Epidemiology of SARS-CoV-2 in Kakuma Refugee Camp Complex, Kenya, 2020-20211.

Understanding SARS-CoV-2 infection in populations at increased risk for poor health is critical to reducing disease. We describe the epidemiology of SARS-CoV-2 infection in Kakuma Refugee Camp Complex, Kenya. We performed descriptive analyses of SARS-CoV-2 infection in the camp and surrounding community during March 16, 2020‒December 31, 2021. We identified cases in accordance with national guidelines.We estimated fatality ratios and attack rates over time using locally weighted scatterplot smoothing for refugees, host community members, and national population. Of the 18,864 SARS-CoV-2 tests performed, 1,024 were positive, collected from 664 refugees and 360 host community members. Attack rates were 325.0/100,000 population (CFR 2.9%) for refugees,150.2/100,000 population (CFR 1.11%) for community, and 628.8/100,000 population (CFR 1.83%) nationwide. During 2020-2021, refugees experienced a lower attack rate but higher CFR than the national population, underscoring the need to prioritize SARS-CoV-2 mitigation measures, including vaccination.

Cholera Outbreak in Dadaab Refugee Camp, Kenya - November 2015-June 2016.

Dadaab Refugee camp in Garissa County, Kenya, hosts nearly 340,000 refugees in five subcamps (Dagahaley, Hagadera, Ifo, Ifo2, and Kambioos) (1). On November 18 and 19, 2015, during an ongoing national cholera outbreak (2), two camp residents were evaluated for acute watery diarrhea (three or more stools in ≤24 hours); Vibrio cholerae serogroup O1 serotype Ogawa was isolated from stool specimens collected from both patients. Within 1 week of the report of index cases, an additional 45 cases of acute watery diarrhea were reported. The United Nations High Commissioner for Refugees and their health-sector partners coordinated the cholera response, community outreach and water, sanitation, and hygiene (WASH) activities; Médecins Sans Frontiéres and the International Rescue Committee were involved in management of cholera treatment centers; CDC performed laboratory confirmation of cases and undertook GIS mapping and postoutbreak response assessment; and the Garissa County Government and the Kenya Ministry of Health conducted a case-control study. To prevent future cholera outbreaks, improvements to WASH and enhanced disease surveillance systems in Dadaab camp and the surrounding area are needed.

A digital microfluidic system for serological immunoassays in remote settings.

Serosurveys are useful for assessing population susceptibility to vaccine-preventable disease outbreaks. Although at-risk populations in remote areas could benefit from this type of information, they face several logistical barriers to implementation, such as lack of access to centralized laboratories, cold storage, and transport of samples. We describe a potential solution: a compact and portable, field-deployable, point-of-care system relying on digital microfluidics that can rapidly test a small volume of capillary blood for disease-specific antibodies. This system uses inexpensive, inkjet-printed digital microfluidic cartridges together with an integrated instrument to perform enzyme-linked immunosorbent assays (ELISAs). We performed a field validation of the system's analytical performance at Kakuma refugee camp, a remote setting in northwestern Kenya, where we tested children aged 9 to 59 months and caregivers for measles and rubella immunoglobulin G (IgG). The IgG assays were determined to have sensitivities of 86% [95% confidence interval (CI), 79 to 91% (measles)] and 81% [95% CI, 73 to 88% (rubella)] and specificities of 80% [95% CI, 49 to 94% (measles)] and 91% [95% CI, 76 to 97% (rubella)] (measles, n = 140; rubella, n = 135) compared with reference tests (measles IgG and rubella IgG ELISAs from Siemens Enzygnost) conducted in a centralized laboratory. These results demonstrate a potential role for this point-of-care system in global serological surveillance, particularly in remote areas with limited access to centralized laboratories.

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.

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.

A rapid assessment of drinking water quality in informal settlements after a cholera outbreak in Nairobi, Kenya.

Populations living in informal settlements with inadequate water and sanitation infrastructure are at risk of epidemic disease. In 2010, we conducted 398 household surveys in two informal settlements in Nairobi, Kenya with isolated cholera cases. We tested source and household water for free chlorine residual (FCR) and Escherichia coli in approximately 200 households. International guidelines are ≥0.5 mg/L FCR at source, ≥0.2 mg/L at household, and <1 E. coli/100 mL. In these two settlements, 82% and 38% of water sources met FCR guidelines; and 7% and 8% were contaminated with E. coli, respectively. In household stored water, 82% and 35% met FCR guidelines and 11% and 32% were contaminated with E. coli, respectively. Source water FCR≥0.5 mg/L (p=0.003) and reported purchase of a household water treatment product (p=0.002) were associated with increases in likelihood that household stored water had ≥0.2 mg/L FCR, which was associated with a lower likelihood of E. coli contamination (p<0.001). These results challenge the assumption that water quality in informal settlements is universally poor and the route of disease transmission, and highlight that providing centralized water with ≥0.5 mg/L FCR or (if not feasible) household water treatment technologies reduces the risk of waterborne cholera transmission in informal settlements.

A national cholera epidemic with high case fatality rates--Kenya 2009.

BACKGROUND: Cholera remains endemic in sub-Saharan Africa. We characterized the 2009 cholera outbreaks in Kenya and evaluated the response. METHODS: We analyzed surveillance data and estimated case fatality rates (CFRs). Households in 2 districts, East Pokot (224 cases; CFR = 11.7%) and Turkana South (1493 cases; CFR = 1.0%), were surveyed. We randomly selected 15 villages and 8 households per village in each district. Healthcare workers at 27 health facilities (HFs) were surveyed in both districts. RESULTS: In 2009, cholera outbreaks caused a reported 11 425 cases and 264 deaths in Kenya. Data were available from 44 districts for 6893 (60%) cases. District CFRs ranged from 0% to 14.3%. Surveyed household respondents (n = 240) were aware of cholera (97.5%) and oral rehydration solution (ORS) (87.9%). Cholera deaths were reported more frequently from East Pokot (n = 120) than Turkana South (n = 120) households (20.7% vs. 12.3%). The average travel time to a HF was 31 hours in East Pokot compared with 2 hours in Turkana South. Fewer respondents in East Pokot (9.8%) than in Turkana South (33.9%) stated that ORS was available in their village. ORS or intravenous fluid shortages occurred in 20 (76.9%) surveyed HFs. CONCLUSIONS: High CFRs in Kenya are related to healthcare access disparities, including availability of rehydration supplies.

Association of the CT values of real-time PCR of viral upper respiratory tract infection with clinical severity, Kenya.

Quantitative real-time polymerase chain reaction (qRT-PCR) assay of the upper respiratory tract is used increasingly to diagnose lower respiratory tract infections. The cycle threshold (CT ) values of qRT-PCR are continuous, semi-quantitative measurements of viral load, although interpretation of diagnostic qRT-PCR results are often categorized as positive, indeterminate, or negative, obscuring potentially useful clinical interpretation of CT values. From 2008 to 2010, naso/oropharyngeal swabs were collected from outpatients with influenza-like illness, inpatients with severe respiratory illness, and asymptomatic controls in rural Kenya. CT values of positive specimens (i.e., CT values < 40.0) were compared by clinical severity category for five viruses using Mann-Whitney U-test and logistic regression. Among children <5 years old we tested with respiratory syncytial virus (RSV), inpatients had lower median CT values (27.2) than controls (35.8, P = 0.008) and outpatients (34.7, P < 0.001). Among children and older patients infected with influenza virus, outpatients had the lowest median CT values (29.8 and 24.1, respectively) compared with controls (P = 0.193 for children, P < 0.001 for older participants) and inpatients (P = 0.009 for children, P < 0.001 for older participants). All differences remained significant in logistic regression when controlling for age, days since onset, and coinfection. CT values were similar for adenovirus, human metapneumovirus, and parainfluenza virus in all severity groups. In conclusion, the CT values from the qRT-PCR of upper respiratory tract specimens were associated with clinical severity for some respiratory viruses.

Global and regional burden of hospital admissions for severe acute lower respiratory infections in young children in 2010: a systematic analysis.

BACKGROUND: The annual number of hospital admissions and in-hospital deaths due to severe acute lower respiratory infections (ALRI) in young children worldwide is unknown. We aimed to estimate the incidence of admissions and deaths for such infections in children younger than 5 years in 2010. METHODS: We estimated the incidence of admissions for severe and very severe ALRI in children younger than 5 years, stratified by age and region, with data from a systematic review of studies published between Jan 1, 1990, and March 31, 2012, and from 28 unpublished population-based studies. We applied these incidence estimates to population estimates for 2010, to calculate the global and regional burden in children admitted with severe ALRI in that year. We estimated in-hospital mortality due to severe and very severe ALRI by combining incidence estimates with case fatality ratios from hospital-based studies. FINDINGS: We identified 89 eligible studies and estimated that in 2010, 11·9 million (95% CI 10·3-13·9 million) episodes of severe and 3·0 million (2·1-4·2 million) episodes of very severe ALRI resulted in hospital admissions in young children worldwide. Incidence was higher in boys than in girls, the sex disparity being greatest in South Asian studies. On the basis of data from 37 hospital studies reporting case fatality ratios for severe ALRI, we estimated that roughly 265,000 (95% CI 160,000-450,000) in-hospital deaths took place in young children, with 99% of these deaths in developing countries. Therefore, the data suggest that although 62% of children with severe ALRI are treated in hospitals, 81% of deaths happen outside hospitals. INTERPRETATION: Severe ALRI is a substantial burden on health services worldwide and a major cause of hospital referral and admission in young children. Improved hospital access and reduced inequities, such as those related to sex and rural status, could substantially decrease mortality related to such infection. Community-based management of severe disease could be an important complementary strategy to reduce pneumonia mortality and health inequities. FUNDING: WHO.

Regional initiatives in support of surveillance in East Africa: The East Africa Integrated Disease Surveillance Network (EAIDSNet) Experience.

The East African Integrated Disease Surveillance Network (EAIDSNet) was formed in response to a growing frequency of cross-border malaria outbreaks in the 1990s and a growing recognition that fragmented disease interventions, coupled with weak laboratory capacity, were making it difficult to respond in a timely manner to the outbreaks of malaria and other infectious diseases. The East Africa Community (EAC) partner states, with financial support from the Rockefeller Foundation, established EAIDSNet in 2000 to develop and strengthen the communication channels necessary for integrated cross-border disease surveillance and control efforts. The objective of this paper is to review the regional EAIDSNet initiative and highlight achievements and challenges in its implementation. Major accomplishments of EAIDSNet include influencing the establishment of a Department of Health within the EAC Secretariat to support a regional health agenda; successfully completing a regional field simulation exercise in pandemic influenza preparedness; and piloting a web-based portal for linking animal and human health disease surveillance. The strategic direction of EAIDSNet was shaped, in part, by lessons learned following a visit to the more established Mekong Basin Disease Surveillance (MBDS) regional network. Looking to the future, EAIDSNet is collaborating with the East, Central and Southern Africa Health Community (ECSA-HC), EAC partner states, and the World Health Organization to implement the World Bank-funded East Africa Public Health Laboratory Networking Project (EAPHLNP). The network has also begun lobbying East African countries for funding to support EAIDSNet activities.

The population-based burden of influenza-associated hospitalization in rural western Kenya, 2007-2009.

OBJECTIVE: To estimate the burden and age-specific rates of influenza-associated hospitalization in rural western Kenya. METHODS: All 3924 patients with respiratory illness (defined as acute cough, difficulty in breathing or pleuritic chest pain) who were hospitalized between June 2007 and May 2009 in any inpatient health facility in the Kenyan district of Bondo were enrolled. Nasopharyngeal and oropharyngeal swabs were collected and tested for influenza viruses using real-time reverse transcriptase polymerase chain reaction (RT-PCR). In the calculation of annual rates, adjustments were made for enrolled patients who did not have swabs tested for influenza virus. FINDINGS: Of the 2079 patients with tested swabs, infection with influenza virus was confirmed in 204 (10%); 176, 27 and 1 were found to be RT-PCR-positive for influenza A virus only, influenza B virus only, and both influenza A and B viruses, respectively. Among those tested for influenza virus, 6.8% of the children aged < 5 years and 14.0% of the patients aged ≥ 5 years were found positive. The case-fatality rate among admitted patients with PCR-confirmed infection with influenza virus was 2.0%. The annual rate of hospitalization (per 100,000 population) was 699.8 among patients with respiratory illness and 56.2 among patients with influenza (with 143.7, 18.8, 55.2, 65.1 and 57.3 hospitalized patients with influenza virus per 100,000 people aged < 5, 5-19, 20-34, 35-49 and ≥ 50 years, respectively). CONCLUSION: In a rural district of western Kenya, the rate of influenza-associated hospitalization was highest among children aged less than 5 years.

Global burden of respiratory infections due to seasonal influenza in young children: a systematic review and meta-analysis.

BACKGROUND: The global burden of disease attributable to seasonal influenza virus in children is unknown. We aimed to estimate the global incidence of and mortality from lower respiratory infections associated with influenza in children younger than 5 years. METHODS: We estimated the incidence of influenza episodes, influenza-associated acute lower respiratory infections (ALRI), and influenza-associated severe ALRI in children younger than 5 years, stratified by age, with data from a systematic review of studies published between Jan 1, 1995, and Oct 31, 2010, and 16 unpublished population-based studies. We applied these incidence estimates to global population estimates for 2008 to calculate estimates for that year. We estimated possible bounds for influenza-associated ALRI mortality by combining incidence estimates with case fatality ratios from hospital-based reports and identifying studies with population-based data for influenza seasonality and monthly ALRI mortality. FINDINGS: We identified 43 suitable studies, with data for around 8 million children. We estimated that, in 2008, 90 million (95% CI 49-162 million) new cases of influenza (data from nine studies), 20 million (13-32 million) cases of influenza-associated ALRI (13% of all cases of paediatric ALRI; data from six studies), and 1 million (1-2 million) cases of influenza-associated severe ALRI (7% of cases of all severe paediatric ALRI; data from 39 studies) occurred worldwide in children younger than 5 years. We estimated there were 28,000-111,500 deaths in children younger than 5 years attributable to influenza-associated ALRI in 2008, with 99% of these deaths occurring in developing countries. Incidence and mortality varied substantially from year to year in any one setting. INTERPRETATION: Influenza is a common pathogen identified in children with ALRI and results in a substantial burden on health services worldwide. Sufficient data to precisely estimate the role of influenza in childhood mortality from ALRI are not available. FUNDING: WHO; Bill & Melinda Gates Foundation.

Risk factors for hospitalized seasonal influenza in rural western Kenya.

BACKGROUND: Risk factors for influenza hospitalization in Africa are unknown, including the role of HIV. METHODS: We conducted a case-control study of risk factors for hospitalized seasonal influenza among persons in rural western Kenya, a high HIV prevalence area, from March 2006-August 2008. Eligible cases were ≥five years old, admitted to health facilities with respiratory symptoms, and had nasopharyngeal/oropharyngeal swab specimens that tested positive for influenza A or B by real-time reverse transcription-PCR. Three randomly selected age-, sex- and neighborhood-matched controls were enrolled per case. A structured questionnaire was administered and home-based HIV testing was performed. Risk factors were evaluated using conditional logistic regression. RESULTS: A total of 64 cases (38 with influenza A and 26 with influenza B) and 190 controls were enrolled. The median age was 16 years (range 5-69 years). Among cases, 24.5% were HIV-infected versus 12.5% of controls (p = 0.004). Among persons ≥18 years old, 13 (59%) of 22 tested cases were HIV-positive compared with 15 (24%) of 62 tested controls (p = 0.005). In multivariable analysis, HIV-infection was associated with hospitalization due to influenza [adjusted Odds Ratio (aOR) 3.56, 95% CI 1.25-10.1]. The mean CD4 count among HIV-infected cases and controls was similar (399 vs. 387, respectively, p = 0.89). Chronic lung disease (aOR 6.83, 95% CI 1.37-34.0) was also associated with influenza hospitalization in multivariable analysis. Active pulmonary tuberculosis was associated with influenza hospitalization in bivariate, but not multivariable, analysis. CONCLUSIONS: People with HIV infection and chronic lung disease were at increased risk of hospitalized influenza in rural Kenya. HIV infection is common in many parts of sub-Saharan Africa. Influenza vaccine might prevent severe influenza in these risk groups.

High mortality in a cholera outbreak in western Kenya after post-election violence in 2008.

In 2008, a cholera outbreak with unusually high mortality occurred in western Kenya during civil unrest after disputed presidential elections. Through active case finding, we found a 200% increase in fatal cases and a 37% increase in surviving cases over passively reported cases; the case-fatality ratio increased from 5.5% to 11.4%. In conditional logistic regression of a matched case-control study of fatal versus non-fatal cholera infection, home antibiotic treatment (odds ratio [OR] 0.049; 95% CI: < 0.001-0.43), hospitalization (OR, 0.066; 95% CI, 0.001-0.54), treatment in government-operated health facilities (OR, 0.15; 95% CI, 0.015-0.73), and receiving education about cholera by health workers (OR, 0.19; 95% CI, 0.018-0.96) were protective against death. Among 13 hospitalized fatal cases, chart review showed inadequate intravenous and oral hydration and substantial staff and supply shortages at the time of admission. Cholera mortality was under-reported and very high, in part because of factors exacerbated by widespread post-election violence.