pathogens (especially, B. anthracis and SFGR) suggests substantial exposure. These pathogens should be considered in the differential diagnosis of febrile illness in Kenya. |
Seroprevalence of infections with dengue, Rift Valley fever and chikungunya viruses in Kenya, 2007
Ochieng C , Ahenda P , Vittor AY , Nyoka R , Gikunju S , Wachira C , Waiboci L , Umuro M , Kim AA , Nderitu L , Juma B , Montgomery JM , Breiman RF , Fields B . PLoS One 2015 10 (7) e0132645 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. |
The unrecognized burden of influenza in young Kenyan children, 2008-2012
McMorrow ML , Emukule GO , Njuguna HN , Bigogo G , Montgomery JM , Nyawanda B , Audi A , Breiman RF , Katz MA , Cosmas L , Waiboci LW , Duque J , Widdowson MA , Mott JA . PLoS One 2015 10 (9) e0138272 Influenza-associated disease burden among children in tropical sub-Saharan Africa is not well established, particularly outside of the 2009 pandemic period. We estimated the burden of influenza in children aged 0-4 years through population-based surveillance for influenza-like illness (ILI) and acute lower respiratory tract illness (ALRI). Household members meeting ILI or ALRI case definitions were referred to health facilities for evaluation and collection of nasopharyngeal and oropharyngeal swabs for influenza testing by real-time reverse transcription polymerase chain reaction. Estimates were adjusted for health-seeking behavior and those with ILI and ALRI who were not tested. During 2008-2012, there were 9,652 person-years of surveillance among children aged 0-4 years. The average adjusted rate of influenza-associated hospitalization was 4.3 (95% CI 3.0-6.0) per 1,000 person-years in children aged 0-4 years. Hospitalization rates were highest in the 0-5 month and 6-23 month age groups, at 7.6 (95% CI 3.2-18.2) and 8.4 (95% CI 5.4-13.0) per 1,000 person-years, respectively. The average adjusted rate of influenza-associated medically attended (inpatient or outpatient) ALRI in children aged 0-4 years was 17.4 (95% CI 14.2-19.7) per 1,000 person-years. Few children who had severe laboratory-confirmed influenza were clinically diagnosed with influenza by the treating clinician in the inpatient (0/33, 0%) or outpatient (1/109, 0.9%) settings. Influenza-associated hospitalization rates from 2008-2012 were 5-10 times higher than contemporaneous U.S. estimates. Many children with danger signs were not hospitalized; thus, influenza-associated severe disease rates in Kenyan children are likely higher than hospital-based estimates suggest. |
Strengthening the influenza vaccine virus selection and development process: Report of the 3rd WHO Informal Consultation for Improving Influenza Vaccine Virus Selection held at WHO headquarters, Geneva, Switzerland, 1-3 April 2014.
Ampofo WK , Azziz-Baumgartner E , Bashir U , Cox NJ , Fasce R , Giovanni M , Grohmann G , Huang S , Katz J , Mironenko A , Mokhtari-Azad T , Sasono PM , Rahman M , Sawanpanyalert P , Siqueira M , Waddell AL , Waiboci L , Wood J , Zhang W , Ziegler T . Vaccine 2015 33 (36) 4368-82 Despite long-recognized challenges and constraints associated with their updating and manufacture, influenza vaccines remain at the heart of public health preparedness and response efforts against both seasonal and potentially pandemic influenza viruses. Globally coordinated virological and epidemiological surveillance is the foundation of the influenza vaccine virus selection and development process. Although national influenza surveillance and reporting capabilities are being strengthened and expanded, sustaining and building upon recent gains has become a major challenge. Strengthening the vaccine virus selection process additionally requires the continuation of initiatives to improve the timeliness and representativeness of influenza viruses shared by countries for detailed analysis by the WHO Global Influenza Surveillance and Response System (GISRS). Efforts are also continuing at the national, regional, and global levels to better understand the dynamics of influenza transmission in both temperate and tropical regions. Improved understanding of the degree of influenza seasonality in tropical countries of the world should allow for the strengthening of national vaccination policies and use of the most appropriate available vaccines. There remain a number of limitations and difficulties associated with the use of HAI assays for the antigenic characterization and selection of influenza vaccine viruses by WHOCCs. Current approaches to improving the situation include the more-optimal use of HAI and other assays; improved understanding of the data produced by neutralization assays; and increased standardization of serological testing methods. A number of new technologies and associated tools have the potential to revolutionize influenza surveillance and response activities. These include the increasingly routine use of whole genome next-generation sequencing and other high-throughput approaches. Such approaches could not only become key elements in outbreak investigations but could drive a new surveillance paradigm. However, despite the advances made, significant challenges will need to be addressed before next-generation technologies become routine, particularly in low-resource settings. Emerging approaches and techniques such as synthetic genomics, systems genetics, systems biology and mathematical modelling are capable of generating potentially huge volumes of highly complex and diverse datasets. Harnessing the currently theoretical benefits of such bioinformatics ("big data") concepts for the influenza vaccine virus selection and development process will depend upon further advances in data generation, integration, analysis and dissemination. Over the last decade, growing awareness of influenza as an important global public health issue has been coupled to ever-increasing demands from the global community for more-equitable access to effective and affordable influenza vaccines. The current influenza vaccine landscape continues to be dominated by egg-based inactivated and live attenuated vaccines, with a small number of cell-based and recombinant vaccines. Successfully completing each step in the annual influenza vaccine manufacturing cycle will continue to rely upon timely and regular communication between the WHO GISRS, manufacturers and regulatory authorities. While the pipeline of influenza vaccines appears to be moving towards a variety of niche products in the near term, it is apparent that the ultimate aim remains the development of effective "universal" influenza vaccines that offer longer-lasting immunity against a broad range of influenza A subtypes. |
Severe acute respiratory illness deaths in sub-Saharan Africa and the role of influenza: a case-series from 8 countries
McMorrow ML , Wemakoy EO , Tshilobo JK , Emukule GO , Mott JA , Njuguna H , Waiboci L , Heraud JM , Rajatonirina S , Razanajatovo NH , Chilombe M , Everett D , Heyderman RS , Barakat A , Nyatanyi T , Rukelibuga J , Cohen AL , Cohen C , Tempia S , Thomas J , Venter M , Mwakapeje E , Mponela M , Lutwama J , Duque J , Lafond K , Nzussouo NT , Williams T , Widdowson MA . J Infect Dis 2015 212 (6) 853-60 BACKGROUND: Data on causes of respiratory deaths in Africa are limited. METHODS: From January to April 2013, 28 African countries were invited to participate in a review of severe acute respiratory illness (SARI) deaths identified from influenza surveillance during 2009 - 2012. RESULTS: Twenty-three (82%) countries responded, 11 (48%) collect mortality data, and 8 provided data. Data were collected from 37,714 SARI cases and 3091 (8.2%, range by country 5.1-25.9%) tested positive for influenza. There were 1073 (2.8%, range by country 0.1-5.3%) deaths reported among whom 57 (5.3%) were influenza-positive. Case fatality proportion (CFP) was higher among countries with systematic death reporting than those with sporadic reporting. The influenza-associated CFP was 1.8% (57/3091) compared to 2.9% (1016/34,623) for influenza-negative cases (p<0.001). Among 834 (77.7%) deaths tested for other respiratory pathogens, rhinovirus (n=107, 12.8%), adenovirus (n=64, 6.0%), respiratory syncytial virus (n=60, 5.6%), and S. pneumoniae (n=57, 5.3%) were most commonly identified. Among 1073 deaths, 402 (37.5%) were aged 0-4 years, 462 (43.1%) aged 5-49 years, and 209 (19.5%) aged 50 years and older. CONCLUSIONS: Few African countries systematically collect data on respiratory hospitalization outcomes. Stronger surveillance for respiratory deaths may identify risk groups for targeted vaccine use and other prevention strategies. |
An outbreak of acute febrile illness caused by Sandfly Fever Sicilian Virus in the Afar region of Ethiopia, 2011.
Woyessa AB , Omballa V , Wang D , Lambert A , Waiboci L , Ayele W , Ahmed A , Abera NA , Cao S , Ochieng M , Montgomery JM , Jima D , Fields B . Am J Trop Med Hyg 2014 91 (6) 1250-3 In malaria-endemic regions, many medical facilities have limited capacity to diagnose non-malarial etiologies of acute febrile illness (AFI). As a result, the etiology of AFI is seldom determined, although AFI remains a major cause of morbidity in developing countries. An outbreak of AFI was reported in the Afar region of Ethiopia in August of 2011. Retrospectively, 12,816 suspected AFI cases were identified by review of medical records. Symptoms were mild and self-limiting within 3 days after the date of onset; no fatalities were identified. All initial test results of AFI patient specimens were negative for selected pathogens using standard microbiological and molecular techniques. High-throughput sequencing of nucleic acid extracts of serum specimens from 29 AFI cases identified 17 (59%) of 29 samples as positive for Sandfly Fever Sicilian Virus (SFSV). These results were further confirmed by specific reverse transcription polymerase chain reaction. This is the first study implicating SFSV as an etiological agent for AFI in Ethiopia. |
Does the length of specimen storage affect influenza testing results by real-time reverse transcription-polymerase chain reaction? An analysis of influenza surveillance specimens, 2008 to 2010
Caselton D , Arunga G , Emukule G , Muthoka P , Mayieka L , Kosgey A , Ochola R , Waiboci L , Feikin D , Mott J , Breiman R , Katz M . Euro Surveill 2014 19 (36) In some influenza surveillance systems, timely transport to laboratories for reverse transcription-polymerase chain reaction (RT-PCR) testing is challenging. Guidelines suggest that samples can be stored at 4°C for up to 96 hours but the effect of longer storage times has not been systematically evaluated. We collected nasopharyngeal and oropharyngeal specimens from patients in Kenya and stored them in viral transport medium at 2 to 8°C before testing for influenza A and B using real-time RT-PCR. From April 2008 to November 2010, we collected 7,833 samples; 940 (12%) were positive for influenza. In multivariable analysis, specimens stored for six days were less likely to be influenza-positive compared to specimens stored between zero and one day (adjusted odds ratio (aOR): 0.49, 95% confidence interval (CI): 0.27–0.93). There was no statistically significant difference in influenza positivity of specimens stored for five days compared to zero to one day. There was no statistically significant relationship between days in refrigeration and cycle threshold (Ct) values for positive samples (p=0.31). We found that samples could remain in storage for at least five days without affecting the proportion-positive of samples, potentially increasing the feasibility of including influenza surveillance sites in remote areas. |
Results from the first six years of national sentinel surveillance for influenza in Kenya, July 2007-June 2013
Katz MA , Muthoka P , Emukule GO , Kalani R , Njuguna H , Waiboci LW , Ahmed JA , Bigogo G , Feikin DR , Njenga MK , Breiman RF , Mott JA . PLoS One 2014 9 (6) e98615 BACKGROUND: Recent studies have shown that influenza is associated with significant disease burden in many countries in the tropics, but until recently national surveillance for influenza was not conducted in most countries in Africa. METHODS: In 2007, the Kenyan Ministry of Health with technical support from the CDC-Kenya established a national sentinel surveillance system for influenza. At 11 hospitals, for every hospitalized patient with severe acute respiratory illness (SARI), and for the first three outpatients with influenza-like illness (ILI) per day, we collected both nasopharyngeal and oropharyngeal swabs. Beginning in 2008, we conducted in-hospital follow-up for SARI patients to determine outcome. Specimens were tested by real time RT-PCR for influenza A and B. Influenza A-positive specimens were subtyped for H1, H3, H5, and (beginning in May 2009) A(H1N1)pdm09. RESULTS: From July 1, 2007 through June 30, 2013, we collected specimens from 24,762 SARI and 14,013 ILI patients. For SARI and ILI case-patients, the median ages were 12 months and 16 months, respectively, and 44% and 47% were female. In all, 2,378 (9.6%) SARI cases and 2,041 (14.6%) ILI cases were positive for influenza viruses. Most influenza-associated SARI cases (58.6%) were in children <2 years old. Of all influenza-positive specimens, 78% were influenza A, 21% were influenza B, and 1% were influenza A/B coinfections. Influenza circulated in every month. In four of the six years influenza activity peaked during July-November. Of 9,419 SARI patients, 2.7% died; the median length of hospitalization was 4 days. CONCLUSIONS: During six years of surveillance in Kenya, influenza was associated with nearly 10 percent of hospitalized SARI cases and one-sixth of outpatient ILI cases. Most influenza-associated SARI and ILI cases were in children <2 years old; interventions to reduce the burden of influenza, such as vaccine, could consider young children as a priority group. |
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
Agoti CN , Mayieka LM , Otieno JR , Ahmed JA , Fields BS , Waiboci LW , Nyoka R , Eidex RB , Marano N , Burton W , Montgomery JM , Breiman RF , Nokes DJ . BMC Infect Dis 2014 14 (1) 178 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. |
Hepatitis E outbreak, Dadaab refugee camp, Kenya, 2012
Ahmed JA , Moturi E , Spiegel P , Schilperoord M , Burton W , Kassim NH , Mohamed A , Ochieng M , Nderitu L , Navarro-Colorado C , Burke H , Cookson S , Handzel T , Waiboci LW , Montgomery JM , Teshale E , Marano N . Emerg Infect Dis 2013 19 (6) 1010-1 Hepatitis E virus (HEV) is transmitted through the fecal-oral route and is a common cause of viral hepatitis in developing countries. HEV outbreaks have been documented among forcibly displaced persons living in camps in East Africa, but for >10 years, no cases were documented among Somali refugees (1,2). On August 15, 2012, the US Centers for Disease Control and Prevention (CDC) in Nairobi, Kenya, was notified of a cluster of acute jaundice syndrome (AJS) cases in refugee camps in Dadaab, Kenya. On September 5, a CDC epidemiologist assisted the United Nations High Commissioner for Refugees (UNHCR) and its partners in assessing AJS case-patients in the camp, enhancing surveillance, and improving medical management of case-patients. We present the epidemiologic and laboratory findings for the AJS cases (defined as acute onset of scleral icterus not due to another underlying condition) identified during this outbreak. | Dadaab refugee camp is located in eastern Kenya near the border with Somalia. It has existed since 1991 and is the largest refugee camp in the world. Dadaab is composed of 5 smaller camps: Dagahaley, Hagadera, Ifo, Ifo II, and Kambioos. As of December 2012, a total of 460,000 refugees, mainly Somalians, were living in the camps; >25% were recent arrivals displaced by the mid-2011 famine in the Horn of Africa (3). Overcrowding and poor sanitation have led to outbreaks of enteric diseases, including cholera and shigellosis (4); in September 2012, an outbreak of cholera occurred simultaneously with the AJS outbreak. |
Epidemiology, seasonality, and burden of influenza and influenza-like illness in urban and rural Kenya, 2007-2010
Katz MA , Lebo E , Emukule G , Njuguna HN , Aura B , Cosmas L , Audi A , Junghae M , Waiboci LW , Olack B , Bigogo G , Njenga MK , Feikin DR , Breiman RF . J Infect Dis 2012 206 Suppl 1 S53-60 BACKGROUND: The epidemiology and burden of influenza remain poorly defined in sub-Saharan Africa. Since 2005, the Kenya Medical Research Institute and Centers for Disease Control and Prevention-Kenya have conducted population-based infectious disease surveillance in Kibera, an urban informal settlement in Nairobi, and in Lwak, a rural community in western Kenya. METHODS: Nasopharyngeal and oropharyngeal swab specimens were obtained from patients who attended the study clinic and had acute lower respiratory tract (LRT) illness. Specimens were tested for influenza virus by real-time reverse-transcription polymerase chain reaction. We adjusted the incidence of influenza-associated acute LRT illness to account for patients with acute LRT illness who attended the clinic but were not sampled. RESULTS: From March 2007 through February 2010, 4140 cases of acute LRT illness were evaluated in Kibera, and specimens were collected from 1197 (27%); 319 (27%) were positive for influenza virus. In Lwak, there were 6733 cases of acute LRT illness, and specimens were collected from 1641 (24%); 359 (22%) were positive for influenza virus. The crude and adjusted rates of medically attended influenza-associated acute LRT illness were 6.9 and 13.6 cases per 1000 person-years, respectively, in Kibera, and 5.6 and 23.0 cases per 1000 person-years, respectively, in Lwak. In both sites, rates of influenza-associated acute LRT illness were highest among children <2 years old and lowest among adults ≥50 years old. CONCLUSION: In Kenya, the incidence of influenza-associated acute LRT illness was high in both rural and urban settings, particularly among the most vulnerable age groups. |
Secondary household transmission of 2009 pandemic influenza A (H1N1) virus among an urban and rural population in Kenya, 2009-2010
Kim CY , Breiman RF , Cosmas L , Audi A , Aura B , Bigogo G , Njuguna H , Lebo E , Waiboci L , Njenga MK , Feikin DR , Katz MA . PLoS One 2012 7 (6) e38166 BACKGROUND: In Kenya, >1,200 laboratory-confirmed 2009 pandemic influenza A (H1N1) (pH1N1) cases occurred since June 2009. We used population-based infectious disease surveillance (PBIDS) data to assess household transmission of pH1N1 in urban Nairobi (Kibera) and rural Lwak. METHODS: We defined a pH1N1 patient as laboratory-confirmed pH1N1 infection among PBIDS participants during August 1, 2009-February 5, 2010, in Kibera, or August 1, 2009-January 20, 2010, in Lwak, and a case household as a household with a laboratory-confirmed pH1N1 patient. Community interviewers visited PBIDS-participating households to inquire about illnesses among household members. We randomly selected 4 comparison households per case household matched by number of children aged <5. Comparison households had a household visit 10 days before or after the matched patient symptom onset date. We defined influenza-like illnesses (ILI) as self-reported cough or sore throat, and a self-reported fever ≤8 days after the pH1N1 patient's symptom onset in case households and ≤8 days before selected household visit in comparison households. We used the Cochran-Mantel-Haenszel test to compare proportions of ILIs among case and comparison households, and log binomial-model to compare that of Kibera and Lwak. RESULTS: Among household contacts of patients with confirmed pH1N1 in Kibera, 4.6% had ILI compared with 8.2% in Lwak (risk ratio [RR], 0.5; 95% confidence interval [CI], 0.3-0.9). Household contacts of patients were more likely to have ILIs than comparison-household members in both Kibera (RR, 1.8; 95% CI, 1.1-2.8) and Lwak (RR, 2.6; 95% CI, 1.6-4.3). Overall, ILI was not associated with patient age. However, ILI rates among household contacts were higher among children aged <5 years than persons aged ≥5 years in Lwak, but not Kibera. CONCLUSIONS: Substantial pH1N1 household transmission occurred in urban and rural Kenya. Household transmission rates were higher in the rural area. |
Detection of influenza A virus in live bird markets in Kenya, 2009-2011
Munyua PM , Githinji JW , Waiboci LW , Njagi LM , Arunga G , Mwasi L , Murithi Mbabu R , Macharia JM , Breiman RF , Njenga MK , Katz MA . Influenza Other Respir Viruses 2012 7 (2) 113-9 BACKGROUND: Surveillance for influenza viruses within live bird markets (LBMs) has been recognized as an effective tool for detecting circulating avian influenza viruses (AIVs). In Sub-Saharan Africa, limited data exist on AIVs in animal hosts, and in Kenya the presence of influenza virus in animal hosts has not been described. OBJECTIVES: This surveillance project aimed to detect influenza A virus in poultry traded in five LBMs in Kenya. METHODS: We visited each market monthly and collected oropharyngeal and cloacal specimens from poultry and environmental specimens for virological testing for influenza A by real time RT-PCR. On each visit, we collected information on the number and types of birds in each market, health status of the birds, and market practices. RESULTS: During March 24, 2009-February 28, 2011, we collected 5221 cloacal and oropharyngeal swabs. Of the 5199 (99.6%) specimens tested, influenza A virus was detected in 42 (0.8%), including 35/4166 (0.8%) specimens from chickens, 3/381 (0.8%) from turkeys, and 4/335 (1.2%) from geese. None of the 317 duck specimens were positive. Influenza was more commonly detected in oropharyngeal [33 (1.3%)] than in cloacal [9 (0.4%)] specimens. None of the 485 environmental specimens were positive. Virus was detected in all five markets during most (14/22) of the months. Ducks and geese were kept longer at the market (median 30 days) than chickens (median 2 days). CONCLUSIONS: Influenza A was detected in a small percentage of poultry traded in LBMs in Kenya. Efforts should be made to promote practices that could limit the maintenance and transmission of AIVs in LBMs. |
Epidemiology of respiratory viral infections in two long-term refugee camps in Kenya, 2007-2010
Ahmed JA , Katz MA , Auko E , Njenga MK , Weinberg M , Kapella BK , Burke H , Nyoka R , Gichangi A , Waiboci LW , Mahamud A , Qassim M , Swai B , Wagacha B , Mutonga D , Nguhi M , Breiman RF , Eidex RB . BMC Infect Dis 2012 12 (1) 7 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 etiology 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 hospitalization for 2007-2010 was 57 per 1000 children per year. Virus-positive hospitalization 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 hospitalization 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 hospitalization 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. |
Hospitalized patients with pandemic (H1N1) 2009, Kenya
Osoro EM , Munyua P , Muthoka P , Gikundi S , Njenga MK , Lifumo S , Achilla R , Waiboci L , Nzioka C , Omolo J , Feikin DR , Breiman RF , Katz MA . Emerg Infect Dis 2011 17 (9) 1744-6 To describe the epidemiology and clinical course of patients hospitalized with pandemic (H1N1) 2009 in Kenya, we reviewed medical records of 49 such patients hospitalized during July-November 2009. The median age (7 years) was lower than that in industrialized countries. More patients had HIV than the general Kenyan population. |
Comparison of nasopharyngeal and oropharyngeal swabs for the diagnosis of eight respiratory viruses by real-time reverse transcription-PCR assays
Kim C , Ahmed JA , Eidex RB , Nyoka R , Waiboci LW , Erdman D , Tepo A , Mahamud AS , Kabura W , Nguhi M , Muthoka P , Burton W , Breiman RF , Njenga MK , Katz MA . PLoS One 2011 6 (6) e21610 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. |
Viral shedding in patients infected with pandemic influenza A (H1N1) virus in Kenya, 2009
Waiboci LW , Lebo E , Williamson JM , Mwiti W , Kikwai GK , Njuguna H , Olack B , Breiman RF , Njenga MK , Katz MA . PLoS One 2011 6 (6) e20320 BACKGROUND: Understanding shedding patterns of 2009 pandemic influenza A (H1N1) (pH1N1) can inform recommendations about infection control measures. We evaluated the duration of pH1N1 virus shedding in patients in Nairobi, Kenya. METHODS: Nasopharyngeal (NP) and oropharyngeal (OP) specimens were collected from consenting laboratory-confirmed pH1N1 cases every 2 days during October 14-November 25, 2009, and tested at the Centers for Diseases Control and Prevention-Kenya by real time reverse transcriptase polymerase chain reaction (rRT-PCR). A subset of rRT-PCR-positive samples was cultured. RESULTS: Of 285 NP/OP specimens from patients with acute respiratory illness, 140 (49%) tested positive for pH1N1 by rRT-PCR; 106 (76%) patients consented and were enrolled. The median age was 6 years (Range: 4 months-41 years); only two patients, both asthmatic, received oseltamivir. The median duration of pH1N1 detection after illness onset was 8 days (95% CI: 7-10 days) for rRT-PCR and 3 days (Range: 0-13 days) for viral isolation. Viable pH1N1 virus was isolated from 132/162 (81%) of rRT-PCR-positive specimens, which included 118/125 (94%) rRT-PCR-positive specimens collected on day 0-7 after symptoms onset. Viral RNA was detectable in 18 (17%) and virus isolated in 7/18 (39%) of specimens collected from patients after all their symptoms had resolved. CONCLUSIONS: In this cohort, pH1N1 was detected by rRT-PCR for a median of 8 days. There was a strong correlation between rRT-PCR results and virus isolation in the first week of illness. In some patients, pH1N1 virus was detectable after all their symptoms had resolved. |
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