On January 30, 2020, the World Health Organization (WHO) declared coronavirus disease 2019 (COVID-19) a Public Health Emergency of International Concern (1). On March 24, 2020, the Global Polio Eradication Initiative (GPEI) suspended all polio supplementary immunization activities and recommended the continuation of polio surveillance (2). In April 2020, GPEI shared revised polio surveillance guidelines in the context of the COVID-19 pandemic, which focused on reducing the risk for transmission of SARS-CoV-2, the virus that causes COVID-19, to health care workers and communities by modifying activities that required person-to-person contact, improving hand hygiene and personal protective equipment use practices, and overcoming challenges related to movement restrictions, while continuing essential polio surveillance functions (3). GPEI assessed the impact of the COVID-19 pandemic on polio surveillance by comparing data from January to September 2019 to the same period in 2020. Globally, the number of acute flaccid paralysis (AFP) cases reported declined 33% and the mean number of days between the second stool collected and receipt by the laboratory increased by 70%. Continued analysis of AFP case reporting and stool collection is critical to ensure timely detection and response to interruptions of polio surveillance.

Background: In Pakistan and other countries using oral polio vaccine (OPV), immunity to type 2 poliovirus is now maintained by a single dose of inactivated polio vaccine (IPV) in routine immunization, supplemented in outbreak settings by monovalent OPV type 2 (mOPV2) and IPV. While well-studied in clinical trials, population protection against poliovirus type 2 achieved in routine and outbreak settings is generally unknown. Methods: We conducted two phases of a population-based serological survey of 7940 children aged 6-11 months old, between November 2016 and October 2017 from 13 polio high-risk locations in Pakistan. Results: Type 2 seroprevalence was 50% among children born after trivalent OPV (tOPV) withdrawal (April 2016), with heterogeneity across survey areas. Supplementary immunization activities (SIAs) with mOPV2 followed by IPV improved population immunity, varying from 89% in Pishin to 64% in Killa Abdullah, with little observed marginal benefit of subsequent campaigns. In the other high-risk districts surveyed, a single SIA with IPV was conducted and appeared to improve immunity to 57% in Karachi to 84% in Khyber. Conclusions: Our study documents declining population immunity following trivalent OPV withdrawal in Pakistan, and wide heterogeneity in the population impact of supplementary immunization campaigns. Differences between areas, attributable to vaccination campaign coverage, were far more important for type 2 humoral immunity than the number of vaccination campaigns or vaccines used. This emphasizes the importance of immunization campaign coverage for type 2 outbreak response in the final stages of polio eradication. Given the declining type 2 immunity in new birth cohorts it is also recommended that 2 or more doses of IPV should be introduced in the routine immunization program of Pakistan.

Human adenoviruses (HAdVs) were previously detected at high prevalence by real-time RT-PCR (rRT-PCR) in the upper respiratory tract of residents of two Kenyan refugee camps under surveillance for acute respiratory illness (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 co-detected 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, that 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 co-detections. These findings suggest that many HAdV detections were incidental and not a primary cause of ARI among camp patients. Species/type, co-detections and viral load determinations may permit more accurate HAdV disease burden estimates in these populations. This article is protected by copyright. All rights reserved.

Following the declaration of eradication of wild poliovirus (WPV) type 2 in September 2015, trivalent oral poliovirus vaccine (tOPV) was withdrawn globally to reduce the risk for type 2 vaccine-derived poliovirus (VDPV2) transmission; all countries implemented a synchronized switch to bivalent OPV (type 1 and 3) in April 2016 (1,2). Any isolation of VDPV2 after the switch is to be treated as a potential public health emergency and might indicate the need for supplementary immunization activities (3,4). On August 9, 2016, VDPV2 was isolated from a sewage sample taken from an environmental surveillance site in Hyderabad, Sindh province, Pakistan. Possible vaccination activities in response to VDPV2 isolation include the use of injectable inactivated polio vaccine (IPV), which poses no risk for vaccine-derived poliovirus transmission. Fractional-dose, intradermal IPV (fIPV), one fifth of the standard intramuscular dose, has been developed to more efficiently manage limited IPV supplies. fIPV has been shown in some studies to be noninferior to full-dose IPV (5,6) and was used successfully in response to a similar detection of a single VDPV2 isolate from sewage in India (7). Injectable fIPV was used for response activities in Hyderabad and three neighboring districts. This report describes the findings of an assessment of preparatory activities and subsequent implementation of the fIPV campaign. Despite achieving high coverage (>80%), several operational challenges were noted. The lessons learned from this campaign could help to guide the planning and implementation of future fIPV vaccination activities.

We used the Centers for Disease Control and Prevention-Kenya Medical Research Institute Acute Respiratory Infection (ARI) Surveillance System data to estimate severe acute respiratory infection (SARI) hospitalization rates, viral etiology, and associated complaints of influenza-like illnesses (ILI) and SARI conditions among those aged 5 years and older in Hagadera, Dadaab refugee camp, Kenya, for 2010-2012. A total of 471 patients aged ≥ 5 years met the case definition for ILI or SARI. SARI hospitalization rates per 10,000 person-years were 14.7 (95% confidence interval [CI] = 9.1, 22.2) for those aged 5-14 years; 3.4 (95% CI = 1.6, 7.2) for those aged 15-24 year; and 3.8 (95% CI = 1.6, 7.2) for those aged ≥ 25 years. Persons between the ages of 5 and 14 years had 3.5 greater odds to have been hospitalized as a result of SARI than those aged ≥ 25 years (odds ratio [OR] = 3.5, P < 0.001). Among the 419 samples tested, 169 (40.3%) were positive for one or more virus. Of those samples having viruses, 36.9% had influenza A; 29.9% had adenovirus; 20.2% had influenza B; and 14.4% had parainfluenza 1, 2, or 3. Muscle/joint pain was associated with influenza A (P = 0.002), whereas headache was associated with influenza B (P = 0.019). ARIs were responsible for a substantial disease burden in Hagadera camp.

BACKGROUND: The refugee complexes of Dadaab, Kenya, and Dollo-Ado, Ethiopia, experienced measles outbreaks during June-November 2011, following a large influx of refugees from Somalia. METHODS: Line-lists from health facilities were used to describe the outbreak in terms of age, sex, vaccination status, arrival date, attack rates (ARs), and case fatality ratios (CFRs) for each camp. Vaccination data and coverage surveys were reviewed. RESULTS: In Dadaab, 1370 measles cases and 32 deaths (CFR, 2.3%) were reported. A total of 821 cases (60.1%) were aged ≥15 years, 906 (82.1%) arrived to the camps in 2011, and 1027 (79.6%) were unvaccinated. Camp-specific ARs ranged from 212 to 506 cases per 100 000 people. In Dollo-Ado, 407 cases and 23 deaths (CFR, 5.7%) were reported. Adults aged ≥15 years represented 178 cases (43.7%) and 6 deaths (26.0%). Camp-specific ARs ranged from 21 to 1100 cases per 100 000 people. Immunization activities that were part of the outbreak responses initially targeted children aged 6 months to 14 years and were later expanded to include individuals up to 30 years of age. CONCLUSIONS: The target age group for outbreak response-associated immunization activities at the start of the outbreaks was inconsistent with the numbers of cases among unvaccinated adolescents and adults in the new population. In displacement of populations from areas affected by measles outbreaks, health authorities should consider vaccinating adults in routine and outbreak response activities.

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.

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.

BACKGROUND: Measles among displaced, malnourished populations can result in a high case fatality ratio (CFR). 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 June 6-September 10, 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. 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<0.0001]). Independent risk factors for measles mortality were neurological complications (OR=12.8, 95% 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.

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.

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.

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.

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.

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.