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.

Reassessment of high prevalence human adenovirus detections among residents of two refugee centers in Kenya under surveillance for acute respiratory infections.

Human adenoviruses (HAdVs) were previously detected at high prevalence by real-time reverse transcription-polymerase chain reaction (rRT-PCR) in the upper respiratory tract of residents of two Kenyan refugee camps under surveillance for acute respiratory infection (ARI) between October 2006 and April 2008. We sought to confirm this finding and characterize the HAdVs detected. Of 2148 respiratory specimens originally tested, 511 (23.8%) screened positive for HAdV and 510 were available for retesting. Of these, 421 (82.4%) were confirmed positive by repeat rRT-PCR or PCR and sequencing. Other respiratory viruses were codetected in 55.8% of confirmed HAdV-positive specimens. Species B and C viruses predominated at 82.8%, and HAdV-C1, -C2, and -B3 were the most commonly identified types. Species A, D, and F HAdVs, which are rarely associated with ARI, comprised the remainder. Viral loads were highest among species B HAdVs, particularly HAdV-B3. Species C showed the widest range of viral loads, and species A, D, and F were most often present at low loads and more often with codetections. These findings suggest that many HAdV detections were incidental and not a primary cause of ARI among camp patients. Species/type, codetections, and viral load determinations may permit more accurate HAdV disease burden estimates in these populations.

Use of TaqMan Array Cards to Screen Outbreak Specimens for Causes of Febrile Illness in Tanzania.

We describe the deployment of a custom-designed molecular diagnostic TaqMan Array Card (TAC) to screen for 31 bacterial, protozoal, and viral etiologies in blood from outbreaks of acute febrile illness in Tanzania during 2015-2017. On outbreaks notified to the Tanzanian Ministry of Health, epidemiologists were dispatched and specimens were collected, transported to a central national laboratory, and tested by TAC within 2 days. This algorithm streamlined investigation, diagnosed a typhoid outbreak, and excluded dozens of other etiologies. This method is usable in-country and may be incorporated into algorithms for diagnosing outbreaks.

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.

Risk factors for measles mortality among hospitalized Somali refugees displaced by famine, Kenya, 2011.

BACKGROUND: Measles among displaced, malnourished populations can result in a high case fatality ratio. In 2011, a large measles outbreak occurred in Dadaab, Kenya, among refugees fleeing famine and conflict in Somalia. The aim of this study was to identify predictors of measles deaths among hospitalized patients during the outbreak. METHODS: A retrospective cohort study design was used to investigate measles mortality among hospitalized measles patients with a date of rash onset during 6 June-10 September 2011. Data were abstracted from medical records and a measles case was defined as an illness with fever, maculopapular rash, and either cough, coryza or conjunctivitis. Vaccination status was determined by patient or parental recall. Independent predictors of mortality were identified using logistic regression analysis. RESULTS: Of 388 hospitalized measles patients, 188 (49%) were from hospital X, 70 (18%) from hospital Y, and 130 (34%) from hospital Z; median age was 22 years, 192 (50%) were 15-29 years of age, and 22 (6%) were vaccinated. The mean number of days from rash onset to hospitalization varied by hospital (hospital X = 5, hospital Y = 3, hospital Z = 6; P < .0001). Independent risk factors for measles mortality were neurological complications (odds ratio [OR], 12.8; 95% confidence interval [CI], 3.1-52.4), acute malnutrition (OR, 7.6; 95% CI, 1.3-44.3), and admission to hospital Z (OR, 4.2; 95% CI, 1.3-13.2). CONCLUSIONS: Among Somali refugees, in addition to timely vaccination at border crossing points, early detection and treatment of acute malnutrition and proper management of measles cases may reduce measles mortality.

A randomized, double-blind, controlled trial of the 17D yellow fever virus vaccine given in combination with immune globulin or placebo: comparative viremia and immunogenicity.

We evaluated whether coadministration of the yellow fever (YF) virus vaccine with human immunoglobulin (Ig) that contained YF virus-neutralizing antibodies would reduce post-vaccination viremia without compromising immunogenicity and thus, potentially mitigate YF vaccine-associated adverse events. We randomized 80 participants to receive either YF vaccine and Ig or YF vaccine and saline placebo. Participants were followed for 91 days for safety and assessments of viremia and immunogenicity. There were no differences found between the two groups in the proportion of vaccinated participants who developed viremia, seroconversion, cluster of differentiation (CD)-8(+) and CD4(+) T-cell responses, and cytokine responses. These results argue against one putative explanation for the increased reporting of YF vaccine side effects in recent years (i.e., a change in travel clinic practice after 1996 when hepatitis A prophylaxis with vaccine replaced routine use of pre-travel Ig, thus potentially removing an incidental YF vaccine-attenuating effect of anti-YF virus antibodies present in Ig).

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.

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.

Case of yellow fever vaccine--associated viscerotropic disease with prolonged viremia, robust adaptive immune responses, and polymorphisms in CCR5 and RANTES genes.

BACKGROUND: The live attenuated yellow fever vaccine 17D (YF-17D) is one of the most effective vaccines. Despite its excellent safety record, some cases of viscerotropic adverse events develop, which are sometimes fatal. The mechanisms underlying such events remain a mystery. Here, we present an analysis of the immunologic and genetic factors driving disease in a 64-year-old male who developed viscerotropic symptoms. METHODS: We obtained clinical, serologic, virologic, immunologic and genetic data on this case patient. RESULTS: Viral RNA was detected in the blood 33 days after vaccination, in contrast to the expected clearance of virus by day 7 after vaccination in healthy vaccinees. Vaccination induced robust antigen-specific T and B cell responses, which suggested that persistent virus was not due to adaptive immunity of suboptimal magnitude. The genes encoding OAS1, OAS2, TLR3, and DC-SIGN, which mediate antiviral innate immunity, were wild type. However, there were heterozygous genetic polymorphisms in chemokine receptor CCR5, and its ligand RANTES, which influence the migration of effector T cells and CD14+CD16bright monocytes to tissues. Consistent with this, there was a 200-fold increase in the number of CD14+CD16bright monocytes in the blood during viremia and even several months after virus clearance. CONCLUSION: In this patient, viscerotropic disease was not due to the impaired magnitude of adaptive immunity but instead to anomalies in the innate immune system and a possible disruption of the CCR5-RANTES axis.

Fatal multiorgan failure due to yellow fever vaccine-associated viscerotropic disease.

Yellow fever vaccine-associated viscerotropic disease (YEL-AVD) is a rare complication of yellow fever (YF) vaccination. A previously healthy 22-year-old female died following YF vaccination despite aggressive measures. Serial viral load titers, cytokine levels and host genetic factors were evaluated in an attempt to understand this unusual and lethal outcome. The patient's high-titer vaccine viremia and possibly related minor genetic anomalies provide clues to exploring the etiology of YEL-AVD.

Neurologic disease associated with 17D-204 yellow fever vaccination: a report of 15 cases.

Yellow fever (YF), can be prevented by an attenuated vaccine (YEL). We reviewed neurologic adverse events (AE) following YEL that were reported to the national Vaccine Adverse Events Reporting System (VAERS). VAERS is a passive reporting system with inherent limitations for causality assessment. Based on defined criteria, five cases of encephalitis were classified as 'definitely' and one of acute disseminated encephalomyelitis (ADEM) as 'probably' caused by YEL. Six cases of Guillain-Barre Syndrome (GBS), one of encephalitis, and two of ADEM, were classified as 'suspect' vaccine-associated disease. Laboratory and epidemiological evidence suggests that YEL caused encephalitis. Additional studies will be required to confirm whether YEL can rarely result in GBS and/or ADEM.